# Patent

## Title
Compositions produced using enteric pathogens and methods of use

## Abstract

The present invention provides compositions including polypeptides having the characteristics of polypeptides expressed by a reference microbe such E coli or Salmonella. Examples of Salmonella strains that can be used include, for instance, S. enterica serovar Newport, S. enterica serovar Enteritidis, S. enterica serovar Typhimurium, and S. enterica serovar Dublin. Also provided are compositions including polypeptides having a particular molecular weight and a mass fingerprint that includes polypeptide fragments having a particular set of masses, or polypeptides having an amino acid sequence with at least about 95% identity with an amino acid sequence, wherein the polypeptide has seroreactive activity. The present invention also provides methods of making and methods of using such compositions.

## Background
RELATED APPLICATIONS
This application is a divisional application of U.S. patent application Ser. No. 10/946,647, filed Sep. 20, 2004, now U.S. Pat. No. 8,119,147, which claims the benefit of U.S. Provisional Application No. 60/504,119, filed Sep. 19, 2003, both of which are incorporated by reference in their entirety.


BACKGROUND
SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on May 18, 2011, is named 29334102.txt and is 636,661 bytes in size.
The transmission of enteric pathogens to human populations by the consumption of contaminated food and water has become a world wide concern. Surveillance data compiled by the World Health Organization estimate that gastrointestinal infections and their sequalae result in approximately 4 million to 6 million deaths annually. More than 80% of these cases are among children under the age of five with mortality reaching 4 million. The majority of these deaths are in children less than 2 years of age. In the United States, diarrhea is the second most common infectious illness, accounting for one out of every six infectious diseases. In some developing countries, children have more than 12 episodes of diarrhea per year and diarrhea diseases account for 15 to 34 percent of all deaths.
In the United States food/waterborne diseases cause approximately 76 million illnesses, 325,000 hospitalizations, and 5000 deaths each year. More than 90% of the foodborne illnesses of known causes are of microbial origin. Costs associated with medical expenses and losses in productivity associated with microbial agents are estimated to be between $5.6 and $9.4 billion dollars annually. The most commonly recognized food/borne pathogens contributing to gastrointestinal infections have been shown to be bacteria (e.g., Salmonella spp., Escherichia coli, Shigella spp., and Vibrio spp.).
The virulence and pathogenesis of enteric pathogens involves both host and pathogen specific factors. Many pathogen-specific virulence determinants contribute to the pathogenesis of these bacteria. The bacterial virulence of these bacteria is the result of many different attributes, which often contribute to different steps in the complicated series of events we recognize as an infection. Infection occurs primarily by the consumption of contaminated water, food or by direct person to person contact. Once ingested the stages of infection common to enteric pathogens can include attachment, colonization, proliferation, tissue damage, invasion and dissemination. Less frequently, enteric pathogens can produce a bacteremic condition inducing reactive arthritis, kidney failure, Guillian-Barre, Reiter syndrome and other extra-intestinal symptoms.
The first host barrier that enteric pathogens must overcome is the mucosal surface. A single epithelial cell layer separates the host from the lumen of the gastrointestinal tract. This barrier and a plethora of other host antimicrobial mechanisms deter commensal, opportunistic and pathogenic microorganisms from establishing infection. Enteric pathogens have evolved some elaborate pathogenic strategies to attach, invade and translocate across the gut epithelium to cause infection. Adherence to mucosal surfaces is a prerequisite of most enteric pathogens to establish infection. In its simplest form adherence or attachment requires two factors: a receptor and an adhesin. A number of specialized structures (adhesins) have been identified in enteric pathogens that enhance intestinal colonization of the organism. These specialized structures (e.g., pili or fimbriae) act as ligands to bind the bacterial cell to specific complex carbohydrate receptors on the epithelial cell surface of the intestine. Once colonization is established enteric pathogens have a multitude of virulence factors that enhance the ability of the pathogen to invade its host. One of the more pronounced clinical manifestations of intestinal colonization is diarrhea. This clinical syndrome is typically induced by the synthesis and excretion of a variety of enterotoxins, (e.g., heat-labile toxin (LT), heat-stable toxin (ST) cholera toxin (CT) and shiga toxin (Stx)) that cause a net secretion of fluid and electrolytes (diarrhea). Many other specific virulence factors of enteric pathogens have been described that affect a wide range of eukaryotic cell processes in the host, to including invasion of specific cell types, cell to cell interactions and signal transduction by integrins, attaching and effacing with destruction of the epithelial surface, elaboration of exotoxins, and actin polymerization enhancing cell to cell spread, etc.
The diversity of enteric pathogens and virulence factors has complicated the development of new and improved vaccines with long lasting protection. The search for a better vaccine is prompted by the results of epidemiological and challenge studies showing that the recovery from natural infection is often followed by long lasting immunity while providing cross-protection against multiple strains and/or serotypes.
Current vaccines under development for such enteric pathogens as Vibrio cholera, Escherichia coli, Salmonella, and Shigella are based on parenteral and oral vaccines. Moderately effective vaccines have been tested and implemented for controlling cholera. The oral vaccines currently under development include two types: killed Vibrio cholera bacteria that are combined with purified cholera B subunit toxin, and live-attenuated strains of V. cholera with known genetic deletions (Butterton et al., Infect. Immun. 65: 2127-2135 (1997)). Field trials sponsored by The World Health Organization using an oral vaccine consisting of a whole-cell B subunit reported levels of only 50% protection in human populations in underdeveloped countries. The vaccine required multiple doses over a four month period; unfortunately, young children were not well protected (Sack et al. Infect. Immun. 66:1968-1972 (1998); Sanchez et al, Lancet. 349: 1825-1830 (1997); and Trach et al. Lancet. 349: 231-235(1997)). A whole-cell vaccine containing four common isolates of V. choleraa not containing B subunit toxin has also been tested in human subjects that showed a protective efficacy of 65% (Taylor et al. Infect. Immun. 65: 3852-3856 (1997)). A whole-cell vaccine containing four common isolates of cholera not containing B subunit toxin has also been tested in human subjects (Taylor et al. Infect. Immun. 65: 3852-3856 (1997)). The vaccine required two administrations 7-14 days apart and induced a protective index of approximately 65%. However, the vaccine was not well tolerated due to its reactve nature upon injection. Several live-attenuated vaccine candidates have been tested in large scale efficacy trials involving more than 60,000 human subjects. Unfortunately, the results of this pivotal trial did not demonstrate the effectiveness of the vaccine in preventing cholera. Further development in live attenuated gene deleted vaccines has recently shown promise against the 01 and 0139 serotypes in human volunteers. However, efficacy of the vaccine in large populations and protection against multiple serotypes have yet to be demonstrated.
There are five categories of diarrheagenic Escherichia coli that cause foodborne and waterborne diseases in humans: the enteropathogenic (EPEC), enterohemorrhagic (EHEC), enterotoxigenic (ETEC), enteroinvasive (EtIC) and enteroaggregative (EAEC) strains. The mechanism of disease associated with these pathogens depends on specific characteristics which involve attaching and effacing adherence of the organism to intestinal epithelial cells and damage to the intestinal microvilli. Of particular interest has been the emergence of the Shiga toxin-producing E. coli, also referred to as EHEC, primarily of the 0157:H7serotype. This strain of E. coli has been shown to synthesize either one or both of the Shiga toxins (Stx-1 and/or Stx-2). This strain has been associated with gastrointestinal infections that begin with diarrhea that can exasperate into hemorrhagic colitis, followed by hemolytic-uremic syndrome (HUS) and/or encephalopathy, particularly in the young, immunocompromized, and elderly adults. The Shiga toxin (Stx) produced by this isolate is believed to be important in the pathogenesis of this organism. Current efforts at vaccine development are primarily focused on animals known to asymptomatically carry these organisms and shed them in their feces. Research has focused on a number of strategies for controlling this organism, which revolve around the concept of preventing colonization by targeting the colonization factor intimin, and immunization of animals with genetically modified non-toxin producing versions of the parent isolate. The intimin protein has been shown to be responsible for the attaching and effacing lesions also characteristic of both Shigella dysenteriae (STEC) and the enteropathogenic (EPEC) strains of E. coli. In addition, researchers have been investigating the expression of intimin in animal feed products such as canola and alfalfa for use as an edible animal vaccine. If any of these strategies work in animals it could find its way to human usage (Acheson et al. Infect. Immun. 64: 355-357(1996); Bokete et al. J. Infect. Dis. 175: 1382-1389 (1997); Bosworth et al. Infect. Immun. 64:55-60 (1996) and Konadu et al. Infect. Immun. 62: 5048-5054(1994)).
The National Institute of Child Health and Human development have proposed the use of conjugate vaccines using the B-subunit of Stx-1 in conjunction with a whole cell as developed for V. cholerae, which has shown promising results in experimental animal models as well as toxoids and immunotherapeutics using antitoxin antibodies as well as human monoclonal antibodies to neutralize the Stx-1 and Stx-2 toxin. Such prophylactic and immunotherapeutic strategies could protect against STEC infection as well as infections caused by closely related organisms such as EPEC and EHEC strains of E. coli. 
Enterotoxigenic (ETEC) strains of E. coli are an important cause of diarrhea in infants in less developed countries. It is estimated that ETEC causes more than 650 million cases of diarrhea per year and more than 800,000 deaths in children less than 5 years of age. ETEC is also the major cause of traveler's diarrhea, which affects at least 8 million United States citizens who travel to endemic regions of the world each year. Virulence factors associated with these strains of E. coli include primarily adhesins and enterotoxins such as LTI, STa and STb. In volunteer studies infection with ETEC generates protective immunity against rechallenge with the same strain. The vaccine candidate currently being developed consists of a mixture of five formalin-inactivated ETEC strains, which together express the required adhesins, combined with a recombinant Cholera toxin B subunit, which generates antibody that cross-reacts with the ETEC-LT toxin. Clinical studies have shown that the vaccine is immunogenic and safe in human volunteers.
Shigella spp. such as S. sonnei, S. flexneri, S. boydii and S. dysenteriae are causative agents of shigellosis or bacillary dysentery. In the United States approximately 13,000 cases of shigellosis were reported in 2002, a 22% increase from 2001 (CDC, Shigella Annual Summary 2002). Nearly 30% of the reported cases occurred in children under the age of five. The mechanism of disease associated with these pathogens is characterized by specific attaching and effacing lesions involving microvilli destruction, and the production of potent exotoxins (Shiga toxin) that frequently results in hemolytic uremic syndrome. A virulence plasmid present in all invasive Shigella strains has been identified that encode a number of outer membrane proteins that mediate attachment to the epithelial cell. Several of the plasmid-encoded proteins initiate parasite-induced phagocytosis which in turn breaks down the membrane of the phagocytic vacuole, allowing bacteria to multiply within the cytoplasm.
Vaccine strategies created to control shigellosis have focused on attenuated strains with known genetic deletions. A deletion mutant of S. flexneri has shown excellent protection after a single oral dose. This vaccine candidate provides protection against severe shigellosis in volunteers challenged with S. flexneri. Other vaccine strategies include the development of auxotrophic mutants and recent studies have shown protection using O-specific polysaccharides conjugates from S. sonnei and S. flexneri. As with many of these diseases a comprehensive vaccine approach to controlling shigellosis must include various bacterial components to protect against the multiple serotypes of Shigella that are responsible for endemic outbreaks of dysentery (Ashkenazi et al., J. Infect. Immun. 179: 1565-1568 (1999); Cohen et al., Lancet. 349: 155-159 (1997); Coster et al., Infect. Immun. 67: 3437-3437 (1999); Kotloff et al., infect Immun. 64: 4542-4548 (1996) and Sansonetti et al., Res. Immunol. 147:595-602 (1996)).
Salmonella infections are the leading cause of bacterial foodborne diseases worldwide and are one of the most common enteric diseases in the United States. There are approximately 2,213 different Salmonella strains currently identified which can be classified according to their adaptation to human and animal hosts. For instance, S. typhi and S. paratyphi causes enteric or typhoid fever only in humans and globally infect 20-30 million people annually and cause 600,000 deaths. In the United States, more than 41,000 cases were reported in 1993 with the highest incidence being in children 5 to 19 years of age. Non-typhoidal Salmonella enterica is one of the most common causes of food poisoning in the United States, responsible for an estimated 1.4 million cases of salmonellosis annually (Mead et al. Emerg. Infect. Dis. 5:607-625 (1999)). The cost of human salmonellosis in the U.S. is estimated to be several billion dollars annually based on healthcare costs and lost productivity.
There has been a number of virulence factors associated with disease caused by Salmonella. Briefly, the pathogenesis of the organism begins with the colonization of the host followed by localized degeneration of the epithelial surface resulting in penetration of the epithelial barrier and proliferation in the lamina propria, multiplication, and stimulation of an inflammatory response. Diarrhea associated with salmonellosis is associated primarily with the inflammatory response, which stimulates the release of prostaglandins and production of cAMP, which increase the secretion of fluid and electrolytes into the lumen of the bowel (diarrhea).
A number of parenteral whole-cell vaccines for typhoid fever have been developed but have been found to be only marginally effective because of severe adverse reactions in vaccinates. Currently the National Institute of Child Health and Human Development has developed and tested a vaccine consisting of the Vi antigen. Clinical trials have demonstrated an efficacy of 72-80% with a single injection. A number of gene deleted mutants have been developed for controlling S. typhi with varying degrees of success (Germanier et al. J. Infect. Dis 131:553-558 (1975); Hohmann et al. J. Infect. Dis. 173:1408-1414 (1996); Nardelli-Haefliger et al. Infect. Immun. 64:5219-5224 (1996); Stocker Vaccine. 6:141-145 (1988); Szu et al. Infect. Immun. 62: 4440-4444 (1994); Tacket et al. Infect Immun. 60: 536-541(1992); and Tacket et al. Vaccine. 10: 443-446 (1992)).
The remaining Salmonella strains commonly referred to as nontyphoidal are primarily transmitted from animals to humans (Calnek et al., Diseases of Poultry-9th ed., pp. 99-130, Iowa StateUniversity, Ames Iowa (1991)). In the United States, the most common serotypes of S. enterica isolated from humans are serotypes Typhimurium, Enteritidis, and Newport (CDC Salmonella Annual Summary, 2002). These three serotypes accounted for 51% of human Salmonella isolates in 2002. Notably, the serotypes Typhimurium and Newport are frequently resistant to multiple antibiotics. In a 2001 annual survey, 53% of Typhimurium isolates were resistant to at least one antibiotic and 30% were resistant to five antibiotics in a manner characterisitic of the DT104 phage type (CDC National Antimicrobial Resistance Monitoring System:Enteric Bacteria, available on the world wide web at cdc.gov/narms/). In addition, 26% of Newport isolates were resistant to at least nine antibiotics in the 2001 annual survey. The Typhimurium and Newport serotypes are primarily associated with the consumption of a variety of different types of animal products that become contaminated during processing or handling. In contrast, Salmonella serotype Enteritidis is almost exclusively associated with the consumption of contaminated chicken eggs. This serotype has a propensity to colonize poultry ovarian tissues for extended periods of time (Okamura et al., Avian Dis., 45: 61-69 (2001) and Okamura et al., Avian Dis., 45: 962-971(2001)), and can gain entry to the egg environment by vertical transmission during egg formation (Gast et al., Avian Dis. 44: 706-710 (2000) and Humphrey et al., Int. J. Food Microbiol. 21: 31-40 (1994)). A recent risk assessment estimated that 2.3 million eggs are contaminated in the United States annually, resulting in approximately 660,000 human infections (Hope et al., Risk Anal., 22:203-218 (2002)). Additional serotypes that have been associated with human salmonellosis derived from poultry and other animals include S. enterica Heidelberg, Hadar, Infantis, Agona, Montevideo, Thompson, and Braenderup. Heidelberg, Hadar, Infantis, Agona, Montevideo, Thompson, and Braenderup.
Research for controlling nontyphoidal Salmonella has been primarily limited to the bacterins, which consist of killed Salmonella cells, and the live attenuated strains of Salmonella. Bacterins typically stimulate antibody responses in vaccinated animals but may be limited in their ability to promote cell-mediated immunity (Babu et al., Vet. Immunol. Immunopathol. 91:39-44 (2003) and Okamura et al., Comp. Immunol. Microbiol. Infect. Dis. 27:255-272 (2004)), an important host response for effective clearance of Salmonella (Lalmanach and Lantier. Microbes Infect. 1:719-726 (1999) and Naiki et al., J. Immunol. 163:2057-2063 (1999)). In addition, bacterins have generally produced inconsistent protection against fecal shedding of Salmonella (House et al., Am. J. Vet. Res. 12: 1897-1902 (2001) and Davison et al., Avian Dis. 43:664-669 (1999)). Other disadvantages of bacterins include injection-site granulomas, weight loss, and serotype-specific protection. The live attenuated Salmonella vaccines are generally considered to provide better cross-protection than observed with the bacterins (Hassan and Curtiss, III. Infect. Immun. 62:5519-5527. (1994)), and additionally stimulate both humoral and cell-mediated immune responses (Curtiss, III et al., Vet Microbiol. 37:397-405 (1993) and Villarreal-Ramos et al., Vaccine 16: 45-54 (1998)). However, there are significant obstacles regarding the safety of introducing these organisms into commercial animals; specifically, there is concern that genetic reversion will occur and render the vaccine strain virulent. A second potential problem with using modified live vaccines is that antibodies generated to the somatic antigen of the vaccination strains can interfere with national and state Salmonella monitoring programs by generating false positive reactions. In addition, antibiotics are often administered in commercial flocks to control infection rates which can eliminate the attenuated vaccine strain; hence, repeated immunizations of live Salmonella vaccines are often required. There have been relatively few attempts to formulate subcellular vaccines for controlling Salmonella in agricultural animals. A few key studies in poultry species utilized crude cell extracts in their vaccinations, showing S. Enteritidis-specific mucosal and/or circulating antibody responses (Fukutome et al., Dev. Comp. Immunol. 25:475-484 (2001) and Ochoa-Reparaz et al., Vet. Res. 35:291-298 (2004)). In other studies, purified outer membrane protein compositions were demonstrated to promote heightened antibody responses and reduced intestinal colonization or fecal shedding following challenge with S. Enteritidis (Charles et al., Am. J. Vet. Res. 55:636-642 (1994), Khan et al., J. Appl. Microbiol. 95:142-145 (2003), and Meenakshi et al., Vet. Res. Commun. 23:81-90 (1999)).
SUMMARY
The present invention provides compositions including a polypeptide having the characteristics of a polypeptide expressed by a reference microbe. The characteristics of the polypeptide include both molecular weight and mass fingerprint. The reference microbe may be, for instance, an E. coli or a Salmonella. Examples of Salmonella strains that can be used include, for instance, S. enterica serovar Newport, S. enterica serovar Enteritidis, S. enterica serovar Typhimurium, and S. enterica serovar Dublin. Preferably, the reference polypeptide is expressed by the microbe during growth in low metal conditions. The present invention also provides compositions including a polypeptide having a particular molecular weight and a mass fingerprint that includes polypeptide fragments having a particular set of masses. The present invention further provides compositions including a polypeptide having an amino acid sequence with at least about 95% identity with a reference amino acid sequence, wherein the polypeptide has seroreactive activity.
The compositions of the present invention may optionally include a pharmaceutically acceptable carrier. The present invention also includes methods for using the polypeptides disclosed herein. Methods include inducing the production of antibody in an animal, treating a gram negative microbial infection in an animal, and decreasing intestinal colonization of an animal.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. The percent mortality in mice showing a dose response to varying concentrations of a composition prepared from Salmonella enterica serovar Newport after challenge. Non-diluted, 1/10, 1/100, and 1/1000 refer to the dilution of the stock vaccine as described in Example 5. Numbers above the bars indicate the percent mortality.
FIG. 2. The difference in fecal shedding between vaccinated and non-vaccinated mice after oral challenge with Salmonella enterica serovar Newport. Log10 CFU, mean number of bacteria in fecal sample.
FIG. 3. The difference in fecal shedding between vaccinated and non-vaccinated mice after oral challenge with E. coli O157:H7. Log10 CFU, mean number of bacteria in fecal sample.
FIG. 4. The serological response in vaccination with a composition derived from S. enterica serovar Newport compared to non-vaccinated controls as evaluated by ELISA.
FIG. 5. The difference in fecal shedding between vaccinated and non-vaccinated calves after oral challenge with a composition derived from S. enterica serovar Newport.
FIG. 6. The difference in fecal shedding between vaccinated and non-vaccinated steers after oral challenge with a nalidixic acid resistant E. coli O157:H7.
FIG. 7. The difference in fecal shedding between vaccinated and non-vaccinated steers after oral challenge with a nalidixic acid resistant E. coli O157:H7.
FIG. 8. Clearance of Salmonella enterica serovar Enteritidis from the Spleens of Control and Vaccinated Groups following Intravenous Challenge in Chickens.
FIG. 9. Clearance of Salmonella enterica serovar Enteritidis from the Ovaries of Control and Vaccinated Groups following Intravenous Challenge in Chickens.
FIG. 10. Difference in Fecal Shedding of Salmonella enterica serovar Enteritidis in Control and Vaccinated Groups following Intravenous Challenge in Chickens.
FIG. 11. Comparison of selected proteins identified using E. coli grown under iron-limiting conditions with proteins from other pathogens.
FIG. 12. Amino acid sequence of SEQ ID NO:1367.
FIG. 13. Amino acid sequence of SEQ ID NO:1368.
FIG. 14. Amino acid sequence of SEQ ID NO:1369.
FIG. 15. Amino acid sequence of SEQ ID NO:1370.
FIG. 16. Amino acid sequence of SEQ ID NO:1371.
FIG. 17. Amino acid sequence of SEQ ID NO:1372.
FIG. 18. Amino acid sequence of SEQ ID NO:1373.
FIG. 19. Amino acid sequence of SEQ ID NO:1374.
FIG. 20. Amino acid sequence of SEQ ID NO:1375.
FIG. 21. Amino acid sequence of SEQ ID NO:1376.
FIG. 22. Amino acid sequence of SEQ ID NO:1377.
FIG. 23. Amino acid sequence of SEQ ID NO:1378.
FIG. 24. Amino acid sequence of SEQ ID NO:1379.
FIG. 25. Amino acid sequence of SEQ ID NO:1380.
FIG. 26. Nucleotide sequence of SEQ ID NO:1382.
FIG. 27. Nucleotide sequence of SEQ ID NO:1383.
FIG. 28. Nucleotide sequence of SEQ ID NO:1384.
FIG. 29. Nucleotide sequence of SEQ ID NO:1385.
FIG. 30. Nucleotide sequence of SEQ ID NO:1386.
FIG. 31. Nucleotide sequence of SEQ ID NO:1387.
FIG. 32. Nucleotide sequence of SEQ ID NO:1388.
FIG. 33. Nucleotide sequence of SEQ ID NO:1389.
FIG. 34. Nucleotide sequence of SEQ ID NO:1390.
FIG. 35. Nucleotide sequence of SEQ ID NO:1391.
FIG. 36. Nucleotide sequence of SEQ ID NO:1392.
FIG. 37. Nucleotide sequence of SEQ ID NO:1393.
FIG. 38. Nucleotide sequence of SEQ ID NO:1394.
FIG. 39. Nucleotide sequence of SEQ ID NO:1395.
FIG. 40. Nucleotide sequence of SEQ ID NO:1396.
FIG. 41. Nucleotide sequence of SEQ ID NO:1397.
FIG. 42. Nucleotide sequence of SEQ ID NO:1398.
FIG. 43. Nucleotide sequence of SEQ ID NO:1399.
FIG. 44. Nucleotide sequence of SEQ ID NO:1400.
FIG. 45. Nucleotide sequence of SEQ ID NO:1401.
FIG. 46. Nucleotide sequence of SEQ ID NO:1402.
FIG. 47. Nucleotide sequence of SEQ ID NO:1403.
FIG. 48. Nucleotide sequence of SEQ ID NO:1404.
FIG. 49. Nucleotide sequence of SEQ ID NO:1405.
FIG. 50. Nucleotide sequence of SEQ ID NO:1406.
FIG. 51. Nucleotide sequence of SEQ ID NO:1407.
FIG. 52. Nucleotide sequence of SEQ ID NO:1408.
FIG. 53. Nucleotide sequence of SEQ ID NO:1409.
FIG. 54. Nucleotide sequence of SEQ ID NO:1410.
FIG. 55. Nucleotide sequence of SEQ ID NO:1411.
FIG. 56. Nucleotide sequence of SEQ ID NO:1412.
FIG. 57. Nucleotide sequence of SEQ ID NO:1413.
FIG. 58. Nucleotide sequence of SEQ ID NO:1414.
FIG. 59. Nucleotide sequence of SEQ ID NO:1415.
FIG. 60. Nucleotide sequence of SEQ ID NO:1416.
FIG. 61. Nucleotide sequence of SEQ ID NO:1417.
FIG. 62. Nucleotide sequence of SEQ ID NO:1418.
FIG. 63. Nucleotide sequence of SEQ ID NO:1419.
FIG. 64. Nucleotide sequence of SEQ ID NO:1420.
FIG. 65. Nucleotide sequence of SEQ ID NO:1421.
FIG. 66. Nucleotide sequence of SEQ ID NO:1422.
FIG. 67. Nucleotide sequence of SEQ ID NO:1423.
FIG. 68. Nucleotide sequence of SEQ ID NO:1424.
FIG. 69. Nucleotide sequence of SEQ ID NO:1425.
FIG. 70. Nucleotide sequence of SEQ ID NO:1426.
FIG. 71. Nucleotide sequence of SEQ ID NO:1427.
FIG. 72. Nucleotide sequence of SEQ ID NO:1428.
FIG. 73. Nucleotide sequence of SEQ ID NO:1429.
FIG. 74. Nucleotide sequence of SEQ ID NO:1430.
FIG. 75. Nucleotide sequence of SEQ ID NO:1431.
FIG. 76. Nucleotide sequence of SEQ ID NO:1432.
FIG. 77. Nucleotide sequence of SEQ ID NO:1433.
FIG. 78. Nucleotide sequence of SEQ ID NO:1434.
FIG. 79. Nucleotide sequence of SEQ ID NO:1435.
FIG. 80. Nucleotide sequence of SEQ ID NO:1436.
FIG. 81. Nucleotide sequence of SEQ ID NO:1437.
FIG. 82. Nucleotide sequence of SEQ ID NO:1438.
FIG. 83. Nucleotide sequence of SEQ ID NO:1439.
FIG. 84. Nucleotide sequence of SEQ ID NO:1440.
FIG. 85. Nucleotide sequence of SEQ ID NO:1441.
FIG. 86. Nucleotide sequence of SEQ ID NO:1442.
FIG. 87. Nucleotide sequence of SEQ ID NO:1443.
FIG. 88. Nucleotide sequence of SEQ ID NO:1444.
FIG. 89. Nucleotide sequence of SEQ ID NO:1445.
FIG. 90. Nucleotide sequence of SEQ ID NO:1446.
FIG. 91. Nucleotide sequence of SEQ ID NO:1447.
FIG. 92. Nucleotide sequence of SEQ ID NO:1448.
FIG. 93. Nucleotide sequence of SEQ ID NO:1381.
FIG. 94. The difference in mortality between vaccinated and non-vaccinated chickens after intravenous challenge with S. enterica serovar Enteritidis.



DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS OF THE INVENTION
The present invention provides polypeptides and compositions including polypeptides. As used herein, “polypeptide” refers to a polymer of amino acids linked by peptide bonds. Thus, for example, the terms peptide, oligopeptide, protein, and enzyme are included within the definition of polypeptide. This term also includes post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations, and the like. The term polypeptide does not connote a specific length of a polymer of amino acids. A polypeptide may be obtainable directly from a natural source, or can be prepared with the aid of recombinant, enzymatic, or chemical techniques. In the case of a polypeptide that is naturally occurring, such polypeptide is typically isolated. An “isolated” polypeptide is one that has been removed from its natural environment. For instance, an isolated polypeptide is a polypeptide that has been removed from the cytoplasm or from the outer membrane of a cell, and many of the polypeptides, nucleic acids, and other cellular material of its natural environment are no longer present. A “purified” polypeptide is one that is at least 60% free, preferably 75% free, and most preferably 90% free from other components with which they are naturally associated. Polypeptides that are produced outside the organism in which they naturally occur, e.g., through chemical or recombinant means, are considered to be isolated and purified by definition, since they were never present in a natural environment. As used herein, a “polypeptide fragment” refers to a portion of a polypeptide that results from digestion of a polypeptide with a protease. Unless otherwise specified, “a,” “an,” “the,” and “at least one” are used interchangeably and mean one or more than one.
A polypeptide of the present invention may be characterized by molecular weight. The molecular weight of a polypeptide, typically expressed in kilodaltons (kDa), can be determined using routine methods including, for instance, gel filtration, gel electrophoresis including sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis, capillary electrophoresis, mass spectrometry, and liquid chromatography including HPLC.
A polypeptide of the present invention may be characterized by mass fingerprint. As used herein, a “mass fingerprint” refers to a population of polypeptide fragments obtained from a polypeptide after digestion with a protease. Typically, the polypeptide fragments resulting from a digestion are analyzed using a mass spectrometric method. Each polypeptide fragment is characterized by a mass, or by a mass (m) to charge (z) ratio, which is referred to as an “m/z ratio” or an “m/z value”. Methods for generating a mass fingerprint of a polypeptide are routine. An example of such a method is disclosed in Example 25.
The polypeptides of the present invention may be metal regulated polypeptides. As used herein, a “metal regulated polypeptide” is a polypeptide that is expressed by a microbe at a greater level when the microbe is grown in low metal conditions compared to growth of the same microbe in high metal conditions. Low metal and high metal conditions are described herein. For instance, a metal regulated polypeptide is not expressed at detectable levels during growth of the microbe in high metal conditions but is expressed at detectable levels during growth in low metal conditions. Another type of metal regulated polypeptide is expressed at detectable levels during growth of the microbe in high metal conditions but expressed at higher levels during growth in low metal conditions. The expression of such polypeptides is referred to herein as “enhanced” during growth in low metal conditions. In general, metal regulated polypeptides typically have a molecular weight of 66 kDa or greater. Polypeptides that are not metal regulated are typically expressed at about the same level when the microbe is grown in low metal and high metal conditions. In general, non-metal regulated polypeptides typically have a molecular weight of less than 66 kDa.
Whether a metal regulated polypeptide is expressed at a detectable level or has enhanced expression during growth in low metal conditions can be determined by methods useful for comparing the presence of polypeptides, including, for example, gel filtration, gel electrophoresis including sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis, capillary electrophoresis, mass spectrometry, and liquid chromatography including HPLC. Separate cultures of a microbe are grown under high metal conditions and under low metal conditions, polypeptides of the present invention are isolated as described herein, and the polypeptides present in each culture are resolved and compared. Typically, an equal amount of polypeptide from each culture is used. For instance, when SDS polyacrylamide gel electrophoresis is used to compare the polypeptides, about 30 μg micrograms of polypeptide from each culture is used and loaded into a well. After running the gel and staining the polypeptides, the two lanes can be compared.
Preferably, polypeptides of the present invention have immunogenic activity. “Immunogenic activity” refers to the ability of a polypeptide to elicit an immunological response in an animal. An immunological response to a polypeptide is the development in an animal of a cellular and/or antibody-mediated immune response to the polypeptide. Usually, an immunological response includes but is not limited to one or more of the following effects: the production of antibodies, B cells, helper T cells, suppressor T cells, and/or cytotoxic T cells, directed to an epitope or epitopes of the polypeptide. “Epitope” refers to the site on an antigen to which specific B cells and/or T cells respond so that antibody is produced.
In one aspect, a polypeptide of the present invention has the characteristics of a polypeptide expressed by a reference microbe. The characteristics include both molecular weight and mass fingerprint. The reference microbe can be Salmonella or an E. coli. Preferred examples of each of these are detailed in Table 1.







TABLE 1







Bacterial strains.








Bacterial cell
Laboratory designation





S. enterica serovar Newport
MS020508 (Accession No. PTA-9496,



American Type Culture Collection,



Manassas, VA, deposited Sep. 16, 2008)


S. enterica serovar Enteritidis
MS010531


S. enterica serovar Typhimurium
MS010427


S. enterica serovar Dublin
IRP SDC Serial


E. coli
BEcO157(stx−), MS040330,



MS040324, or MS040827









When the reference microbe is S. enterica serovar Newport, for instance MS020508(ATCC Accession No. PTA-9496), a candidate polypeptide is considered to be a polypeptide of the present invention if it has a molecular weight of 82 kDa, 80 kDa, 74 kDa, 65 kDa, 56 kDa, 55kDa, 52 kDa, 45 kDa, 38 kDa, 36 kDa, 22 kDa, 18 kDa, or 12 kDa, and has a mass fingerprint that is similar to the mass fingerprint of a polypeptide expressed by a reference microbe and having a molecular weight of 80 kDa, 74 kDa, 65 kDa, 56 kDa, 55 kDa, 52 kDa, 45 kDa, 38 kDa, 36 kDa, 22 kDa, 18 kDa, or 12 kDa, respectively.
When the reference microbe is S. enterica serovar Enteritidis, for instance MS010531, a polypeptide is considered to be a polypeptide of the present invention if it has a molecular weight of 92 kDa, 91 kDa, 86 kDa, 83 kDa, 78 kDa, 55 kDa, 40 kDa, 39 kDa, or 38 kDa, and has a mass fingerprint that is similar to the mass fingerprint of a polypeptide expressed by a reference microbe and having a molecular weight of 92 kDa, 91 kDa, 86 kDa, 83 kDa, 78 kDa, 55 kDa, 40 kDa, 39 kDa, or 38 kDa, respectively.
When the reference microbe is S. enterica serovar Typhimurium, for instance MS010427, a polypeptide is considered to be a polypeptide of the present invention if it has a molecular weight of 86 kDa, 82 kDa, 77 kDa, 40 kDa, 39 kDa, or 38 kDa, and has a mass fingerprint that is similar to the mass fingerprint of a polypeptide expressed by a reference microbe and having a molecular weight of 86 kDa, 82 kDa, 77 kDa, 40 kDa, 39 kDa, or 38 kDa, respectively.
When the reference microbe is S. enterica serovar Dublin, for instance IRP SDC Serial, a polypeptide is considered to be a polypeptide of the present invention if it has a molecular weight of 96 kDa kDa, 89 kDa, 81 kDa, 61 kDa, 56 kDa, 51 kDa, 43 kDa, 40 kDa, or 38 kDa, and has a mass fingerprint that is similar to the mass fingerprint of a polypeptide expressed by a reference microbe and having a molecular weight of 96 kDa kDa, 89 kDa, 81 kDa, 61 kDa, 56 kDa, 51 kDa, 43 kDa, 40 kDa, or 38 kDa, respectively.
When the reference microbe is an E. coli, for instance BEcO157(stx-), a polypeptide is considered to be a polypeptide of the present invention if it has a molecular weight of 90 kDa, 86 kDa, 83 kDa, 79 kDa, 66 kDa, 56 kDa, 38 kDa, 37 kDa, or 29 kDa, and has a mass fingerprint that is similar to the mass fingerprint of a polypeptide expressed by a reference microbe and having a molecular weight of 90 kDa, 86 kDa, 83 kDa, 79 kDa, 66 kDa, 56 kDa, 38 kDa, 37 kDa, or 29 kDa, respectively.
When the reference microbe is an E. coli, for instance MS040330, a polypeptide is considered to be a polypeptide of the present invention if it has a molecular weight of 92 kDa, 80 kDa, 77 kDa, 72 kDa, 66 kDa, 50 kDa, 42 kDa, 38 kDa, 36 kDa, 35 kDa, 30 kDa, 19 kDa, or 16 kDa, and has a mass fingerprint that is similar to the mass fingerprint of a polypeptide expressed by a reference microbe and having a molecular weight of 92 kDa, 80 kDa, 77 kDa, 72 kDa, 66 kDa, 50 kDa, 42 kDa, 38 kDa, 36 kDa, 35 kDa, 30 kDa, 19 kDa, or 16 kDa, respectively.
When the reference microbe is an E. coli, for instance MS040324, a polypeptide is considered to be a polypeptide of the present invention if it has a molecular weight of 88 kDa, 82 kDa, 79 kDa, 60 kDa, 54 kDa, 46 kDa, 45 kDa, 38 kDa, 37 kDa, 31 kDa, 30 kDa, 19 kDa, 16 kDa, and has a mass fingerprint that is similar to the mass fingerprint of a polypeptide expressed by a reference microbe and having a molecular weight of 88 kDa, 82 kDa, 79 kDa, 60 kDa, 54 kDa, 46 kDa, 45 kDa, 38 kDa, 37 kDa, 31 kDa, 30 kDa, 19 kDa, 16 kDa, respectively.
When the reference microbe is an E. coli, for instance MS040827, a polypeptide is considered to be a polypeptide of the present invention if it has a molecular weight of 101 kDa, 88 kDa, 85 kDa, 77 kDa, 67 kDa, 38 kDa, 35 kDa, and has a mass fingerprint that is similar to the mass fingerprint of a polypeptide expressed by a reference microbe and having a molecular weight of 101 kDa, 88 kDa, 85 kDa, 77 kDa, 67 kDa, 38 kDa, 35 kDa, respectively.
The polypeptides expressed by a reference microbe and referred to above by molecular weight can be obtained by growth of the reference microbe under low metal conditions and the subsequent isolation of a polypeptide by the processes disclosed herein. A candidate polypeptide can be obtainable from a microbe, preferably a gram negative microbe, more preferably, a member of the family Enterobacteriaceae, for instance, a member of the tribe Escherichieae or Salmonelleae. A candidate polypeptide may also be produced using recombinant, enzymatic, or chemical techniques.
A candidate polypeptide may be evaluated by mass spectrometric analysis to determine whether the candidate polypeptide has a mass fingerprint similar to one of the polypeptides expressed by a reference microbe and referred to above by molecular weight. Typically, the candidate polypeptide is purified, for instance by resolving the candidate polypeptide by gel electrophoresis and excising the portion of the gel containing the candidate polypeptide. Any gel electrophoresis method that separates polypeptides based on differing characteristics can be used, including 1 dimensional or 2 dimensional gel electrophoresis, as well as separation based on, for instance, hydrophobicity, pI, or size. The candidate polypeptide is fragmented, for instance by digestion with a protease. Preferably, the protease cleaves the peptide bond on the carboxy-terminal side of the amino acid lysine and the amino acid arginine, except when the amino acid following the lysine or the arginine is a proline. An example of such a protease is trypsin. Methods for digesting a polypeptide with trypsin are routine and known to the art. An example of such a method is disclosed in Example 24.
Methods for the mass spectrometric analysis of polypeptides are routine and known to the art and include, but are not limited to, matrix assisted laser desorption/ionization time of flight mass spectroscopy (MALDI-TOF MS). Typically, a mixture containing the polypeptide fragments obtained from a candidate polypeptide is mixed with a matrix that functions to transform the laser energy to the sample and produce ionized, preferably monoisotopic, polypeptide fragments. Examples of matrices that can be used include, for instance, sinapinic acid and cyano-4-hydroxycinnamic acid. An example of a method for the analysis of polypeptides by MALDI-TOF MS is described in Example 24. The ionized polypeptide fragments are separated according to their m/z ratio, and detected to yield a spectrum of m/z ratio versus intensity. The spectrum includes m/z values that represent the polypeptide fragments derived from the candidate polypeptide. For any given polypeptide, the amount of each polypeptide fragment resulting from a trypsin digestion should be equimolar. However, it is known that trypsin digestion is not 100% efficient, for instance, some sites are more efficiently cleaved. Thus, when MALDI-TOF MS is used to determine m/z values, the intensity of each m/z value is typically not identical. Generally, a spectrum has a background level of noise present across most of the x-axis (i.e., the axis having the values of the m/z ratios). This background level of noise varies depending on the running conditions and the machine used, and is easily identified by visual inspection of the spectrum. An m/z value is generally considered to represent a polypeptide fragment when the intensity is at least 2 times greater, 3 times greater, or 4 times greater than the background level of noise. The spectrum usually includes other m/z values that are artifacts resulting from, for instance, incomplete digestion, over digestion, other polypeptides that may be present in the mixture, or the protease used to digest the polypeptide including m/z values resulting from autolysis of the protease. This method of digesting a polypeptide with a protease is recognized by the art as resulting in a mass fingerprint of great specificity that can be used to accurately characterize the polypeptide and distinguish it from other polypeptides.
In this aspect of the invention, when a candidate polypeptide is analyzed by mass spectroscopy, preferably both the candidate polypeptide and the polypeptide from the reference microbe are prepared and analyzed together, thereby decreasing any potential artifacts resulting from differences in sample handling and running conditions. Preferably, all reagents used to prepare and analyze the two polypeptides are the same. For instance, the polypeptide from the reference microbe and the candidate polypeptide are isolated under substantially the same conditions, fragmented under substantially the same conditions, and analyzed by MALDI-TOF MS on the same machine under substantially the same conditions. A mass fingerprint of a candidate polypeptide is considered to be similar to the mass fingerprint of a polypeptide from a reference microbe when 80%, 90%, 95%, or substantially all of the m/z values present in the spectrum of the reference microbe polypeptide and above the background level of noise are also present in the spectrum of the candidate polypeptide.
In another aspect, a polypeptide is considered to be a polypeptide of the present invention if it has a molecular weight of a reference polypeptide described in Table 2, 3, 4, 5, 6, 7, 8, or 9 and has a mass fingerprint that includes the population of polypeptide fragments of the reference polypeptide as listed in Table 2, 3, 4, 5, 6, 7, 8, or 9. For instance, a polypeptide of the present invention includes a polypeptide of 82 kDa and a mass fingerprint that includes polypeptide fragments having masses of 629.39, 644.37, 772.42, 831.45, 873.46, 991.55, 1083.61, 1208.58, 1325.75, 1378.66, 1500.71, 1619.77, 1634.84, 1619.77, 1728.83, 1872.88, 1981.96, 1998.06, 2193.94, and 2332.05. The mass fingerprint of a candidate polypeptide can be determined by a mass spectrometric method as described herein, preferably, by MALDI-TOF MS. The mass fingerprint of a candidate polypeptide will generally have additional polypeptide fragments and therefore additional m/z values other than those listed for a polypeptide in Table 2, 3, 4, 5, 6, 7, 8, or 9. Preferably, when the candidate polypeptide is being compared to a polypeptide in Table 2, 3, 4, or 5, the candidate polypeptide is obtained from an S. enterica serovar Newport, an S. enterica serovar Enteritidis, an S. enterica serovar Typhimurium, or an S. enterica serovar Dublin, respectively. Preferably, when the candidate polypeptide is being compared to a polypeptide in Table 6, 7, 8, or 9, the candidate polypeptide is obtained from an E. coli. A candidate polypeptide can be obtained by growth of a microbe under low metal conditions and the subsequent isolation of a polypeptide by the processes described herein.
It is well known in the art that modifications of amino acids can be accidentally introduced during sample handling, such as oxidation, and formation of carbamidomethyl derivatives. Further, these types of modifications alter the m/z value of a polypeptide fragment. For instance, if a polypeptide fragment contains a methoinine that is oxidized the m/z value will be increased by 16 relative to the same fragment that does not contain the oxidized methionine. It is understood that the polypeptide fragments of Tables 2, 3, 4, 5, 6, 7, 8, and 9 can be modified during sample handling.







