bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic Analyses of aListeria monocytogenesMutant Lacking σBIdentify New Components of the σBRegulon and Highlight a Role for σBin the Utilization of Glycerol
Authors: Abram F. , Su Wan-Lin , Wiedmann M. , Boor K. J. , Coote P. , Botting C. , Karatzas K. A. G. , O'Byrne C. P. 
Published: December 2007

ABSTRACTInListeria monocytogenesthe alternative sigma factor σBplays important roles in both virulence and stress tolerance. In this study a proteomic approach was used to define components of the σBregulon inL. monocytogenes10403S (serotype 1/2a). Using two-dimensional gel electrophoresis and the recently developed isobaric tags for relative and absolute quantitation technique, the protein expression profiles of the wild type and an isogenic ΔsigBdeletion strain were compared. Overall, this study identified 38 proteins whose expression was σBdependent; 17 of these proteins were found to require the presence of σBfor full expression, while 21 were expressed at a higher level in the ΔsigBmutant background. The data obtained with the two proteomic approaches showed limited overlap (four proteins were identified by both methods), a finding that highlights the complementarity of the two technologies. Overall, the proteomic data reaffirmed a role for σBin the general stress response and highlighted a probable role for σBin metabolism, especially in the utilization of alternative carbon sources. Proteomic and physiological data revealed the involvement of σBin glycerol metabolism. Five newly identified members of the σBregulon were shown to be under direct regulation of σBusing reverse transcription-PCR (RT-PCR), while random amplification of cDNA ends-PCR was used to map four σB-dependent promoters upstream from lmo0796, lmo1830, lmo2391, and lmo2695. Using RT-PCR analysis of known and newly identified σB-dependent genes, as well as proteomic analyses, σBwas shown to play a major role in the stationary phase of growth in complex media.
Evaluation of Murine Norovirus, Feline Calicivirus, Poliovirus, and MS2 as Surrogates for Human Norovirus in a Model of Viral Persistence in Surface Water and Groundwater
Authors: Bae Jinhee , Schwab Kellogg J. 
Published: December 2007

ABSTRACT

Human noroviruses (NoVs) are a significant cause of nonbacterial gastroenteritis worldwide, with contaminated drinking water a potential transmission route. The absence of a cell culture infectivity model for NoV necessitates the use of molecular methods and/or viral surrogate models amenable to cell culture to predict NoV inactivation. The NoV surrogates murine NoV (MNV), feline calicivirus (FCV), poliovirus (PV), and male-specific coliphage MS2, in conjunction with Norwalk virus (NV), were spiked into surface water samples (
n
= 9) and groundwater samples (
n
= 6). Viral persistence was monitored at 25°C and 4°C by periodically analyzing virus infectivity (for all surrogate viruses) and nucleic acid (NA) for all tested viruses. FCV infectivity reduction rates were significantly higher than those of the other surrogate viruses. Infectivity reduction rates were significantly higher than NA reduction rates at 25°C (0.18 and 0.09 log
10
/day for FCV, 0.13 and 0.10 log
10
/day for PV, 0.12 and 0.06 log
10
/day for MS2, and 0.09 and 0.05 log
10
/day for MNV) but not significant at 4°C. According to a multiple linear regression model, the NV NA reduction rates (0.04 ± 0.01 log
10
/day) were not significantly different from the NA reduction rates of MS2 (0.05 ± 0.03 log
10
/day) and MNV (0.04 ± 0.03 log
10
/day) and were significantly different from those of FCV (0.08 ± 0.03 log
10
/day) and PV (0.09 ± 0.03 log
10
/day) at 25°C. In conclusion, MNV shows great promise as a human NoV surrogate due to its genetic similarity and environmental stability. FCV was much less stable and thus questionable as an adequate surrogate for human NoVs in surface water and groundwater.
Characterization of
htrB
and
msbB
Mutants of the Light Organ Symbiont
Vibrio fischeri
Authors: Adin Dawn M. , Phillips Nancy J. , Gibson Bradford W. , Apicella Michael A. , Ruby Edward G. , McFall-Ngai Margaret J. , Hall Daniel B. , Stabb Eric V. 
Published: December 2007