TABLE 2







Characteristics of polypeptides obtained from


Salmonella enterica serovar Newport.












mass of





polypeptide
predicted



approximate
fragments
amino acid



molecular
resulting
sequence



weight in
from
of the


polypeptide
kilodaltons
trypsin
polypeptide


designation
(kDa)1
digest2
fragment













Lw221
82
628.39
IEVLR





(SEQ ID NO: 1)


 




643.37
QIDIR





(SEQ ID NO: 2)


 




771.42
DINGVVR





(SEQ ID NO: 3)


 




830.45
DVSEIIR





(SEQ ID NO: 4)


 




872.46
LGWRGER





(SEQ ID NO: 5)


 




990.55
EIGLEFKR





(SEQ ID NO: 6)


 




1082.61
IEAGTVPLQR





(SEQ ID NO: 7)


 




1207.58
TGSYADTLPAGR





(SEQ ID NO: 8)


 




1324.75
NKIEAGTVPLQR





(SEQ ID NO: 9)


 




1377.66
TDVYQWENVPK





(SEQ ID NO: 10)


 




1463.74
LYGNLDKTQADAR





(SEQ ID NO: 15)


 




1499.71
GDTAWVPPEMIER





(SEQ ID NO: l1)


 




1618.77
TMPGVNLTGNSTSGQR





(SEQ ID NO: 13)


 




1633.84
NVSLTGGVDNLFDKR





(SEQ ID NO: 14)


 




1727.83
TNFSLNGPLGGDFSFR





(SEQ ID NO: 16)


 




1871.88
DTRGDTAWVPPEMIER





(SEQ ID NO: 17)


 




1980.96
WDFAPLQSLELEAGYS





R





(SEQ ID NO: 18)


 




1997.06
GMGPENTLILIDGKPV





TSR





(SEQ ID NO: 19)


 




2192.94
DTQTGAYKAGAGAYTY





NEPGR





(SEQ ID NO: 21)


 




2331.05
KGGSEWHGSWNTYFNA





PEHK





(SEQ ID NO: 22)


 


Lw223A
80
848.45
LYGNLNR





(SEQ ID NO: 23)


 




918.45
LGFYYEK





(SEQ ID NO: 24)


 




1040.60
IVAGDQIIGR





(SEQ ID NO: 25)


 




1097.62
QQPGVSIITR





(SEQ ID NO: 26)


 




1309.63
ITNDQTFTTNR





(SEQ ID NO: 27)


 




1335.71
NPPVNDLADIIR





(SEQ ID NO: 28)


 




1341.66
DSNIAGIPGSAANR





(SEQ ID NO: 29)


 




1364.60
SAEGANTYNEPGR





(SEQ ID NO: 30)


 




1528.70
GDTNWVPPEMVER





(SEQ ID NO: 31)


 




1564.76
SASGAYVLQWQNGGK





(SEQ ID NO: 32)


 




1735.86
GNFSLSGPLAGDTLTM





R





(SEQ ID NO: 33)


 




1750.86
EGVTNKDINSVFSWR





(SEQ ID NO: 34)


 




1754.83
MTPQQILDFEAGYSR





(SEQ ID NO: 35)


 




1845.91
APNLYQTSEGYLLYSK





(SEQ ID NO: 36)


 




1911.98
ALIEGIEASMAVPLMP





DR





(SEQ ID NO: 37)


 




1929.04
GPAAARYGSGAAGGVV





NIITK





(SEQ ID NO: 38)


 




1935.01
DDIQKNPPVNDLADII





R





(SEQ ID NO: 39)


 




2030.93
QNYGLTHNGIWDWGQS





R





(SEQ ID NO: 40)


 




2416.14
RPTNDWHGSLSLYTNQ





PESSK





(SEQ ID NO: 41)


 




2587.35
IVAGDQIIGRSASGAY





VLQWQNGGK





(SEQ ID NO: 42)


 




2701.36
SEISALYVEDNIEPMA





GTNIIPGLR





(SEQ ID NO: 43)


 




2909.36
FDYLSESGSNFSPSLN





LSQELGEYVK





(SEQ ID NO: 44)


 




2943.50
NKSEISALYVEDNIEP





MAGTNIIPGLR





(SEQ ID NO: 45)


 


Lw223B
74
605.33
NAVFR





(SEQ ID NO: 46)


 




616.37
VPVFR





(SEQ ID NO: 47)


 




808.41
IEGFTSR





(SEQ ID NO: 48)


 




1063.48
YFMAVDYR





(SEQ ID NO: 49)


 




1158.55
QNYALSHNGR





(SEQ ID NO: 50)


 




1210.55
YFMAVDYRF





(SEQ ID NO: 51)


 




1314.62
LSLNYTYNDGR





(SEQ ID NO: 52)


 




1329.77
IFEPLALTTGIR





(SEQ ID NO: 53)


 




1345.55
DDYGYTEDGRR





(SEQ ID NO: 54)


 




1526.73
EVPGVQLTNEGDNR





(SEQ ID NO: 55)


 




1649.90
GLDSSYTLILIDGKR





(SEQ ID NO: 56)


 




1677.74
DEQQSSATTATGETPR





(SEQ ID NO: 57)


 




1740.90
DAPASISVITQQDLQR





(SEQ ID NO: 58)


 




1744.69
MDDHETYGDHWSPR





(SEQ ID NO: 59)


 




1750.84
WHGSVTVDSTIQEHR





(SEQ ID NO: 60)


 




1792.88
GEEGILEGVEASVTTF





R





(SEQ ID NO: 61)


 




1814.85
TSASQYALFLEDEWR





(SEQ ID NO: 82)


 




1906.92
TPGGYVVWDTGAAWQA





TK





(SEQ ID NO: 63)


 




1934.88
EKDEQQSSATTATGET





PR





(SEQ ID NO: 64)


 




1952.94
HNDFDLNWIPVDAIER





(SEQ ID NO: 65)


 




1987.04
IQGVETELKVPFNEAW





K





(SEQ ID NO: 66)


 




2242.03
TPDVNAAPGYSNFVGF





ETNSR





(SEQ ID NO: 67)


 




2538.26
IVGSPDLKPETSESWE





LGLYYR





(SEQ ID NO: 68)


 




2587.24
DRGDTYNGQFFTSGPL





IDGVLGMK





(SEQ ID NO: 69)


 




2710.17
DGNVEFAWTPNENHDV





TAGYGFDR





(SEQ ID NO: 70)


 


P4
65
1303.65
WQSTSVNDVLR





(SEQ ID NO: 71)


 




1398.57
YDSDYSAYPYR





(SEQ ID NO: 72)


 




1508.73
TLYGALEHTFSDR





(SEQ ID NO: 73)


 




1792.85
QWEGAFEGLTAGVSWR





(SEQ ID NO: 74)


 




1868.85
QTTTPGTGYVPEGYDQ





R





(SEQ ID NO: 75)


 




1932.87
TDYDAYYSPGSPLIDT





R





(SEQ ID NO: 76)


 




2023.92
HGTWQTSAGWEFIEGY





R





(SEQ ID NO: 77)


 




2086.08
LPGVDIAQSGGAGQNS





SIFIR





(SEQ ID NO: 78)


 




2257.21
LNLAGVSGSADLSQFP





VSLVQR





(SEQ ID NO: 79)


 


Lw224
56
1100.52
DDAAGQAIANR





(SEQ ID NO: 80)


 




1131.59
SQSALGTAIER





(SEQ ID NO: 81)


 




1254.69
IDAALAQVDALR





(SEQ ID NO: 82)


 




1715.73
IEDSDYATEVSNMSR





(SEQ ID NO: 83)


 




1756.93
QINSQTLGLDSLNVQK





(SEQ ID NO: 84)


 




1958.86
SRIEDSDYATEVSNMS





R





(SEQ ID NO: 85)


 




2034.01
FNSAITNLGNTVNNLS





EAR





(SEQ ID NO: 86)


 




2669.30
NANDGISIAQTTEGAL





NEINNNLQR





(SEQ ID NO: 87)


 




2804.34
ELAVQSANSTNSQSDL





DSIQAEITQR





(SEQ ID NO: 88)


 




2859.59
AQILQQAGTSVLAQAN





QVPQNVLSLLR





(SEQ ID NO: 89)


 




3059.51
VRELAVQSANSTNSQS





DLDSIQAEITQR





(SEQ ID NO: 90)


 


Lw225
55
958.48
SDLGAVQNR





(SEQ ID NO: 91)


 




1100.52
DDAAGQAIANR





(SEQ ID NO: 92)


 




1131.59
SQSALGTAIER





(SEQ ID NO: 93)


 




1143.59
TALNQLGGADGK





(SEQ ID NO: 94)


 




1254.69
IDAALAQVDALR





(SEQ ID NO: 95)


 




1603.77
ADVDADGNVSLATGAT





K





(SEQ ID NO: 96)


 




1613.81
INSAKDDAAGQAIANR





(SEQ ID NO: 97)


 




1621.82
AGITGTTTETGSVKDG





K





(SEQ ID NO: 98)


 




1639.79
YDVDSTGVTQSLDLK





(SEQ ID NO: 99)


 




1708.75
NYYVEVDFTDTTDK





(SEQ ID NO: 100)


 




1715.73
IEDSDYATEVSNMSR





(SEQ ID NO: 101)


 




1770.95
QINSQTLGLDTLNVQK





(SEQ ID NO: 102)


 




1903.98
LNEIDRVSGQTQFNGV





K





(SEQ ID NO: 103)


 




1958.86
SRIEDSDYATEVSNMS





R





(SEQ ID NO: 104)


 




2084.12
AQVINTNSLSLLTQNN





LNK





(SEQ ID NO: 105)


 




2195.17
IDAALAQVDALRSDLG





AVQNR





(SEQ ID NO: 106)


 




2669.30
NANDGISIAQTTEGAL





NEINNNLQR





(SEQ ID NO: 107)


 




2804.34
ELAVQSANSTNSQSDL





DSIQAEITQR





(SEQ ID NO: 108)


 




3059.51
VRELAVQSANSTNSQS





DLDSIQAEITQR





(SEQ ID NO: 109)


 


Lw226
52
787.46
SVVQTVR





(SEQ ID NO: 110)


 




799.43
QQLANAR





(SEQ ID NO: 111)


 




801.43
LSQDLAR





(SEQ ID NO: 112)


 




827.45
LSNPELR





(SEQ ID NO: 113)


 




913.53
NLSLLQAR





(SEQ ID NO: 114)


 




1089.50
ANSNNGNPFR





(SEQ ID NO: 115)


 




1285.63
NNLDNAVEELR





(SEQ ID NO: 116)


 




1381.76
YTYLINQLNIK





(SEQ ID NO: 117)


 




1549.77
AQYDTVLANEVTAR





(SEQ ID NO: 118)


 




1615.87
FNVGLVAITDVQNAR





(SEQ ID NO: 119)


 




1661.90
VLNAIDVLSYTQAQK





(SEQ ID NO: 120)


 




1737.90
TIVDVLDATTTLYDAK





(SEQ ID NO: 121)


 




1828.90
SSFNNINASISSINAY





K





(SEQ ID NO: 122)


 




2033.96
QAQYNFVGASEQLESA





HR





(SEQ ID NO: 123)


 




2184.09
SPLLPQLGLGADYTYS





NGYR





(SEQ ID NO: 124)


 




2208.09
QVTGNYYPELASLNVE





HFK





(SEQ ID NO: 125)


 




2226.06
QAVVSAQSSLDANEAG





YSVGTR





(SEQ ID NO: 126)


 




2684.26
DANGINSNETSASLQL





TQTLFDMSK





(SEQ ID NO: 127)


 




2748.32
QAQDGHLPTLNLTAST





GISDTSYSGSK





(SEQ ID NO: 128)


 




2886.44
AAGIQDVTYQTDQQTL





ILNTANAYFK





(SEQ ID NO: 129)


 


Lw227
45
665.35
WGYIK





(SEQ ID NO: 130)


 




730.43
LSLAATR





(SEQ ID NO: 131)


 




812.44
IFATYAK





(SEQ ID NO: 132)


 




858.46
LGQEVWK





(SEQ ID NO: 133)


 




963.46
VDFHGYAR





(SEQ ID NO: 134)


 




1150.53
DTANDVFDVR





(SEQ ID NO: 135)


 




1223.60
WDEKWGYIK





(SEQ ID NO: 136)


 




1411.67
YAAATNSGISTNSR





(SEQ ID NO: 137)


 




1422.69
WGYIKDGDNISR





(SEQ ID NO: 138)


 




1658.80
FVVQYATDAMTTQGK





(SEQ ID NO: 139)


 




1683.90
NLIEWLPGSTIWAGK





(SEQ ID NO: 140)


 




1780.79
DGWMFTAEHTQSMLK





(SEQ ID NO: 141)


 




1964.99
WTPIMSTLLEVGYDNV





K





(SEQ ID NO: 142)


 




2086.07
LAGLQTNPDGVLELGV





DYGR





(SEQ ID NO: 143)


 




2181.97
STEAGGSYTESSQNIY





DEVK





(SEQ ID NO: 144)


 




2296.21
ITLAQQWQAGDSIWSR





PAIR





(SEQ ID NO: 145)


 




3100.35
SFYFDTNVAYSVNQQN





DWESTDPAFR





(SEQ ID NO: 146)


 




3314.49
STEAGGSYTESSQNIY





DEVKDTANDVFDVR





(SEQ ID NO: 147)


 


Lw228A
38
718.44
LAFAGLK





(SEQ ID NO: 148)


 




867.44
TTGVATYR





(SEQ ID NO: 149)


 




1057.56
NAEVWAAGLK





(SEQ ID NO: 150)


 




1103.50
NMSTFVDYK





(SEQ ID NO: 151)


 




1121.57
DGNKLDLYGK





(SEQ ID NO: 152)


 




1296.54
FADYGSFDYGR





(SEQ ID NO: 153)


 




1638.83
VSTDNIVAVGLNYQF





(SEQ ID NO: 154)


 




2218.07
NTDFFGLVEGLNFAAQ





YQGK





(SEQ ID NO: 155)


 




2382.03
VHAQHYFSDDNGSDGD





KTYAR





(SEQ ID NO: 156)


 




2389.09
GETQINDQLTGFGQWE





YEFK





(SEQ ID NO: 157)


 




2603.24
NTDFFGLVEGLNFAAQ





YQGKNDR





(SEQ ID NO: 158)


 




2716.25
GETQINDQLTGFGQWE





YEFKGNR





(SEQ ID NO: 159)


 




2757.28
NLGTYGDQDLVEYIDV





GATYYFNK





(SEQ ID NO: 160)


 




2805.41
TQNFEAVAQYQFDFGL





RPSIAYLK





(SEQ ID NO: 161)


 




2834.36
LGFKGETQINDQLTGF





GQWEYEFK





(SEQ ID NO: 162)


 




3065.32
DGAYESNGDGFGLSAT





YEYEGFGVGAAYAK





(SEQ ID NO: 163)


 




3450.49
NDRDGAYESNGDGFGL





SATYEYEGFGVGAAYA





K





(SEQ ID NO: 164)


 


Lw228B
38
704.42
VAFAGLK





(SEQ ID NO: 165)


 




793.37
LYGNOOR





(SEQ ID NO: 166)


 




900.41
GNGYATYR





(SEQ ID NO: 167)


 




908.50
ATVYTGGLK





(SEQ ID NO: 168)


 




1105.58
DGNKLDLFGK





(SEQ ID NO: 169)


 




1204.51
FADAGSFDYGR





(SEQ ID NO: 171)


 




1800.82
DISNGYGASYGDQDIV





K





(SEQ ID NO: 174)


 




1834.81
FGTSNGSNPSTSYGFA





NK





(SEQ ID NO: 175)


 




1944.95
LDLFGKVDGLNYFSDD





K





(SEQ ID NO: 170)


 




1985.93
GKDISNGYGASYGDQD





IVK





(SEQ ID NO: 176)


 




2247.08
NTDFFGLVDGLDFALQ





YQGK





(SEQ ID NO: 177)


 




2382.01
VDGLNYFSDDKGSDGD





QTYMR





(SEQ ID NO: 178)


 




3004.51
AQNFEVVAQYQFDFGL





RPSVAYLQSK





(SEQ ID NO: 180)


 




3133.52
SLLNQNGDGYGGSLTY





AIGEGFSVGGAITTSK





(SEQ ID NO: 181)


 


Lw230A
36
817.43
LGGMVWR





(SEQ ID NO: 182)


 




871.51
RVEIEVK





(SEQ ID NO: 183)


 




914.52
AQGVQLTAK





(SEQ ID NO: 184)


 




1024.46
DNTWYAGAK





(SEQ ID NO: 185)


 




1082.54
SDVLFNFNK





(SEQ ID NO: 186)


 




1156.59
AALIDCLAPDR





(SEQ ID NO: 187)


 




1263.65
DGSVVVLGFTDR





(SEQ ID NO: 188)


 




1377.76
RAQSVVDYLISK





(SEQ ID NO: 189)


 




1380.65
IGSDAYNQGLSEK





(SEQ ID NO: 190)


 




1536.75
IGSDAYNQGLSEKR





(SEQ ID NO: 191)


 




1639.81
LGYPITDDLDVYTR





(SEQ ID NO: 192)


 




2302.20
FGQQEAAPVVAPAPAP





APEVQTK





(SEQ ID NO: 193)


 




2615.29
DHDTGVSPVFAGGIEY





AITPEIATR





(SEQ ID NO: 194)


 




2672.37
STLKPEGQQALDQLYS





QLSNLDPK





(SEQ ID NO: 195)


 




3422.69
LEYQWTNNIGDANTIG





TRPDNGLLSVGVSYR





(SEQ ID NO: 196)


 


Lw233
22
1050.53
VRPYVGVGVNYTTFFD





NDPNDNGK





(SEQ ID NO: 202)


 




1221.57
NAGLSDLSFKDSWGAA





GQVGVDYLINR





(SEQ ID NO: 203)


 




1587.75
VGTGATGDIATVHLLP





PTLMAQWYFGDSSSK





(SEQ ID NO: 204)


 




1734.82
MSGFNLK





(SEQ ID NO: 205)


 




1819.89
FQTTDYPTYK





(SEQ ID NO: 206)


 




2737.28
GQYYGITAGPAYR





(SEQ ID NO: 207)


 




2852.41
SVDVGTWIAGVGYR





(SEQ ID NO: 208)


 




3219.59
SVDVGTWIAGVGYRF





(SEQ ID NO: 209)


 


Lw234
18
795.39
LNDWASIYGVVGVGYG





K





(SEQ ID NO: 210)


 




1262.58
YEQDDNPLGVIGSFTY





TEK





(SEQ ID NO: 211)


 




1415.68
YEQDDNPLGVIGSFTY





TEKDR





(SEQ ID NO: 212)


 




1478.75
YRYEQDDNPLGVIGSF





TYTEK





(SEQ ID NO: 213)


 




1625.82
LDNQATK





(SEQ ID NO: 214)


 




1796.91
SDVQAAKDDAAR





(SEQ ID NO: 215)


 




2175.00
ANQRLDNQATK





(SEQ ID NO: 216)


 




2446.13
VDQLSNDVNAMR





(SEQ ID NO: 217)


 




2494.17
IDQLSSDVQTLNAK





(SEQ ID NO: 218)


 


Lw235
12
788.40
VDQLSNDVNAMRSDVQ





AAK





(SEQ ID NO: 219)


 




1245.59
IDQLSSDVQTLNAKVD





QLSNDVNAMR





(SEQ ID NO: 220)





1. Molecular weight as determined by SDS-PAGE.


2. The mass of a polypeptide fragment can be converted to m/z value by adding 1 to the mass. Each mass includes a range of plus or minus 300 parts per million (ppm).













TABLE 3







Characteristics of polypeptides obtained from


S. enterilidis serovar Enteritidis.












mass of





poly-




peptide
predicted



approximate
fragments
amino acid



molecular
resulting
sequence



weight in
from
of the


polypeptide
kilodaltons
trypsin
polypeptide


designation
(kDa)1
digest2
fragment













Lw 98
92
728.43
WVVLGR





(SEQ ID NO: 221)


 




815.38
SYYLDR





(SEQ ID NO: 222)


 




888.41
YGYAYPR





(SEQ ID NO: 223)


 




957.50
AGLGYVHNK





(SEQ ID NO: 224)


 




972.50
QNLEASGVR





(SEQ ID NO: 225)


 




986.54
LAGDLETLR





(SEQ ID NO: 226)


 




998.45
GYFPTDGSR





(SEQ ID NO: 227)


 




1008.47
WGYGDGLGGK





(SEQ ID NO: 228)


 




1047.53
GFQSNTIGPK





(SEQ ID NO: 229)


 




1076.59
LVFQEGVSAK





(SEQ ID NO: 230)


 




1113.56
DIHFEGLQR





(SEQ ID NO: 231)


 




1180.59
AEQFQFNIGK





(SEQ ID NO: 232)


 




1219.61
IEPGELYNGTK





(SEQ ID NO: 233)


 




1276.60
GLEDFYYSVGK





(SEQ ID NO: 234)


 




1282.74
VAVGAALLSMPVR





(SEQ ID NO: 235)


 




1338.66
ALFATGNFEDVR





(SEQ ID NO: 236)


 




1384.65
VTIPGSDNEYYK





(SEQ ID NO: 237)


 




1401.71
VPGSPDQVDVVYK





(SEQ ID NO: 238)


 




1402.67
LSNMQPQIAMDR





(SEQ ID NO: 239)


 




1470.69
DEVPWWNVVGDR





(SEQ ID NO: 240)


 




1519.80
ERPTIASITFSGNK





(SEQ ID NO: 241)


 




1527.72
LGFFETVDTDTQR





(SEQ ID NO: 242)


 




1648.75
TGDTVNDEDISNTIR





(SEQ ID NO: 243)


 




1691.87
FNIDSTQVSLTPDKK





(SEQ ID NO: 244)


 




1712.86
GIYITVNITEGDQYK





(SEQ ID NO: 1352)


 




1732.81
QMEGAWLGSDLVDQGK





(SEQ ID NO: 1353)


 




1758.82
YDGDKAEQFQFNIGK





(SEQ ID NO: 1354)


 




1786.87
VSLDTATYVPIDNDHK





(SEQ ID NO: 1355)


 




1894.97
LSGVQVSGNLAGHSAEI





EK





(SEQ ID NO: 1356)


 




1953.86
EMPFYENFYAGGSSTVR





(SEQ ID NO: 1357)


 




2159.05
SYGTDVTLGFPINEYNT





LR





(SEQ ID NO: 1358)


 




2254.95
IFYNDFEADDADLSDYT





NK





(SEQ ID NO: 1359)


 




2284.27
LLIASLLFSSATVYGAE





GFVVK





(SEQ ID NO: 1360)


 




2793.46
IQQINIVGNHAFSTEEL





ISHFQLR





(SEQ ID NO: 1361)


 




2881.34
NDYQTYSELSVTNPYFT





VDGVSLGGR





(SEQ ID NO: 1362)


 


Lw 99
91
904.51
LVQLNYR





(SEQ ID NO: 1363)


 




924.43
SGVQYDTR





(SEQ ID NO: 1364)


 




945.53
SGFLIPNAK





(SEQ ID NO: 1365)


 




1004.49
WGSLNTEAK





(SEQ ID NO: 1366)


 




1050.50
IYDDAAVER





(SEQ ID NO: 197)


 




1075.60
VDGKLIFER





(SEQ ID NO: 198)


 




1109.55
QAEGQPEPVR





(SEQ ID NO: 199)


 




1199.63
VQYLYVPYR





(SEQ ID NO: 200)


 




1276.56
YGSSTDGYATQK





(SEQ ID NO: 201)


 




1294.58
GNIMWENEFR





(SEQ ID NO: 245)


 




1307.68
LQADEVQLHQK





(SEQ ID NO: 246)


 




1343.65
EEQVAEIWNAR





(SEQ ID NO: 247)


 




1375.72
IYGQAVHFVNTK





(SEQ ID NO: 248)


 




1417.75
IASANQVTTGVTTR





(SEQ ID NO: 249)


 




1450.68
RGNIMWENEFR





(SEQ ID NO: 250)


 




1509.63
VSDSSYFNDFDSK





(SEQ ID NO: 251)


 




1510.72
TGSLVWAGDTYWR





(SEQ ID NO: 252)


 




1601.89
VHLEPTINLPLSNR





(SEQ ID NO: 253)


 




1618.81
EEQVAEIWNARFK





(SEQ ID NO: 254)


 




1624.79
GLSSNYGLGTQEMLR





(SEQ ID NO: 255)


 




1668.72
DTNVWEGDYQMVGR





(SEQ ID NO: 256)


 




1766.91
NGINQVGAVASWPIADR





(SEQ ID NO: 257)


 




1766.91
NGINQVGAVASWPIADR





(SEQ ID NO: 258)


 




1792.85
DMAMLAPGYTQTLEPR





(SEQ ID NO: 259)


 




1808.87
FNVSVGQIYYFTESR





(SEQ ID NO: 260)


 




1832.89
FSVGYAVQNFDATVSTK





(SEQ ID NO: 261)


 




2013.02
TVDALGNVHYDDNQVIL





K





(SEQ ID NO: 262)


 




2088.13
VGPVPIFYSPYLQLPVG





DK





(SEQ ID NO: 263)


 




2269.01
GNYPDDAVFTGNVDIMQ





GNSR





(SEQ ID NO: 264)


 




2298.03
WENDDKTGSLVWAGDTY





WR





(SEQ ID NO: 265)


 




2453.09
LMATHYQQTNLDSYNSD





PNNK





(SEQ ID NO: 266)


 




2554.16
DQSGIYNYDSSLLQSDY





NGLFR





(SEQ ID NO: 267)


 




2572.20
YASPEYIQATLPSYYST





AEQYK





(SEQ ID NO: 268)


 


Lw 101
86
643.37
QIDIR





(SEQ ID NO: 269)


 




872.46
LGWRGER





(SEQ ID NO: 270)


 




950.49
ETNRLYR





(SEQ ID NO: 271)


 




990.55
EIGLEFKR





(SEQ ID NO: 272)


 




1082.61
IEAGTVPLQR





(SEQ ID NO: 273)


 




1084.57
GNNRQIDIR





(SEQ ID NO: 274)


 




1095.49
DNYGKETNR





(SEQ ID NO: 275)


 




1151.68
IEVLRGPAAAR





(SEQ ID NO: 276)


 




1181.55
NINQGHQSER





(SEQ ID NO: 277)


 




1207.58
TGSYADTLPAGR





(SEQ ID NO: 278)


 




1324.75
NKIEAGTVPLQR





(SEQ ID NO: 279)


 




1365.74
NPPARDVSEIIR





(SEQ ID NO: 280)


 




1377.66
TDVYQWENVPK





(SEQ ID NO: 281)


 




1411.78
EGVINKDINGVVR





(SEQ ID NO: 282)


 




1432.77
YGNGAAGGVVNIITK





(SEQ ID NO: 283)


 




1463.74
LYGNLDKTQADAR





(SEQ ID NO: 284)


 




1499.71
GDTAWVPPEMIER





(SEQ ID NO: 285)


 




1560.86
YGNGAAGGVVNIITKK





(SEQ ID NO: 286)


 




1560.86
YGNGAAGGVVNIITKK





(SEQ ID NO: 287)


 




1584.74
KYDYQGNPVTGTDK





(SEQ ID NO: 288)


 




1618.77
TMPGVNLTGNSTSGQR





(SEQ ID NO: 289)


 




1633.84
NVSLTGGVDNLFDKR





(SEQ ID NO: 290)


 




1633.84
NVSLTGGVDNLFDKR





(SEQ ID NO: 291)


 




1727.83
TNFSLNGPLGGDFSFR





(SEQ ID NO: 292)


 




1870.95
APSLYQTNPNYILYSK





(SEQ ID NO: 293)


 




1903.94
INNGKTDVYQWENVPK





(SEQ ID NO: 294)


 




1974.95
NSRMPEGLAGGTEGIFD





PK





(SEQ ID NO: 295)


 




1980.96
WDFAPLQSLELEAGYSR





(SEQ ID NO: 296)


 




1997.06
GMGPENTLILIDGKPVT





SR





(SEQ ID NO: 297)


 




2078.00
QGNLYAGDTQNTNTNQL





VK





(SEQ ID NO: 298)


 




2192.94
DTQTGAYMAGAGAYTYN





EPGR





(SEQ ID NO: 299)


 




2233.14
AYKAPSLYQTNPNYILY





SK





(SEQ ID NO: 300)


 




2371.13
NINQGHQSERTGSYADT





LPAGR





(SEQ ID NO: 301)


 




2531.24
TNFSLNGPLGGDFSFRL





YGNLDK





(SEQ ID NO: 302)


 




2622.42
QIDIRGMGPENTLILID





GKPVTSR





(SEQ ID NO: 303)


 




2632.20
MKDQLSNSQTFMGGNIP





GYSSTNR





(SEQ ID NO: 304)


 




3098.47
FDHHSIVGDNWSPSLNL





SQGLGDDFTLK





(SEQ ID NO: 305)


 




3211.45
QNYSLTWNGGWNNGVTT





SNWVQYEHTR





(SEQ ID NO: 306)


 




3473.51
DTQTGAYMAGAGAYTYN





EPGRTWYMSINTHF





(SEQ ID NO: 307)


 


Lw 102
83
610.29
YSWR





(SEQ ID NO: 308)


 




628.39
IEVIR





(SEQ ID NO: 309)


 




848.45
LYGNLNR





(SEQ ID NO: 310)


 




918.45
LGFYYEK





(SEQ ID NO: 311)


 




1040.60
IVAGDQIIGR





(SEQ ID NO: 312)


 




1097.62
QQPGVSIITR





(SEQ ID NO: 313)


 




1141.60
NLDPEISINK





(SEQ ID NO: 314)


 




1153.63
DTGNPLSIIPK





(SEQ ID NO: 315)


 




1162.50
MNEGLSGGGEGR





(SEQ ID NO: 316)


 




1218.66
LNVGISNIFDK





(SEQ ID NO: 317)


 




1309.63
ITNDQTFTTNR





(SEQ ID NO: 318)


 




1335.71
NPPVNDLADIIR





(SEQ ID NO: 319)


 




1341.66
DSNIAGIPGSAANR





(SEQ ID NO: 320)


 




1364.60
SAEGANTYNEPGR





(SEQ ID NO: 321)


 




1405.76
YGSGAAGGVVNIITK





(SEQ ID NO: 322)


 




1460.70
MPGVNLTGNSASGTR





(SEQ ID NO: 323)


 




1528.70
GDTNWVPPEMVER





(SEQ ID NO: 324)


 




1564.76
SASGAYVLQWQNGGK





(SEQ ID NO: 325)


 




1564.76
SASGAYVLQWQNGGK





(SEQ ID NO: 326)


 




1735.86
GNFSLSGPLAGDTLTMR





(SEQ ID NO: 327)


 




1750.86
EGVTNKDINSVFSWR





(SEQ ID NO: 328)


 




1754.83
MTPQQILDFEAGYSR





(SEQ ID NO: 329)


 




1845.91
APNLYQTSEGYLLYSK





(SEQ ID NO: 330)


 




1880.96
ALGAYSLVGANVNYDIN





K





(SEQ ID NO: 331)


 




1911.98
ALIEGIEASMAVPLMPD





R





(SEQ ID NO: 332)


 




1954.02
GMGPENTLVLIDGVPVT





SR





(SEQ ID NO: 333)


 




2030.93
QNYGLTHNGIWDWGQSR





(SEQ ID NO: 334)


 




2261.06
EIGLEFTVDDYHASVTY





FR





(SEQ ID NO: 335)


 




2397.12
LYGNLNPTDADSWDINS





SAGTK





(SEQ ID NO: 336)


 




2416.14
RPTNDWHGSLSLYTNQP





ESSK





(SEQ ID NO: 337)


 




2701.36
SEISALYVEDNIEPMAG





TNIIPGLR





(SEQ ID NO: 338)


 




2909.36
FDYLSESGSNFSPSLNL





SQELGEYVK





(SEQ ID NO: 339)


 




2943.50
NKSEISALYVEDNIEPM





AGTNIIPGLR





(SEQ ID NO: 340)


 


Lw 103
78
605.33
NAVFR





(SEQ ID NO: 341)


 




614.38
IEVVR





(SEQ ID NO: 342)


 




616.37
VPVFR





(SEQ ID NO: 343)


 




808.41
IEGFTSR





(SEQ ID NO: 344)


 




836.42
GGWATAFK





(SEQ ID NO: 345)


 




989.50
VPFNEAWK





(SEQ ID NO: 346)


 




1060.52
WDLGNSELK





(SEQ ID NO: 347)


 




1063.48
YFMAVDYR





(SEQ ID NO: 348)


 




1140.66
LRAGVLNVGDK





(SEQ ID NO: 349)


 




1158.55
QNYALSHNGR





(SEQ ID NO: 350)


 




1177.52
QDRDSDSLDK





(SEQ ID NO: 351)


 




1177.52
QDRDSDSLDK





(SEQ ID NO: 352)


 




1210.55
YFMAVDYRF





(SEQ ID NO: 353)


 




1314.62
LSLNYTYNDGR





(SEQ ID NO: 354)


 




1329.77
IFEPLALTTGIR





(SEQ ID NO: 355)


 




1345.55
DDYGYTEDGRR





(SEQ ID NO: 356)


 




1493.80
GLDSSYTLILIDGK





(SEQ ID NO: 357)


 




1526.73
EVPGVQLTNEGDNR





(SEQ ID NO: 358)


 




1570.82
AYLVYNATDTLTVK





(SEQ ID NO: 359)


 




1649.90
GLDSSYTLILIDGKR





(SEQ ID NO: 360)


 




1654.83
EVPGVQLTNEGDNRK





(SEQ ID NO: 361)


 




1740.90
DAPASISVITQQDLQR





(SEQ ID NO: 362)


 




1744.69
MDDHETYGDHWSPR





(SEQ ID NO: 363)


 




1750.84
WHGSVTVDSTIQEHR





(SEQ ID NO: 364)


 




1792.88
GEEGILEGVEASVTTFR





(SEQ ID NO: 365)


 




1814.85
TSASQYALFLEDEWR





(SEQ ID NO: 366)


 




1906.92
TPGGYVVWDTGAAWQAT





K





(SEQ ID NO: 367)


 




1952.94
HNDFDLNWIPVDAIER





(SEQ ID NO: 368)


 




2242.03
TPDVNAAPGYSNFVGFE





TNSR





(SEQ ID NO: 369)


 




2538.26
IVGSPDLKPETSESWEL





GLYYR





(SEQ ID NO: 370)


 




2710.17
DGNVEFAWTPNENHDVT





AGYGF





(SEQ ID NO: 371)


 


Lw 104
55
787.46
SVVQTVR





(SEQ ID NO: 372)


 




801.43
LSQDLAR





(SEQ ID NO: 373)


 




913.53
NLSLLQAR





(SEQ ID NO: 374)


 




1179.55
SAADRDAAFEK





(SEQ ID NO: 375)


 




1226.55
ANSNNGNPFRH





(SEQ ID NO: 376)


 




1226.55
ANSNNGNPFRH





(SEQ ID NO: 377)


 




1285.63
NNLDNAVEELR





(SEQ ID NO: 378)


 




1381.76
YTYLINQLNIK





(SEQ ID NO: 379)


 




1549.77
AQYDTVLANEVTAR





(SEQ ID NO: 380)


 




1615.87
FNVGLVAITDVQNAR





(SEQ ID NO: 381)


 




1661.90
VLNAIDVLSYTQAQK





(SEQ ID NO: 382)


 




1737.90
TIVDVLDATTTLYDAK





(SEQ ID NO: 383)


 




1828.90
SSFNNINASISSINAYK





(SEQ ID NO: 384)


 




2033.96
QAQYNFVGASEQLESAH





R





(SEQ ID NO: 385)


 




2184.09
SPLLPQLGLGADYTYSN





GYR





(SEQ ID NO: 386)


 




2208.09
QVTGNYYPELASLNVEH





FK





(SEQ ID NO: 387)


 




2226.06
QAVVSAQSSLDAMEAGY





SVGTR





(SEQ ID NO: 388)


 




2748.32
QAQDGHLPTLNLTASTG





ISDTSYSGSK





(SEQ ID NO: 389)


 




2886.44
AAGIQDVTYQTDQQTLI





LNTANAYFK





(SEQ ID NO: 390)


 


Lw 106A
40
691.39
LDLFGK





(SEQ ID NO: 391)


 




704.42
VAFAGLK





(SEQ ID NO: 392)


 




900.41
GNGYATYR





(SEQ ID NO: 393)


 




908.50
ATVYTGGLK





(SEQ ID NO: 394)


 




973.45
STSYGFANK





(SEQ ID NO: 395)


 




1105.58
DGNKLDLFGK





(SEQ ID NO: 396)


 




1128.45
GSDGDQTYMR





(SEQ ID NO: 397)


 




1190.53
NGSVSGENTNGR





(SEQ ID NO: 398)


 




1204.51
FADAGSFDYGR





(SEQ ID NO: 399)


 




1438.68
YVDVGATYYFNK





(SEQ ID NO: 400)


 




1800.82
DISNGYGASYGDQDIVK





(SEQ ID NO: 401)


 




1890.93
VAFAGLKFADAGSFDYG





R





(SEQ ID NO: 402)


 




1989.84
TADQNNTADEHLYGNGD





R





(SEQ ID NO: 403)


 




2247.08
NTDFFGLVDGLDFALQY





QGK





(SEQ ID NO: 404)


 




2339.08
YDANNIYLAAQYSQTYN





ATR





(SEQ ID NO: 405)


 




2405.02
VDGLHYFSDDKGSDGDQ





TYMR





(SEQ ID NO: 406)


 




3004.51
AQNFEVVAQYQFDFGLR





PSVAYL





(SEQ ID NO: 407)


 


Lw 106B
39
718.44
LAFAGLK





(SEQ ID NO: 408)


 




867.44
TTGVATYR





(SEQ ID NO: 409)


 




1057.56
NAEVWAAGLK





(SEQ ID NO: 410)


 




1103.50
NMSTFVDYK





(SEQ ID NO: 411)


 




1121.57
DGNKLDLYGK





(SEQ ID NO: 412)


 




1279.63
INLLDDSDFTK





(SEQ ID NO: 413)


 




1296.54
FADYGSFDYGR





(SEQ ID NO: 414)


 




1638.83
VSTDNIVAVGLNYQF





(SEQ ID NO: 415)


 




1890.78
VHAQHYFSDDNGSDGDK





(SEQ ID NO: 416)


 




2218.07
NTDFFGLVEGLNFAAQY





QGK





(SEQ ID NO: 417)


 




2218.07
NTDFFGLVEGLNFAAQY





QGK





(SEQ ID NO: 418)


 




2382.03
VHAQHYFSDDNGSDGDK





TYAR





(SEQ ID NO: 419)


 




2389.09
GETQINDQLTGFGQWEY





EFK





(SEQ ID NO: 420)


 




2757.28
NLGTYGDQDLVEYIDVG





ATYYFNK





(SEQ ID NO: 421)


 




2805.41
TQNFEAVAQYQFDFGLR





PSIAYLK





(SEQ ID NO: 422)


 




3067.50
TTGVATYRNTDFFGLVE





GLNFAAQYQGK





(SEQ ID NO: 423)


 


Lw 108
38
817.43
LGGMVWR





(SEQ ID NO: 424)


 




1024.46
DNTWYAGAK





(SEQ ID NO: 425)


 




1082.54
SDVLFNFNK





(SEQ ID NO: 426)


 




1156.59
AALIDCLAPDR





(SEQ ID NO: 427)


 




1221.66
AQSVVDYLISK





(SEQ ID NO: 428)


 




1232.63
LGGMVWRADTK





(SEQ ID NO: 429)


 




1263.65
DGSVVVLGFTDR





(SEQ ID NO: 430)


 




1377.76
RAQSVVDYLISK





(SEQ ID NO: 431)


 




1380.65
IGSDAYNQGLSEK





(SEQ ID NO: 432)


 




1469.70
MPYKGDNINGAYK





(SEQ ID NO: 433)


 




1536.75
IGSDAYNQGLSEKR





(SEQ ID NO: 434)


 




1639.81
LGYPITDDLDVYTR





(SEQ ID NO: 435)


 




2302.20
FGQQEAAPVVAPAPAPA





PEVQTK





(SEQ ID NO: 436)


 




2615.29
DHDTGVSPVFAGGIEYA





ITPEIATR





(SEQ ID NO: 437)


 




2672.37
STLKPEGQQALDQLYSQ





LSNLDPK





(SEQ ID NO: 438)


 




3422.69
LEYQWTNNIGDANTIGT





RPDNGLLSVGVSYR





(SEQ ID NO: 439)





1. Molecular weight as determined by SDS-PAGE.


2. The mass of a polypeptide fragment can be converted to m/z value by adding 1 to the mass. Each mass includes a range of plus or minus 1 Dalton.














TABLE 4







Characteristics of polypeptides obtained



from S. enterilidis serovar Typhimurium.













mass value of






polypeptide



approximate
fragments
predicted amino



molecular
resulting
acid sequence of


polypeptide
weight in
from trypsin
the polypeptide


designation
kilodaltons (kDa)1
digest2
fragment














Lw 111
86
990.55
EIGLEFKR






(SEQ ID NO: 440)


 




1082.61
IEAGTVPLQR





(SEQ ID NO: 441)


 




1181.55
NINQGHQSER





(SEQ ID NO: 442)


 




1207.58
TGSYADTLPAGP





(SEQ ID NO: 443)


 




1306.65
DGWLAGVTWFR





(SEQ ID NO: 444)


 




1324.75
NKIEAGTVPLQR





(SEQ ID NO: 445)


 




1377.66
TDVYQWENVPK





(SEQ ID NO: 446)


 




1432.77
YGNGAAGGVVNIITK





(SEQ ID NO: 447)


 




1477.74
NVSLTGGVDNLFDK





(SEQ ID NO: 448)


 




1499.71
GDTAWVPPEMIER





(SEQ ID NO: 449)


 




1584.74
KYDYQGNPVTGTDK





(SEQ ID NO: 450)


 




1617.77
MPEGLAGGTEGIFDPK





(SEQ ID NO: 451)


 




1618.77
TMPGVNLTGNSTSGQR





(SEQ ID NO: 452)


 




1633.84
NVSLTGGVDNLFDKR





(SEQ ID NO: 453)


 




1658.79
QDVSLQSTFTWYGK





(SEQ ID NO: 454)


 




1727.83
TNFSLNGPLGGDFSFR





(SEQ ID NO: 455)


 




1870.95
APSLYQTNPNYILYSK





(SEQ ID NO: 456)


 




1980.96
WDFAPLQSLELEAGYSR





(SEQ ID NQ:457)


 




1997.06
GMGPENTLILIDGKPVTSR





(SEQ ID NO: 458)


 




2021.05
QAVSPYSIVGLSATWDVTK





(SEQ ID NO: 459)


 




2078.00
QGNLYAGDTQNTNTNQLVK





(SEQ ID NO: 460)


 




2118.15
LSIIPQYTLNSTLSWQVR





(SEQ ID NO: 461)


 




2192.94
DTQTGAYMAGAGAYTYNEP





GR





(SEQ ID NO: 462)


 




2202.95
GGSEWHGSWNTYFNAPEHK





(SEQ ID NO: 463)


 




2331.05
KGGSEWHGSWNTYFNAPEH





K





(SEQ ID NO: 464)


 




2373.07
DQLSNSQTFMGGNIPGYSS





TNE





(SEQ ID NO: 465)


 




2632.20
MKDQLSNSQTFMGGNIPGY





SSTNR





(SEQ ID NO: 466)


 




3098.47
FDHHSIVGDNWSPSLNLSQ





GLGDDFTLK





(SEQ ID NO: 467)


 


Lw 112
82
610.29
YSWR





(SEQ ID NO: 468)


 




848.45
LYGNLNR





(SEQ ID NO: 469)


 




918.45
LGFYYEK





(SEQ ID NO: 470)


 




1040.60
IVAGDQIIGR





(SEQ ID NO: 471)


 




1094.54
DINSVESWK





(SEQ ID NO: 472)


 




1097.62
QQPGVSIITR





(SEQ ID NO: 473)


 




1153.63
DTGNPLSIIPK





(SEQ ID NO: 474)


 




1162.50
MNEGLSGGGEGR





(SEQ ID NO: 475)


 




1208.64
QKPRTHAESR





(SEQ ID NO: 476)


 




1218.66
LNVGISNIFDK





(SEQ ID NO: 477)


 




1309.63
ITNDQTFTTNR





(SEQ ID NO: 478)


 




1335.71
NPPVNDLADIIR





(SEQ ID NO: 479)


 




1341.66
DSNIAGIPGSAANR





(SEQ ID NO: 480)


 




1364 . 60
SAEGANTYNEPGR





(SEQ ID NO: 481)


 




1405.76
YGSGAAGGVVNIITK





(SEQ ID NO: 482)


 




1528.70
GDTNWVPPEMVER





(SEQ ID NO: 483)


 




1564 .76
SASGAYVLQWQNGGE





(SEQ ID NO: 484)


 




1566.68
TDADSWDINSSAGTK





(SEQ ID NO: 485)


 




1735.86
GNFSLSGPLAGDTLTMR





(SEQ ID NO: 486)


 




1754 .83
MTPQQILDFEAGYSR





(SEQ ID NO: 487)


 




1845. 91
APNLYQTSEGYLLYSK





(SEQ ID NO: 488)


 




1880.96
ALGAYSLVGANVNYDINK





(SEQ ID NO: 489)


 




1882.89
LNWNTNATYMIASEQK





(SEQ ID NO: 490)


 




1911.98
ALIEGIEASMAVPLMPDR





(SEQ ID NO: 491)


 




1929.95
ITNDQTFTTNRLTSYR





(SEQ ID NO: 492)


 




1954 .02
GMGPENTLVLIDGVPVTSR





(SEQ ID NO: 493)


 




2030.93
QNYGLTHNGIWDWGQSR





(SEQ ID NO: 494)


 




2192.12
AFKAPNLYQTSEGYLLYSK





(SEQ ID NO: 495)


 




2261.06
EIGLEFTVDDYHASVTYFR





(SEQ ID NO: 496)


 




2416.14
RPTNDWHGSLSLYTNQPES





SK





(SEQ ID NO: 497)


 




2449.22
DITSGGCYLVGNKNLDPEI





SINK





(SEQ ID NO: 498)


 




2701.36
SEISALYVEDNIEPMAGTN





IIPGLR





(SEQ ID NO: 499)


 




2909.36
FDYLSESGSNFSPSLNLSQ





ELGEYVK





(SEQ ID NO: 500)


 




2943.50
NKSEISALYVEDNIEPMAG





TNIIPGLR





(SEQ ID NO: 501)


 


Lw 113
77
957.55
GQRVPVFR





(SEQ ID NO: 502)


 




1158.55
QNYALSHNGR





(SEQ ID NO: 503)


 




1177.52
QDRDSDSLDK





(SEQ ID NO: 504)


 




1210.55
YFMAVDYRF





(SEQ ID NO: 505)


 




1308.79
RPVQNLKDVLK





(SEQ ID NO: 506)


 




1314.62
LSLNYTYNDGR





(SEQ ID NO: 507)


 




1329.77
IFEPLALTTGIR





(SEQ ID NO: 508)


 




1345.55
DDYGYTEDGRR





(SEQ ID NO: 509)


 




1397.75
VPVFRYYNVNK





(SEQ ID NO: 510)


 




1526.73
EVPGVQLTNEGDNR





(SEQ ID NO: 511)


 




1649.90
GLDSSYTLILIDGKR





(SEQ ID NO: 512)


 




1654.83
EVPGVQLTNEGDNRK





(SEQ ID NO: 513)


 




1744.69
MDDHETYGDHWSPR





(SEQ ID NO: 514)


 




1750.84
WHGSVTVDSTIQEHR





(SEQ ID NO: 515)


 




1792.88
GEEGILEGVEASVTTFR





(SEQ ID NO: 516)


 




1952.94
HNDFDLNWIPVDAIER





(SEQ ID NO: 517)


 




2021.97
WHGSVTVDSTIQEHRDR





(SEQ ID NO: 518)


 




2201.06
QNYALSHNGRWDLGNSELK





(SEQ ID NO: 519)


 




2242.03
TPDVNAAPGYSNFVGFETN





SR





(SEQ ID NO: 520)


 


Lw 115A
40
851.30
NDFTR





(SEQ ID NO: 521)


 




704.42
VAFAGLE





(SEQ ID NO: 522)


 




793.37
LYGNGDR





(SEQ ID NO: 523)


 




900.41
GNGYATYR





(SEQ ID NO: 524)


 




908.50
ATVYTGGLK





(SEQ ID NO: 525)


 




1105.58
DGNKLDLFGK





(SEQ ID NO: 526)


 




1119.49
NMSTYVDYK





(SEQ ID NO: 527)


 




1128.45
GSDGDQTYMR





(SEQ ID NO: 528)


 




1174.53
TADQNNTANAR





(SEQ ID NO: 529)


 




1204.51
FADAGSFDYGR





(SEQ ID NO: 530)


 




1347.71
INLLDKNDFTR





(SEQ ID NO: 531)


 




1438.68
YVDVGATYYFNK





(SEQ ID NO: 532)


 




1800.82
DISNGYGASYGDQDIVK





(SEQ ID NO: 533)


 




1834 .81
FGTSNGSNPSTSYGFANK





(SEQ ID NO: 534)


 




1985.93
GKDISNGYGASYGDQDIVK





(SEQ ID NO: 535)


 




2247.08
NTDFFGLVDGLDFALQYQG





K





(SEQ ID NO: 536)


 




2339.08
YDANNIYLAAQYSQTYNAT





R





(SEQ ID NO: 537)


 




2405.02
VDGLHYFSDDKGSDGDQTY





MR





(SEQ ID NO: 538)


 




3004 .51
AQNFEVVAQYQFDFGLRPS





VAYLQSK





(SEQ ID NO: 539)


 




3133.52
SLLNQNGDGYGGSLTYAIG





EGESVGGAITTSK





(SEQ ID NO: 540)


 


Lw 115B
39
718.44
LAFAGLK





(SEQ ID NO: 541)


 




867.44
TTGVATYR





(SEQ ID NO: 542)


 




1057.56
NAEVWAAGLK





(SEQ ID NO: 543)


 




1103.50
NMSTFVDYK





(SEQ ID NO: 544)


 




1121.57
DGNKLDLYGK





(SEQ ID NO: 545)


 




1161.54
GNRTESQGADK





(SEQ ID NO: 546)


 




1279.63
INLLDDSDFTK





(SEQ ID NO: 547)


 




1296.54
FADYGSFDYGR





(SEQ ID NO: 548)


 




2218.07
NTDEFGLVEGLNFAAQYQG





K





(SEQ ID NO: 549)


 




2382.03
VHAQHYFSDDNGSDGDKTY





AR





(SEQ ID NO: 550)


 




2389.09
GETQINDQLTGFGQWEYEF





K





(SEQ ID NO: 551)


 




2757.28
NLGTYGDQDLVEYIDVGAT





YYFNK





(SEQ ID NO: 552)


 




2805.41
TQNFEAVAQYQFDFGLRPS





IAYLK





(SEQ ID NO: 553)


 




3450.49
NDRDGAYESNGDGFGLSAT





YEYEGKGVGAAYAK





(SEQ ID NO: 554)


 


Lw 117
38
644.36
HFTLK





(SEQ ID NO: 555)


 




817.43
LGGMVWR





(SEQ ID NO: 556)


 




871.51
RVEIEVK





(SEQ ID NO: 557)


 




914.52
AQGVQLTAK





(SEQ ID NO: 558)


 




942.48
SNVPGGPSTK





(SEQ ID NO: 559)


 




1024.46
DNTWYAGAK





(SEQ ID NO: 560)


 




1042.58
GIPSDKISAR





(SEQ ID NO: 561)


 




1082.54
SDVLFNFNK





(SEQ ID NO: 562)


 




1140.61
GVKDVVTQPQA





(SEQ ID NO: 563)


 




1221.66
AQSVVDYLISK





(SEQ ID NO: 564)


 




1263.65
DGSVVVLGFTDR





(SEQ ID NO: 565)


 




1377.76
RAQSVVDYLISK





(SEQ ID NO: 566)


 




1380.65
IGSDAYNQGLSEK





(SEQ ID NO: 567)


 




1469.70
MPYKGDNINGAYK





(SEQ ID NO: 568)


 




1469.70
MPYKGDNINGAYK





(SEQ ID NO: 569)


 




1536.75
IGSDAYNQGLSEKR





(SEQ ID NO: 570)


 




1639.81
LGYPITDDLDVYTR





(SEQ ID NO: 571)


 




1708.89
HFTLKSDVLFNFNK





(SEQ ID NO: 572)


 




2302.20
FGQQEAAPVVAPAPAPAPE





VQTK





(SEQ ID NO: 573)


 




2615.29
DNDTGVSPVFAGGIEYAIT





PEIATE





(SEQ ID NO: 574)


 




2626.29
DGSVVVLGFTDRIGSDAYN





QGLSEK





(SEQ ID NO: 575)


 




2672.37
STLKPEGQQALDQLYSQLS





NLDPK





(SEQ ID NO: 576)


 




3422.69
LEYQWTNNIGDANTIGTRP





DNGLLSVGVSYR





(SEQ ID NO: 577)


 




3539.75
SNVPGGPSTKDHDTGVSPV





FAGGIEYAITPEIATR





(SEQ ID NO: 578)





1Molecular weight as determined by SDS-PAGE.


2The mass of a polypeptide fragment can be converted to m/z value by adding 1 to the mass. Each mass includes a range of plus or minus 1 Dalton.














TABLE 5







Characteristics of polypeptides obtained



from S. enteritidis serovar Dublin.













mass value of






polypeptide



approximate
fragments
predicted amino



molecular
resulting
acid sequence of


polypeptide
weight in
from trypsin
the polypeptide


designation
kilodaltons (kDa)1
digest2
fragment














Dublin 1
96
1082.61
IEAGTVPLQR



(SD1)


(SEQ ID NO: 579)


 




1207.58
TGSYADTLPAGR





(SEQ ID NO: 580)


 




1298.57
TWYMSINTHF





(SEQ ID NO: 581)


 




1377.66
TDVYQWENVPK





(SEQ ID NO: 582)


 




1499.71
GDTAWVPPEMIER





(SEQ ID NO: 583)


 




1617.77
MPEGLAGGTEGIFDPK





(SEQ ID NO: 585)


 




1727.83
TNFSLNGPLGGDFSFR





(SEQ ID NO: 586)


 




1870.95
APSLYQTNPNYILYSK





(SEQ ID NO: 587)


 




1956.05
GPAAARYGNGAAGGVVNII





TK





(SEQ ID NO: 588)


 




1980.96
WDFAPLQSLELEAGYSR





(SEQ ID NO: 589)


 




1997.06
GMGPENTLILIDGKPVTSR





(SEQ ID NO: 590)


 




2118.15
LSIIPQYTLNSTLSWQVR





(SEQ ID NO: 592)


 




2192.94
DTQTGAYMAGAGAYTYNEP





GR





(SEQ ID NO: 593)


 




2202.95
GGSEWHGSWNTYFNAPEHK





(SEQ ID NO: 594)


 




2331.05
KGGSEWHGSWNTYFNAPEH





K





(SEQ ID NO: 596)


 


Dublin-2
89
610.29
YSWR


(SD2)


(SEQ ID NO: 597)


 




628.39
IEVIR





(SEQ ID NO: 598)


 




848.45
LYGNLNR





(SEQ ID NO: 599)


 




918.45
LGFYYEK





(SEQ ID NO: 600)


 




1040.60
IVAGDQIIGR





(SEQ ID NO: 601)


 




1097.62
QQPGVSIITR





(SEQ ID NO: 602)


 




1218.66
LNVGISNIFDK





(SEQ ID NO: 603)


 




1309.63
ITNDQTFTTNR





(SEQ ID NO: 604)


 




1335.71
NPPVNDLADIIR





(SEQ ID NO: 605)


 




1341.66
DSNIAGIPGSAANR





(SEQ ID NO: 606)


 




1364.60
SAEGANTYNEPGR





(SEQ ID NO: 607)


 




1528.70
GDTNWVPPEMVER





(SEQ ID NO: 608)


 




1564.76
SASGAYVLQWQNGGK





(SEQ ID NO: 609)


 




1735.86
GNFSLSGPLAGDTLTMR





(SEQ ID NO: 610)


 




1750.86
EGVTNKDINSVESWR





(SEQ ID NO: 611)


 




1845.91
APNLYQTSEGYLLYSK





(SEQ ID NO: 612)


 




1880.96
ALGAYSLVGANVNYDINK





(SEQ ID NO: 613)


 




1911.98
ALIEGIEASMAVPLMPDR





(SEQ ID NO: 614)


 




2261.06
EIGLEFTVDDYHASVTYFR





(SEQ ID NO: 615)


 




2416.14
RPTNDWHGSLSLYTNQPES





SK





(SEQ ID NO: 616)


 




2701 .36
SEISALYVEDNIEPMAGTN





IIPGLR





(SEQ ID NO: 617)


 




2909.36
FDYLSESGSNFSPSLNLSQ





ELGEYVK





(SEQ ID NO: 618)


 


Dublin-3
81
605.33
NAVFR


(SD3)


(SEQ ID NO: 619)


 




616.37
VPVFR





(SEQ ID NO: 620)


 




989.50
VPFNEAWK





(SEQ ID NO: 621)


 




1063.48
YFMAVDYR





(SEQ ID NO: 622)


 




1177.52
QDRDSDSLDK





(SEQ ID NO: 623)


 




1314.62
LSLNYTYNDGR





(SEQ ID NO: 624)


 




1329.77
IFEPLALTTGIR





(SEQ ID NO: 625)


 




1526.73
EVPGVQLTNEGDNR





(SEQ ID NO: 626)


 




1649.90
GLDSSYTLILIDGKR





(SEQ ID NO: 627)


 




1740.90
DAPASISVITQQDLQR





(SEQ ID NO: 628)


 




1744.69
MDDHETYGDHWSPR





(SEQ ID NO: 629)


 




1750.84
WHGSVTVDSTIQEHR





(SEQ ID NO: 630)


 




1792.88
GEEGILEGVEASVTTFR





(SEQ ID NO: 631)


 




1814.85
TSASQYALFLEDEWR





(SEQ ID NO: 632)


 




1906.92
TPGGYVVWDTGAAWQATK





(SEQ ID NO: 633)


 




1934.88
EKDEQQSSATTATGETPR





(SEQ ID NO: 634)


 




1952.94
HNDFDLNWIPVDAIER





(SEQ ID NO: 635)


 




2196.14
YVLPLASVNQFLTFGGEWR





(SEQ ID NO: 636)


 




2242.02
TPDVNAAPGYSNFVGFETN





SR





(SEQ ID NO: 637)


 




2551.23
ADSATAKTPGGYVVWDTGA





AWQATK





(SEQ ID NO: 638)


 




2S87.24
DRGDTYNGQFFTSGPLIDG





VLGMI





(SEQ ID NO: 639)


 




2710.17
DGNVEFAWTPNENHDVTAG





YGFDR





(SEQ ID NO: 640)


 


Dublin-4
61
631.37
LSSGLR


(SD4)


(SEQ ID NO: 641)


 




944.50
SSLGAIQNR





(SEQ ID NO: 642)


 




1100.52
DDAAGQAIANR





(SEQ ID NO: 643)


 




1115.56
SIQDEIQQR





(SEQ ID NO: 644)


 




1163.58
SQSSLSSAIER





(SEQ ID NO: 645)


 




1316.67
SLGLDGFNVNGPK





(SEQ ID NO: 646)


 




1473.77
STANPLASIDSALSK





(SEQ ID NO: 647)


 




1763.81
NVTGYDTYAAGADKYR





(SEQ ID NO: 648)


 




1832.86
NVYTSVVNGQFTFDDK





(SEQ ID NO: 649)


 




2007.00
FDSAITNLGNTVTNLNSAR





(SEQ ID NO: 650)


 




2084.12
AQVINTNSLSLLTQNNLNK





(SEQ ID NO: 651)


 




2669.30
NANDGISIAQTTEGALNEI





NNNLQR





(SEQ ID NO: 652)


 




2682.28
VYVNAANGQLTTDDAENNT





AVDLFK





(SEQ ID NO: 653)


 




2859.59
AQILQQAGTSVLAQANQVP





QNVLSLLR





(SEQ ID NO: 654)


 


Dublin-5
56
913.53
NLSLLQAR


(SD5)


(SEQ ID NO: 655)


 




988.49
QLDQTTQR





(SEQ ID NO: 656)


 




1285.63
NNLDNAVEELR





(SEQ ID NO: 657)


 




1381.76
YTYLINQLNIK





(SEQ ID NO: 658)


 




1549.77
AQYDTVLANEVTAR





(SEQ ID NO: 659)


 




1615.87
FNVGLVAITDVQNAR





(SEQ ID NO: 670)


 




1661.90
VENAIDVLSYTQAQK





(SEQ ID NO: 671)


 




1737.90
TIVDVLDATTTLYDAK





(SEQ ID NO: 672)


 




1828.90
SSFNNINASISSINAYK





(SEQ ID NO: 673)


 




2033.96
QAQYNFVGASEQLESAHR





(SEQ ID NO: 674)


 




2184.09
SPLLPQLGLGADYTYSNGY





R





(SEQ ID NO: 675)


 




2208.09
QVTGNYYPELASLNVEHFK





(SEQ ID NO: 676)


 


Dublin-6
51
944.50
SSLGAIQNR


(SD6)


(SEQ ID NO: 677)


 




1115.56
SIQDEIQQR





(SEQ ID NO: 678)


 




1220.61
VSNQTQFNGVK





(SEQ ID NO: 679)


 




1316.67
SLGLDGFNVNGPK





(SEQ ID NO: 680)


 




1444.65
NVTGYDTYAAGADK





(SEQ ID NO: 681)


 




1473.77
STANPLASIDSALSK





(SEQ ID NO: 682)


 




1813.94
IQVGANDGETITIDLQK





(SEQ ID NO: 683)


 




1832.86
NVYTSVVNGQFTFDDK





(SEQ ID NO: 684)


 




2007.00
FDSAITNLGNTVTNLNSAR





(SEQ ID NO: 685)


 




2669.30
NANDGISIAQTTEGALNEI





NNNLQR





(SEQ ID NO: 686)


 




2682.20
VYVNAANGQLTTDDAENNT





AVDLFK





(SEQ ID NO: 687)


 




2859.59
AQILQQAGTSVLAQANQVP





QNVLSLL





(SEQ ID NO: 688)


 


Dublin-7
43
1171.64
ELVNMIVAQR


(SD7)


(SEQ ID NO: 689)


 




1342.65
LVDSNGSVFYSR





(SEQ ID NO: 691)


 




1375.61
SGTASFADMFAGSK





(SEQ ID NO: 692)


 




1422.73
GLDVAISQNGFFR





(SEQ ID NO: 694)


 




1526.84
TQDQILNTLVNLR





(SEQ ID NO: 695)


 




1853.88
VAGITQDFTDGTTTNTGR





(SEQ ID NO: 696)


 




2344.08
GTVTVYDSQGNAHDMNVYF





VK





(SEQ ID NO: 697)


 




3078.44
TKDNEWAVYTHDSSDPAAT





APTTASTTLK





(SEQ ID NO: 699)


 


Dublin-8
40
1204.51
FADAGSFDYGR


(SD8)


(SEQ ID NO: 700)


 




1347.71
INLLDKNDFTR





(SEQ ID NO: 701)


 




1438.68
YVDVGATYYFNK





(SEQ ID NO: 702)


 




1800.82
DISNGYGASYGDQDIVK





(SEQ ID NO: 703)


 




1834.81
FGTSNGSNPSTSYGFANK





(SEQ ID NO: 704)


 




2247.08
NTDFFGLVDGLDFALQYQG





K





(SEQ ID NO: 705)


 




2339.08
YDANNIYLAAQYSQTYNAT





P





(SEQ ID NO: 706)


 




2405.02
VDGLHYFSDDKGSDGDQTY





MR





(SEQ ID NO: 707)


 




3004.51
AQNFEVVAQYQFDFGLRPS





VAYLQSK





(SEQ ID NO: 708)


 


Dublin-10
38
817.43
LGGMVWR


(SD9)


(SEQ ID NO: 709)


 




1263.65
DGSVVVLGFTDR





(SEQ ID NO: 710)


 




1639.81
LGYPITDDLDVYTR





(SEQ ID NO: 711)


 




2302.20
FGQQEAAPVVAPAPAPAPE





VQTK





(SEQ ID NO: 712)


 




2615.29
DHDTGVSPVFAGGIEYAIT





PEIATR





(SEQ ID NO: 713)


 




2672.37
STLKPEGQQALDQLYSQLS





NLDPK





(SEQ ID NO: 714)


 




3422.69
LEYQWTNNIGDANTIGTRP





DNGLLSVGVSYR





(SEQ ID NO: 715)





1Molecular weight as determined by SDS-PAGE.


2The mass of a polypeptide fragment can be converted to m/z value by adding 1 to the mass. Each mass includes a range of plus or minus 300 ppm for the polypeptide fragments from the 96 kDa reference polypeptide; plus or minus 1 Dalton for the polypeptide fragments from the 89 kDa, 81 kDa, 61 kDa, 56 kDa, 51 kDa, 40 kDa, and 38 kDa reference polypeptides; and plus or minus 450 ppm for the polypeptide fragments from the 43 kDa polypeptide.














TABLE 6







Characteristics of polypeptides



obtained from an E. coli.













mass value of






polypeptide



approximate
fragments
predicted amino



molecular
resulting
acid sequence of


polypeptide
weight in
from trypsin
the polypeptide


designation
kilodaltons (kDa)1
digest2
fragment














Lw118
90
628.39
IEVLR






(SEQ ID NO: 716)


 




771.42
DINGVVR





(SEQ ID NO: 717)


 




830.45
DVSEIIR





(SEQ ID NO: 718)


 




990.55
EIGLEEKR





(SEQ ID NO: 719)


 




1177.61
AGTYATTLPAGR





(SEQ ID NO: 720)


 




1284.56
TWYMSVNTHF





(SEQ ID NO: 721)


 




1320.66
DOWLAGITWER





(SEQ ID NO: 722)


 




1367.75
NPVARDVSEIIR





(SEQ ID NO: 723)


 




1432.77
YGNGAAGGVVNIITK





(SEQ ID NO: 724)


 




1515.70
GDTSWVPPEMIER





(SEQ ID NO: 725)


 




1618.77
TMPGVNLTGNSTSGQR





(SEQ ID NO: 726)


 




1633.84
NVSLTGGVDNLEDKR





(SEQ ID NO: 727)


 




1705.77
EDLSMQTTFTWYGK





(SEQ ID NO: 728)


 




1786.85
TNFSLTGPLGDEFSFR





(SEQ ID NO: 729)


 




1796.82
TQADAWDINQGHQSAR





(SEQ ID NO: 730)


 




1870.95
APSLYQTNPNYILYSK





(SEQ ID NO: 731)


 




1965.01
EISPYSIVGLSATWDVTK





(SEQ ID NO: 732)


 




1980.96
WDFAPLQSLELEAGYSR





(SEQ ID NO: 733)


 




2087.91
QGNLYAGDTQNTNSDAYTR





(SEQ ID NO: 734)


 




2173.92
GSGEWHGSWDAYENAPEHK





(SEQ ID NO: 735)


 




2302.02
KGSGEWHGSWDAYFNAPEH





K





(SEQ ID NO: 736)


 




2600.24
LYGNLDKTQADAWDINQGN





QSAR





(SEQ ID NO: 737)


 




2706.33
IEAGYVAVGQNAVGTDLYQ





WDNVPE





(SEQ ID NO: 738)


 




2843.31
AGNAQTTGDLAGANYIAGA





GAYTYNEPGR





(SEQ ID NO: 739)


 




3081.49
FDHHSIVGNNWSPALNISQ





GLGDDFTLK





(SEQ ID NO: 740)


 




3212.43
QNYSLTWNGGWDNGVTTSN





WVQYEHTR





(SEQ ID NO: 741)


 


Lw119
86
975.44
DPANSGPYR





(SEQ ID NO: 742)


 




991.55
QVVATATFR





(SEQ ID NO: 743)


 




1094.51
DDKQFTWR





(SEQ ID NO: 744)


 




1246.63
RLPTDFNEGAK





(SEQ ID NO: 745)


 




1277.70
VGSYTVVDALVR





(SEQ ID NO: 746)


 




1358.69
GASNTYDHLIIR





(SEQ ID NO: 747)


 




1395.61
YDWADQESLNR





(SEQ ID NO: 748)


 




1435.73
EALSYTPGVSVGTR





(SEQ ID NO: 749)


 




1492.65
YTGSSYGDPANSFK





(SEQ ID NO: 750)


 




1571.87
RPTTEPLKEVQFK





(SEQ ID NO: 751)


 




1649.82
YAIAPAFTWRPDDK





(SEQ ID NO: 752)


 




1664.78
QTGVYVQDQAQWDK





(SEQ ID NO: 753)


 




1809.86
GFAAEGQSQNNYLNGLK





(SEQ ID NO: 754)


 




1912.96
VGMAGSNVALHVNNLFDR





(SEQ ID NO: 755)


 




2133.15
YVPEDRPIVVTGAVYNLTK





(SEQ ID NO: 756)


 




2209.96
TSQNSVYGYGVCSDPANAY





SK





(SEQ ID NO: 757)


 




2269.03
TNNLMADPEGSFFSVEGGE





IR





(SEQ ID NO: 758)


 


LW-1A-3
83
836.45
TLRYER





(SEQ ID NO: 759)


 




883.47
WGLAGQPR





(SEQ ID NO: 760)


 




1047.46
SEQRDGDNK





(SEQ ID NO: 761)


 




1126.59
DKWGLAGQPR





(SEQ ID NO: 762)


 




1337.62
DGQLGSLTGGYDR





(SEQ ID NO: 763)


 




1350.68
DGVVLASTGETFR





(SEQ ID NO: 764)


 




1396.63
SYLNWNETENK





(SEQ ID NO: 765)


 




1471.73
FTQNYSSLSAVQK





(SEQ ID NO: 766)


 




1604.85
GMPASYTLILIDGVR





(SEQ ID NO: 767)


 




1649.85
AYLVWDVADAWTLK





(SEQ ID NO: 768)


 




1721.84
IPYPTESQNYNLGAR





(SEQ ID NO: 769)


 




1726.76
YEHHEQFGGHFSPR





(SEQ ID NO: 770)


 




1758.89
WLSSVNAGLNLQESNK





(SEQ ID NO: 771)


 




1812.80
ASEQDVLWFDMDTTR





(SEQ ID NO: 772)


 




2266.14
GPMSTLYGSDAMGGVVNII





TRE





(SEQ ID NO: 774)


 




2512.18
STLYAGDYFQTGSSTTGYV





IPER(SEQ ID NO: 775)


 


Lw121
79
715.38
HFSIGR





(SEQ ID NO: 776)


 




951.48
IYWSEVR





(SEQ ID NO: 777)


 




1134.55
IWGWDVMTK





(SEQ ID NO: 778)


 




1154.67
DLPITLLGGTR





(SEQ ID NO: 779)


 




1221.63
MSRPQFTSLR





(SEQ ID NO: 780)


 




1335.64
DLLQEGQSSGFR





(SEQ ID NO: 781)


 




1395.64
INAQNTGSSGEYR





(SEQ ID NO: 782)


 




1446.71
TENLDGIVAWSSR





(SEQ ID NO: 783)


 




1511.74
LAPQGNDWLNADAK





(SEQ ID NO: 784)


 




1531.71
EYWSPQGIPQDGR





(SEQ ID NO: 785)


 




1652.79
QEQHPGGATTGFPQAK





(SEQ ID NO: 786)


 




1656.77
FDDLMLSNDALEFK





(SEQ ID NO: 787)


 




1676.80
YTTDLFSLDVAYNR





(SEQ ID NO: 788)


 




1716.88
GTWQIDSAQSLSGLVR





(SEQ ID NO: 789)


 




1778.88
IDFSSGWLQDEITLR





(SEQ ID NO: 790)


 




1859.83
NPQTVEASESSNPMVDR





(SEQ ID NO: 791)


 




1962.95
VFGTGGTGDHSLGLGASAF





GR





(SEQ ID NO: 792)


 




2261 .08
QPGYGVNDFYVSYQGQQAL





K





(SEQ ID NO: 793)


 




2397.13
STLFADSFASHLLTYGGEY





YR





(SEQ ID NO: 794)


 


EW-1A-5A
66
631.37
LSSGLR





(SEQ ID NO: 795)


 




944.50
SSLGAIQNR





(SEQ ID NO: 796)


 




1190.59
NQSALSSSIER





(SEQ ID NO: 797)


 




1237.66
LNTTTGLYDLK





(SEQ ID NO: 798)


 




1439.81
AQIIQQAGNSVLAK





(SEQ ID NO: 799)


 




1560.83
VSGQTQFNGVNVLAK





(SEQ ID NO: 800)


 




1646.83
DYAPAIGTAVNVNSAGK





(SEQ ID NO: 801)


 




1790.92
KIDSDTLGLNGFNVNGK





(SEQ ID NO: 802)


 




2060.95
TIGFTAGESSDAAKSYVDD





K





(SEQ ID NO: 803)


 




2084.12
AQVINTNSLSLITQNNINK





(SEQ ID NO: 804)


 




2189.01
AASEGSDGASLTFNGTEYT





IAK





(SEQ ID NO: 805)


 




2248.09
LDSAVTNLNNTTTNLSEAQ





SR





(SEQ ID NO: 806)


 




2454.34
ATPATTTPVAPLIPGGITY





QATVSK





(SEQ ID NO: 807)


 




2628.27
NANDGISVAQTTEGALSEI





NNNLQR





(SEQ ID NO: 808)


 


LW-2A-5B
66
678.37
VEYIE





(SEQ ID NO: 809)


 




1294.63
LYSQSWDAGLR





(SEQ ID NO: 810)


 




1298.53
DYNYDPHYGR





(SEQ ID NO: 811)


 




1303.65
WQSTSVNDVLR





(SEQ ID NO: 812)


 




1422.73
KLYSQSWDAGLR





(SEQ ID NO: 813)


 




1549.86
GTNASHVLVLIDGVR





(SEQ ID NO: 814)


 




1919.86
QWEGAFEGLTAGVNWR





(SEQ ID NO: 815)


 




1892.00
SAVYGSDAIGGVVNIITTR





(SEQ ID NO: 816)


 




1917.87
TNYDAYYSPGSPLVDTR





(SEQ ID NO: 817)


 




2158.14
LPGVDITQNGGSGQLSSIF





IR





(SEQ ID NO: 818)


 




2323.11
IANLFDKDYETVYGYQTAG





R





(SEQ ID NO: 819)


 




2357.17
NTGIYLTGLQQVGDFTFEG





AAR





(SEQ ID NO: 820)


 




2698.25
GVEATANFDTGPLTHTVSY





DYVDAR





(SEQ ID NO: 821)


 


LW-1A-6
56
1284.64
NNLDNAVEQLR





(SEQ ID NO: 822)


 




1394.76
YNYLINQLNIK





(SEQ ID NO: 823)


 




1549.77
AQYDTVLANEVTAR





(SEQ ID NO: 824)


 




1615.87
FNVGLVAITDVQNAR





(SEQ ID NO: 825)


 




1828.90
SSFNNINASISSINAYK





(SEQ ID NO: 826)


 




2033.96
QAQYNFVGASEQLESAHR





(SEQ ID NO: 827)


 




2123.10
VGLSFSLPIYQGGMVNSQV





K





(SEQ ID NO: 828)


 




2183.09
QITGNYYPELAALNVENFK





(SEQ ID NO: 829)


 




2226.05
QAVVSAQSSLDANEAGYSV





GTR





(SEQ ID NO: 830)


 


Lw123
38
704.42
VAFAGLE





(SEQ ID NO: 831)


 




884.41
GNGFATYR





(SEQ ID NO: 832)


 




930.49
VGSLGWANK





(SEQ ID NO: 833)


 




938.47
AETYTGGLK





(SEQ ID NO: 834)


 




1119.49
NMSTYVDYK





(SEQ ID NO: 835)


 




1121.57
DGNKLDLYGK





(SEQ ID NO: 836)


 




1123.50
NYDDEDILK





(SEQ ID NO: 837)


 




1170.50
SVDGDQTYMR





(SEQ ID NO: 838)


 




1289.57
FQDVGSFDYGR





(SEQ ID NO: 839)


 




1347.68
INLLDDNQFTR





(SEQ ID NO: 840)


 




1378.59
NGSVSGEGMTNNGR





(SEQ ID NO: 841)


 




1378.59
NGSVSGEGMTNNGR





(SEQ ID NO: 842)


 




1438.68
YVDVGATYYFNK





(SEQ ID NO: 843)


 




1663.74
TDDQNSPLYIGNGDR





(SEQ ID NO: 844)


 




1819.84
RTDDQNSPLYIGNGDR





(SEQ ID NO: 845)


 




1819.84
RTDDQNSPLYIGNGDR





(SEQ ID NO: 846)


 




2232.09
NTDEFGLVDGLNFAVQYQG





K





(SEQ ID NO: 847)


 




2353.10
YDANNIYLAAQYTQTYNAT





R





(SEQ ID NO: 848)


 




2447.07
VDGLHYFSDDKSVDGDQTY





MR





(SEQ ID NO: 849)


 




2584.20
TDDQNSPLYIGNGDRAETY





TGGLK





(SEQ ID NO: 850)


 




2791.30
QNGDGVGGSITYDYEGFGI





GAAVSSSKR





(SEQ ID NO: 851)


 




2990.49
AQNFEAVAQYQFDFGLRPS





LAYLQSK





(SEQ ID NO: 852)


 




3104.47
EALRQNGDGVGGSITYDYE





GFGIGAAVSSSK





(SEQ ID NO: 853)


 


Lw124
37
817.43
LGGMVWR





(SEQ ID NO: 854)


 




914.52
AQGVQLTAK





(SEQ ID NO: 855)


 




1026.58
GIPADEISAR





(SEQ ID NO: 856)


 




1054.47
DNTWYTGAK





(SEQ ID NO: 857)


 




1082.54
SDVLFNFNK





(SEQ ID NO: 858)


 




1154.63
GIKDVVTQPQA





(SEQ ID NO: 859)


 




1221.66
AQSVVDYLISK





(SEQ ID NO: 860)


 




1279.64
DGSVVVLGYTDR





(SEQ ID NO: 861)


 




1377.76
RAQSVVDYLISK





(SEQ ID NO: 862)


 




1408.66
IGSDAYNQGLSER





(SEQ ID NO: 863)


 




1442.69
MPYKGSVENGAYK





(SEQ ID NO: 864)


 




1564.76
IGSDAYNQGLSERR





(SEQ ID NO: 865)


 




1653.82
LGYPITDDLDIYTR





(SEQ ID NO: 866)


 




3708.89
HFTLKSDVLFNFNK





(SEQ ID NO: 867)


 




2231.16
FGQGEAAPVVAPAPAPAPE





VQTK





(SEQ ID NO: 868)


 




2599.35
ATLKPEGQAALDQLYSQLS





NLDPK





(SEQ ID NO: 869)


 




2600.29
NHDTGVSPVFAGGVEYAIT





PEIATR





(SEQ ID NO: 870)


 




2670.29
DGSVVVLGYTDRIGSDAYN





QGLSER





(SEQ ID NO: 871)


 




3477.67
LEYQWTNNIGDAHTIGTRP





DNGMLSLGVSYR





(SEQ ID NO: 872)


 


LW-1A-10
29
950.52
ATNLLYTR





(SEQ ID NO: 873)


 




1019.54
YAIVANDVR





(SEQ 3D NO: 874)


 




1484.73
TALIDHLDTMAER





(SEQ ID NO: 875)(


 




1516.89
QVIQFIDLSLITK





(SEQ ID NO: 877)


 




1675.81
GANFIAVHEMLDGFR





(SEQ ID NO: 878)





1Molecular weight as determined by SDS-PAGE.


2The mass of a polypeptide fragment can be converted to m/z value by adding 1 to the mass. Each mass includes a range of plus or minus 300 ppm (the 83 kDa and 29 kDa polypeptides), 450 ppm (the 66 kDa and 56 kiDa polypeptides), or 1 Dalton (the remaining polypeptide).














TABLE 7







Characteristics of polypeptides



obtained from an E. coli.













mass value of
predicted





polypeptide
amino acid



approximate
fragments
sequence



molecular
resulting
of the


polypeptide
weight in
from trypsin
polypeptide


designation
kilodaltons (kDa)1
digest2
fragment














AB1-1
92
904.51
LVQLNYR






(SEQ ID NO: 880)


 




908.44
GGIQYDTR





(SEQ ID NO: 881)


 




1050.50
IYDDAAVER





(SEQ ID NO: 882)


 




1078.54
EAPGQPEPVR





(SEQ ID NO: 883)


 




1171.60
AQYLYVPYR





(SEQ ID NO: 884)


 




1276.56
YGSSTDGYATQK





(SEQ ID NO: 885)


 




1343.65
EEQVAEIWNAR





(SEQ ID NO: 886)


 




1403.73
IYGQAVHFVNTR





(SEQ ID NO: 887)


 




1450.67
RGNIMWENEFR





(SEQ ID NO: 888)


 




1479.76
YASPEYIQATLPK





(SEQ ID NO: 889)


 




1510.72
TGSLVWAGDTYWR





(SEQ ID NO: 890)


 




1546.66
VSDPSYFNDFDNK





(SEQ ID NO: 891)


 




1567.75
LDNVATSNSSIEYR





(SEQ ID NO: 892)


 




1624.79
GLSSNYGLGTQEMLR





(SEQ ID NO: 893)


 




1668.72
DTNVWEGDYQMVGR





(SEQ ID NO: 895)


 




1739.90
NGISQVGAVASWPIADR





(SEQ ID NO: 897)


 




1822.89
FNISVGQIYYFTESR





(SEQ ID NO: 898)


 




1858.93
QHAVYDNAIGFNIELR





(SEQ ID NO: 899)


 




2122.02
LLATHYQQTNLDWYNSR





(SEQ ID NO: 900)


 




2140.01
IYNYDSSLLQSDYSGLFR





(SEQ ID NO: 901)


 


AB12
80
628.39
IEVER





(SEQ ID NO: 902)


 




830.45
DVSEIIR





(SEQ ID NO: 903)


 




1177.61
AGTYATTLPAGR





(SEQ ID NO: 904)


 




1633.84
NVSLTGGVDNLFDKR





(SEQ ID NO: 905)


 




1786.85
TNFSLTGPLGDEFSFR





(SEQ ID NO: 906)


 




1796.82
TQADAWDINQGHQSAR





(SEQ ID NO: 907)


 




1870.95
APSLYQTNPNYILYSK





(SEQ ID NO: 908)


 




1980.96
WDFAPLQSLELEAGYSR





(SEQ ID NO: 909)


 




2087.91
QGNLYAGDTQNTNSDAYTR





(SEQ ID NO: 910)


 




2091.10
LSIIPEYTLNSTLSWQAR





(SEQ ID NO: 911)


 




2173.92
GSGEWHGSWDAYFNAPEHK





(SEQ ID NO: 912)


 




2302.02
KGSGEWHGSWDAYFNAPEH





K





(SEQ ID NO: 913)


 




2843.31
AGNAQTTGDLAGANYIAGA





GAYTYNEPGR





(SEQ ID NO: 914)


 


AB1-3
77
1380.59
SSEGANTYNEPGR





(SEQ ID NO: 915)


 




1525.72
GDTNWVPPEQVER





(SEQ ID NO: 916)


 




1688.88
ANFSLSGPLAGNALTTR





(SEQ ID NO: 917)


 




1748.79
TNNTRNNEGLSGGGEGR





(SEQ ID NO: 918)


 




1831.90
APNLYQSSEGYLLYSK





(SEQ ID NO: 919)


 




1889.03
IVAGDNVIGQTASGAYILK





(SEQ ID NO: 920)


 




1929.04
GPAAARYGSGAAGGVVNII





TK





(SEQ ID NO: 921)


 




1968.03
GMGPENTLILIDGVPVTSR





(SEQ ID NO: 922)


 




2030.93
QNYGITHNGIWDWGQSR





(SEQ ID NO: 924)


 




2917.36
QNYGITHNGIWDWGQSEFG





VYYEK





(SEQ ID NO: 925)


 




2959.54
NHSQISALYIEDNIEPVPG





TNIIPGLR





(SEQ ID NO: 928)


 


AB14
72
628.39
IEVIR





(SEQ ID NO: 927)


 




807.40
YWANVR





(SEQ ID NO: 928)


 




871.47
QIWAAQR





(SEQ ID NO: 929)


 




888.44
FVFEYGK





(SEQ ID NO: 930)


 




1738.77
DKYNHWDLNYESR





(SEQ ID NO: 931)


 




1762.81
LDNHEIYGSYWNPR





(SEQ ID NO: 932)


 




1872.93
FGNSTTNDFYLSGPLIK





(SEQ ID NO: 933)


 




1999.02
DVEGISITGGNEKPDISIR





(SEQ ID NO: 934)


 




2103.95
SEDIDTIDGNWQVDEGRR





(SEQ ID NO: 935)


 




2141.02
EVSPGFGTLTQGGASIMYG





NR





(SEQ ID NO: 936)


 




2207.09
DPVTGLNTFIYDNVGEANI





R





(SEQ ID NO: 937)


 




2415.19
ESRPNGSGGFEAGFIPPVE





AIER





(SEQ ID NO: 938)


 




2439.29
VTAFLPENVLTIGGQFQHA





ELR





(SEQ ID NO: 939)


 


ABI-5
66
614.38
VEIVR





(SEQ ID NO: 940)


 




715.38
HESIGE





(SEQ ID NO: 941)


 




770.48
RVEIVR





(SEQ ID NO: 942)


 




830.38
ASYFDTK





(SEQ ID NO: 943)


 




941.46
IFVSYQW





(SEQ ID NO: 944)


 




951.48
IYWSEVR





(SEQ ID NO: 945)


 




1025.62
GVLVLVDGVR





(SEQ ID NO: 946)


 




1134.55
IWGWDVMTK





(SEQ ID NO: 947)


 




1154.67
DLPITLLGGTR





(SEQ ID NO: 948)


 




1221.63
MSRPQFTSLR





(SEQ ID NO: 949)


 




1335.64
DLLQEGQSSGFR





(SEQ ID NO: 950)


 




1395.64
INAQNTGSSGEYR





(SEQ ID NO: 951)


 




1531.71
EYWSPQGIPQDGR





(SEQ ID NO: 952)


 




1656.77
FDDLMLSNDALEFK





(SEQ ID NO: 953)


 




1676.80
YTTDLFSLDVAYNR





(SEQ ID NO: 955)


 




1716.88
GTWQIDSAQSLSGLVR





(SEQ ID NO: 956)


 




1778.88
IDFSSGWLQDEITLR





(SEQ ID NO: 957)


 




1962.95
VFGTGGTGDHSLGLGASAF





GR





(SEQ ID NO: 958)


 




1997.02
QGTDTGHLNGTFLOPALIK





(SEQ ID NO: 959)


 




2261.08
QPGYGVNDFYVSYQGQQAL





K





(SEQ ID NO: 960)


 




2397.13
STLFADSFASHLLTYGGEY





YR





(SEQ ID NO: 961)


 




3304.56
FYTNYWVPNPNLRPETNET





QEYGFGLR





(SEQ ID NO: 962)


 


AB1-6
50
787.46
SVVQTVR





(SEQ ID NO: 963)


 




801.43
LSQDLAR





(SEQ ID NO: 964)


 




827.45
LSNPELR





(SEQ ID NO: 965)


 




913.53
NLSLLQAR





(SEQ ID NO: 966)


 




1179.55
SAADRDAAFEK





(SEQ ID NO: 967)


 




1344.62
TTTSNGHNPFRN





(SEQ ID NO: 968)


 




1736.92
TIVDVLDATTTLYNAK





(SEQ ID NO: 969)


 




1828.90
SSFNNINASISSINAYK





(SEQ ID NO: 970)


 




2033.96
QAQYNFVGASEQLESAHR





(SEQ ID NO: 971)


 




2033.96
QAQYNFVGASEQLESAHR





(SEQ ID NO: 972)


 




2183.09
QITGNYYPELAALNVENFK





(SEQ ID NO: 973)


 




2183.09
QITGNYYPELAALNVENFK





(SEQ ID NO: 974)


 




2184.09
SPLLPQLGLGADYTYSNGY





R





(SEQ ID NO: 975)


 




2226.06
QAVVSAQSSLDANEAGYSV





GTR





(SEQ ID NO: 976)


 




2226.06
QAVVSAQSSLDANEAGYSV





GTR





(SEQ ID NO: 977)


 


AB1-7
42
631.37
LSSGLR





(SEQ ID NO: 978)


 




708.38
FTSNIK





(SEQ ID NO: 979)


 




715.40
GLTQAAR





(SEQ ID NO: 980)


 




759.38
LDEIDR





(SEQ ID NO: 981)


 




930.49
SSLGAVQNR





(SEQ ID NO: 982)


 




1002.51
SRLDEIDR





(SEQ ID NO: 983)


 




1019.54
AIAQVDTFR





(SEQ ID NO: 984)


 




2248.09
LDSAVTNLNNTTTNLSEAQ





SR





(SEQ ID NO: 985)


 




2642.29
NANDGISLAQTTEGALSEI





NNNLQR





(SEQ ID NO: 986)


 




2700.24
GAATSQFVVQSGNDFYSAS





INHTDGK





(SEQ ID NO: 987)


 




2814 .50
VVVELSTAKPTAQFSGASS





ADPLALLDK





(SEQ ID NO: 988)


 


AB1-8
38
704.42
VAFAGLK





(SEQ ID NO: 989)


 




841.48
NLGVINGR





(SEQ ID NO: 990)


 




884.41
GNGFATYR





(SEQ ID NO: 991)


 




1289.57
EQDVGSFDYGR





(SEQ ID NO: 992)


 




1438.68
YVDVGATYYFNK





(SEQ ID NO: 993)


 




2353. 10
YDANNIYLAAQYTQTYNAT





R





(SEQ ID NO: 994)


 




2990.49
AQNFEAVAQYQFDFGLRPS





LAYLQSK





(SEQ ID NO: 995)


 


AB1-9
36
718.44
LAFAGLK





(SEQ ID NO: 996)


 




867.42
DLGVHGDR





(SEQ ID NO: 997)


 




1057.56
NAEVWAAGLK





(SEQ ID NO: 998)


 




1248.54
FGDYGSIDYGR





(SEQ ID NO: 999)


 




1438.68
YVDVGATYYFNK





(SEQ ID NO: 1000)


 




1933.77
HYFSSNDADDGDTTYAR





(SEQ ID NO: 1001)


 




2217.05
NNDFFGLVDGLNFAAQYQG





K





(SEQ ID NO: 1002)


 




2389.09
GETQINDQLTGFGQWEYEF





K





(SEQ ID NO: 1003)


 




2834.36
LGFKGETQINDQLTGFGQW





EYEFK





(SEQ ID NO: 1004)


 


AB1-10
35
817.43
LGGMVWR





(SEQ ID NO: 1005)


 




871.51
RVEIEVK





(SEQ ID NO: 1007)


 




1054.47
DNTWYTGAK





(SEQ ID NO: 1008)


 




1279.64
DGSVVVLGYTDR





(SEQ ID NO: 1009)


 




1377.76
RAQSVVDYLISK





(SEQ ID NO: 1010)


 




1422.67
IGSDAYNQALSER





(SEQ ID NO: 1011)


 




1639.81
LGYPITDDLDVYTR





(SEQ ID NO: 1012)


 




2231.16
FGQGEAAPVVAPAPAPAPE





VQTK





(SEQ ID NO: 1013)


 




2599.35
ATLKPEGQAALDQLYSQLS





NLDPI





(SEQ ID NO: 1014)


 




3477.67
LEYQWTNNIGDAHTIGTRP





DNGMLSLGVSYR





(SEQ ID NO: 1015)


 


AB1-11
30
706.34
YWNPK





(SEQ ID NO: 1016)


 




776.48
ILPVGTK





(SEQ ID NO: 1017)


 




929.52
LENSLGGIK





(SEQ ID NO: 1018)


 




964.57
VHIINLEK





(SEQ ID NO: 1019)


 




1065.58
MKPEIEGAR





(SEQ ID NO: 1020)


 




1108.55
AGVHFGHQTR





(SEQ ID NO: 1022)


 




1204.61
WLGGMLTNWK





(SEQ ID NO: 1023)


 




1403.81
AVTLYLGAVAATVR





(SEQ ID NO: 1025)


 




1560.82
WLGGMLTNWKTVR





(SEQ ID NO: 1026)


 




1575.79
TVPMFNEALAELNK





(SEQ ID NO: 1027)


 




2376.17
DMGGLPDALFVIDADHEHI





AIK





(SEQ ID NO: 1028)


 


Lw214
19
914.52
ATVELLNR





(SEQ ID NO: 1029)


 




941.43
QAHWNMR





(SEQ ID NO: 1030)


 




950.52
ATNLLYTR





(SEQ ID NO: 1031)


 




1019.54
YAIVANDVR





(SEQ ID NO: 1032)


 




1484.73
TALIDHLDTMAER





(SEQ ID ND: 1033)


 




1516.89
QVIQFIDLSLITK





(SEQ ID NO: 1034)


 




1603.83
ELADRYAIVANDVR





(SEQ ID NO: 1035)


 




1675.81
GANFIAVHEMLDGFR





(SEQ ID NO: 1036)


 




1677.85
SYPLDIHNVQDHLK





(SEQ ID NO: 1037)


 




1677.85
SYPLDIHNVQDHLK





(SEQ ID NO: 1038)


 




2413. 39
ATVELLNRQVIQFIDLSLI





TK





(SEQ ID NO: 1039)


 


Lw215
16
602.30
ELADR





(SEQ ID NO: 1040)


 




914.52
ATVELLNR





(SEQ ID NO: 1041)


 




941.43
QAHWNMR





(SEQ ID N0: 1042)


 




950.52
ATNLLYTR





(SEQ ID NO: 1043)


 




1019.54
YAIVANDVR





(SEQ ID NO: 1044)


 




1042.61
KATVELLNR





(SEQ ID NO: 1045)


 




1147.63
YAIVANDVRK





(SEQ ID NO: 1046)


 




1362.63
DDDTADILTAASR





(SEQ ID NO: 1047)


 




1484.73
TALIDHLDTMAER





(SEQ ID NO: 1048)


 




1516.89
QVIQFIDLSLITK





(SEQ ID NO: 1049)


 




1603.83
ELADRYAIVANDVR





(SEQ ID NO: 1050)


 




1675.81
GANFIAVHEMLDGFR





(SEQ ID NO: 1051)


 




1767.87
DLDKFLWFIESNIE





(SEQ ID NO: 1052)


 




1931.94
AIGEAKDDDTADILTAASR





(SEQ ID NO: 1053)


 




2262.14
SYPLDIHNVQDHLKELADR





(SEQ ID NO: 1054)





1Molecular weight as determined by SDS-PAGE.


2The mass of a polypeptide fragment can be converted to m/z value by adding 1 to the mass. Each mass includes a range of plus or minus 250 ppm (the 92 kDa polypeptide), plus or minus 300 ppm (the 80 kDa and 30 kDa polypeptides), plus or minus 400 ppm (the 77 kDa, 72 kDa, 42 kDa, and 35 kDa polypeptides), plus or minus 450 ppm (the 50 kDa and 36 kDa polypeptides), plus or minus 500 ppm (the 66 kDa and 38 kDa polypeptides) or 1 Dalton (the 19 kDa and 16 kDa polypeptides).














TABLE 8







Characteristics of polypeptides



obtained from an E. coli.













mass value of
predicted





polypeptide
amino acid



approximate
fragments
sequence



molecular
resulting
of the


polypeptide
weight in
from trypsin
polypeptide


designation
kilodaltons (kDa)1
digest2
fragment














J4-1
82
628.39
IEVLR






(SEQ ID NO: 1055)


 




1306.65
DGWLAGVTWFR





(SEQ ID NO: 1056)


 




1515.70
GDTSWVPPEMIER





(SEQ ID NO: 1057)


 




1577.83
AETSINKEIGLEFK





(SEQ ID NO: 1058)


 




1633.84
NVSLTGGVDNLFDKR





(SEQ ID NO: 1059)


 




1786.85
TNFSLTGPLGDEFSFR





(SEQ ID NO: 1060)


 




1796.82
TQADAWDINQGHQSAR





(SEQ ID NO: 1061)


 




1980.96
WDFAPLQSLELEAGYSR





(SEQ ID NO: 1062)


 




2087.91
QGNLYAGDTQNTNSDAYTR





(SEQ ID NO: 1063)


 




2091.10
LSIIPEYTLNSTLSWQAR





(SEQ ID NO: 1064)


 




2126.08
GDTSWVPPEMIERIEVLR





(SEQ ID NO: 1065)


 




2843.31
AGNAQTTGDLAGANYIAGA





GAYTYNEPGR





(SEQ ID NO: 1066)


 


J4-2
79
685.41
ITLSPR





(SEQ ID NO: 1067)


 




736.37
NYWVR





(SEQ ID NO: 1068)


 




841.51
RITLSPR





(SEQ ID NO: 1069)


 




860.45
GIYAGQPR





(SEQ ID NO: 1070)


 




1146.60
IPGFMLWGAR





(SEQ ID NO: 1071)


 




1207.57
WQSTRPYDR





(SEQ ID NO: 1073)


 




1243.56
ENDVFEHAGAR





(SEQ ID NO: 1074)


 




1278.57
YLNESTHEMR





(SEQ ID NO: 1075)


 




1472.74
IDIGNWTITPGMR





(SEQ ID NO: 1076)


 




1486.76
FNIQGFYTQTLR





(SEQ ID NO: 1077)


 




1578.82
YGPQSVGGVVNFVTR





(SEQ ID NO: 1078)


 




1615.78
EDALTVVGDWLGDAR





(SEQ ID NO: 1079)


 




1717.84
LASLGYQFQPDSQHK





(SEQ ID NO: 1080)


 




2013.89
ADYDADEWQSTRPYDR





(SEQ ID NO: 1081)


 




2035.91
YYTATSSGQLPSGSSPYDR





(SEQ ID NO: 1082)


 




2110.03
YSQIFMIGPSAHEVGVGYR





(SEQ ID NO: 1083)


 


J4-3
88
649.35
GFSAIR





(SEQ ID NO: 1085)


 




649.35
GFSAIR





(SEQ ID NO: 1086)


 




671.36
IPGTER





(SEQ ID NO: 1087)


 




820.42
FTGNNLR





(SEQ ID NO: 1088)


 




1123.53
VDSYELGWR





(SEQ ID NO: 1089)


 




1278.78
GRPLVVLVDGVR





(SEQ ID NO: 1090)


 




1296.65
FYPFPTVNANK





(SEQ ID NO: 1091)


 




1324.64
IDDFIGYAQQR





(SEQ ID NO: 1092)


 




1380.62
SQGDDDYGLNLGK





(SEQ ID NO: 1093)


 




1423.72
IAGAVSGGNEHISGR





(SEQ ID NO: 1094)


 




1550.73
GTSTPFVSNGLNSDR





(SEQ ID NO: 1095)


 




1702.85
ATAYIGWAPDPWSLR





(SEQ ID NO: 1096)


 




1731.80
VQSTTSFDVSDAQGYK





(SEQ ID NO: 1097)


 




2023.96
APLYYSPGYGPASLYDYK





(SEQ ID NO: 1098)


 




2019.88
QVTAFSSSQQDTDQYGMK





(SEQ ID NO: 1099)


 




2234.98
GQPETMMEFEAGTKSGFSS





SK





(SEQ ID NO: 1100)


 




2785.41
HLISLQYSDSAFLGQELVG





QVYYR





(SEQ ID NO: 1101)


 




2847.27
FGGWFDGNGDATLLDNTQT





CLQYSDR





(SEQ ID NO: 1102)


 


J4-4
60
675.33
FEQPR





(SEQ ID NO: 1103)


 




678.37
VEYIE





(SEQ ID NO: 1104)


 




1755.80
YDKDYSSYPYQTVK





(SEQ ID NO: 1105)


 




1819.86
QWEGAFEGLTAGVNWR





(SEQ ID NO: 1106)


 




1892.00
SAVYGSDAIGGVVNIITTR





(SEQ ID NO: 1107)


 




1930.95
QDIDRWQSTSVNDVLR





(SEQ ID NO: 1108)


 




2023.92
HGTWQTSAGWEFIEGYR





(SEQ ID NO: 1109)


 




2158.14
LPGVDITQNGGSGQLSSIF





HR





(SEQ ID NO: 1110)


 




2206. 07
APNLGQLYGFYGNPNLDPE





K





(SEQ ID NO: 1111)


 




2255.23
LNLAGVSGSADLSQFPIAL





VQR(SEQ ID NO: 1112)


 




2323.11
IANLFDKDYETVYGYQTAG





R





(SEQ ID NO: 1113)


 




2357.17
NTGIYLTGLQQVGDFTFEG





AAR





(SEQ ID NO: 1114)


 




2698.25
GVEATANFDTGRLTHTVSY





DYVDAR





(SEQ ID NO: 1115)


 


J4-5
54
787.46
SVVQTVR





(SEQ ID NO: 1116)


 




801.43
ESQOLAR





(SEQ ID NO: 1117)


 




827.45
LSNPELR





(SEQ ID NO: 1118)


 




913.53
NLSLLQAR





(SEQ ID NO: 1119)


 




1230.57
TTTSNGHNPFR





(SEQ ID NO: 1120)


 




1284.64
NNLDNAVEQLR





(SEQ ID NO: 1121)


 




1322.76
TDKPQPVNALLK





(SEQ ID NO: 1122)


 




1344.62
TTTSNGHNPFRN





(SEQ ID NO: 1123)


 




1549.77
AQYDTVLANEVTAR





(SEQ ID NO: 1124)


 




1615.87
FNVGLVAITDVQNAR





(SEQ ID NO: 1125)


 




1736.92
TIVDVLDATTTLYNAK





(SEQ ID NO: 1126)


 




1828.90
SSFNNINASISSINAYK





(SEQ ID NO: 1127)


 




2033.96
QAQYNFVGASEQLESAHR





(SEQ ID NO: 1128)


 




2123.10
VGLSFSLPIYQGGMVNSQV





K





(SEQ ID NO: 1129)


 




2183.09
QITGNYYPELAALNVENFK





(SEQ ID NO: 1130)


 




2226.05
QAVVSAQSSLDANEAGYSV





GTR





(SEQ ID NO: 1131)


 


J4-6
46
730.43
LSLAATR





(SEQ ID NO: 1132)


 




858.46
LGQEVWK





(SEQ ID NO: 1133)


 




963.46
VDFHGYAR





(SEQ ID NO: 1134)


 




1562.74
FAYNINNNGHNLR





(SEQ ID NO: 1135)


 




1660.77
EVVQYATDSNTSQGK





(SEQ ID NO: 1137)


 




1683.90
NLIEWLPGSTIWAGK





(SEQ ID NO: 1138)


 




1730.86
DGWLETAEHTQSVLK





(SEQ ID NO: 1139)


 




2132.06
LAQNEINPGGTLELGVDYG





R





(SEQ ID NO: 1140)


 




2209.07
LGNECETYAELKLGQEVWK





(SEQ ID NO: 1142)


 




2355.08
WTPINSTVMEIGYDNVESQ





R





(SEQ ID NO: 1143)


 




3216.38
SSEAGGSSSFASNNIYDYT





NETANDVFDVR





(SEQ ID NO: 1145)


 


J47
45
785.41
YALTYR





(SEQ ID NO: 1146)


 




1024.46
GNYSSDLNR





(SEQ ID NO: 1147)


 




1029.51
SISIPDQDR





(SEQ ID NO: 1148)


 




1254 .61
ATSTSGDTLEQK





(SEQ ID NO: 1149)


 




1496.68
INEGPYQFESEGK





(SEQ ID NO: 1150)


 




1504.74
FWLSAGTTYAFNK





(SEQ ID NO: 1151)


 




1586.77
TGIAFDDSPVPAQNR





(SEQ ID NO: 1152)


 




1651.74
AYSGEGAIADDAGNVSR





(SEQ ID NO: 1153)


 




1777.83
DASVDVGVSYMHGQSVK





(SEQ ID NO: 1154)


 




1898.94
LNNAWSFGLGFNAVYAR





(SEQ ID NO: 1155)


 




1997.92
IALGTTYYYDDNWTFR





(SEQ ID NO: 1156)


 


Lw216
38
867.44
TTGVATYR





(SEQ ID NO: 1157)


 




1248.54
FGDYGSIDYGR





(SEQ ID NO: 1158)


 




1438.68
YVDVGATYYFNK





(SEQ ID NO: 1159)


 




1933.77
HYFSSNDADDGDTTYAR





(SEQ ID NO: 1160)


 




2217.05
NNDFFGLVDGLNFAAQYQG





K





(SEQ ID NO: 1161)


 




2389.09
GETQINDQLTGFGQWEYEF





K





(SEQ ID NO: 1162)


 




2602.22
NNDFFGLVDGLNFAAQYQG





KNDR





(SEQ ID NO: 1163)


 




2976.48
AQNFEAVAQYQFDFGLRPS





VAYLQSK





(SEQ ID NO: 1164)


 




3306.53
YDANNIYLATTYSETQNMT





VFGNNHIANK





(SEQ ID NO: 1165)


 


Lw217
37
817.43
LGGMVWR





(SEQ ID NO: 1166)


 




1279.64
DGSVVVLGYTDR





(SEQ ID NO: 1167)


 




1377.69
ADTKANVPGGASYK





(SEQ ID NO: 1168)


 




2231.16
FGQGEAAPVVAPAPAPAPE





VQTK





(SEQ ID NO: 1169)


 




2599.35
ATLKPEGQAALDQLYSQLS





NLDPK





(SEQ ID NO: 1170)


 




2601.27
DHDTGVSPVFAGGVEYAIT





PEIATR





(SEQ ID NO: 1171)


 


J411
31
706.34
YWNPK





(SEQ ID NO: 1172)


 




776.48
ILFVGTK





(SEQ ID NO: 1173)


 




929.52
LENSLGGIK





(SEQ ID NO: 1174)


 




964.57
VHIINLEK





(SEQ ID NO: 1175)


 




1065.58
MKPFIFGAR





(SEQ ID NO: 1176)


 




1108.55
AGVHFGHQTR





(SEQ ID NO: 1178)


 




1204 .61
WLGGMLTNWK





(SEQ ID NO: 1179)


 




1403.81
AVTLYLGAVAATVR





(SEQ ID NO: 1181)


 




1575.80
TVPMFNEALAELNK





(SEQ ID NO: 1182)


 




2376.17
DMGGLPDALFVIDADHEHI





AIK





(SEQ ID NO: 1184)


 


J412
30
716.40
FGPQIR





(SEQ ID NO: 1185)


 




1338.68
LTNTDLSFGPFK





(SEQ ID NO: 1186)


 




1462.66
NDTYLEYEAFAK





(SEQ ID NO: 1187)


 




1840.79
EWYFANNYIYDMGR





(SEQ ID NO: 1188)


 




1881.92
GIWNHGSPLFMEIEPR





(SEQ ID NO: 1190)


 




2262.94
YQWQNYGAANENEWDGYR





(SEQ ID NO: 1192)


 




2824 .20
YWHDGGQWNDDAELNFGNG





NFNVR





(SEQ ID NO: 1193)


 




2867.41
TNNSIASSHILALNYDHWH





YSVVAR





(SEQ ID NO: 1194)


 


Lw218
19
914.52
ATVELLNR





(SEQ ID NO: 1195)


 




941.43
QAHWNMR





(SEQ ID NO: 1196)


 




950.52
ATNLLYTR





(SEQ ID NO: 1197)


 




1019.54
YAIVANDVR





(SEQ ID NO: 1198)


 




1362.63
DDDTADILTAASR





(SEQ ID NO: 1199)


 




1484.73
TALIDHLDTMAER





(SEQ ID NO: 1200)


 




1516.89
QVIQFIDLSLITK





(SEQ ID NO: 1201)


 




1603.83
ELADRYAIVANDVR





(SEQ ID NO: 1202)


 




1675.81
GANFIAVHEMLDGFR





(SEQ ID NO: 1203)


 




1677.85
SYPLDIHNVQDHLK





(SEQ ID NO: 1204)


 




1754.99
AVQLGGVALGTTQVINSK





(SEQ ID NO: 1205)


 




1931.94
AIGEAKDDDTADILTAASR





(SEQ ID NO: 1206)


 




2262.14
SYPLDIHNVQDHLKELADR





(SEQ ID NO: 1207)


 


Lw219
16
602.30
ELADR





(SEQ ID NO: 1208)


 




914.52
ATVELLNR





(SEQ ID NO: 1209)


 




941.43
QAHWNMR





(SEQ ID NO: 1210)


 




950.52
ATNLLYTR





(SEQ ID NO: 1211)


 




1019.54
YAIVANDVR





(SEQ ID NO: 1212)


 




1042.61
KATVELLNR





(SEQ ID NO: 1213)


 




1147.63
YAIVANDVRK





(SEQ ID NO: 1214)


 




1362.63
DDDTADILTAASR





(SEQ ID NO: 1215)


 




1484.73
TALIDHLDTMAER





(SEQ ID NO: 1216)


 




1516.89
QVIQFIDLSLITK





(SEQ ID NO: 1217)


 




1603.83
ELADRYAIVANDVR





(SEQ ID NO: 1218)


 




1675.81
GANFIAVHEMLDGFR





(SEQ ID NO: 1219)


 




1754.99
AVQLGGVALGTTQVINSK





(SEQ ID NO: 1220)


 




1767.87
DLDKFLWFIESNIE





(SEQ ID NO: 1221)


 




1931.94
AIGEAKDDDTADILTAASR





(SEQ ID NO: 1222)


 




2262.14
SYPLDIHNVQDHLKELADR





(SEQ ID NO: 1223)





1Molecular weight as determined by SDS-PAGE.


2The mass of a polypeptide fragment can be converted to m/z value by adding a to the mass. Each mass includes a range of plus or minus 300 ppm (the 88 kDa, 79 kDa, 60 kDa, 38 Wa, and 31 kDa polypeptides), plus or minus 350 ppm (the 46 kDa polypeptide), plus or minus 400 ppm (the 82 kDa, 54 kDa, 45 kDa, and 30 kDa polypeptides), or plus or minus 1 Dalton (the 37 kDa, 19 kDa and 16 kDa polypeptides).














TABLE 9







Characteristics of polypeptides



obtained from an E. coli.













mass value of
predicted





polypeptide
amino acid



approximate
fragments
sequence



molecular
resulting
of the


polypeptide
weight in
from trypsin
polypeptide


designation
kilodaltons (kDa)1
digest2
fragment














Lw189A
101
888.41
YGYAYPR






(SEQ ID NO: 1224)


 




986.54
LAGDLETLR





(SEQ ID NO: 1225)


 




998.45
GYFPTDGSR





(SEQ ID NO: 1226)


 




1008.47
WGYGDGLGGK





(SEQ ID NO: 1227)


 




1113.56
DIHFEGLQR





(SEQ ID NO: 1228)


 




1276.60
GLEDFYYSVGK





(SEQ ID NO: 1229)


 




1338.66
ALFATGNFEDVR





(SEQ ID NO: 1230)


 




1401.71
VPGSPDQVDVVYK





(SEQ ID NO: 1231)


 




1470.69
DEVPWWNVVGDR





(SEQ ID NO: 1232)


 




1519.80
ERPTIASITFSGNK





(SEQ ID NO: 1233)


 




1527.72
LGFFETVDTDTQR





(SEQ ID NO: 1234)


 




1698.85
GIYVTVNITEGDQYK





(SEQ ID NO: 1235)


 




1758.82
YDGDKAEQFQFNIGK





(SEQ ID NO: 1236)


 




1770.75
TDDFTFNYGWTYNK





(SEQ ID NO: 1237)


 




1953.86
EMPFYENFYAGGSSTVR





(SEQ ID NO: 1238)


 




2145.04
SYGTDVTLGFPINEYNSLR





(SEQ ID NO: 1239)


 




2154 .96
TDDFTENYGWTYNKLDR





(SEQ ID NO: 1240)


 




2238.15
LSGVEVSGNLAGHSAEIEQ





LTK





(SEQ ID NO: 1241)


 




2253.97
LFYNDFQADDADLSDYTNK





(SEQ ID NO: 1242)


 




2911.42
LGFFETVDTDTQRVPGSPD





QVDVVYK





(SEQ ID NO: 1243)


 


Lw189B
101
904.51
LVQLNYR





(SEQ ID NO: 1244)


 




1171.60
AQYLYVPYR





(SEQ ID NO: 1245)


 




1276.56
YGSSTDGYATQK





(SEQ ID NO: 1246)


 




1294.58
GNIMWENEFR





(SEQ ID NO: 1247)


 




1307.68
LQADEVQLHQK





(SEQ ID NO: 1248)


 




1343.65
EEQVAEIWNAR





(SEQ ID NO: 1249)


 




1403.73
IYGQAVHFVNTR





(SEQ ID NO: 1250)


 




1450.68
RGNIMWENEFR





(SEQ ID NO: 1251)


 




1546.66
VSDPSYFNDFDNK





(SEQ ID NO: 1252)


 




1668.72
DTNVWEGDYQMVGR





(SEQ ID NO: 1253)


 




1717.73
VYEDEHPNDDSSRR





(SEQ ID NO: 1254)


 




1763.82
WSIVGAYYYDTNANK





(SEQ ID NO: 1255)


 




1822.89
FNISVGQIYYFTESR





(SEQ ID NO: 1256)


 




1831.91
FSVGYAVQNFNATVSTK





(SEQ ID NO: 1257)


 




1858.93
QHAVYDNAIGFNIELR





(SEQ ID NO: 1258)


 




2013.02
TVDALGNVHYDDNQVILK





(SEQ ID NO: 1259)


 




2088.13
VGPVPIFYSPYLQLPVGDK





(SEQ ID NO: 1260)


 


Lw190
88
1177.81
AGTYATTLPAGR





(SEQ ID NO: 1261)


 




1177.61
AGTYATTLPAGR





(SEQ ID NO: 1262)


 




1306.65
DGWLAGVTWFR





(SEQ ID NO: 1263)


 




1515.70
GDTSWVPPEMIER





(SEQ ID NO: 1264)


 




1577.83
AETSINKEIGLEFK





(SEQ ID NO: 1265)


 




1633.84
NVSLTGGVDNLFDKR





(SEQ ID NO: 1266)


 




1786.85
TNFSLTGPLGDEFSFR





(SEQ ID NO: 1267)


 




1796.82
TQADAWDINQGHQSAR





(SEQ ID NO: 1268)


 




1870.95
APSLYQTNPNYILYSK





(SEQ ID NO: 1269)


 




1980.96
WDFAPLQSLELEAGYSR





(SEQ ID NO: 1270)


 




2126.08
GDTSWVPPEMIERIEVLR





(SEQ ID NO: 1271)


 




2173.92
GSGEWHGSWDAYFNAPEHK





(SEQ ID NO: 1272)


 




2302.02
KGSGEWHGSWDAYFNAPEH





K





(SEQ ID NO: 1273)


 




2706.33
IEAGYVAVGQNAVGTDLYQ





WDNVPK





(SEQ ID NO: 1274)


 




2843.31
AGNAQTTGDLAGANYIAGA





GAYTYNEPGR





(SEQ ID NO: 1275)


 




3081.49
FDHHSIVGNNWSPALNISQ





GLGDDFTLK





(SEQ ID NO: 1276)


 




3196.44
QNYALTWNGGWDNGVTTSN





WVQYENTR





(SEQ ID NO: 1277)


 


Lw191
85
564.28
FWGR





(SEQ ID NO: 1278)


 




685.41
ITLSPR





(SEQ ID NO: 1279)


 




736.37
NYWVR





(SEQ ID NO: 1280)


 




860.45
GIYAGQRR





(SEQ ID NO: 1281)


 




861.43
TWELGTP





(SEQ ID NO: 1282)


 




1146.60
IPGFMLWGAR





(SEQ ID NO: 1283)


 




1207.57
WQSTRPYDR





(SEQ ID NO: 1284)


 




1243.56
ENDVFEHAGAR





(SEQ ID NO: 1285)


 




1278.57
YLNESTNEMR





(SEQ ID NO: 1286)


 




1278.57
YLNESTHEMR





(SEQ ID NO: 1287)


 




1329.64
NIFDQDYFIR





(SEQ ID NO: 1288)


 




1486.76
FNIQGFYTQTLR





(SEQ ID NO: 1289)


 




1578.82
YGPQSVGGVVNFVTR





(SEQ ID NO: 1290)


 




1615. 78
EDALTVVGDWLGDAR





(SEQ ID NO: 1291)


 




1650.83
EKGDTYGNLVPFSPK





(SEQ ID NO: 1292)


 




1696.78
SYDDNNKGIYAGQPR





(SEQ ID NO: 1293)


 




1717.84
LASLGYQFQPDSQHK





(SEQ ID NO: 1294)


 




2013.89
ADYDADRWQSTRPYDR





(SEQ ID NO: 1295)


 




2035.91
YYTATSSGQLPSGSSPYDR





(SEQ ID NO: 1296)


 




2110.03
YSQIFMIGPSAHEVGVGYR





(SEQ ID NO: 1297)


 




2221.11
ALNQYAAHSGFTLSVDASL





TR





(SEQ ID NO: 1298)


 




2408.09
YYTATSSGQLPSGSSPYDR





DTR





(SEQ ID NO: 172)


 




2581 .22
ETHNLMVGGTADNGEGTAL





LYSGTR





(SEQ ID NO: 1299)


 




2603.31
AIPQDFGIEAGVEGQLSPT





SSQNNPK





(SEQ ID NO: 1300)


 




2946.40
SGTEAHAWYLDDKIDIGNW





TITPGMR





(SEQ ID NO: 1301)


 




3021.50
YDLGTLTPTLDNVSIYASY





AYVNAEIR





(SEQ ID NO: 1302)


 




3144.41
YAPDEVIATFNSLLQYYDGE





ADMPGGLSR





(SEQ ID NO: 1303)


 


Lw193
77
523.26
YDVK





(SEQ ID NO: 1304)


 




649.35
GESAIR





(SEQ ID NO: 1305)


 




820.42
FTGNNLR





(SEQ ID NO: 1306)


 




1123.53
VDSYELGWR





(SEQ ID NO: 1307)


 




1159.59
TFGLNYSVLF





(SEQ ID NO: 1308)


 




1278.78
GRPLVVLVDGVR





(SEQ ID NO: 1309)


 




1296.65
FYPFPTVNANK





(SEQ ID NO: 1310)


 




1324.64
IDDFIGYAQQR





(SEQ ID NO: 1311)


 




1372.71
GRTFGLNYSVLF





(SEQ ID NO: 1312)


 




1380.62
SQGDODYGLNLGK





(SEQ ID NO: 1313)


 




1423.72
IAGAVSGGNEHISGR





(SEQ ID NO: 1314)


 




1509.83
GIYGAAVNGHLPLTK





(SEQ ID NO: 1315)


 




1550.73
GTSTRFVSNGLNSDR





(SEQ ID NO: 1316)


 




1553.84
DALAQLIPGLDVSSR





(SEQ ID NO: 1317)


 




1649.84
LEGVKVDSYELGWR





(SEQ ID NO: 1318)


 




1702.85
ATAYIGWAPDPWSLR





(SEQ ID NO: 1319)


 




1924.08
ELKDALAQLIPGLDVSSR





(SEQ ID NO: 1320)


 




2013.00
QQAWLNFSQGVELPDPGK





(SEQ ID NO: 1321)


 




2023.96
APLYYSPGYGRASLYDYK





(SEQ ID NO: 1322)


 




2204.08
GTSTPFVSNGLNSDRIPGT





ER





(SEQ ID NO: 1323)


 




2251.05
YQYTENKIDDFIGYAQQR





(SEQ ID NO: 1324)


 




2552.24
QQAWLNESQGVELPDPGKY





YGR





(SEQ ID NO: 1325)


 




2785.41
HLISLQYSDSAFLGQELVG





QVYYR





(SEQ ID NO: 1326)


 




2847.27
FGGWFDGNGDATLLDNTQT





GLQYSDR





(SEQ ID NO: 1327)


 




3194.53
ATSADAIPGGSVDYDNFLF





NAGLLMHITER





(SEQ ID NO: 1328)


 




3335.85
YPSYDITNLAAFLQSGYDI





NNLFTLNGGVR





(SEQ ID NO: 1329)


 




3385.69
HLISLQYSDSAFLGQELVG





QVYYRDESLR





(SEQ ID NO: 1330)


 


Lw194
67
678.37
VEYIR





(SEQ ID NO: 1331)


 




1112.62
NAITDTPLLR





(SEQ ID NO: 1332)


 




1135.55
FIASYGTSYK





(SEQ ID NO: 1333)


 




1243.71
STVLAPTTVVTR





(SEQ ID NO: 1334)


 




1249.63
SQLITSYSHSK





(SEQ ID NO: 1335)


 




1294.63
LYSQSWDAGLR





(SEQ ID NO: 1336)


 




1298.53
DYNYDPHYOR





(SEQ ID NO: 1337)


 




1303.65
WQSTSVNDVLR





(SEQ ID NO: 1338)


 




1349.61
DYSSYPYQTVK





(SEQ ID NO: 1339)


 




1422.73
KLYSQSWDAGLR





(SEQ ID NO: 1340)


 




1521 .67
DYETVYGYQTAGR





(SEQ ID NO: 1341)


 




1549.86
GTNASHVLVLIDGVR





(SEQ ID NO: 1342)


 




1755.80
YDKDYSSYPYQTVK





(SEQ ID NO: 1343)


 




1761 .81
NDVSDLIDYDDHTLK





(SEQ ID NO: 1344)


 




1886.83
QTTTPGTGYVEDGYDQR





(SEQ ID NO: 1345)


 




1892.00
SAVYGSDAIGGVVNIITTR





(SEQ ID NO: 1346)


 




1931.89
TNYDAYYSPGSPLLDTR





(SEQ ID NO: 1347)


 




2023.92
HGTWQTSAGWEFIEGYR





(SEQ ID NO: 1348)


 




2158.14
LPGVDITQNGGSGQLSSIF





IR





(SEQ ID NO: 1349)


 




2206.07
APNLGQLYGFYGNPNLDPE





K





(SEQ ID NO: 1350)


 




2255.23
LNLAGVSGSADLSQFPIAL





VQR





(SEQ ID NO: 1351)


 




2323.11
IANLFDKDYETVYGYQTAG





R





(SEQ ID NO: 12)


 


Lw195
38
1057.56
NAEVWAAGLK





(SEQ ID NO: 20)


 




1248.54
FGDYGSIDYGR





(SEQ ID NO: 584)


 




1438.68
YVDVGATYYFNK





(SEQ ID NO: 591)


 




1933.77
HYFSSNDADDGDTTYAR





(SEQ ID NO: 595)


 




1960.03
TDTQVNAGKVLPEVFASGK





(SEQ ID NO: 690)


 




2217.05
NNDFFGLVDGLNFAAQYQG





K





(SEQ ID NO: 693)


 




2389.09
GETQINDQLTGFGQWEYEF





K





(SEQ ID NO: 698)


 




2976.48
AQNFEAVAQYQFDFGLRPS





VAYLQSK





(SEQ ID NO: 773)


 




3340.53
YDANNIYLATTYSETQNMT





VFADHFVANK





(SEQ ID NO: 876)


 




3549.48
SDFDNYTEGNGDGFGFSAT





YEYEGFGIGATYAK





(SEQ ID NO: 879)


 


Lw196
35
644.36
HFTLK





(SEQ ID NO: 894)


 




817.43
LGGMVWR





(SEQ ID NO: 896)


 




871.51
RVEIEVK





(SEQ ID NO: 923)


 




914.52
AQGVQLTAK





(SEQ ID NO: 954)


 




1054.47
DNTWYTGAK





(SEQ ID NO: 1006)


 




1082.54
SDVLFNFNK





(SEQ ID NO: 1021)


 




1154.63
GIKDVVTQPQA





(SEQ ID NO: 1024)


 




1213.61
AALIDCLAPDR





(SEQ ID NO: 1072)


 




1221.66
AQSVVDYLISK





(SEQ ID NO: 1084)


 




1232.63
LGGMVWRADTK





(SEQ ID NO: 1136)


 




1279.64
DGSVVVLGYTDR





(SEQ ID NO: 1141)


 




1369.71
AALIDCLAPDRR





(SEQ ID NO: 1144)


 




1377.76
RAQSVVDYLISK





(SEQ ID NO: 1177)


 




1408.66
IGSDAYNQGLSER





(SEQ ID NO: 1180)


 




1653.82
LGYPITDDLDIYTR





(SEQ ID NO: 1183)


 




2062 . 92
GMGESNPVTGNTCDNVKQR





(SEQ ID NO: 1189)


 




2231.16
FGQGEAAPVVAPAPAPAPE





VQTK





(SEQ ID NO: 1191)


 




2600.29
NHDTGVSPVFAGGVEYAIT





PEIATR





(SEQ ID NO: 173)


 




3477.67
LEYQWTNNIGDAHTIGTRP





DNGMLSLGVSYR





(SEQ ID NO: 179)





1Molecular weight as determined by SDS-PAGE.


2The mass of a polypeptide fragment can be converted to m/z value by adding 1 to the mass. Each mass includes a range of plus or minus 150 ppm (the 38 kDa and 35 kiDa polypeptide), plus or minus 300 ppm (the 101 kDa polypeptides), or plus or minus I Dalton (the 88 kDa, 85 kDa, 77 kDa, and 67 kDa polypeptides).






In yet another aspect, the present invention further includes polypeptides having similarity with an amino acid sequence. The similarity is referred to as structural similarity and is generally determined by aligning the residues of the two amino acid sequences (i.e., a candidate amino acid sequence and a reference amino acid sequence) to optimize the number of identical amino acids along the lengths of their sequences; gaps in either or both sequences are permitted in making the alignment in order to optimize the number of identical amino acids, although the amino acids in each sequence must nonetheless remain in their proper order. Reference amino acid sequences are disclosed in Tables 10, 11, 12, 13, 14, 15, 16, and 17. Two amino acid sequences can be prepared using commercially available algorithms. Preferably, two amino acid sequences are compared using the Blast program of the BLAST 2 search algorithm, as described by Tatusova, et al., (FEMS Microbiol Lett 1999, 174:247-250) Preferably, the default values for all BLAST 2search parameters are used, including matrix =BLOSUM62; open gap penalty =11, extension gap penalty =1, gap x_dropoff =50, expect =10, wordsize =3, and optionally, filter on. In the comparison of two amino acid sequences using the BLAST search algorithm, structural similarity is referred to as “identities.” Preferably, a candidate amino acid sequence has at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to a reference amino acid sequence. Preferably, the molecular weight of the candidate amino acid sequence and the reference amino acid sequence are substantially the same value. Preferably, the molecular weight of the candidate amino acid sequence and the reference amino acid sequence is determined by SDS polyacrylamide gel electrophoresis. A candidate polypeptide can be obtained by growth of a microbe under low metal conditions and the subsequent isolation of a polypeptide by the procedures disclosed herein.
Typically, a candidate amino acid sequence having structural similarity to a reference amino acid sequence has seroreactive activity. As used herein, “seroreactive activity” refers to the ability of a candidate polypeptide to react with antibody present in convalescent serum from an animal infected with an S. enterica serovar Newport (preferably, MS020508, ATCC Accession No. PTA-9496), an S. enterica serovar Enteritidis (preferably, MS010531), an S. enterica serovar Typhimurium (preferably, MS010427), an S. enterica serovar Dublin (preferably, IRP SDC Serial), or an E. coli (preferably, BEcO157(stx-), MS040330, MS040324, or MS040827). Preferably, when the candidate polypeptide is compared to a reference polypeptide from table 10, 11, 12, 13, 14, 15, 16, or 17, the convalescent serum is from an animal infected with MS020508 (ATCC Accession No. PTA-9496), MS010531, MS010427, IRP SDC Ser., BEcO157(stx-), MS040330, MS040324, or MS040827, respectively.







TABLE 10







S. enterica serovar Newport










Molecular
NCBI sequence identifier of




weight of
polypeptide identified by the




reference
computer algorithm as having




polypeptide
best match to mass fingerprint




(kDa)
of reference polypeptide
Figure
SEQ ID NO:













82
25300748
12
1367


80
20196197
13
1368


74
25300749
14
1369


65
16767394
15
1370


56
1706868
16
1371


55
16226009
17
1372


52
25298420
18
1373


45
1941972
19
1374


38
16420094
20
1375


38
7428872
21
1376


36
25298549
22
1377


22
7162107
23
1378


18
25301837
24
1379


12
25298585
25
1380
















TABLE 11







S. enterica serovar Enteritidis










Molecular
NCBI sequence identifier of




weight of
polypeptide identified by the




reference
computer algorithm as having




polypeptide
best match to mass fingerprint




(kDa)
of reference polypeptide
Figure
SEQ ID NO:





92
29136388
93
1381


91
25008880
26
1382


86
16419095
27
1383


83
20196197
28
1384


78
29136792
29
1385


55
29139082
30
1386


40
19743622
31
1387


39
17865737
32
1388


38
20141670
33
1389
















TABLE 12







S. enterica serovar Typhimurium










Molecular
NCBI sequence identifier of




weight of
polypeptide identified by the




reference
computer algorithm as having




polypeptide
best match to mass fingerprint




(kDa)
of reference polypeptide
Figure
SEQ ID NO:





86
29138313
34
1390


82
16421325
35
1391


77
29136792
36
1392


40
16761195
37
1393


39
17865737
38
1394


38
20141670
39
1395
















TABLE 13







S. enterica serovar Dublin










Molecular
NCBI sequence identifier of




weight of
polypeptide identified by the




reference
computer algorithm as having




polypeptide
best match to mass fingerprint




(kDa)
of reference polypeptide
Figure
SEQ ID NO:













96
16419095
40
1396


89
16421325
41
1397


81
16765529
42
1398


61
479267
43
1399


56
2495191
44
1400


51
531889
45
1401


43
16764533
46
1402


40
47797
47
1403


38
16764429
48
1404
















TABLE 14







E. coli










Molecular
NCBI sequence identifier of




weight of
polypeptide identified by the




reference
computer algorithm as having




polypeptide
best match to mass fingerprint




(kDa)
of reference polypeptide
Figure
SEQ ID NO:













90
25300745
49
1405


86
15799834
50
1406


83
3661500
51
1407


79
1655877
52
1408


66
12516024
53
1409


66
15804564
54
1410


56
15803582
55
1411


38
25298428
56
1412


37
25298543
57
1413


29
232021
58
1414
















TABLE 15







E. coli










Molecular
NCBI sequence identifier of




weight of
polypeptide identified by the




reference
computer algorithm as having




polypeptide
best match to mass fingerprint




(kDa)
of reference polypeptide
Figure
SEQ ID NO:













92
26106377
59
1415


80
26106960
60
1416


77
25987939
61
1417


72
26250982
62
1418


66
13363854
63
1419


50
15803582
64
1420


42
6009835
65
1421


38
6650193
66
1422


36
26107830
67
1423


35
7188818
68
1424


30
26246115
69
1425


19
3660175
70
1426


16
232021
71
1427
















TABLE 16







E. coli










Molecular
NCBI sequence identifier of




weight of
polypeptide identified by the




reference
computer algorithm as having




polypeptide
best match to mass fingerprint




(kDa)
of reference polypeptide
Figure
SEQ ID NO:













82
26106960
72
1428


79
7429053
73
1429


88
78355
74
1430


60
7429052
75
1431


54
15803582
76
1432


46
3114532
77
1433


45
1799743
78
1434


38
26107830
79
1435


37
37624562
80
1436


31
1552746
81
1437


30
25348404
82
1438


19
3660175
83
1439


16
232021
84
1440
















TABLE 17







E. coli










Molecular
NCBI sequence identifier of




weight of
polypeptide identified by the




reference
computer algorithm as having




polypeptide
best match to mass fingerprint




(kDa)
of reference polypeptide
Figure
SEQ ID NO:













101
21307716
85
1441


101
7430186
86
1442


88
6730010
87
1443


85
7429053
88
1444


77
38016693
89
1445


67
7429052
90
1446


38
33112659
91
1447


35
72585
92
1448









Also provided by the present invention are whole cell preparations of a microbe, where the microbe expresses one or more of the polypeptides of the present invention. The cells present in a whole cell preparation are preferably inactivated such that the cells cannot replicate, but the immunogenic activity of the polypeptides of the present invention expressed by the microbe is maintained. Typically, the cells are killed by exposure to agents such as glutaraldehyde, formalin, or formaldehyde.
Compositions
A composition of the present invention may include at least one polypeptide described herein, or a number of polypeptides that is an integer greater than 1 (e.g., at least 2, at least 3, at least 4, etc.) up to 15. A composition can include polypeptides obtainable from 1microbe, or can be obtainable from a combination of 2 or more microbes. For instance, a composition can include polypeptides obtainable from 2 or more E. coli strains, or from 1 or more E. coil and 1 or more Salmonella spp.
Optionally, a polypeptide of the present invention can be covalently bound to a carrier polypeptide to improve the immunological properties of the polypeptide. Useful carrier polypeptides are known to the art. The chemical coupling of a polypeptide of the present invention can be carried out using known and routine methods. For instance, various homobifunctional and/or heterobifunctional cross-linker reagents such as bis(sulfosuccinimidyl)suberate, bis(diazobenzidine), dimethyl adipimidate, dimethyl pimelimidate, dimethyl superimidate, disuccinimidyl suberate, glutaraldehyde, m-maleimidobenzoyl-N-hydroxysuccinimide, sulfo-m-maleimidobenzoyl-N-hydroxysuccinimide, sulfosuccinimidyl 4-(N-maleimidomethyl)cycloheane-1-carboxylate, sulfosuccinimidyl 4-(p-maleimido-phenyl)butyrate and (1-ethyl-3-(dimethyl-aminopropyl) carbodiimide can be used (Harlow and Lane, Antibodies, A Laboratory Manual, generally and Chapter 5, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., N.Y. (1988)).
Preferably, such compositions of the present invention include low concentrations of lipopolysaccharide (LPS). LPS is a component of the outer membrane of most gram negative microbes (see, for instance, Nikaido and Vaara, Outer Membrane, In: Escherichia coli and Salmonella typhimurium, Cellular and Molecular Biology, Neidhardt et al., (eds.) American Society for Microbiology, Washington, D.C., pp. 7-22 (1987), and typically includes polysaccharides (O-specific chain, the outer and inner core) and the lipid A region. The lipid A component of LPS is the most biologically active component of the LPS structure and together induce a wide spectrum of pathophysiological effects in mammals. The most dramatic effects are fever, disseminated intravascular coagulation, complement activation, hypotensive shock, and death. The non-specific immunostimulatory activity of LPS can enhance the formation of a granuloma at the site of administration of compositions that include LPS. Such reactions can result in undue stress on the animal by which the animal may back off feed or water for a period of time, and exasperate infectious conditions in the animal. In addition, the formation of a granuloma at the site of injection can increase the likelihood of possible down grading of the carcass due to scaring or blemishes of the tissue at the injection site (see, for instance, Rae, Injection Site Reactions, available at www.animal.ufl.edu/short94/rae.htm).
The concentration of LPS can be determined using routine methods known to the art. Such methods typically include measurement of dye binding by LPS (see, for instance, Keler and Nowotny, Analyt. Biochem., 156, 189-193 (1986)) or the use of a Limulus amebocyte lysate (LAL) test (see, for instance, Endotoxins and Their Detection With the Limulus AmebocyteLysate Test, Watson et al., (eds.), Alan R. Liss, Inc., 150 Fifth Avenue, New York, NY (1982)). There are four basic commercially available methods that are typically used with an LAL test: the gel-clot test; the turbidimetric (spectrophotometric) test; the colorimetric test; and the chromogenic test. An example of a gel-clot assay is available under the tradename E-TOXATE (Sigma Chemical Co., St. Louis, MO; see Sigma Technical Bulletin No. 210), and PYROTELL (Associates of Cape Cod, Inc., East Falmouth, MA). Typically, assay conditions include contacting the composition with a preparation containing a lysate of the circulating amebocytes of the horseshoe crab, Limulus polyphemus. When exposed to LPS, the lysate increases in opacity as well as viscosity and may gel. About 0.1 milliliter of the composition is added to lysate. Typically, the pH of the composition is between 6 and 8, preferably, between 6.8 and 7.5. The mixture of composition and lysate is incubated for about 1 hour undisturbed at about 37° C. After incubation, the mixture is observed to determine if there was gelation of the mixture. Gelation indicates the presence of endotoxin. To determine the amount of endotoxin present in the composition, dilutions of a standardized solution of endotoxin are made and tested at the same time that the composition is tested. Standardized solutions of endotoxin are commercially available from, for instance, Sigma Chemical (Catalog No. 210-SE), U.S. Pharmacopeia (Rockville, MD, Catalog No. 235503), and Associates of Cape Cod, Inc., (Catalog No. E0005). In general, when a composition of the present invention is prepared by isolating polypeptides from a microbe by a method as described herein (e.g., a method that includes disrupting and solubilizing the cells, and collecting the insoluble polypeptides), the amount of LPS in a composition of the present invention is less than the amount of LPS present in a mixture of the same amount of the microbe that has been disrupted under the same conditions but not solubilized. Typically, the level of LPS in a composition of the present invention is decreased by, in increasing order of preference, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% relative to the level of LPS in a composition prepared by disrupting, but not solubilizing, the same microbe.
The present invention also provides compositions including a whole cell preparation of at least 1 Salmonella spp., at least about 1 E. coli, or the combination thereof. In some aspects, a composition can include whole preparations from 2, 3, 4, 5, or 6 E. coli strains.
The compositions of the present invention optionally further include a pharmaceutically acceptable carrier. “Pharmaceutically acceptable” refers to a diluent, carrier, excipient, salt, etc, that is compatible with the other ingredients of the composition, and not deleterious to the recipient thereof. Typically, the composition includes a pharmaceutically acceptable carrier when the composition is used as described herein. The compositions of the present invention may be formulated in pharmaceutical preparations in a variety of forms adapted to the chosen route of administration, including routes suitable for stimulating an immune response to an antigen. Thus, a composition of the present invention can be administered via known routes including, for example, oral; parental including intradermal, subcutaneous, intramuscular, intravenous, intraperitoneal, etc., and topically, such as, intranasal, intrapulmonary, intramammary, intravaginal, intrauterine, intradermal, and rectally etc. It is foreseen that a composition can be administered to a mucosal surface, such as by administration to the nasal or respiratory mucosa (e.g. spray or aerosol), to stimulate mucosal immunity, such as production of secretory IgA antibodies, throughout the animal's body.
A composition of the present invention can also be administered via a sustained or delayed release implant. Implants suitable for use according to the invention are known and include, for example, those disclosed in Emery and Straub (WO 01/37810 (2001)), and Emery et al., (WO 96/01620 (1996)). Implants can be produced at sizes small enough to be administered by aerosol or spray. Implants also include nanospheres and microspheres.
A composition of the present invention is administered in an amount sufficient to treat certain conditions as described herein. The amount of polypeptides or whole cells present in a composition of the present invention can vary. For instance, the dosage of polypeptides can be between 0.01 micrograms (μg) and 300 mg, typically between 0.1 mg and 10 mg. When the composition is a whole cell preparation, the cells can be present at a concentration of 106 bacteria/ml, 107 bacteria/ml, 108 bacteria/ml, or 109 bacteria/ml. For an injectable composition (e.g. subcutaneous, intramuscular, etc.) the polypeptides may be present in the composition in an amount such that the total volume of the composition administered is 0.5 ml to 5.0 ml, typically 1.0-2.0 ml. When the composition is a whole cell preparation, the cells are preferably present in the composition in an amount that the total volume of the composition administered is 0.5 ml to 5.0 ml, typically 1.0-2.0 ml. The amount administered will vary depending on various factors including, but not limited to, the specific polypeptides chosen, the weight, physical condition and age of the animal, and the route of administration. Thus, the absolute weight of the polypeptide included in a given unit dosage form can vary widely, and depends upon factors such as the species, age, weight and physical condition of the animal, as well as the method of administration. Such factors can be determined by one of skill in the art. Other examples of dosages suitable for the invention are disclosed in Emery et al., (U.S. Pat. No. 6,027,736).
The formulations may be conveniently presented in unit dosage form and may be prepared by methods well known in the art of pharmacy. All methods of preparing a composition including a pharmaceutically acceptable carrier include the step of bringing the active compound (e.g., a polypeptide or whole cell of the present invention) into association with a carrier that constitutes one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing the active compound into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product into the desired formulations.
A composition including a pharmaceutically acceptable carrier can also include an adjuvant. An “adjuvant” refers to an agent that can act in a nonspecific manner to enhance an immune response to a particular antigen, thus potentially reducing the quantity of antigen necessary in any given immunizing composition, and/or the frequency of injection necessary in order to generate an adequate immune response to the antigen of interest. Adjuvants may include, for example, IL-1, IL-2, emulsifiers, muramyl dipeptides, dimethyldiocradecylammonium bromide (DDA), pyridine, aluminum hydroxide, oils, saponins, alpha-tocopherol, polysaccharides, emulsified paraffins (including, for instance, those available from under the tradename EMULSIGEN from MVP Laboratories, Ralston, Nebr.), ISA-70, RIBI and other substances known in the art.
In another embodiment, a composition of the invention including a pharmaceutically acceptable carrier can include a biological response modifier, such as, for example, IL-2, IL-4 and/or IL-6, TNF, IFN-alpha, IFN-gamma, and other cytokines that effect immune cells. An immunizing composition can also include other components known to the art such as an antibiotic, a preservative, an anti-oxidant, or a chelating agent.
Methods of Making
The polypeptides and whole cells of the present invention are obtainable from a member of the family Enterobacteriaceae, for instance, a member of the tribe Escherichieae or Salmonelleae. Preferred examples of members of the tribe Escherichieae are E. coli and Salmonella spp. A Salmonella spp. can be a member of serogroup A, B, C1, C2, C3, D1, D2, D3, E1, B2, E3, E4, G1, G2, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60. Preferred examples of Salmonella spp. are S. cholerasuis, S. typhi, or one of the S. enterica serovars, e.g., Bredeney, Dublin, Agona, Blockley, Enteriditis, Typhimurium, Hadar, Heidelberg, Montevideo, Muenster, Newport, or Senftenberg, most preferably, S. enterica serovar Newport, S. enterica serovar Enteritidis, S. enterica serovar Typhimurium, and S. enterica serovar Dublin. Microbes useful for obtaining polypeptides of the present invention and making whole cell preparations are commercially available from a depository such as American Type Culture Collection (ATCC). In addition, such microbes are readily obtainable by techniques routine and known to the art. The microbes may be derived from an infected animal as a field isolate, and used to obtain polypeptides and/or whole cell preparations of the present invention, or stored for future use, for example, in a frozen repository at −20° C. to −95° C., or −40° C. to −50° C. in bacteriological media containing 20% glycerol, and other like media.
When a polypeptide of the present invention is to be obtained from a microbe, the microbe can be incubated under low metal conditions. As used herein, the phrase “low metal conditions” refers to an environment, typically bacteriological media, that contains amounts of a free metal that cause a microbe to express metal regulated polypeptides. As used herein, the phrase “high metal conditions” refers to an environment that contains amounts of a free metal that cause a microbe to either not express one or more of the metal regulated polypeptides described herein, or to decrease expression of such a polypeptide. Metals are those present in the periodic table under Groups 1 through 17 (IUPAC notation; also referred to as Groups I-A, II-A, III-B, IV-B, V-B, VI-B, VII-B, VIII, I-B, II-B, III-A, IV-A, V-A, VI-A, and VII-A, respectively, under CAS notation). Preferably, metals are those in Groups 2 through 12, more preferably, Groups 3-12. Even more preferably, the metal is iron, zinc, copper, magnesium, nickel, cobalt, manganese, molybdenum, or selenium, most preferably, iron.
Low metal conditions are generally the result of the addition of a metal chelating compound to a bacteriological medium. High metal conditions are generally present when a chelator is not present in the medium, a metal is added to the medium, or the combination thereof. Examples of metal chelators include natural and synthetic compounds. Examples of natural compounds include plant phenolic compounds, such as flavonoids. Examples of flavonoids include the copper chelators catechin and naringenin, and the iron chelators myricetin and quercetin. Examples of synthetic copper chelators include, for instance, tetrathiomolybdate, and examples of synthetic zinc chelators include, for instance, N,N,N′,N′-Tetrakis (2-pyridylmethyl)-ethylene diamine. Examples of synthetic iron chelators include 2,2′-dipyridyl (also referred to in the art as α,α′-bipyridyl), 8-hydroxyquinoline, ethylenediamine-di-O-hydroxyphenylacetic acid (EDDHA), desferrioxamine methanesulphonate (desferol), transferrin, lactoferrin, ovotransferrin, biological siderophores, such as, the catecholates and hydroxamates, and citrate. Preferably, 2,2′-dipyridyl is used for the chelation of iron. Typically, 2,2′-dipyridyl is added to the media at a concentration of at least 0.0025 micrograms/milliliter (μg/ml), at least 0.025 μg/ml, or at least 0.25 μg/ml. High levels of 2,2′-dipyridyl can be 10 μg/ml, 20 μg/ml, or 30 μg/ml.
It is expected that a Salmonella spp. or E. coli with a mutation in a fur gene will result in the constitutive expression of many, if not all, of the metal regulated polypeptides of the present invention. The production of a fur mutation in a Salmonella spp. or E. coli can be produced using routine methods including, for instance, transposon, chemical, or site-directed mutagenesis useful for generating gene knock-out mutations in gram negative bacteria.
The medium used to incubate the microbe and the volume of media used to incubate the microbe can vary. When a microbe is being evaluated for the ability to produce one or more of the polypeptides described herein, the microbe can be grown in a suitable volume, for instance, 10 milliliters to 1 liter of medium. When a microbe is being grown to obtain polypeptides for use in, for instance, administration to animals, the microbe may be grown in a fermentor to allow the isolation of larger amounts of polypeptides. Methods for growing microbes in a fermentor are routine and known to the art. The conditions used for growing a microbe preferably include a metal chelator, more preferably an iron chelator, for instance 2,2′-dipyridyl, a pH of between 6.5 and 7.5, preferably between 6.9 and 7.1, and a temperature of 37° C.
In some aspects of the invention, a microbe may be harvested after growth. Harvesting includes concentrating the microbe into a smaller volume and suspending in a media different than the growth media. Methods for concentrating a microbe are routine and known to the art, and include, for example, filtration or centrifugation. Typically, the concentrated microbe is suspended in decreasing amounts of buffer. Preferably, the final buffer includes a metal chelator, preferably, ethylenediaminetetraacetic acid (EDTA). An example of a buffer that can be used contains Tris-base (7.3 grams/liter) and EDTA (0.9 grams/liter), at a pH of 8.5. Optionally, the final buffer also minimizes proteolytic degradation. This can be accomplished by having the final buffer at a pH of greater than 8.0, preferably, at least 8.5, and/or including one or more proteinase inhibitors (e.g. phenylmethanesulfonyl fluoride). Optionally and preferably, the concentrated microbe is frozen at −20° C. or below until disrupted.
When the microbe is to be used as a whole cell preparation, the harvested cells may be processed using routine and known methods to inactivate the cells. Alternatively, when a microbe is to be used to prepare polypeptides of the present invention, the microbe may be disrupted using chemical, physical, or mechanical methods routine and known to the art, including, for example, french press, sonication, or homoginization. Preferably, homoginization is used. As used herein, “disruption” refers to the breaking up of the cell. Disruption of a microbe can be measured by methods that are routine and known to the art, including, for instance, changes in optical density. Typically, a microbe is subjected to disruption until the percent transmittance is increased by 20% when a 1:100 dilution is measured. The temperature during disruption is typically kept low, preferably at 4° C., to further minimize proteolytic degradation.
The disrupted microbe is solubilized in a detergent, for instance, an anionic, zwitterionic, nonionic, or cationic detergent. Preferably, the detergent is sarcosine, more preferably, sodium lauroyl sarcosinate. As used herein, the term “solubilize” refers to dissolving cellular materials (e.g., polypeptides, nucleic acids, carbohydrates) into the aqueous phase of the buffer in which the microbe was disrupted, and the formation of aggregates of insoluble cellular materials. The conditions for solubilization preferably result in the aggregation of polypeptides of the present invention into insoluble aggregates that are large enough to allow easy isolation by, for instance, centrifugation.
Preferably, the sarcosine is added such that the final ratio of sarcosine to gram weight of disrupted microbe is between 1.0 gram sarcosine per 4.5 grams pellet mass and 6.0 grams sarcosine per 4.5 grams pellet mass, preferably, 4.5 gram sarcosine per 4.5 grams pellet mass. The solubilization of the microbe may be measured by methods that are routine and known to the art, including, for instance, changes in optical density. Typically, the solubilization is allowed to occur for at least 24 hours, more preferably, at least 48 hours, most preferably, at least 60 hours. The temperature during disruption is typically kept low, preferably at 4° C.
The insoluble aggregates that include one or more of the polypeptides of the present invention may be isolated by methods that are routine and known to the art. Preferably, the insoluble aggregates are isolated by centrifugation. Typically, centrifugation of outer membrane polypeptides that are insoluble in detergents requires centrifugal forces of at least 50,000×g, typically 100,000×g. The use of such centrifugal forces requires the use of ultracentrifuges, and scale-up to process large volumes of sample is often difficult and not economical with these types of centrifuges. The methods described herein provide for the production of insoluble aggregates large enough to allow the use of significantly lower centrifugal forces (for instance, 46,000×g). Methods for processing large volumes at these lower centrifugal forces are available and known to the art. Thus, the insoluble aggregates can be isolated at a significantly lower cost.
Optionally and preferably, the sarcosine is removed from the isolated polypeptides. Methods for removing sarcosine from the isolated polypeptides are known to the art, and include, for instance, diafiltration, precipitation, hydrophobic chromatography, ion-exchange chromatography, or affinity chromatography, and ultra filtration and washing the polypeptides in alcohol by diafiltration. After isolation, the polypeptides suspended in buffer and stored at low temperature, for instance, −20° C. or below.
Polypeptides of the present invention may also be isolated from microbes using methods that are known to the art. The isolation of the polypeptides may be accomplished as described in, for instance, Emery et al., (U.S. Pat. No. 5,830,479) and Emery et al., (U.S. Patent Application US 20030036639 A 1).
In those aspects of the present invention where a whole cell preparation is to be made, after growth a microbe can be killed with the addition of an agent such as glutaraldehyde, formalin, or formaldehyde, at a concentration sufficient to inactivate the cells in the culture. For instance, formalin can be added at a concentration of 3% (vol:vol). After a period of time sufficient to inactivate the cells, the cells can be harvested by, for instance, diafiltration and/or centrifugation, and washed.
Methods of Use
An aspect of the present invention is further directed to methods of using the compositions of the present invention. The methods include administering to an animal an effective amount of a composition of the present invention. The animal can be, for instance, avian (including, for instance, chickens or turkeys), bovine (including, for instance, cattle), caprine (including, for instance, goats), ovine (including, for instance, sheep), porcine (including, for instance, swine), bison (including, for instance, buffalo), a companion animal (including, for instance, horses), members of the family Cervidae (including, for instance, deer, elk, moose, caribou and reindeer), or human.
In some aspects, the methods may further include additional administrations (e.g., one or more booster administrations) of the composition to the animal to enhance or stimulate a secondary immune response. A booster can be administered at a time after the first administration, for instance, 1 to 8 weeks, preferably 2 to 4 weeks, after the first administration of the composition. Subsequent boosters can be administered one, two, three, four, or more times annually. Without intending to be limited by theory, it is expected that in some aspects of the present invention annual boosters will not be necessary, as an animal will be challenged in the field by exposure to microbes expressing polypeptides present in the compositions having epitopes that are identical to or structurally related to epitopes present on polypeptides of the composition administered to the animal.
In one aspect, the invention is directed to methods for inducing the production of antibody in an animal or by recombinant techniques. The antibody produced includes antibody that specifically binds at least one polypeptide present in the composition. In this aspect of the invention, an “effective amount” is an amount effective to result in the production of antibody in the animal. Methods for determining whether an animal has produced antibodies that specifically bind polypeptides present in a composition of the present invention can be determined as described herein.
The method may be used to produce antibody that specifically binds polypeptides expressed by a microbe other than the microbe from which the polypeptides of the composition were isolated. As used herein, an antibody that can “specifically bind” a polypeptide is an antibody that interacts with the epitope of the antigen that induced the synthesis of the antibody, or interacts with a structurally related epitope. At least some of the polypeptides present in the compositions of the present invention typically include epitopes that are conserved in the polypeptides of different species and different genera of microbes (see Example 26). Accordingly, antibody produced using a composition derived from one microbe is expected to bind to polypeptides expressed by other microbes and provide broad spectrum protection against gram negative organisms. Examples of gram negative microbes to which the antibody specifically binds are enteropathogens, for instance, members of the family Enterobacteriaceae.
In another aspect, the present invention is directed to methods for treating one or more symptoms of certain conditions in animals that may be caused by, or associated with, a microbe. Such conditions include, for instance, gram negative microbial infections. Examples of conditions caused by microbial infections include mastitis, intestinal colonization by a microbe, metritis, strangles, intrauterine infections, odema disease, enteritis, chronic reproductive infections, laminitis, mastitis, and acute or chronic chlamydiosis, colibacillosis, ehrlichiosis, leptospirosis, pasteurellosis, pseudotuberculosis, and salmonellosis. Examples of conditions that may be caused by microbial infections include performance characteristics such as decreased milk production, high somatic cell counts, poor milk quality, and weight loss. Treatment of these conditions can be prophylactic or, alternatively, can be initiated after the development of a condition described herein. Treatment that is prophylactic, for instance, initiated before a subject manifests symptoms of a condition caused by a microbe, is referred to herein as treatment of a subject that is “at risk” of developing the condition. Typically, an animal “at risk” of developing a condition is an animal present in an area where the condition has been diagnosed and/or is likely to be exposed to a microbe causing the condition. Accordingly, administration of a composition can be performed before, during, or after the occurrence of the conditions described herein. Treatment initiated after the development of a condition may result in decreasing the severity of the symptoms of one of the conditions, or completely removing the symptoms. In this aspect of the invention, an “effective amount” is an amount effective to prevent the manifestation of symptoms of a disease, decrease the severity of the symptoms of a disease, and/or completely remove the symptoms. The potency of a composition of the present invention can be tested according to established standard methods detailed at Title 9 of the Code of Federal Regulations, section 113. For instance, 9 CFR §113.120(c) and 9 CFR §113.123(c) describe standard methods for determining the potency of the composition against a standard reference bacterin of Salmonella enterica serovar Typhimurium and Salmonella enterica serovar Dublin, respectively. Methods for determining whether an animal has the conditions disclosed herein and symptoms associated with the conditions are routine and known to the art (see, for instance, Zhang et al., Infect. Immun., 71:1-12 (2003)).
In one aspect the invention is also directed to treating a gram negative microbial infection in an animal in an animal. The method includes administering an effective amount of a composition of the present invention to an animal having or at risk of having a gram negative infection, and determining whether at least one symptom of the gram negative infection is reduced. The successful treatment of a gram negative microbial infection in an animal is disclosed in Examples 3-9. Working Examples 3-5, 6, and 9 demonstrate the protection against disease by caused by Salmonella enterica serovar Newport and by Salmonella enterica serovar Dublin in mouse models by administering a composition of the present invention. Working Examples 7-8 demonstrate the protection against disease by caused by E. coli O157:H7 in a mouse model by administering a composition of the present invention. These mouse models are a commonly accepted model for the study of human disease caused by these microbes.
The present invention is also directed to decreasing colonization of the intestinal tract or reproductive tract of an animal by a gram negative microbe. The method includes administering an effective amount of a composition of the present invention to an animal colonized by, or at risk of being colonized by a gram negative microbe. In this aspect of the invention, an “effective amount” is an amount effective to decrease colonization of the animal by the microbe. Colonization of an animal's intestinal tract by a microbe can be determined by measuring the presence of the microbe in the animal's feces. The successful decrease of colonization by Salmonella and by E. coli is disclosed in Examples 6, 7-8, 10-15, and 16-19. Working Examples 6 and 10-15 demonstrate the decreased colonization by Salmonella in mice and in cattle. Working Examples 7-8 and 16-19 demonstrate the decreased colonization by E. coli O157:H7 in mice and in cattle. Cattle are considered to be one of the important natural reservoirs of E. coli O157:H7 that contaminate food and cause human disease. Methods for evaluating the colonization of an animal's reproductive tract by a microbe are routine and known to the art. It is expected that decreasing the colonization of an animal by a microbe will reduce transmission of the microbe to humans.
A composition of the invention can be used to provide for active or passive immunization against bacterial infection. Generally, the composition can be administered to an animal to provide active immunization. However, the composition can also be used to induce production of immune products, such as antibodies, which can be collected from the producing animal and administered to another animal to provide passive immunity. Immune components, such as antibodies, can be collected to prepare antibody compositions from serum, plasma, blood, colostrum, etc. for passive immunization therapies. Antibody compositions comprising monoclonal antibodies and/or anti-idiotypes can also be prepared using known methods. Passive antibody compositions and fragments thereof, e.g., scFv, Fab, F(ab′)2 or Fv or other modified forms thereof, may be administered to a recipient in the form of serum, plasma, blood, colostrum, and the like. However, the antibodies may also be isolated from serum, plasma, blood, colostrum, and the like, using known methods for later use in a concentrated or reconstituted form such as, for instance, lavage solutions, impregnated dressings and/or topical agents and the like. Passive immunizing preparations may be particularly advantageous for treatment of acute systemic illness, or passive immunization of young animals that failed to receive adequate levels of passive immunity through maternal colostrum. Antibodies useful for passive immunization may also be useful to conjugate to various drugs or antibiotics that could be directly targeted to bacteria expressing these proteins during a systemic or localized infection.
Another aspect of the present invention provides methods for detecting antibody that specifically binds polypeptides of the present invention. These methods are useful in, for instance, detecting whether an animal has antibody that specifically bind polypeptides of the present invention, and diagnosing whether an animal may have a condition caused by a microbe expressing polypeptides described herein, or expressing polypeptides that share epitopes with the polypeptides described herein. Such diagnostic systems may be in kit form. The methods include contacting an antibody with a preparation that includes polypeptides of the present invention to result in a mixture. The antibody may be present in a biological sample, for instance, blood, milk, or colostrum. The method further includes incubating the mixture under conditions to allow the antibody to specifically bind the polypeptide to form a polypeptide:antibody complex. As used herein, the term “polypeptide:antibody complex” refers to the complex that results when an antibody specifically binds to a polypeptide. The preparation that includes the polypeptides of the present invention may also include reagents, for instance a buffer, that provide conditions appropriate for the formation of the polypeptide:antibody complex. The polypeptide:antibody complex is then detected. The detection of antibodies is known in the art and can include, for instance, immunofluorescence and peroxidase. The methods for detecting the presence of antibodies that specifically bind to polypeptides of the present invention can be used in various formats that have been used to detect antibody, including radioimmunoassay and enzyme-linked immunosorbent assay.
The present invention also provides a kit for detecting antibody that specifically binds polypeptides of the present invention. The kit includes at least one of the polypeptides of the present invention, or a number of polypeptides that is an integer greater than 1 (e.g., at least 2, at least 3, etc.), in a suitable packaging material in an amount sufficient for at least one assay. Optionally, other reagents such as buffers and solutions needed to practice the invention are also included. Instructions for use of the packaged polypeptides are also typically included. As used herein, the phrase “packaging material” refers to one or more physical structures used to house the contents of the kit. The packaging material is constructed by well known methods, generally to provide a sterile, contaminant-free environment. The packaging material has a label which indicates that the polypeptides can be used for detecting antibody that specifically binds polypeptides of the present invention. In addition, the packaging material contains instructions indicating how the materials within the kit are employed to detect the antibody. As used herein, the term “package” refers to a solid matrix or material such as glass, plastic, paper, foil, and the like, capable of holding within fixed limits the polypeptides. Thus, for example, a package can be a microtiter plate well to which microgram quantities of polypeptides have been affixed. “Instructions for use” typically include a tangible expression describing the reagent concentration or at least one assay method parameter, such as the relative amounts of reagent and sample to be admixed, maintenance time periods for reagent/sample admixtures, temperature, buffer conditions, and the like.
The present invention is illustrated by the following examples. It is to be understood that the particular examples, materials, amounts, and procedures are to be interpreted broadly in accordance with the scope and spirit of the invention as set forth herein.
EXAMPLE 1
Production and Isolation of Metal Regulated Proteins
Gram negative enteric bacteria belonging to the families Enterobacteriaceae and Vibrionaceae as well as other gram negative bacteria can be grown under controlled fermentation conditions so as to express proteins, including proteins associated with the outer membrane. The bacteria can be harvested and the proteins can then be isolated and used as immunogens in a composition described in detail in the following example.
The immunizing compositions used in the following examples were prepared using the proteins derived from two enteric pathogens; a multi-drug resistant isolate of Salmonella enterica serovar Newport and an Escherichia coli O157:H7 isolate, both originating from a bovine species.
Salmonella enterica serovar Newport was isolated from fecal cultures of cows at a commercial dairy showing clinical signs of salmonellosis. This isolate was also recovered from the owners of the dairy who became sick after ingesting raw milk. Isolation was accomplished using Brilliant Green Sulfa broth and Brilliant Green Selective agar plates. The isolate was serotyped by the Centers for Veterinary Biologics Laboratory (Ames, Iowa) and by the Minnesota Poultry Testing Laboratory, Minnesota Board of Animal Health (Willmar, Minn.). The Escherichia coli isolate O157:H7 originated from steers isolated from a commercial feed lot. As detected by PCR, the strin was found to be serotype O157:H7, and possessed the eaeA and hlyA genes but not the stx1 and stx2 genes.
Master seed stocks of the Salmonella Newport and E. coli 0157:H7 isolates were prepared by inoculating each of the isolates into 200 ml of Tryptic Soy Broth (Difco Laboratories, Detroit, MI) containing 50 micrograms per milliliter (μg/ml) of 2,2-dipyridyl (Sigma-Aldrich St. Louis, MO). The cultures were grown while stirring at 200 rpm for 6 hours at 37° C. The bacteria were collected by centrifugation at 10,000 x g. The bacterial pellets from each isolate was resuspended into 100 ml physiological saline (0.85%) containing 20% glycerol, and sterilely dispensed into 2 ml cryogenic vials (1 ml per vial) and stored at −90° C. Each isolate was given an identification number designating it as a master seed. The master seed number for Salmonella Newport was MS020508 (ATCC Accession No. PTA-9496) while the 0157:H7isolate was designated as BEc0157(stx-). Each master seed was expanded into a working seed that was then used for the production of metal regulated proteins. A large-scale production process was developed involving fermentation, bacterial harvest, disruption, solubilization, concentration, diafiltration, and isolation of fmal product.
Fermentation
A cryogenic vial of the working seed (1ml at 109 CFU/ml) was used to inoculate 500 ml of 37° C. tryptic soy broth (TSB) without dextrose (Difco) containing 50 micrograms 2,2-dipyridyl (Sigma), 2.7 grams BITEK yeast extract (Difco) and glycerol (3% vol/vol). The culture was incubated at 37° C. for 12 hours while stirring at 200 rpm, and then added to 2 liters of the above media. This second culture was allowed to grow for an additional 4 hours at 37° C. This culture was used to inoculate a 20-liter VIRTIS bench-top feHnentor, (Virtis, Gardiner, NY) charged with 13 liters of the above-described media. The pH was held constant between 6.9 and 7.1 by automatic titration with 30% NaOH and 10% HCL. The stirring speed was adjusted to 400 revolutions per minute (rev/minute), and the culture aerated with 11 liters air/minute at 37° C. Foaming was controlled automatically by the addition of 11 ml defoamer (MAZU DF 204 Chem/Serv, Minneapolis, MN). The culture was allowed to grow continuously at these conditions for 4 hours at which time was sterilely pumped into a 150-liter fermentor (W. B. Moore, Easton, PA). The fennentor was charged with 115 liters TSB without dextrose (3,750.0 grams), BITEK yeast extract (625 grams), glycerol (3750 ml), 2,2-dypyrdyl (3.13 grams) and MAZU DF 204 defoamer (100 ml). The parameters of the fermentation were as follows: dissolved oxygen (DO) was maintained at 30% +/- 10% by increasing agitation to 220 rev/minute sparged with 60 liters of air/minute and 10 pounds per square inch (psi) back pressure. The pH was held constant between 6.9 and 7.1 by automatic titration with 30% NaOH and 10% HCL. The temperature was maintained at 37° C. At hour 4.5(optical density 8-9 at 540 nanometers), the culture was supplemented with additional nutrients by feeding 7 liters of media containing 1,875 grams TSB without dextrose, 313 grams yeast extract 3.13 grams 2,2-dipyridyl and 1,875 ml of glycerol. The rate of feed was adjusted to 29ml/minute while increasing agitation to 675 rpm. At the end of the feed (hour 8.5) the fermentation was allowed to continue for an additional three hours at which point the fermentation was terminated by lowing the temperature of the fermentor to 10° C. (optical density 35-40 at 540 nanometers at a 1:100 dilution). The culture was sterilely transferred to a 200-liter tank (LEE Process Systems and Equipment model 2000LDBT) in preparation for harvest.
Harvest
The bacterial fermentation was concentrated and washed using a PALL FILTRON TANGENTIAL FLOW MAXESET-25 (Pall Filtron Corporation, Northboro, MA) equipped with two 30 ft2 Alpha 300-K open channel filters, catalog No. AS30005C5, (Pall Filtron) connected to a Waukesha Model U-60 feed pump (Waukesha Cherry-Burrell, Delevan, WI) The original culture volume of 125 liters was reduced to 25 liters (2.5 liters/minute) using a filter inlet pressure of 15 psi and a retentate pressure of 0psi. The bacterial retentate was adjusted back up to 50 liters using physiological saline (0.85%) and then concentrated again to 15 liters to help remove any contaminating exogenous proteins, etc. The retentate (15 liters) was adjusted to 35 liters using sterile Osmotic Shock Buffer (OMS) containing 7.26 grams/liter Tris-base and 0.93 grams/liter EDTA adjusted to a pH of 8.5..The EDTA in the OMS serves to remove much of LPS from the cell wall, while the elevated pH prevents much of the proteolytic degradation after freezing and disruption. Protease inhibitors may be used instead of, or in addition to, an elevated pH. The retentate was mixed thoroughly while in the 200-liter tank using a bottom mount magnetically driven mixer. The retentate was sterilely dispensed (3.5 liters) into sterile 4 liter NALGENE containers No. 2122 and placed into a −20° C. freezer for storage. Freezing the bacterial pellet serves to weaken the cell wall structure making downstream disruption more efficient. The pellet mass was calculated by centrifuging 30 ml samples of the fermented culture and final harvest. Briefly, pre-weighted 50ml NALGENE conical tubes were centrifuged at 39,000 x g for 90 minutes in a BECKMAN J2-21 centrifuge using a JA-21 rotor (Beckman Instruments, Palo Alto CA). At the end of the run, the supernate was poured off and the tubes were weighed again. The pellet mass was calculated for each stage. The fermentation process yielded a wet pellet mass of 9.0 kilograms.
Disruption (Homogenization)
Twenty kilograms of frozen bacterial cell slurry in OMS were thawed at 4° C. (20 kg of pellet mass). The liquid culture suspension from each container was aseptically aspirated into a steam in place 250 liter jacketed process tank (Lee, Model 259LU) with a top mounted mixer (Eastern, Model TME-1/2, EMI Incorporated, Clinton, Conn.) containing 222 liters OMS pH 8.5 containing 0.1 grams thimerosal/liter as preservative. The volume of OMS was determined by dividing the pellet mass (in grams) by 900 and then multiplying the result by 10 to get the homogenizing volume in liters (gram pellet mass/900×10=liters homogenizing volume). The bulk bacterial suspension was chilled to 4° C. with continuous mixing for 18 hours at 200 rpm at which time it was disrupted by homogenization. Briefly, the 250 liter tank containing the bacterial suspension was connected to a model 12.51 H Rannie Homogenizer, (APV Systems, Rosemont, Ill.). A second 250 liter jacketed process tank (empty) was connected to the homogenizer such that the fluid in the process tank could be passed through the homogenizer, into the empty tank and back again, allowing for multiple homogenizing passes while still maintaining a closed system. The temperature during homogenization was kept at 4° C. At the start of each pass, fluid was circulated at 70 psi via a Waukesha model IODO pump (Waukesha) through the homogenizer (160 gallons/hour) and back to the tank of origin, while the homogenizer pressure was adjusted to 13,500 psi. Prior to the first pass, two pre-homogenizing samples were withdrawn from the homogenizer to establish a baseline for determining the degree of disruption and monitoring of pH. The degree of disruption was monitored by transmittance (% T at 540 nm at 1:100 dilution) compared to the non-homogenized sample. The number of passes through the homogenizer was standardized for different organisms based on the integrity of the cell wall and variation in the degree of disruption, which had a direct correlation in the efficiency of solubilization and quality of end product. For example, the disruption of Salmonella passed three times through the homogenizer gave a final percent transmittance between 78-83% T at a 1:100 dilution. E. coli having the same pellet mass and starting OD gave a % T of 86-91% (at a 1:100 dilution) after the third pass. It has been observed that bacteria differ in their cell wall integrity and vary in their capacity of disruption under identical condition. This variation can effect the degree and efficiency of solubilization and recovery of metal regulated proteins. In general, cells were passed through the homogenizer until the transmittance did not increase after an additional pass.
After homogenization, Sodium Lauroyl Sarcosinate (HAMPOSYL L-30, Chem/Serv) was aseptically added to the homogenized bacterial suspension for solubilization. The amount of sarcosine (30%) added equaled 0.0664 times the solubilizing volume, in liters, (1.0 gram sarcosine/4.5 grams pellet mass). The tank was removed from the homogenizer and put onto a chiller loop at 4° C. and mixed at 240 rpm for 60-70 hours. This time period was important for complete solubilization. It was discovered that increasing the solubilization time in OMS at an elevated pH (8.0-8.5) that metal regulated proteins aggregated together forming large insoluble aggregates that were easily removed by centrifugation. The optimal OD after solubilization was usually between 25-30%T at 540nm.
Protein Harvest
The aggregated metal regulated proteins within the solubilized process fluid were collected by centrifugation using T-1 SHARPLES, (Alfa Laval Seperations, Warminster, PA). Briefly, the tank of solubilized homogenate was fed into six SHARPLES with a feed rate of 250 ml/minute at 17 psi at a centrifugal force of 46,000 x g. The effluent was collected into a second 250 liter jacketed process tank through a closed sterile loop allowing for multiple passes through the centrifuges while maintaining a closed system. The temperature during centrifugation was kept at 4° C. The solubilized homogenate was passed 8times across the centrifuges. Fifty percent of the protein was collected after the second pass, at which point the solubilized fluid was concentrated to 1⁄3of its original volume. This decrease in volume shortened the process time for the next 6 passes. Briefly, the solubilized homogenate tank was aseptically disconnected from the centrifuges and connected to a MILLIPORE PELLICON TANGENTIAL FLOW FILTER assembly (Millipore Corporation, Bedford, MA), equipped with a 25ft2 screen-channel series Alpha 10K Centrasette filter (Pall Filtron) connected to a Waukesha Model U30 feed pump for concentration. After concentration, centrifugation was continued until the process was completed. Protein was collected after each pass. The protein was collected, resuspended and dispensed in 50 liters Tris-buffer pH 8.5 containing 0.3% formalin (Sigma) as preservative.
Diafiltration
The protein suspension was washed by diafiltration at 4° C. to remove any contaminating sarcosine that may have been bound to the protein. Briefly, the 50 liters of protein was sterilely aspirated into a 200 liter process tank containing 50 liters sterile Tris-buffer, pH 8.5, equipped with a bottom mount Dayton mixer, Model 2Z846 (Dayton Electric, Chicago, IL) rotating at 125rev/minute. The process tank was sterilely connected to a MILLIPORE PELLICON TANGENTIAL FLOW FILTER assembly (Millipore Corporation), equipped with a 25 ft2 screen-channel series Alpha 10K Centrasette filter (Pall Filtron) connected to a Waukesha Model U30 feed pump. The 100 liter protein solution was concentrated by filtration to a target volume of 5.45 times the protein pellet mass, at which point Tris-buffer, pH 7.4, containing 5% isopropyl alcohol was slowly added to the concentrate from a second process tank. Isopropyl alcohol is believed to cause a slight unfolding of the protein structure allowing for the removal of bound sarcosine without compromising the immunogenicity of the protein. Diafiltration continued until the pH stabilized to 7.4 at which point 50 liters Tris-buffer pH 7.4 was slowly added by diafiltration to remove residual alcohol.
The protein suspension was then concentrated to approximately 25 liters. The protein concentrate was aseptically dispensed (3.5 liters) into sterile 4 liter NALGENE containers and placed into a −20° C. freezer for storage.
This process produces a composition containing metal regulated proteins with a decrease in the amount of LPS and very little to no sarcosine residue. The protein was examined by SDS-PAGE for purity and banding profile, and also examined for bacterial contamination, residual sarcosine and LPS. The banding profile of the finished product showed consistent patterns as examined by electrophoresis. The composition was tested for sarcosine by the use of a modified agar gel diffusion test in which sheep red blood cells (5%) were incorporated into an agar base (1.5%). Wells were cut into the agar and samples of the finished product along with control samples of known concentrations of sarcosine at 0.05, 0.1, 0.2, 0.3, 0.4, 0.5 1.0 and 2.0% were placed into the wells. The gel was incubated at 25° C. for 24 hours and the degree of hemolysis was determined compared to the controls. The process removes the level of detectable sarcosine below 0.05%, which at this concentration showed minimal hemolysis in control samples. The concentration of LPS is examined by a Limulus amebocyte lysate (LAL) test available under the tradename PYROTELL (Associates of Cape Cod, Inc., East Falmouth, Mass.).
The compositions used in the following examples were prepared and harvested as described in Example 1. The efficacy of each composition was evaluated in separate experiments based on the route of challenge. Data was collected on the following parameters: 1) the potency of the immunizing compositions, which was evaluated against a live virulent challenge given intraperitoneally to measure systemic protection, 2) the efficacy of each composition, which was evaluated after administering the challenge dose orally to evaluate the effect on colonization or fecal shedding of the challenge organism, and 3) examination of the injection sites for any adverse tissue reaction.
EXAMPLE 2
Preparation of the Immunizing Compositions Derived from S. Enterica Serovar Newport and E. Coli O157:H7
The proteins made from S. enterica serovar Newport and E. coli as described in Example 1 were used to prepare two compositions for administration to animals. The composition prepared from S. enterica serovar Newport contained the proteins described in Table 2, and the composition prepared from E. coli 0157:H7 contained the proteins described in Table 6. A stock vaccine was prepared from each composition by emulsifying the aqueous protein suspension (500 μg total protein/ml) into the commercial adjuvant, EMULSIGEN, (MVP Laboratories, Ralston, Nebraska) using an IKA ULTRA-TURRAX T-50homogenizing vessel (IKA, Cincinnati, OH). The stock vaccine was used at two different injectable volumes depending on the target animal it would be used in. A mouse dose was administered to give a final dose of 50 μg total protein in a 0.1 ml injectable volume with an adjuvant concentration of 22.5% vol/vol. The bovine dose was given using a two milliliter injectable volume to provide a dose of 1000 μg total protein. A placebo was prepared by replacing the antigen with physiological saline in the above foimulation and emulsifying the suspension into EMULSIGEN to give an adjuvant concentration of 22.5%.
A standard reference bacterin of Salmonella enterica serovar Dublin was obtained from the Center of Veterinary Biologics-Laboratory (United States Department of Agriculture, Ames, Iowa, strain APHIS NVSL #82, Salmonella Dublin, Lot Number IRP DSC #5) for use as a control reference in accordance with the standardized mouse model described in 9 CFR 113.123. This was provided as a whole cell bacterin prepared in AlOH.
EXAMPLE 3
Mouse Vaccination and Challenge Study
(Systemic Evaluation)
The efficacy of the S. enterica serovar Newport vaccine was carried out against a live virulent challenge in mice. One hundred twenty five (N=125) female CF-1 mice obtained from Harlan Breeding Laboratories (Indianapolis, Ind.) weighing 16-22 grams were equally distributed into five groups (25 mice/group). Mice were housed in polycarbonate mouse cages (Ancore Corporation, Bellmore, N.Y.). Two cages were used for each treatment group to minimize the number of mice for each cage. Groups were designated as 1-5. Food and water were supplied ad libitum to all mice.
The potency of the vaccine was tested at four different concentrations; non-diluted stock vaccine (Group 1, 50 μg/0.1 ml), 1:10 (volume diluent: volume protein solution) (Group 2, 5.0μg/0.1 ml), 1:100 (Group 4, 0.5 μg/0.1 ml), 1:1000 (Group 4, 0.05 μg/0.1 ml) and a Placebo (non-vaccinated/challenged control group) (Group 5). EMULSIGEN as used as the diluent for diluting the stock vaccine so as to maintain the concentration of adjuvant at a 22.5% for each treatment group. Mice were vaccinated intraperitoneally two times at 14 day intervals. The volume administered was 0.1 ml/mouse.
EXAMPLE 4
Preparation of Challenge Organism
The S. enterica serovar Newport as described above was used for challenge. Briefly, the isolate from a frozen stock was streaked onto a blood agar plate and incubated at 37° C. for 18 hours. A single colony was subcultured into 50 ml Tryptic Soy Broth (Difco) containing 25 μg/ml 2,2′ dipyridyl. The culture was incubated at 37° C. for 6 hours while rotating at 200 rpm, at which point was centrifuged at 10,000×g for 10 minutes at 4° C. to pellet the bacteria. The bacterial pellet was washed twice by centrifugation in physiological saline at 4° C. The final pellet was resuspended in 25 ml of physiological saline and used for challenge. Just prior to challenge, 1 ml of the above bacterial suspension was serially diluted ten fold to enumerate the number of CFU/mouse dose.
EXAMPLE 5
Challenge
Fourteen days after the 2nd vaccination, mice in groups 1-5 were intraperitoneally challenged with 0.2 ml of S. enterica serovar Newport at 7.6×108 colony forming units (CFU) prepared as described at example 4. Mortality was recorded daily for 14 days after challenge. The results showed a strong protective index that correlated with dilution of the vaccine (Table 18). Twenty five (100%) of the non-vaccinated mice (Group 5) died within 14 days after challenge. In contrast, only 1 mouse (4.0%) died given the non-diluted vaccine of Group 1. Mortality increased with each 10 fold serial dilution as seen in FIG. 1 (Group 2, 8.0%), (Group 3, 48.0%) and (Group 4, 80.0%). The vaccine showed a high degree of systemic protection as compared to non-vaccinated mice of Group 5 (Placebo). The vaccine prepared from S. enterica serovar Newport was highly efficacious in preventing mortality associated with a lethal S. enterica serovar Newport challenge.







TABLE 18







Mortality of Vaccinated and Non-Vaccinated Mice Following


IP Challenge with S. enterica serovar Newport










Groups
# Mice
# Dead
Percent mortality (%)













Group 1 (non-diluted)
25
 1/25
4.3


Group 2 (1:10)
25
 2/25
8.3


Group 3 (1:100)
25
12/25
48.0


Group 4 (1:1000)
25
15/25
88.0


Group 5 (non-vaccinated/
25
25/25
100.0


challenged)









EXAMPLE 6
Mouse Vaccination and Oral Challenge Study with S. Enterica Serovar Newport
(Evaluation of Fecal Shedding)
In this experiment the efficacy of the S. enterica serovar Newport vaccine was carried out against a live oral challenge in mice. The outcome parameters used to evaluate vaccine efficacy in this experiment were 1) individual mouse mortality, and 2) differences in the concentration of Salmonella being shed between treatment groups after challenge. Twenty (N=20) female CF-1 mice obtained from Harlan Breeding Laboratories (Indianapolis, Ind.) weighing 16-22 grams were equally distributed into two groups (10 mice/group). Mice were housed in polycarbonate mouse cages (Ancore Corporation, Bellmore, N.Y.). Two cages were used, one for each treatment group. Groups were designated as placebo, non-vaccinated (Group 1) and vaccinated (Group 2). Food and water were supplied ad libitum to all mice.
Mice were vaccinated three times at 14 day intervals subcutaneously with the placebo and/or the S. enterica serovar Newport vaccines of Example 2. The volume of vaccine administered was 0.1 ml/mouse. Seven days after the third vaccination, mice in groups 1 and 2 were orally challenged with S. enterica serovar Newport at 2.8×108 colony forming units (CFU) in a volume of 0.2 cc. The challenge organism was prepared as described in example 4.
To enumerate the difference in fecal shedding between the control and vaccinated groups, mouse droppings were collected at 12, 24, 36 and 48 hours post challenge. Droppings were collected by placing a sterile pad on the floor of each cage 1 hour prior to collection. At each time period the pad was removed and placed into a laminar flow hood. Using sterilely flamed forceps, twenty individual droppings were randomly collected. The forceps were flamed between each collection so as not to cross-contaminate samples. Individual droppings were placed into sterile saline dilution blanks (0.9 ml), two droppings per tube to give ten tubes. Each sample was macerated using a sterile 1 ml pipette and serially diluted 10 fold. Dilutions were plated on Brilliant Green Sulfur Agar (Difco Laboratories, Detroit, Mich.) incubated at 37 C for 48 hours. The number of bacteria was enumerated for each sample and the log10 colony forming units were averaged for each treatment group at each time period.
Table 19 shows the difference in the fecal shedding between vaccinated and non-vaccinated mice after an oral challenge with S. enterica serovar Newport at each time period. There was a large difference between treatment groups in the amount of Salmonella shedding in feces post-challenge. The challenge dose represented as time 0 in Table 4 shows the initial inoculum given to each mouse. Within twelve hours post challenge there was a dramatic decrease in the amount of Salmonella being shed from the vaccinated group as compared to the Placebo group. Averaged across the study period and accounting for repeated estimates, vaccinates shed less Salmonella at each sampling period when compared to non-vaccinates, with a degree of significance of P=0.02. The amount of Salmonella being shed in the vaccinated group dramatically declined with each sampling period as compared to the non-vaccinated Placebo group (FIG. 2). At 48 hours post challenge the difference in the amount of Salmonella being shed between the vaccinated and non-vaccinated group was greater then 4 log CFU (Table 19, FIG. 2).







TABLE 19







The Difference in Shedding of Salmonella Newport Between the Non-


Vaccinated and Vaccinated Treatment Groups after Oral Challenge.










Mean log10 Colony Forming Units













Group 1
Group 2



Sampling Times
(Non-vaccinated)
(Vaccinated)















Challenge Dose (time 0)
8.4
8.4



12 hours
5.5
3.1



24 hours
4.2
0.8



36 hours
3.7
0.43



48 hours
5.0
0.16










At the 12 hour sampling period three mice (30%) died in the vaccinated group with no further mortality occurring within 14 days after challenge. Nevertheless, in the non-vaccinated Placebo group three mice died within 12 and 24 hours and 4 mice died between 48 and 56 hours (70% total). It's interesting to note that mortality seemed to be directly correlated with the amount of Salmonella being shed. This is illustrated in the vaccinated group where mortality occurred at an early stage where the level of Salmonella being shed was high (Table 19, FIG. 2). This observation was observed in both groups where three mice died within 24 hours while the amount of Salmonella being shed was high. However, as the incidence of shedding declined in the vaccinated group so did mortality. In contrast, as the incidence of shedding increased in the Placebo as seen at 48 hours, it appeared to be directly correlated with mortality, since 4 mice died within this time period.
Due to the unequal distribution in the number of mice between groups after 48 hours no further sampling was carried out beyond this time period. Nevertheless, the results clearly demonstrate that subcutaneous vaccination with the composition can prevent colonization by Salmonella. In addition, the secondary sequalae due to systemic infection was also inhibited as seen in the difference in mortality between the two groups.
EXAMPLE 7
Mouse Vaccination and Oral Challenge Study with Escherichia Coli O157:H7
(Evaluation of Fecal Shedding)
In this experiment, the efficacy of the Escherichia coli O157:H7 vaccine of example 2 was carried out against a live oral challenge in mice. The outcome parameter used to evaluate the efficacy of the vaccine in this experiment was to enumerate differences in the concentration of the challenge organism being shed between treatment groups after challenge. Twenty (N=20) female CF-1 mice obtained from Harlan Breeding Laboratories (Indianapolis, Ind.) weighing 16-22 grams were equally distributed into two groups (10 mice/group). Mice were housed in polycarbonate mouse cages (Ancore Corporation, Bellmore, N.Y.). Two cages were used, one for each treatment group. Groups were designated as placebo, non-vaccinated (Group 1) and vaccinated (Group 2). Food and water were supplied ad libitum to all mice.
Mice were vaccinated three times at 14 day intervals subcutaneously with the placebo and/or the E. coli O157:H7 vaccines of Example 2. The volume of vaccine administered was 0.1 ml/mouse.
EXAMPLE 8
Preparation of E. Coli O157:H7 Challenge Organism
To enhance the isolation rate of the E. coli O157:H7 challenge organism from fecal samples the isolate was made nalidixic acid resistant. Briefly, the isolate from a frozen stock was streaked onto Eosin Methylene Blue (EMB) agar plate and incubated at 37° C. for 18 hours. A single colony was subcultured into 50 ml Tryptic Soy Broth (Difco) containing 25 μg/ml 2,2′ dipyridyl. The culture was incubated at 37° C. for 6 hours while rotating at 200 rpm, at which point was subcultured into Tryptic Soy Broth containing 25 μg/ml 2,2 dipyridyl and 100 μg/ml nalidixic acid and again incubated at 37° C. for 18 hours. One hundred microliters of the above culture containing approximately 108 CFU/ml viable organisms was spread over the surface of an EMB agar plate containing 500 μg nalidixic acid. The plates were incubated at 37° C. for 48 hours and the colonies that grew were cloned by plating on EMB containing 100 μg/ml nalidixic acid. A number of nalidixic acid resistant colonies were amplified by sub-culturing into TSB containing 25 μg/ml 2,2 dipyridyl and 100 μg/ml nalidixic acid. A stable nalidixic acid resistant isolate was selected as the challenge organism by sub-culturing the isolate continuously in TSB containing 100 μg/ml nalidixic acid to enhance the stability of the organism. The outer membrane protein profile of the nalidixic acid resistant isolate expressed identical banding profiles as the parent wild type grown under iron-restriction having molecular weights of 89 kDa, 85 kDa, 81 kDa, 78 kDa and porins at 36-39 kDa. The nalidixic acid resistant isolate of E. coliO157:H7 was maintained as a frozen stock culture in TSB containing 25 μg/ml 2,2 dipyridyl, 100 μg/ml nalidixic acid and 20% glycerol stored at −90° C.
The nalidixic acid resistant isolate of E. coli O157:H7 as described above was used for challenge. The isolate from the frozen stock was sub-cultured onto an EMB agar plate containing 150 μg/ml nalidixic acid and incubated at 37° C. for 18 hours. A single colony was subcultured into 50 ml Tryptic Soy Broth (Difco) containing 25μ/ml 2,2′ dipyridyl and 250 μg nalidixic acid. The culture was incubated at 37° C. for 6 hours while rotating at 200 rpm, at which point was centrifuged at 10,000×g for 10 minutes at 4° C. to pellet the bacteria. The bacterial pellet was washed twice by centrifugation in physiological saline at 4° C. The final pellet was resuspended in 25 ml of physiological saline containing 250 μg nalidixic acid and used for challenge. Just prior to challenge, 1 ml of the above bacterial suspension was serially diluted ten fold to enumerate the number of CFU/mouse dose.
Seven days after the third vaccination, mice in groups 1 and 2 were orally challenged with 0.2 ml of the nalidixic acid resistant isolate of E. coli at 2.0×108 CFU.
To enumerate the difference in fecal shedding between the control and vaccinated groups, mouse droppings were collected at 12, 24, 36, 48, 56 and 72 hours post challenge. Droppings were collected as before by placing a sterile pad on the floor of each cage 1 hour prior to collection. At each time period the pad was removed and placed into a laminar flow hood. Using sterilely flamed forceps twenty individual droppings were randomly collected. The forceps were flamed between each collection so as not to cross-contaminate samples. Individual droppings were placed into sterile saline dilution blanks (0.9 ml), two droppings per tube to give ten tubes. Each sample was macerated using a sterile 1 ml pipette and serially diluted 10 fold. Dilutions were plated on EMB agar containing 150 μg nalidixic acid/ml incubated at 37 C for 48 hours. The number of bacteria was enumerated for each sample and the log10 colony forming units were averaged for each treatment group at each time period.
Table 20 shows the difference in the fecal shedding between vaccinated and non-vaccinated mice after an oral challenge with the nalidixic acid resistant isolate of E. coli. There was a significant difference in the amount of E. coli O157:H7 being shed between groups at each sampling period. The challenge dose represented as time 0 in Table 20 shows the initial inoculum given to each mouse. Within twelve hours post challenge there was a dramatic decrease in the amount of E. coli O157:H7 being shed from the vaccinated group as compared to the Placebo group with a degree of significance of P=0.03. The amount of E. coli O157:H7 being shed in the vaccinated group dramatically declined with each sampling period as compared to the non-vaccinated mice (FIG. 3). Averaged across the study period, vaccinates shed approximately 2 logs less E. coli when compared to the non-vaccinated controls. At 56 and 72 hours post challenge the shedding incidence of the challenge organism in the vaccinated group was undetectable as compared to the non-vaccinated controls which continued to shed for the duration of the study period.







TABLE 20







The Difference in Shedding of E. coli O157:H7 Between the Non-


Vaccinated and Vaccinated Treatment Groups after Challenge.










Mean log10 Colony Forming Units













Group 1
Group 2



Sampling Times
(Non-vaccinated)
(Vaccinated)















Challenge Dose (time 0)
8.3
8.3



12 hours
6.2
5.1



24 hours
3.9
1.7



36 hours
2.1
0.63



48 hours
3.2
0.1



56 hours
2.1
0



72 hours
1.2
0










Between the 12 and 24 hour sampling period two mice (20.0%) died in the vaccinated group with no further mortality occurring within 14 days after challenge. However, in the non-vaccinated Placebo group five mice (50.0%) died during the sampling period with no further mortality occurring after 72 hours or within the 14 day observation period.
These results demonstrate for the first time that a vaccine composition as described herein can prevent the colonization and/or growth of E. coli O157:H7 through a subcutaneous vaccination as well as reduce mortality due to the secondary sequalae from systemic infection.
EXAMPLE 9
The Cross Protective Nature of Metal Regulated Proteins against a Homologous and Heterologous Salmonella Challenge in Mice
The vaccine Example 2 derived from S. enterica serovar Newport was evaluated against a homologous and heterologous challenge using S. enterica serovar Dublin in a standardized mouse model as described in the Code of Federal Regulations, Title 9, section 113.123.
Two hundred ten (N=210) female Harlan CF-1 mice obtained from Harlan Breeding Laboratories (Indianapolis, IN) weighing 16-22 grams were equally divided into 9 treatment groups (20 mice/group) designated as groups 1-9. The efficacy of each vaccine was tested at four different concentrations. The whole cell S. enterica serovar Dublin reference bacterin as described in example 2 was administered to four groups designated as groups 1-4; Group 1 (non-diluted, 50 pg total protein), Group 2, (1:10 dilution, 5.0 μg total protein), Group 3, (1:100dilution, 0.5 μg total protein) and Group 4, (1:1000 dilution, 0.05 μg total protein). The S. enterica serovar Newport vaccine was also administered at the same dilutions as described above in the same number of mice, designated as groups 5-8 Group 5 (non-diluted), Group 6 (1:10), Group 7 (1:100) and Group 8 (1:1000) respectively. Group 9 was the control group that was not vaccinated, but challenged. Since the Salmonella reference bacterin was prepared using whole cells and supplied from an outside source the protein concentration was unknown. EMULISIGEN was used as the diluent for diluting the composition prepared using MS020508(ATCC Accession No. PTA-9496) at a 22.5% concentration prepared in physiological saline. The S. enterica serovar Dublin reference bacterin was diluted using phosphate buffered saline (PBS). All mice in groups 1-4 and 5-8 were vaccinated with the appropriate vaccine intraperitoneally and revaccinated 14 days after the first vaccination. The volume administered was 0.25 ml per mouse.
Fourteen days after the second vaccination, all mice in groups 1-9 were intraperitoneally challenged with 9.8×107 colony forming units (CFU) of a virulent Salmonella enterica serovar Dublin isolate to evaluate the cross-protective nature of the S. enterica serovar Newport vaccine against a S. enterica serovar Dublin challenge (S. enterica serovar Newport vaccinated/S. enterica serovar Dublin challenged) compared to the homologous group (S. enterica serovar Dublin vaccinated/S. enterica serovar Dublin challenged) The virulent Salmonella enterica serovar Dublin isolate was obtained from The Center of Veterinary Biologics-Laboratory (IRP SDC #5, United States Department of Agriculture, Ames, Iowa). Mortality was recorded daily for 2 weeks post-challenge. Table 21 shows the percent mortality in mice following a homologous and/or heterologous challenge with S. enterica serovar Dublin.







TABLE 21







Mortality in mice following a homologous and/or heterologous


challenge with Salmonella Dublin










Groups
# Mice
# Dead
Percent mortality (%)










Groups 5-8


(Reference Bacterin Vaccinated/


Challenged with S. enterica serovar Dublin)


Homologous Challenge










Group 5 (non-diluted)
20
10/20
50


Group 6 (1:10)
20
11/20
55


Group 7 (1:100)
20
16/20
80


Group 8 (1:1000)
20
16/20
80


Group 9 (non-vaccinated)
20
20/20
100







Groups 1-4


(S. enterica serovar Newport composition Vaccinated/


Challenged with S. enterica serovar Dublin)


Heterologous Challenge










Group 1 (non-diluted)
20
10/20
50


Group 2 (1:10)
20
17/20
85


Group 3 (1:100)
20
20/20
100


Group 4 (1:1000)
20
18/20
90









Twenty (100%) of the non-vaccinated mice (Group 9) died within 3 days after challenge (Table 21). Mice vaccinated with the composition derived from S. enterica serovar Newport and challenged with S. enterica serovar Dublin showed a high degree of cross-protection, (Group 1) when compared to mice vaccinated with the S. enterica serovar Dublin reference bacterin (Group 5). There was no difference in mortality between these two groups. This data shows that the composition derived from S. enterica serovar Newport was protective against a live S. enterica serovar Dublin challenge as compared to the non-vaccinated control mice. Further, the composition derived from S. enterica serovar Newport protected against a different serogroup of Salmonella showing heterologous protection: S. enterica serovar Newport is typed as serogroup C2 whereas S. enterica serovar Dublin is a D1 serogroup.
The results from this study provide strong evidence that the composition includes highly protective antigens that protect against a homologous and heterologous Salmonella challenge in mammals.
EXAMPLE 10
Experimental S. Enterica Serovar Newport Challenge in Calves
The purpose of this study was to evaluate the efficacy of the Salmonella Newport vaccine described in Example 2 against a homologous S. enterica serovar Newport challenge in calves. The parameters used to evaluate vaccine efficacy were 1) individual calf morbidity as evidenced by rectal temperature, and 2) serological response to vaccination and quantitative enumeration of fecal shedding of S. enterica serovar Newport.
Thirty male Holstein steers (N=30) 4 to 6 months of age were randomly assigned to two treatment groups, designated as Group 1 and Group 2. Group 1, which consisted of 20 steers, received the immunizing composition derived from S. enterica serovar Newport strain MS020508 (ATCC Accession No. PTA-9496) as described in Example 2. Steers in Group 2, which consisted of 10 steers (N=10), were vaccinated with a placebo (control group) made by preparing the immunizing composition of example 2 without the addition of the composition derived from S. enterica serovar Newport. The antigen in the control formulation was replaced with saline while keeping the adjuvant concentration the same (22.5%). All calves in groups 1 and 2 were vaccinated with the appropriate vaccine subcutaneously and revaccinated 21 days after the first vaccination.
EXAMPLE 11
Blood and Fecal Sample Collection
Blood samples were collected from all steers on day 7 and again at 28, 42 and 49 days after the first vaccination. The second vaccination was 28 days after the first vaccination. All blood was collected in sterile 13×75 mm vacutainer collection tubes, (SST No. 369783, Becton Dickinson, Franklin Lakes, N.J.). After clotting the blood tubes were centrifuged at 800×g for 30 minutes and frozen at −20° C. until analysis.
Individual fecal samples were taken aseptically by rectal extraction using sterile shoulder length gloves and placed in sterile whirl pack bags. Fecal samples were taken from all steers at three day intervals (3, 6, 9, 12, 15 and 18) (Table 22).
Ten grams of feces from each sample was placed into 90 ml of Bismuth Sulfate Broth (BSG) (Difco). Samples were mixed thoroughly and serially diluted ten fold (10−2 to 10−6) using BSG as diluent. Samples were incubated at 37 C for 24 hours. The end point for each sample was enumerated by plating in duplicate each dilution on Brilliant Green Salmonella selective agar. Positive cultures were confirmed by agglutination using Salmonella O antiserum (poly A-I and Vi). The highest dilution that had a positive Salmonella culture was determined as the end point.







TABLE 22







Schedule of Events








Daily



Schedule
Description of Events





Day (−20)
Calves were purchased from a local sales barn and upon


to day (−1)
entering trial facility were treated as necessary for



respiratory or enteric disease, and treated for internal and



external parasites.


Day 0
Calves were ear-tagged, randomized, and assigned to group


(1st
A or B. Each calf received an initial vaccination with the


vaccination)
appropriate vaccine (test and/or placebo) subcutaneously in



the neck. Serum and fecal samples were collected.


Day 1, 7, 14
Monitored for adverse reactions to vaccination (local and



systemic).


Day 21
Appropriate booster vaccination (test or placebo) was given


(2nd
to each calf (second vaccination). Serum samples collected.


Vaccination)


Day 22,
Monitored for adverse reactions to vaccination (local and


28, 37
systemic).


Day 37
All groups were orally challenged with 1012 CFU of



S. enterica serovar Newport challenge organism.



Calves weighed and serum samples collected.


Days 38-55
Animals were monitored daily for morbidity and mortality.



Dead calves were examined post-mortem and internal



organs cultured for salmonella to confirm cause of death.



Feces from all surviving calves were sampled every 3 days



and cultured for recovery of Salmonella.


Day 56
Termination of trial. Remaining calves were weighed,



serum collected, and treated if necessary. Group B calves



were vaccinated with S. enterica serovar Newport



bacterial vaccine. All surviving calves were returned to a



normal cattle production environment.









EXAMPLE 12
Preparation of S. Enterica Serovar Newport Challenge Organism
A frozen culture of S. enterica serovar Newport challenge organism (MS020508, ATCC Accession No. PTA-9496) was streaked on a Blood agar plate and incubated at 37° C. Several isolated colonies were transferred onto 100 ml of Tryptic Soy Broth (TSB) containing 25 μg/ml 2, 2′ dipyridyl and incubated on and orbital shaker at 200 rpm/min for 12 hours. Twenty five milliliters of this culture was transferred into 3500 ml of pre-warmed TSB. The culture was incubated at 37° C. for 5 hours at which point the cells were collected by centrifugation at 10,000×g for 20 minutes. The bacterial pellet was washed twice by centrifugation with the final pellet resuspended into 3000 ml of sterile physiological saline (0.85%). Just prior to challenge, 1 ml of the above bacterial suspension was serially diluted ten fold to enumerate the number of CFU per ml.
EXAMPLE 13
S. enterica serovar Newport Challenge in Holstein Calves
Sixteen days after the second vaccination all calves were orally lavaged with 100 ml of the above bacterial suspension containing 1.0×1012 Colony Forming Units (CFU) of S. enterica serovar Newport. Calves were monitored daily for signs of morbidity and rectal temperatures for 18 days post-challenge. Rectal temperatures were taken at three day intervals. Fecal samples were collected approximately every 3 days for the isolation of Salmonella. Rectal temperature and the quantitative enumeration of Salmonella was analyzed using linear regression, while the likelihood of being culture-positive (yes/no) was analyzed using logistic regression.
EXAMPLE 14
Enzyme-Linked Immunosorbent Assay (ELISA)
An Enzyme-Linked Immunosorbent Assay (ELISA) was used to monitor the serological response to vaccination. Three highly conserved proteins present in the composition prepared as described in Example 1 were used. Briefly, the proteins migrating at 82 kDa, 80 kDa, and 74 kDa were cut from unstained polyacrylamide gels. The location of these proteins was determined using a stained indicator lane which was cut away from the original gel and stained. Elution of the protein from the macerated gel was carried out according to the manufacturer's recommendation using a model 422 electro-eluter (Bio-Rad, Laboratories, Hercules, Calif.). These proteins were then used as the capture molecule in an indirect ELISA test. A polyclonal antiserum was raised against the composition derived from S. enterica serovar Newport as described in Example 1 and used as the ELISA positive control serum.
The optimum working concentrations of the purified protein and chromogenic conjugate was determined by several checkerboard titrations using the positive and negative control dialysates. A prediction curve was then established to calculate protein-ELISA titers at a 1:500 dilution. All subsequent tests were performed at a single serum dilution (1:500) and protein titers were calculated as an average of the test absorbance values for each treatment.
The ELISA was performed by adding 100 μl of diluted protein in 0.05M carbonate buffer (pH 9.6) to each well of a 96-well flat bottom plate (IMMULON 2, Dynex Technologies). After overnight incubation at 4° C., excess protein was removed and the plate was washed. All subsequent washing steps were done three times in phosphate buffered saline (pH 7.4) with 0.05% TWEEN-20 . The plates were blocked for one hour at 37° C. with 4% fish gelatin (Sigma) in PBS and then washed. Serum samples were tested in parallel at single-point dilutions (1:500) using 100 μl/well and incubated for 45 minutes at 37° C. The first two columns of each plate contained the negative and positive control samples while the rest of the plate was used for the test samples. The plate was incubated for 45 minutes at 37° C. while stirring at 200 rpm. After washing, 100 μl of a Monoclonal Anti-bovine IgG clone BG-18 Alkaline phosphatase conjugate (Sigma Chemical) at a 1:15,000 dilution was added to each well. After incubation for 45 minutes at 37° C., the plates were washed and 100 μl PnPP substrate (Sigma Chemical), prepared in 0.1 M glycine buffer, was added to each well. The substrate was allowed to react for 45 minutes at 37° C. while stirring at 100 rpm. The reaction was terminated by the addition of 25u1 of 3.0 N NaOH. The absorbance was read at 405 nm.
EXAMPLE 15
Results
Calves vaccinated with the composition derived from S. enterica serovar Newport showed an enhanced serological response to vaccination which increased after the second vaccination showing an anamnestic response after the second vaccination (FIG. 4). In contrast, the placebo non-vaccinated control calves showed no antibody response.
There was a significant difference between the rectal temperature of the vaccinates (Table 23) compared to the non-vaccinated calves (Placebo) during the post challenge period (Table 24). Averaged across the study period the rectal temperatures for the non-vaccinates was approximately 0.4 F (95% CI=0.01-0.79 F) higher when compared to vaccinates (P=0.045).







TABLE 23







The Rectal Temperature of Vaccinated Calved following an


Oral Challenge with Salmonella enterica serovar Newport









Days Post Challenge
















Calf #
0
3
4
5
6
9
12
14
18



















 2
103
105.1
104.8
103.7
103.7
103.7
103.1
103.5
102.4


 3
103.1
103.9
104.2
103.9
103.5
103.7
103.7
103.3
102.4


 5
103.3
105.1
103.7
105.5
103.5
104.2
103
03.1
102.4


 6
105.1
104.2
103.9
104.9
102.4
103.3
103
102.4
102.2


 8
103.1
104.6
103.3
104.6
102.6
103.7
103.3
102.5
101.9


 9
103.3
104.2
104.2
103
103.1
104.6
103
102.2
102.8


11
102.8
106.4
103.3
103.3
101.5
103
103.3
103
101.5


12
103.3
105.8
105.1
103.9
102.6
103
102.8
102.2
101.9


14
103.7
105.1
103
103.5
103
105.1
104.8
103.3
103.3


15
105.5
104.2
103.7
103.5
102.4
103
102.4
102.6
102.4


17
103.7
105.1
103.9
104.2
102.4
103.3
103.3
102.4
101.3


18
103.5
106.2
104.9
105.1
101.7
103
103.5
103.3
103.3


20
103.5
106.6
105.3
106.2
102.8
103.3
104.2
103.3
103.7


21
103.3
104.8
103.3
102.2
103
104
103.3
103
101.3


23
N/S
105.5
105.8
103.3
102.4
103.7
103.1
102.4
102.1


24
N/S
105.1
105.5
104.4
103.3
103.3
103.3
102.4
102.2


26
102.8
103.9
103.5
103.5
105.1
103.7
103.3
102.4
101.4


27
103
104.2
103.3
103.7
103.3
103.3
103.3
103.7
102.4


29
103.3
105.5
104
105.5
105.5
106
104.6
103
103.3


Mean
103.5
105.0
104.1
104.1
103.0
103.8
103.4
103
103.3





Cumulative Mean = 103.6


Standard Deviation = 0.64













TABLE 24







The Rectal Temperature of Placebo-Vaccinated Calves following


an Oral Challenge with Salmonella enterica serovar Newport









Days Post Challenge
















Calf #
0
3
4
5
6
9
12
14
18



















 1
103.7
106.9
105.1
105.1
103.3
104.4
103.3
102.6
102.2


 4
104.2
106.6
105.7
104.9
103.9
104.8
104.4
103.3
102.4


 7
103.7
106.4
105.7
103.3
102.8
103.7
104.2
103.3
103.9


10
103.1
104.9
103.3
104.2
103
103.7
102.2
102.4
101.9


13
103.3
106.6
105.5
104.2
103
105.1
104.2
102.1
103.3


16
103.7
106
104
103
102.2
103.7
102.6
102.2
102.1


22
103.5
107.5
106.7
105.7
104.8
105.1
103.3
103.3
104.8


25
102.8
106.9
102.8
103.3
102.4
104.9
103.5
103.3
103.3


28
104.8
105.5
104.2
103.9
103.1
104.2
N/A
N/A
N/A


Mean
103.5
106.5
104.9
104.1
103.2
104.4
103.5
102.8
103





Cumulative Mean = 104.0


Standard Deviation = 1.16






There was a significant difference in the amount of Salmonella being shed between the vaccinated group compared to the non-vaccinated Placebo group after challenge (FIG. 5). Averaged across the study period and accounting for repeated estimates, vaccinates shed less Salmonella per gram of feces as compared to non-vaccinates (average log10=0.91, 95% CI log10=0.17-64, P=0.04). Overall, among vaccinates there were about twice as many culture-negative days. About 40% of cultured days were negative for vaccinates (55/162) compared to non-vaccinates with 21% of cultures days were negative (10/48). These data show that the odds of being culture-positive for Salmonella among non-vaccinates was approximately 2.5 times greater when compared to the vaccinated group (OR=2.5, 95% CI=1.24-4.93, P=0.02). These data illustrate the proof of concept that a composition administered through vaccination prevented the colonization of Salmonella in calves after experimental challenge.
EXAMPLE 16
Decreased Fecal Shedding of E. Coli O157:H7 Through Vaccination in Holstein Steers
The purpose of this study was to evaluate the efficacy of the composition derived from E. coli O157:H7 in eliminating the fecal shedding of a homologous oral challenge of E. coliO157:H7 in Holstein steers. The immunizing composition was prepared from E. coli O157:H7 as described in Examples 1 and 2. The experimental trial was initiated in starter calves on a commercial feed lot. The feed lot consisted of 500 Holstein steers separated into separate grow out facilities based on the age and weight of the steers. Twelve steers (N=12) with an average weight of approximately 300 pounds were randomly selected and distributed into a single pen. Steers were ear tagged for identification and randomly allocated into three groups designated as groups 1-3. Steers in Group 1 were designated as non-vaccinated and remained as the control group. Steers in groups 1 and 2 were given two different vaccine formulations prepared in using two different adjuvant formulations. Steers in Group 2 were vaccinated with the vaccine adjuvanted with EMULSIGEN as described previously in Example 2, while steers in Group 3 were vaccinated with the vaccine prepared in aluminum hydroxide (REHYDRAGEL HPA, Reheis, NJ). Briefly, the composition was suspended in 0.02M phosphate buffered saline pH 7.2 and absorbed onto aluminum hydroxide (25% vol/vol) to provide a total dose of 1000 μg in a 2 ml injectable volume. Steers were vaccinated subcutaneously 3 times at 21 day intervals. The outcome parameters used to evaluate vaccine efficacy were frequency and concentration of fecal shedding of the challenge organism, serological response to vaccination, and injection site reactions.
EXAMPLE 17
Blood and Fecal Sample Collection
Blood samples were collected from all test steers on the initial day of immunization (day-0) and again at 7, 14, 21, 28, 35, 42, and 54 days after the first vaccination to monitor the serological response to vaccination. An Enzyme-Linked Immunosorbent Assay (ELISA) monitored the serological response to vaccination as described in Example 14 with the following modification: metal regulated proteins derived from E. coli O157:H7 having molecular weights of 89 kDa, 85 kDa, 81 kDa, 78 kDa, were used as the capture molecule in the assay. All blood was collected in sterile 13×75 millimeter vacutainer collection tubes (SST No. 369783, Becton Dickinson, Franklin Lakes, N.J.). After clotting, the blood tubes were centrifuged at 800×g for thirty minutes and frozen at −20° C.
Individual fecal samples were taken aseptically by rectal extraction using sterile shoulder length gloves and placed in sterile whirl pack bags. Fecal samples were taken from all steers on the initial day of challenge and again at 12, 24, 48, 72, 96, 120, 144 and 168 hours post challenge. Briefly, ten grams of feces from each sample was placed into 90 ml of physiological saline (0.85%). Samples were mixed thoroughly and serially diluted 10-fold in saline. Each dilution was plated in duplicate on Eosin Methylene Blue Agar (EMB) agar containing 150 μg nalidixic acid/ml incubated at 37° C. for 48 hours. The number of bacteria was enumerated for each sample and the log10 colony forming units was averaged for each treatment group at each time period.
Seven days after the third vaccination steers were transported from the commercial feedlot to a Biosafety level 2 isolation facility. Steers were equally divided among three isolation rooms so that each room had at least one treatment group. Four days after arriving at the isolation facility all steers were challenged. Twelve hours prior to challenge feed and water was removed from each isolation room. The E. coli O157:H7 isolate as described in Example 1 was used for challenge.
EXAMPLE 18
Preparation of E. Coli O157:H7 Challenge Organism
To enhance the isolation rate of the E. coli O157:H7 challenge organism from fecal samples the nalidixic acid resistant isolate as described in Example 8 was used for challenge. Forty eight hours before challenge the isolate was removed from a frozen stock and sub-cultured onto an EMB agar plate containing 150 μg/ml nalidixic acid and incubated at 37° C. for 18 hours. A single colony was subcultured into 100 ml Tryptic Soy Broth (Difco) containing 25 μg/ml 2,2′ dipyridyl and 150 μg nalidixic acid. The culture was incubated at 37° C. for 12 hours while rotating at 200 rpm, at which point was subcultured into 4 liters Tryptic Soy Broth (Difco) containing 25 μg/ml 2,2′ dipyridyl and 150 μg nalidixic acid incubated at 37° C. for 6 hours while continuously stirring. At the end of the incubation period the culture was centrifuged at 10,000×g for 20 minutes at 4° C. to pellet the bacteria. The final bacterial pellet was resuspended in 3600 ml of phosphate buffered saline containing 250 μg/ml nalidixic acid. Just prior to challenge, 1 ml of the above bacterial suspension was serially diluted ten fold to enumerate the number of CFU/calf dose.
EXAMPLE 19
E. Coli O157:H7 Challenge in Holstein Calves
All steers were orally lavaged with 100 ml of the above bacterial suspension containing 4.5×109 CFU. To enumerate the difference in fecal shedding between the control and vaccinated steers, individual fecal samples were collected aseptically by rectal extraction at the time of challenge and again at 12, 24, 48, 72, 96, 120, 144 and 168 hours post challenge. Blood samples were taken at the time of challenge and again at termination of the trial (168 hours).
Table 25 shows the difference in the fecal shedding between the non-vaccinated controls (Group 1) and the vaccinated steers (Groups 2 and 3). There was a highly statistical difference in the amount of E. coli O157:H7 being shed between the steers in Group 2 as compared to the non-vaccinated/challenged controls. Averaged across the study period, steers in Group 2 shed less E. coli per gram of feces as compared to the non-vaccinated steers of Group 1, with a degree of significance of P=0.02 FIG. 6.







TABLE 25







The Difference in Shedding of E. coli O157:H7 Between the Non-


Vaccinated and Vaccinated Treatment Groups after Challenge









Mean log10 Colony Forming Units











Group 1
Group 2
Group 3


Sampling Times
(Non-Vaccinated)
(Vaccinated)1
(Vaccinated)2













Challenge
9.7
9.7
9.7


(Time 0)


12 hours
5.89
4.84
5.7


24 hours
5.51
5.3
4.77


48 hours
6.03
3.92
4.44


72 hours
6.12
2.1
5.4


96 hours
4.68
2.94
5


120 hours 
3.72
2.3
5.4


144 hours 
5.55
1.4
4.4


168 hours 
4.36
1.4
4.03





1Steers in treatment Group 2 were vaccinated with the composition formulated in the EMULSIGEN adjuvant (22.5% vol/vol).


2Steers in treatment Group 3 were vaccinated with the composition formulated in aluminum hydroxide (25% vol/vol).






There was no statistical difference in the fecal shedding between the non-vaccinated controls as compared to the shedding incidence of steers in Group 3 given the vaccine prepared in aluminum hydroxide (FIG. 7). This difference could possibly be explained due to the different adjuvants. It is well known that oil based adjuvants often provide a much better immune response than aluminum hydroxide based adjuvants and could simply be due to a difference in antibody response. Nevertheless, these data illustrate for the first time that a composition as described herein administered as a vaccine composition can prevent the colonization of E. coli O157:H7 in calves after experimental challenge given orally.
EXAMPLE 20
Preparation of the Immunizing Compositions Derived from Salmonella Enterica Serovar Enteritidis
Metal regulated proteins were prepared from S. enterica serovar Enteritidis using the methods described in Example 1. The bacterial isolate used in this experimental study originated from a natural field outbreak in a commercial chicken layer flock. Identity of the isolate was confirmed by the Minnesota Poultry Testing Laboratory located in Willmar, Minnesota and designated as MS010531. The composition prepared from this isolate (S. enterica serovar Enteritidis) contained the proteins described in Table 3. Two stock vaccines were prepared that represented standard adjuvant formulations used in the poultry industry; a water-in-oil emulsion and an aqueous aluminum hydroxide formulation. The water-in-oil formulation was prepared by suspending the protein suspension in physiological saline (0.85%) containing 0.1% formalin. The protein concentration was standardized to contain 100 μg of protein per bird dose. Briefly, the aqueous protein suspension 250 ml was emulsified in a water-in-mineral oil adjuvant containing 50% DRAKEOL 6 mineral oil (Univar USA, St. Paul MN), 44.5% aqueous protein suspension, 2.56% TWEEN 85 (Ruger Chemical Co, Irvington, NJ) and 3.0% SPAN Span 85 (Ruger Chemical Co, Irvington, NJ). The mixture was emulsified using an ULTRA-TURRAX T-50 homogenizing vessel (IKA, Cincinnati, OH). The water-in-oil emulsion was stored at 4° C.
The aqueous aluminum hydroxide formulation was prepared by suspending the S. Enteritidis antigen in 0.02M phosphate buffered saline pH 7.2 to a fmal volume of 250 ml containing 25% vol/vol aluminum hydroxide (REHYDRAGEL HPA, Reheis, NJ) to give a final protein concentration of 200 ug protein/ml.
EXAMPLE 21
Chicken Vaccination and Challenge Study
Evaluation of the efficacy of the S. enterica serovar Enteritidis vaccines was carried out against a live virulent challenge in Specific Pathogen Free Chickens (SPF). Three hundred and fifty (N=350) 1-day old SPF chicks were obtained from Charles River Spafas Inc (Roanoke, Ill.). Chicks were randomly assigned to three treatment groups, designated A, B, and C, with 116 birds in each group. Birds in Group A received a 0.1 ml dose, delivered subcutaneously, of the aluminum hydroxide adjuvant vaccine at day one, followed by a 0.5 cc booster at 10 weeks of age (day 70). Birds in Group B received a 0.5 cc dose, delivered subcutaneously, of the oil emulsified vaccine at 6 weeks of age (Day 42), followed by a 0.5 cc booster vaccination at 10 weeks of age (Day 70). Group C served as non-vaccinated controls.
EXAMPLE 22
Intravenous Challenge with S. Enteritidis Serovar Enteritidis
To enhance the isolation rate of the S. enterica serovar Enteritidis challenge organism from challenged birds the isolate was made nalidixic acid resistant as described in example 8 with the following modification. The S. enterica serovar Enteritidis culture was plated on Brilliant Green Agar (BG) plates rather then Eosin Methylene Blue (EMB). The nalidixic acid resistant S. enterica serovar Enteritidis isolate as prepared by the method described above was stored at −90° C. until used for challenge. Briefly, the isolate from a frozen stock was streaked onto a blood agar plate and incubated at 37° C. for 18 hours. A single colony was subcultured into 100 ml Tryptic Soy Broth (Difco) containing 25 μg/ml 2,2′ dipyridyl. The culture was incubated at 37° C. for 12 hours while rotating at 200 rpm, at which point 10 ml was sub-cultured into 500 ml pre-warmed Tryptic Soy Broth containing 25 μg/ml 2,2′ dipyridyl. The culture was incubated at 37° C. for 6 hours while rotating at 200 rpm at which point it was centrifuged at 10,000×g for 10 minutes at 4° C. to pellet the bacteria. The bacterial pellet was washed twice by centrifugation in physiological saline at 4° C. The final pellet was resuspended and aliquoted into two 200 ml samples in physiological saline. Each sample was adjusted to give a low and high challenge dose, i.e. low dose was adjusted to 3.45×107 CFU/ml while the high dose was adjusted to give 3.45×109 CFU/ml.
EXAMPLE 23
Challenge
At 12 weeks of age (day 84), all groups (A, B, and C) were separated into two sub-groups based on the challenge dose given, i.e. Group A was designated as A1 and A2 while birds in Groups B and C were designated as B1, B2, C1 and C2 respectively. All birds in groups A1, B1, and C1 (60 birds/group) were intravenously challenged using the low dose of S. enterica serovar Enteritidis. Each bird was given 1 ml containing 3.45×107 CFU by intravenous injection (refer to table 26). The outcome parameters used to evaluate vaccine efficacy in these groups was based on the differences in the quantitative clearance of the challenged organism from internal organs (spleen and ovaries) and difference in fecal shedding as examined by culturing the cecal junction. Birds in Groups A2, B2, and C2 (40 birds/group) were intravenously challenged with the high dose of S. enterica serovar Enteritidis (3.45×109 CFU/ml) to evaluate the difference in mortality between vaccinated and non-vaccinated treatment groups. Mortality was recorded daily for 7 days (table 26).







TABLE 26







Treatment Groups, Adjuvants, and Antigen Doses










# of Birds:
















Treatment
Low

High
Adjuvant
Antigen
Priming
Booster
Administration


Group
chlg.

chlg.
Formulation
Treatments
Dose
Dose
Day





Group A
60
+
40
Al—OH
20 and 100 μg
0.1 ml
0.5 ml
Days 1, 70


Group B
60
+
40
Oil Emulsion
100 and 100 μg
0.5 ml
0.5 ml
Days 42, 70


Group C
60
+
40
non-vac
non-vac
—
—
—









To enumerate differences in systemic clearance of the challenge microbe from internal organs and intestinal colonization between vaccinates and non-vaccinates challenged with the low dose, ten birds/group were euthanized by CO2 at 12, 24 and 48 hours after challenge and the spleen, left ovary and cecal junction were aseptically removed from each bird. Each sample was individually weighted and adjusted to give a 1:10 dilution (wt/vol) in physiological saline. Each sample was macerated and serially diluted ten fold. Each diluted sample was plated in duplicate on BG agar plates containing 150 ug nalidixic acid. The number of bacteria was enumerated for each sample and the log10 CFU was averaged for each treatment group at each time period.
FIG. 8 shows the quantitative clearance of S. enterica serovar Enteritidis in spleens of vaccinated and non-vaccinated chickens, 12, 24 and 48 hours after challenge. The results show a steady decline in the number of CFU of S. enterica serovar Enteritidis in the vaccinated groups for each treatment group that was statistically significant at each sampling period as compared to the non-vaccinated controls. The aluminum hydroxide vaccinated birds of group A1 compared to the non-vaccinated controls (C1) showed a highly statistical difference at each sampling period (12, 24 and 48 hours post challenge) with degrees of significance of P=0.036, 0.0003 and 0.024 respectively. A similar scenario was observed in birds vaccinated with the oil-emulsified vaccine (group B1) showing statistically significant differences at 24 and 48 hours after challenge have degrees of significance of P=0.00072 and 0.0123, respectively, when compared to the non-vaccinated controls (group C1). There was no significant difference at the 12 hour sampling period due to a large variation in plate counts at this time period.
FIG. 9 shows the difference in the number of CFU of S. enterica serovar Enteritidis in ovaries between vaccinated and non-vaccinated birds among the different treatment groups. The aluminum hydroxide vaccinated birds of group A1 showed statistical differences at the 24 and 48 hour sampling periods as compared to the non-vaccinated birds of group C1 with degrees of significance of P=0.005 and 0.04 respectively. The oil emulsified vaccinated birds of group B1 also showed degrees of significance at the 24 and 48 hour sampling periods with degrees of significance of P=0.0048 and 0.045. As before, there was no significant difference at the 12 hour sampling period due to variation in plate counts.
FIG. 10 shows the colonization differences or the fecal shedding of S. enterica serovar Enteritidis in the cecal junction between vaccinated and non-vaccinated control birds. Statistical differences were seen in both treatment groups (A1 and B1) when compared to non-vaccinated controls at the 48 hour only sampling period with degrees of significance of P=0.01 and 0.0096 respectively.
Birds in Groups A2, B2 and C2 (40 birds/group) were intravenously challenged with the high dose of S. enterica serovar Enteritidis (3.45×109 CFU/ml) to evaluate the difference in mortality between vaccinated and non-vaccinated treatment groups (table 27). Mortality was recorded at 12 hour intervals for a period of seven 7 days. There was a significant difference in the observed mortality between birds given the aluminum hydroxide (A2) versus the oil-emulsified adjuvanted vaccine (B2) (Table 27). Total 7 day mortality in the aluminum hydroxide (A2) group was 45% compared to 23% in the oil-emulsified groups (B2) and 95% in the non-vaccinated controls of group C2 (FIG. 94). The degree of significance of group A2 compared to the non-vaccinated control group C2 was (p=5.67×10−7) while the degree of significance of group B2 compared to C2 was (p=6.79×10−12).







TABLE 27







The cumulative mortality between vaccinated treatment groups


compared to non-vaccinated controls following intravenous challenge


with S. enterica serovar Enteritidis










Time Post


Aluminum


Challenge
Controls (C2)
Oil Emulsion (B2)
Hydroxide (A2)














12
hour
0
0
0


24
hours
14 
0
0


36
hours
3
0
0


48
hours
5
0
0


60
hours
2
0
0


72
hours
7
0
1


84
hours
4
0
2


96
hours
1
1
1


108
hours
1
0
5


120
hours
1
1
3


132
hours
0
2
1


144
hours
0
1
3


156
hours
0
3
1


168
hours
0
1
1










Total mortality
38/40
9/40
18/40



(95%)
(23%)
(45%)









The results of this study demonstrate that a vaccine including proteins isolated from S. enterica serovar Enteritidis grown under iron-limiting conditions is protective against subsequent challenge by the pathogen in layer chickens. Birds immunized with the vaccine prepared in two commonly used adjuvants showed a significant reduction in the number of colony forming units of the challenge organism (S. enterica serovar Enteritidis) from internal organs (spleen and ovaries) following intravenous challenge compared to the non-vaccinated controls. In addition, vaccination also reduced the fecal shedding or colonization of S. enterica serovar Enteritidis after challenge as compared to the non-vaccinated controls. Both vaccination regiments used in this study resulted in good protection against an intravenous challenge in chickens. In addition, there was minimal adverse reaction at the site of injection, which is a major advantage of the compositions described herein when compared to commercially available bacterins.
EXAMPLE 24
Characterization of Metal Regulated Proteins of an S. Enterica Serovar Newport Isolate
The proteins of the composition prepared as described in Example 1 from the S. enterica serovar Newport strain were characterized using matrix assisted laser desorption/ionization time-of-flight spectrometry (MALDI-TOF MS). A portion of the composition was resolved using a sodium dodecyl sulfate-polyacrylamide gel. After the proteins of a composition had been resolved, the gel stained with either coomasie brilliant blue or silver to visualize the proteins. This method was also used to characterize compositions obtained from S. enterica serovar Enteritidis strain MS010531, S. enterica serovar Typhimurium strain MS010427, and S. enterica serovar IRP SDC Serial.
Materials and Methods
Excision and washing. The gel was washed for 10 minutes with water twice. Each protein band of interest was excised by cutting as close to the protein band as possible to reduce the amount of gel present in the sample. Fourteen gel fragments were prepared, and included polypeptides having the following approximate molecular weights (in kilodaltons): 82 and 79 (excised together in a single gel slice), 74, 65, 56, 55, 45, 38 and 38 (excised together in a single gel slice), 36, 22, 18, and 12.
Each gel slice was cut into 1×1 mm cubes and placed in 1.5 ml tube. The gel pieces were washed with water for 15 minutes. All the solvent volumes used in the wash steps were approximately equal to twice the volume of the gel slice. The gel slice was next washed with water/acetonitrile (1:1) for 15 minutes. When the proteins had been stained with silver, the water/acetonitrile mixture was removed, the gel pieces dried in a SPEEDVAC (ThermoSavant, Holbrook, NY) and then reduced and alkylated as described below. When the gel pieces were not silver-stained, the water/acetonitrile mixture was removed, and acetonitrile was added to cover until the gel pieces turned a sticky white, at which time the acetonitrile was removed. The gel pieces were rehydrated in 100 mM NH4HCO3, and after 5 minutes, a volume of acetonitrile equal to twice the volume of the gel pieces was added. This was incubated for 15 minutes, the liquid removed, and the gel pieces dried in a SPEEDVAC.
Reduction & alkylation. The dried gel pieces were rehydrated in 10mM DTT and 100mM NH4HCO3, and incubated for 45 minutes at 56° C. After allowing the tubes to cool to room temperature, the liquid was removed and the same volume of a mixture of 55mM iodoacetamide and 100 mM NH4HCO3 was immediately added. This was incubated for 30 minutes at room temperature in the dark. The liquid was removed, acetonitrile was added to cover until the gel pieces turned a sticky white, at which time the acetonitrile was removed. The gel pieces were rehydrated in 100 mM NH4HCO3, and after 5 minutes, a volume of acetonitrile equal to twice the volume of the gel pieces was added. This was incubated for 15 minutes, the liquid removed, and the gel pieces dried in a SPEED VAC. If the gel was stained with coomasie blue, and residual coomassie still remained, the wash with 100 mM NH4HCO3/acetonitrile was repeated.
In-gel digestion. Gel pieces were completely dried down in a SPEEDVAC. The pieces were rehydrated in digestion buffer (50 mM NH4HCO3, 5 mM CaCl 2, 12.5nanograms per microliter (ng/μl) trypsin) at 4° C. Enough buffer was added to cover the gel pieces, and more was added as needed. The gel pieces were incubated on ice for 45 minutes, and the supernatant removed and replaced with 5-2 μl of same buffer without trypsin. This was incubated at 37° C. overnight in an air incubator.
Extraction of peptides. A sufficient volume of 25 mM NH4HCO3 was added to cover gel pieces, and incubated for 15 minutes (typically in a bath sonicator). The same volume of acetonitrile was added and incubated for 15 minutes (in a bath sonicator if possible), and the supernatant was recovered. The extraction was repeated twice, using 5% formic acid instead of NH4HCO3. A sufficient volume of 5% formic acid was added to cover gel pieces, and incubated for 15 minutes (typically in a bath sonicator). The same volume of acetonitrile was added and incubated for 15 minutes (typically in a bath sonicator), and the supernatant was recovered. The extracts were pooled, and 10 mM DTT was added to a final concentration of 1 mM DTT. The sample was dried in a SPEEDVAC to a final volume of approximately 5 μl.
Desalting of peptides. The samples were desalted using a ZIPTIP pipette tips (C18, Millipore, Billerica, Mass.) as suggested by the manufacturer. Briefly, a sample was reconstituted in reconstitution solution (5:95 acetonitrile:H2O, 0.1%-0.5% trifluoroacetic acid), centrifuged, and the pH checked to verify that it was less than 3. A ZIPTIP was hydrated by aspirating 10 μl of solution 1 (50:50 acetonitrile:H2O, 0.1% trifluoroacetic acid) and discarding the aspirated aliquots. This was followed by aspirating 10 μl of solution 2 (0.1% trifluoroacetic acid in deionized H2O) and discarding the aspirated aliquots. The sample was loaded into the tip by aspirating 10 μl of the sample slowly into the tip, expelling it into the sample tube, and repeating this 5 to 6 times. Ten microliters of solution 2 was aspirated into the tip, the solution discarded by expelling, and this process was repeated 5-7 times to wash. The peptides were eluted by aspirating 2.5 μl of ice cold solution 3 (60:40, acetonitrile:H2O, 0.1% trifluoroacetic acid), expelling, and then re-aspirating the same aliquot in and out of the tip 3 times. After the solution has been expelled from the tip, the tube is capped and stored on ice.
Mass spectrometric peptide mapping. The peptides were suspended in 10 μl to 30 μl of 5% formic acid, and analyzed by MALDI-TOF MS (Bruker Daltonics Inc., Billerica, Mass.). The mass spectrum of the peptide fragments was determined as suggested by the manufacturer. Briefly, a sample containing the peptides resulting from a tryptic digest were mixed with matrix cyano-4-hydroxycinnamic acid, transferred to a target, and allowed to dry. The dried sample was placed in the mass spectrometer, irradiated, and the time of flight of each ion detected and used to determine a peptide mass fingerprint for each protein present in the composition. Known polypeptides were used to standardize the machine.
Data analysis. The experimentally observed masses for the peptides in each mass spectrum were compared to the expected masses of proteins using the Peptide Mass Fingerprint search method of the MASCOT search engine (Matrix Science Ltd., London, UK, and www.matrixscience.com, see Perkins et al., Electrophoresis 20, 3551-3567 (1999)). The search parameters included: database, NCBInr; taxonomy, bacteria (eubacteria); type of search, peptide mass fingerprint; enzyme, trypsin; fixed modifications, carbamidomethyl (C) or none; variable modifications, oxidation (M), carbamidomethyl (C), the combination, or none; mass values, monoisotopic; protein mass, unrestricted; peptide mass tolerance, between ±100 ppm and ±300ppm or 450 ppm, or ±1 Da; peptide charge state, Mr; max missed cleavages, 0 or 1; number of queries, 25.
Results
The result of this search was a mass fingerprint for each protein present in the composition (Table 28-31).







TABLE 28







Experimental data from MALDI-TOF MS analysis of S. enterica


serovar Newport










Approximate




molecular
m/z value of polypeptide


Polypeptide
weight in kilodaltons
fragments resulting from


Designation
(kDa)1
trypsin digestion2












Lw221 (±300 ppm)
82
629.5




644.5




772.5




831.5




873.5




991.6




1083.6




1208.6




1325.8




1378.7




1464.8




1500.7




1516.7




1619.9




1634.9




1635.9




1728.9




1873.1




1982.1




1998.2




2014.1




2194.1




2332.3


Lw223A (±300 ppm)
80
849.5




919.5




1041.7




1098.7




1310.7




1336.8




1342.7




1365.7




1529.8




1565.9




1737.1




1752.0




1756.1




1847.2




1913.2




1930.2




1936.3




2032.3




2417.5




2588.6




2702.9




2910.8




2945.0


Lw223B (±300 ppm)
74
606.5




617.5




809.5




1064.5




1159.6




1211.6




1315.7




1330.8




1346.7




1528.0




1651.1




1679.0




1742.1




1745.9




1752.0




1794.1




1816.1




1908.2




1936.3




1954.2




1988.2




2243.4




2539.6




2588.6




2711.6


P4 (±300 ppm)
65
1304.60




1399.55




1509.71




1793.82




1869.90




1933.90




2024.94




2087.08




2258.20


Lw224 (±300 ppm)
56
1101.6




1132.8




1255.9




1717.1




1758.2




1960.2




2035.4




2670.8




2805.8




2861.1




3061.1


Lw225 (±300 ppm)
55
959.6




1101.6




1132.7




1144.7




1255.8




1605.0




1615.0




1623.1




1641.0




1710.0




1717.0




1772.2




1905.2




1960.2




2085.4




2196.4




2670.7




2805.7




3060.9


Lw226 (±300 ppm)
52
788.5




800.5




802.5




828.5




914.6




1090.5




1286.7




1382.8




1550.8




1616.9




1663.0




1739.0




1830.0




2035.1




2185.3




2209.3




2227.2




2685.6




2749.6




2887.6


Lw227 (±300 ppm)
45
666.5




731.5




813.5




859.5




964.5




1151.5




1224.6




1412.7




1423.8




1659.9




1685.0




1781.9




1966.2




2087.3




2183.2




2297.4




3101.7




3315.9


Lw228A (±300 ppm)
38
719.6




868.5




1058.6




1104.5




1122.6




1297.6




1639.9




2219.3




2383.2




2390.2




2604.4




2717.4




2758.5




2806.6




2835.5




3066.6




3451.7


Lw228B (±300 ppm)
38
705.6




794.5




901.5




909.6




1106.6




1205.6




1801.9




1835.9




1946.1




1987.0




2248.3




2383.2




3005.7




3134.7


Lw230A (±300 ppm)
36
818.5




872.6




915.5




1025.5




1083.6




1157.6




1264.6




1378.7




1381.6




1537.7




1640.8




2303.3




2616.3




2673.4




3423.9


Lw233 (±300 ppm)
22
1051.7




1222.7




1588.9




1736.0




1821.1




2738.6




2853.7




3220.9


Lw234 (±300 ppm)
18
796.4




1263.6




1416.6




1479.7




1626.8




1797.9




2176.0




2447.1




2495.1


Lw235 (±300 ppm)
12
789.5




1246.6




1258.6




1361.7




1531.9




2061.1




2874.6





1Molecular weight, in kilodaltons, of polypeptide obtained from S. enterica serovar Newport.


2m/z, mass (m) to charge (z) ratio. Each m/z value includes a range of plus or minus 300 ppm.













TABLE 29







Experimental data from MALDI-TOF MS analysis of S. enterica


serovar Enteritidis










Approximate molecular
m/z value of polypeptide


Polypeptide
weight in kilodaltons
fragments resulting from


Designation
(kDa)1
trypsin digestion2












Lw98 (±1 Da)
92
729.61




816.54




889.51




958.56




973.62




987.62




999.54




1009.56




1048.62




1077.64




1114.61




1181.55




1220.62




1277.56




1283.77




1339.65




1385.61




1402.70




1403.69




1471.70




1520.84




1528.74




1649.80




1692.96




1713.93




1733.89




1759.91




1787.97




1895.03




1955.01




2160.25




2255.09




2286.19




2794.68




2882.59


Lw99 (±1 Da)
91
905.48




925.41




946.49




1005.46




1051.45




1077.49




1110.47




1200.52




1277.51




1295.47




1308.60




1344.52




1376.58




1418.64




1451.54




1510.49




1511.63




1602.79




1619.68




1625.71




1669.65




1767.85




1768.86




1793.81




1809.83




1833.85




2014.04




2089.13




2269.98




2299.06




2454.09




2255.19




2573.21


Lw101 (±1 Da)
86
644.6




873.5




951.5




991.5




1083.6




1085.5




1096.4




1152.6




1182.4




1208.5




1325.6




1366.5




1378.5




1412.6




1433.6




1464.6




1500.5




1561.7




1562.7




1585.6




1619.6




1634.7




1728.7




1871.8




1904.9




1975.9




1981.9




1998.0




2078.9




2193.0




2234.1




2372.0




2532.2




2623.3




2634.1




3099.3




3212.4




3474.5


Lw102 (±1 Da)
83
611.5




629.6




849.4




919.4




1041.5




1098.5




1142.4




1154.5




1163.4




1219.5




1310.4




1336.5




1342.5




1365.4




1406.6




1461.6




1529.5




1565.6




1736.7




1752.7




1755.7




1846.8




1881.9




1912.9




1954.9




2031.9




2262.0




2399.0




2417.1




2702.3




2910.4




2944.5


Lw103 (±1 Da)
78
606.5




615.6




617.6




809.4




837.4




990.4




1061.4




1064.4




1142.4




1159.4




1178.5




1211.4




1315.5




1330.6




1346.4




1494.6




1527.6




1571.7




1650.8




1655.8




1741.8




1745.6




1751.8




1793.9




1815.8




1907.9




1953.9




2243.1




5239.4




2711.3


Lw104 (±1 Da)
55
788.5




802.5




914.6




1180.5




1227.5




1286.5




1382.6




1550.7




1616.8




1662.8




1738.8




1829.9




2035.0




2185.1




2209.0




2227.1




2749.3




2887.5


Lw106A (±1 Da)
40
692.5




705.6




901.5




909.6




974.5




1106.6




1129.4




1192.5




1205.5




1439.6




1801.9




1891.9




1991.0




2248.2




2340.3




2406.2




3005.7


Lw106B (±1 Da)
39
719.6




868.5




1058.5




1104.5




1122.5




1280.5




1297.5




1640.8




1891.9




2219.2




2383.2




2390.2




2758.5




2806.6




3067.6


Lw108 (±1 Da)
38
818.5




1025.5




1083.6




1222.7




1233.6




1264.7




1378.8




1381.7




1470.8




1537.9




1641.0




2303.5




2616.7




2673.8




3424.3





1Molecular weight, in kilodaltons, of polypeptide obtained from S. enterica serovar Enteritidis.


2m/z, mass (m) to charge (z) ratio. Each m/z value includes a range of plus or minus 1 Dalton.













TABLE 30







Experimental data from MALDI-TOF MS analysis of S. enterica


serovar Typhimurium










Approximate molecular
m/z value of polypeptide


Polypeptide
weight in kilodaltons
fragments resulting from


Designation
(kDa)1
trypsin digestion2












Lw111 (±1 Da)
86
991.6




1083.7




1182.6




1208.6




1307.7




1325.8




1378.7




1433.8




1478.8




1500.8




1585.8




1618.9




1619.9




1634.9




1659.9




1729.0




1872.1




1982.1




1998.2




2022.2




2079.2




2119.4




2194.2




2204.2




2332.3




2374.3




2633.5




3099.9


Lw112 (±1 Da)
82
611.5




849.5




919.5




1041.6




1095.6




1098.6




1154.7




1163.6




1209.6




1219.7




1310.7




1336.7




1342.7




1365.7




1406.8




1529.8




1565.9




1566.9




1737.0




1756.0




1847.1




1882.2




1884.1




1913.2




1931.2




1955.2




2032.2




2192.4




2262.3




2417.4




2449.4




2702.2




2910.7




2944.9


Lw113 (±1 Da)
77
958.5




1159.5




1179.5




1211.5




1309.7




1315.6




1330.7




1346.5




1398.7




1527.7




1650.9




1655.9




1745.7




1751.9




1793.7




1954.0




2022.1




2202.1




2243.1


Lw115A (±1 Da)
40
652.6




705.7




794.6




901.6




909.6




1106.7




1120.6




1129.5




1175.6




1205.5




1348.8




1439.8




1802.0




1835.9




1987.1




2248.1




2340.2




2406.1




3005.6




3134.5


Lw115B (±1 Da)
39
719.7




868.6




1058.7




1104.6




1122.7




1161.6




1280.7




1297.5




2219.1




2383.1




2390.1




2758.3




2806.4




3451.5


Lw117 (±1 Da)
38
645.6




818.5




872.6




915.6




943.5




1025.5




1043.6




1083.5




1141.6




1222.6




1264.6




1378.7




1381.6




1470.6




1537.7




1640.7




1709.8




2303.2




2616.3




2627.2




2673.4




3423.7




3540.8





1Molecular weight, in kilodaltons, of polypeptide obtained from S. enterica serovar Typhimurium.


2m/z, mass (m) to charge (z) ratio. Each m/z value includes a range of plus or minus 1 Dalton.













TABLE 31







Experimental data from MALDI-TOF MS analysis of S. enterica


serovar Dublin.












Approximate
m/z value




molecular
of polypeptide




weight in
fragments




kilodaltons
resulting from



Polypeptide Designation
(kDa)1
trypsin digestion2















Dublin-1 (±300 ppm)
96
1083.43





1208.36





1315.32





1378.40





1500.50





1516.48





1634.65





1728.66





1871.78





1956.88





1981.83





1997.93





2013.92





2119.03





2193.82





2203.84





2209.82





2331.9



Dublin-2 (±1 Da)
89
611.32





629.38





849.27





919.23





1041.34





1098.34





1219.28





1310.27





1336.36





1342.31





1365.25





1529.35





1565.39





1736.52





1752.52





1846.58





1881.64





1912.69





2262.75





2416.81





2702.01





2910.99



Dublin-3 (±1 Da)
81
606.31





617.37





990.19





1064.17





1178.19





1315.21





1330.34





1527.30





1650.36





1741.45





1745.26





1751.39





1793.44





1815.42





1907.47





1936.49





1953.31





2196.69





2242.57





2552.77





2587.73





2710.65



Dublin-4 (±1 Da)
61
632.32





945.20





1101.13





1116.16





1164.15





1317.16





1475.24





1764.30





1833.30





2007.47





2084.57





2669.63





2683.59





2859.91



Dublin-5 (±1 Da)
56
914.20





989.18





1286.12





1382.20





1550.21





1616.31





1662.31





1738.31





1829.32





2034.37





2185.46





2208.44



Dublin-6 (±1 Da)
51
945.18





1116.13





1221.10





1317.12





1445.06





1475.17





1815.31





1833.26





2007.39





2669.52





2683.47





2859.77



Dublin-7 (±450 ppm)
43
1172.16





1188.14





1343.12





1376.05





1392.04





1423.19





1527.29





1854.31





2344.42





2360.41





3078.65



Dublin-8 (±1 Da)
40
1205.09





1348.22





1439.14





1802.27





1836.26





2247.49





2339.52





2405.42





3004.81



Dublin-9, 10, 11 (±1 Da)
38
818.24





1025.36





1083.42





1264.26





1378.64





1381.53





1640.41





2302.91





2615.82





2672.85





3423.18







1Molecular weight, in kilodaltons, of polypeptide obtained from S. enterica serovar Dublin.



2m/z, mass (m) to charge (z) ratio. Each m/z value includes a range of plus or minus 300 ppm (the polypeptide Dublin-1), 450 ppm (the polypeptide Dublin-7), or 1 Dalton (the remaining polypeptides).






EXAMPLE 25
Characterization of Metal Regulated Proteins of E. Coli 
The proteins of the composition prepared as described in Example 1 from the E. coli strain BEcO157(stx-) were characterized using MALDI-TOF MS as described in Example 24. Twelve gel fragments were prepared, and included polypeptides having the following approximate molecular weights (in kilodaltons): 90, 86, 83, 79, a doublet at 66, 56, 38, 37, and 29. These methods were also used for the characterization of proteins of the E. coli strains MS040330, MS040324, and MS040827.
Results
The result of this search was a mass fingerprint for each protein present in the composition (Table 32-35).







TABLE 32







Experimental data from MALDI-TOF MS analysis of E. coli strain


BEcO157(stx-).












Approximate
m/z value of




molecular
polypeptide




weight in
fragments




kilodaltons
resulting from



Polypeptide Designation
(kDa)1
trypsin digestion2















Lw118 (±1 Da)
90
629.7





772.6





831.5





991.6





1178.6





1285.6





1321.7





1369.7





1433.8





1516.8





1619.9





1634.9





1706.9





1788.0





1798.0





1872.1





1966.2





1982.1





2089.1





2175.1





2303.2





2601.5





2706.6





2844.6





3082.8





3213.8



Lw119 (±1 Da)
86
976.5





992.6





1095.5





1247.6





1278.7





1359.7





1396.5





1436.7





1493.6





1572.9





1650.8





1665.8





1810.9





1914.0





2134.3





2211.2





2270.1



LW-1A-3 (±300 ppm)
83
837.27





884.29





1048.20





1127.26





1338.26





1351.29





1397.26





1472.33





1621.46





1650.47





1722.49





1727.41





1759.47





1813.46





1829.43





2282.75





2512.79



Lw121 (±1 Da)
79
716.5





952.5





1135.5





1155.7





122.6





1336.6





1396.6





1447.7





1512.7





1532.7





1653.8





1657.8





1677.9





1717.9





1780.0





1861.0





1964.1





2262.2





2398.2



LW-1A-5A (±450 ppm)
66
632.33





945.20





1191.31





1238.16





1440.25





1561.26





1647.24





1792.36





2062.63





2085.55





2190.41





2248.51





2454.66





2628.63



LW-1A-5B (±450 ppm)
66
679.45





1295.14





1299.04





1304.17





1423.20





1550.34





1820.33





1892.48





1918.33





2159.57





2323.52





2357.55





2699.58



LW-1A-6 (±450 ppm)
56
1285.15





1395.19





1550.25





1616.35





1829.34





2034.42





2139.53





2183.52





2242.47



Lw123 (±1 Da)
38
705.5





885.4





931.5





939.4





1120.4





1122.5





1124.4





1171.4





1290.4





1348.5





1379.4





1380.5





1439.5





1664.6





1820.7





1821.7





2232.9





2353.9





2447.9





2585.1





2792.1





2991.3





3106.3



Lw124 (±1 Da)
37
818.4





915.4





1027.5





1055.3





1083.4





1155.4





1222.5





1280.4





1378.5





1409.4





1443.5





1565.5





1654.6





1709.7





2231.9





2600.1





2601.0





2671.0





3478.4



LW-1A-10 (±300 ppm)
29
951.32





1020.31





1485.37





1501.36





1517.50





1676.54





1692.47







1Molecular weight, in kilodaltons, of polypeptide obtained from E. coli strain BEcO157(stx-).



2m/z, mass (m) to charge (z) ratio. Each m/z value includes a range of plus or minus 300 ppm (the 83 kDa and 29 kDa polypeptides), 450 ppm (the 66 kDa and 56 kDa polypeptides), or 1 Dalton (the remaining polypeptide).













TABLE 33







Experimental data from MALDI-TOF MS analysis of E. coli strain


MS040330.












Approximate
m/z value of




molecular
polypeptide




weight in
fragments




kilodaltons
resulting from



Polypeptide Designation
(kDa)1
trypsin digestion2















AB1-1 (±250 ppm)
92
905.38





909.28





1051.29





1079.32





1172.32





1277.26





1344.32





1404.39





1467.34





1480.42





1511.37





1547.30





1568.40





1625.45





1641.44





1669.39





1685.37





1740.54





1823.54





1859.56





2122.66





2140.64



AB1-2 (±300 ppm)
80
629.56





831.31





1178.28





1634.37





1787.37





1787.37





1797.30





1871.47





1981.45





2088.38





2091.59





2174.41





2303.43





2843.60



AB1-3 (±400 ppm)
77
1381.12





1526.19





1689.32





1750.32





1832.33





1889.45





1929.36





1968.43





1984.43





2031.32





2918.52





2959.75



AB1-4 (±400 ppm)
72
629.51





808.24





872.25





889.19





1739.11





1763.14





1873.25





1999.31





2104.23





2141.27





2207.32





2415.36





2439.43



AB1-5 (±500 ppm)
66
615.37





716.27





771.26





831.08





942.06





952.10





1026.17





1150.99





1155.12





1222.04





1335.99





1395.96





1531.96





1657.93





1673.00





1677.03





1717.11





1779.09





1963.12





1998.11





2261.12





2397.12





3305.10



AB1-6 (±450 ppm)
50
788.24





802.23





828.20





914.20





1180.04





1345.96





1737.18





1829.11





2035.14





2184.22





2185.23





2227.19



AB1-7 (±400 ppm)
42
632.41





709.30





716.31





760.25





931.16





1003.12





1020.15





2248.21





2642.26





2700.21





2815.45



AB1-8 (±500 ppm)
38
705.30





842.18





885.07





1289.95





1439.00





2553.13





2990.28



AB1-9 (±450 ppm)
36
719.37





868.16





1058.17





1249.01





1439.07





1934.06





2217.24





2389.19





2834.32



AB1-10 (±400 ppm)
35
818.29





834.28





872.28





1055.16





1280.19





1378.26





1423.20





1640.26





2231.49





2599.58





3495.73



AB1-11 (±300 ppm)
30
707.41





777.48





930.38





965.44





1066.41





1082.38





1109.37





1205.37





1221.32





1404.52





1577.47





1592.47





2392.78



Lw214 (±1 Da)
19
915.8





942.7





951.8





1020.9





1486.2





1518.3





1605.2





1677.4





1679.3



Lw215 (±1 Da)
16
603.5





915.6





942.5





951.6





1020.6





1043.7





1148.7





1363.7





1485.8





1518.0





1604.9





1677.0





1769.0





1933.1





2263.3







1Molecular weight, in kilodaltons, of polypeptide obtained from E. coli strain MS040330.



2m/z, mass (m) to charge (z) ratio. Each m/z value includes a range of plus or minus 250 ppm (the 92 kDa polypeptide), plus or minus 300 ppm (the 80 kDa and 30 kDa polypeptides), plus or minus 400 ppm (the 77 kDa, 72 kDa, 42 kDa, and 35 kDa polypeptides), plus or minus 450 ppm (the 50 kDa and 36 kDa polypeptides), plus or minus 500 ppm (the 66 kDa and 38 kDa polypeptides) or 1 Dalton (the 19 kDa and 16 kDa polypeptides).













TABLE 34







Experimental data from MALDI-TOF MS analysis of E. coli strain


MS040324.












Approximate
m/z value of




molecular
polypeptide




weight in
fragments




kilodaltons
resulting from



Polypeptide Designation
(kDa)1
trypsin digestion2















J4-1 (±400 ppm)
82
629.46





1307.21





1532.22





1579.33





1634.33





1787.34





1797.32





1981.42





2089.41





2091.56





2126.48





2843.61



J4-2 (±300 ppm)
79
686.54





737.44





842.49





861.44





1147.48





1163.44





1208.43





1244.42





1279.62





1473.59





1487.60





1579.67





1616.67





1718.71





2014.87





2036.81





2110.97





2126.95



J4-3 (±300 ppm)
88
650.52





672.53





821.37





1124.32





1279.50





1297.39





1325.37





1381.37





1424.43





1551.45





1703.56





1732.51





2024.70





2036.67





2251.76





2787.11





2847.98



J4-4 (±300 ppm)
60
676.37





679.52





1756.36





1820.39





1892.53





1932.42





2024.43





2159.65





2207.56





2255.71





2323.60





2357.64





2699.70



J4-5 (±400 ppm)
54
788.28





802.28





828.24





914.26





1231.12





1285.15





1323.25





1346.10





1550.24





1616.31





1737.36





1829.31





2034.39





2139.50





2183.47





2242.46



J4-6 (±350 ppm)
46
731.33





859.24





964.18





1563.21





1579.20





1677.22





1684.35





1731.31





2132.45





2148.46





2210.46





2371.41





2387.42





3216.50



J4-7 (±400 ppm)
45
786.26





1025.13





1030.16





1255.15





1497.14





1505.19





1587.22





1652.17





1794.25





1899.36





1998.32



Lw216 (±300 ppm)
38
868.5





1249.7





1439.8





1935.1





2218.4





2390.4





2602.6





2977.6





3308.1



Lw217 (±1 Da)
37
818.4





1280.6





1378.7





2232.2





2600.5





2602.4



J4-11 (±300 ppm)
31
707.35





777.40





930.33





965.35





1066.31





1082.29





1109.27





1205.26





1221.24





1404.42





1576.39





1576.39





1592.38





2392.69



J4-12 (±400 ppm)
30
717.33





1339.16





1463.13





1841.21





1857.18





1882.30





1898.31





2263.24





2825.38





2868.54



Lw218 (±1 Da)
19
915.6





942.5





951.6





1020.6





1363.7





1485.8





1518.0





1604.9





1677.0





1679.0





1756.1





1933.2





2263.4



Lw219 (±1 Da)
16
603.3





915.5





942.4





951.5





1020.5





1043.6





1148.6





1363.5





1485.6





1517.8





1604.8





1676.8





1755.9





1768.9





1932.9





2263.1







1Molecular weight, in kilodaltons, of polypeptide obtained from E. coli strain MS040324.



2m/z, mass (m) to charge (z) ratio. Each m/z value includes a range of plus or minus 300 ppm (the 88 kDa, 79 kDa, 60 kDa, 38 kDa, and 31 kDa polypeptides), plus or minus 350 ppm (the 46 kDa polypeptide), plus or minus 400 ppm (the 82 kDa, 54 kDa, 45 kDa, and 30 kDa polypeptides), or plus or minus 1 Dalton (the 37 kDa, 19 kDa and 16 kDa polypeptides).













TABLE 35







Experimental data from MALDI-TOF MS analysis of E. coli strain


MS040827.












Approximate
m/z value of




molecular
polypeptide




weight in
fragments




kilodaltons
resulting from



Polypeptide Designation
(kDa)1
trypsin digestion2















Lw189A (±300 ppm)
101
889.38





987.47





999.42





1009.40





1114.54





1277.56





1339.61





1402.67





1471.65





1520.80





1528.76





1699.95





1759.95





1771.84





1955.01





2146.22





2156.16





2239.30





2255.14





2912.67



Lw189B (±300 ppm)
101
905.46





1172.53





1277.56





1295.50





1308.56





1344.62





1404.72





1451.67





1547.72





1669.78





1718.76





1764.93





1823.94





1833.02





1860.08





2014.15





2089.24



Lw190 (±1 Da)
88
1178.44





1307.50





1517.55





1579.72





1634.75





1787.82





1797.76





1871.89





1981.92





2127.06





2174.98





2303.05





2707.40





2844.30





3082.43





3197.45



Lw191 (±1 Da)
85
565.45





686.41





737.43





861.47





862.47





1147.52





1208.53





1244.54





1279.54





1280.52





1330.57





1487.72





1579.76





1616.78





1651.80





1697.79





1718.84





2014.99





2036.95





2111.03





2222.12





2409.18





2582.31





2684.41





2947.43





3022.60





3145.50



Lw193 (±1 Da)
77
524.21





650.30





821.32





1124.35





1160.35





1279.56





1297.44





1325.41





1373.52





1381.40





1424.49





1510.59





1551.48





1554.63





1650.61





1703.67





1924.87





2013.84





2024.77





2204.93





2251.87





2553.03





2786.14





2848.01





3195.23





3337.27





3386.31



Lw194 (±1 Da)
67
679.56





1113.58





1136.53





1244.65





1260.59





1295.59





1299.46





1304.58





1350.56





1423.69





1522.66





1550.84





1756.84





1762.81





1887.91





1893.05





1932.95





2025.00





2159.25





2207.14





2256.18





2324.18



Lw195 (±150 ppm)
38
1058.57





1249.50





1439.66





1934.81





1960.97





2218.06





2390.13





2977.49





3357.61





3550.53



Lw196 (±1 Da)
35
645.43





818.41





834.41





872.52





915.47





1055.45





1083.47





1155.48





1214.51





1222.57





1249.47





1280.55





1370.65





1378.65





1409.55





1654.76





2062.93





2078.94





2232.10





2601.21





3494.61







1Molecular weight, in kilodaltons, of polypeptide obtained from E. coli strain MS040827.



2m/z, mass (m) to charge (z) ratio. Each m/z value includes a range of plus or minus 150 ppm (the 38 kDa and 35 kDa polypeptide), plus or minus 300 ppm (the 101 kDa polypeptides), or plus or minus 1 Dalton (the 88 kDa, 85 kDa, 77 kDa, and 67 kDa polypeptides).






EXAMPLE 26
Comparison of Proteins Similar to Those Expressed by E. Coli with Other Proteins
The proteins derived from E. coli and Salmonella grown under iron-limiting conditions were identified by MALDI-TOF MS. These analyses resulted in protein sequences that represent the best protein match for each peptide mass fingerprint (see Tables 10-17). The public availability of genomic sequence data allows for a database search for these proteins in other organisms. Thus, nine of the proteins (ChuA, Imp, TolC, R4, LamB, BtuB, lutA, FepA, and FecA) identified from the E. coli strains were used in BLAST searches to determine which other pathogens may also express these proteins. Eight of the ten selected proteins were very similar to proteins from Shigella spp., with 98 to 99% identity at the amino acid level (FIG. 11). Several of the E. coli proteins were also similar to proteins from Salmonella, Yersinia, Klebsiella, and Pseudomonas spp. These analyses suggest that compositions derived from E. coli grown under iron-limiting conditions may constitute antigens that will protect against other pathogens, particularly Shigella species.
The complete disclosure of all patents, patent applications, publications, and electronically available material (including, for instance, nucleotide sequence submissions in, e.g., GenBank and RefSeq, and amino acid sequence submissions in, e.g., SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq) cited herein are incorporated by reference. The foregoing detailed description and examples have been given for clarity of understanding only. No unnecessary limitations are to be understood therefrom. The invention is not limited to the exact details shown and described, for variations obvious to one skilled in the art will be included within the invention defined by the claims.
All headings are for the convenience of the reader and should not be used to limit the meaning of the text that follows the heading, unless so specified.

## Claims

1. A method for decreasing intestinal colonization of an animal intestinally colonized by, or at risk of being intestinally colonized by a Salmonella spp., the method comprising parenterally administering an effective amount of a composition to the animal, wherein the composition comprises:
a first isolated iron-regulated polypeptide from Salmonella enterica serovar Newport having a molecular weight of about 82 kDa as measured following electrophoresis on an SDS-polyacrylamide gel, wherein the first isolated iron-regulated polypeptide, if digested with trypsin, produces polypeptide fragments having masses of 628.39 Da±300 parts per million (ppm), 643.37 Da±300 ppm, 771.42 Da±300 ppm, 830.45 Da±300 ppm, 872.46 Da±300 ppm, 990.55 Da±300 ppm, 1082.61 Da±300 ppm, 1207.58 Da±300 ppm, 1324.75 Da±300 ppm, 1377.66 Da±300 ppm, 1463.74 Da±300 ppm, 1499.71 Da±300 ppm, 1633.84 Da±300 ppm, 1618.77 Da±300 ppm, 1727.83 Da±300 ppm, 1871.88 Da±300 ppm, 1980.96 Da±300 ppm, 1997.06 Da±300 ppm, 2192.94 Da±300 ppm, and 2331.05 Da±300 ppm;
a second isolated iron-regulated polypeptide from Salmonella enterica serovar Newport having a molecular weight of about 80 kDa as measured following electrophoresis on an SDS-polyacrylamide gel, wherein the second isolated iron-regulated polypeptide, if digested with trypsin, produces polypeptide fragments having masses of 848.45 Da±300 ppm, 918.45 Da±300 ppm, 1040.60 Da±300 ppm, 1097.62 Da±300 ppm, 1309.63 Da±300 ppm, 1335.71 Da±300 ppm, 1341.66 Da±300 ppm, 1364.60 Da±300 ppm, 1528.70 Da±300 ppm, 1564.76 Da±300 ppm, 1735.86 Da±300 ppm, 1750.86 Da±300 ppm, 1754.83 Da±300 ppm, 1845.91 Da±300 ppm, 1911.98 Da±300 ppm, 1929.04 Da±300 ppm, 1935.01 Da±300 ppm, 2030.93 Da±300 ppm, 2416.14 Da±300 ppm, 2587.35 Da±300 ppm, 2701.36 Da±300 ppm, 2909.36 Da±300 ppm, and 2943.50 Da±300 ppm;
a third isolated iron-regulated polypeptide from Salmonella enterica serovar Newport having a molecular weight of about 74 kDa as measured following electrophoresis on an SDS-polyacrylamide gel, wherein the third isolated iron-regulated polypeptide, if digested with trypsin, produces polypeptide fragments having masses of 605.33 Da±300 ppm, 616.37 Da±300 ppm, 808.41 Da±300 ppm, 1063.48 Da±300 ppm, 1158.55 Da±300 ppm, 1210.55 Da±300 ppm, 1314.62 Da±300 ppm, 1329.77 Da±300 ppm, 1345.55 Da±300 ppm, 1526.73 Da±300 ppm, 1649.90 Da±300 ppm, 1677.74 Da±300 ppm, 1740.90 Da±300 ppm, 1744.69 Da±300 ppm, 1750.84 Da±300 ppm, 1792.88 Da±300 ppm, 1814.85 Da±300 ppm, 1906.92 Da±300 ppm, 1934.88 Da±300 ppm, 1952.94 Da±300 ppm, 1987.04 Da±300 ppm, 2242.03 Da±300 ppm, 2538.26 Da±300 ppm, 2587.24 Da±300 ppm, and 2710.17 Da±300 ppm; and
a fourth isolated iron-regulated polypeptide from Salmonella enterica serovar Newport having a molecular weight of about 65 kDa as measured following electrophoresis on an SDS-polyacrylamide gel, wherein the fourth isolated iron-regulated polypeptide, if digested with trypsin, produces polypeptide fragments having masses of 1303.65 Da±300 ppm, 1398.57 Da±300 ppm, 1508.73 Da±300 ppm, 1792.85 Da±300 ppm, 1868.85 Da±300 ppm, 1932.87 Da±300 ppm, 2023.92 Da±300 ppm, 2086.08 Da±300 ppm, and 2257.21 Da±300 ppm.

2. The method of claim 1 wherein the animal is avian, bovine, caprine, ovine, porcine, bisontine, cervine, equine, a companion animal, or human.

3. The method of claim 2 wherein the avian animal is a chicken or turkey.

4. The method of claim 1 further comprising one or more additional administrations of the composition to the animal.

5. The method of claim 1 wherein the parenteral administration comprises subcutaneous administration.

6. A method of decreasing mortality due to infection by a Salmonella spp. in an animal, the method comprising parenterally administering an effective amount of a composition to the animal, wherein the composition comprises:
a first isolated iron-regulated polypeptide from Salmonella enterica serovar Newport having a molecular weight of about 82 kDa as measured following electrophoresis on an SDS-polyacrylamide gel, wherein the first isolated iron-regulated polypeptide, if digested with trypsin, produces polypeptide fragments having masses of 628.39 Da±300 parts per million (ppm), 643.37 Da±300 ppm, 771.42 Da±300 ppm, 830.45 Da±300 ppm, 872.46 Da±300 ppm, 990.55 Da±300 ppm, 1082.61 Da±300 ppm, 1207.58 Da±300 ppm, 1324.75 Da±300 ppm, 1377.66 Da±300 ppm, 1463.74 Da±300 ppm, 1499.71 Da±300 ppm, 1633.84 Da±300 ppm, 1618.77 Da±300 ppm, 1727.83 Da±300 ppm, 1871.88 Da±300 ppm, 1980.96 Da±300 ppm, 1997.06 Da±300 ppm, 2192.94 Da±300 ppm, and 2331.05 Da±300 ppm;
a second isolated iron-regulated polypeptide from Salmonella enterica serovar Newport having a molecular weight of about 80 kDa as measured following electrophoresis on an SDS-polyacrylamide gel, wherein the second isolated iron-regulated polypeptide, if digested with trypsin, produces polypeptide fragments having masses of 848.45 Da±300 ppm, 918.45 Da±300 ppm, 1040.60 Da±300 ppm, 1097.62 Da±300 ppm, 1309.63 Da±300 ppm, 1335.71 Da±300 ppm, 1341.66 Da±300 ppm, 1364.60 Da±300 ppm, 1528.70 Da±300 ppm, 1564.76 Da±300 ppm, 1735.86 Da±300 ppm, 1750.86 Da±300 ppm, 1754.83 Da±300 ppm, 1845.91 Da±300 ppm, 1911.98 Da±300 ppm, 1929.04 Da±300 ppm, 1935.01 Da±300 ppm, 2030.93 Da±300 ppm, 2416.14 Da±300 ppm, 2587.35 Da±300 ppm, 2701.36 Da±300 ppm, 2909.36 Da±300 ppm, and 2943.50 Da±300 ppm;
a third isolated iron-regulated polypeptide from Salmonella enterica serovar Newport having a molecular weight of about 74 kDa as measured following electrophoresis on an SDS-polyacrylamide gel, wherein the third isolated iron-regulated polypeptide, if digested with trypsin, produces polypeptide fragments having masses of 605.33 Da±300 ppm, 616.37 Da±300 ppm, 808.41 Da±300 ppm, 1063.48 Da±300 ppm, 1158.55 Da±300 ppm, 1210.55 Da±300 ppm, 1314.62 Da±300 ppm, 1329.77 Da±300 ppm, 1345.55 Da±300 ppm, 1526.73 Da±300 ppm, 1649.90 Da±300 ppm, 1677.74 Da±300 ppm, 1740.90 Da±300 ppm, 1744.69 Da±300 ppm, 1750.84 Da±300 ppm, 1792.88 Da±300 ppm, 1814.85 Da±300 ppm, 1906.92 Da±300 ppm, 1934.88 Da±300 ppm, 1952.94 Da±300 ppm, 1987.04 Da±300 ppm, 2242.03 Da±300 ppm, 2538.26 Da±300 ppm, 2587.24 Da±300 ppm, and 2710.17 Da±300 ppm; and
a fourth isolated iron-regulated polypeptide from Salmonella enterica serovar Newport having a molecular weight of about 65 kDa as measured following electrophoresis on an SDS-polyacrylamide gel, wherein the fourth isolated iron-regulated polypeptide, if digested with trypsin, produces polypeptide fragments having masses of 1303.65 Da±300 ppm, 1398.57 Da±300 ppm, 1508.73 Da±300 ppm, 1792.85 Da±300 ppm, 1868.85 Da±300 ppm, 1932.87 Da±300 ppm, 2023.92 Da±300 ppm, 2086.08 Da±300 ppm, and 2257.21 Da±300 ppm.

7. The method of claim 6 wherein the animal is avian, bovine, caprine, ovine, porcine, bisontine, cervine, equine, a companion animal, or human.

8. The method of claim 7 wherein the avian animal is a chicken or turkey.

9. The method of claim 6 further comprising one or more additional administrations of the composition to the animal.

10. The method of claim 6 wherein the parenteral administration comprises subcutaneous administration.