ABSTRACT

Bacterial lipid A is an important mediator of bacterium-host interactions, and secondary acylations added by HtrB and MsbB can be critical for colonization and virulence in pathogenic infections. In contrast,
Vibrio fischeri
lipid A stimulates normal developmental processes in this bacterium's mutualistic host,
Euprymna scolopes
, although the importance of lipid A structure in this symbiosis is unknown. To further examine
V. fischeri
lipid A and its symbiotic function, we identified two paralogs of
htrB
(designated
htrB1
and
htrB2
) and an
msbB
gene in
V. fischeri
ES114 and demonstrated that these genes encode lipid A secondary acyltransferases.
htrB2
and
msbB
are found on the
Vibrio
“housekeeping” chromosome 1 and are conserved in other
Vibrio
species. Mutations in
htrB2
and
msbB
did not impair symbiotic colonization but resulted in phenotypic alterations in culture, including reduced motility and increased luminescence. These mutations also affected sensitivity to sodium dodecyl sulfate, kanamycin, and polymyxin, consistent with changes in membrane permeability. Conversely,
htrB1
is located on the smaller, more variable vibrio chromosome 2, and an
htrB1
mutant was wild-type-like in culture but appeared attenuated in initiating the symbiosis and was outcompeted 2.7-fold during colonization when mixed with the parent. These data suggest that
htrB2
and
msbB
play conserved general roles in vibrio biology, whereas
htrB1
plays a more symbiosis-specific role in
V. fischeri
.
Plasmids of the pRM/pRF Family Occur in DiverseRickettsiaSpecies
Authors: Baldridge Gerald D. , Burkhardt Nicole Y. , Felsheim Roderick F. , Kurtti Timothy J. , Munderloh Ulrike G. 
Published: December 2007

ABSTRACTThe recent discoveries of the pRF and pRM plasmids ofRickettsia felisandR. monacensishave contravened the long-held dogma that plasmids are not present in the bacterial genusRickettsia(Rickettsiales;Rickettsiaceae). We report the existence of plasmids inR. helvetica, R. peacockii, R. amblyommii, andR. massiliaeisolates from ixodid ticks and in anR. hoogstraaliiisolate from an argasid tick.R. peacockiiand four isolates ofR. amblyommiifrom widely separated geographic locations contained plasmids that comigrated with pRM during pulsed-field gel electrophoresis and larger plasmids with mobilities similar to that of pRF. TheR. peacockiiplasmids were lost during long-term serial passage in cultured cells.R. montanensisdid not contain a plasmid. Southern blots showed that sequences similar to those of a DnaA-like replication initiator protein, a small heat shock protein 2, and the Sca12 cell surface antigen genes on pRM and pRF were present on all of the plasmids except for that ofR. massiliae, which lacked the heat shock gene and was the smallest of the plasmids. TheR. hoogstraaliiplasmid was most similar to pRM and contained apparent homologs of proline/betaine transporter and SpoT stringent response genes on pRM and pRF that were absent from the other plasmids. TheR. hoogstraalii, R. helvetica, andR. amblyommiiplasmids contained homologs of a pRM-carried gene similar to aNitrobactersp. helicase RecD/TraA gene, but none of the plasmids hybridized with a probe derived from a pRM-encoded gene similar to aBurkholderiasp. transposon resolvase gene.
PneumocystisEncodes a FunctionalS-Adenosylmethionine Synthetase Gene
Authors: Kutty Geetha , Hernandez-Novoa Beatriz , Czapiga Meggan , Kovacs Joseph A. 
Published: December 2007

ABSTRACTS-Adenosylmethionine (AdoMet) synthetase (EC 2.5.1.6) is the enzyme that catalyzes the synthesis of AdoMet, a molecule important for all cellular organisms. We have cloned and characterized an AdoMet synthetase gene (sam1) fromPneumocystisspp. This gene was transcribed primarily as an ∼1.3-kb mRNA which encodes a protein containing 381 amino acids inP. cariniiorP. murinaand 382 amino acids inP. jirovecii. sam1was also transcribed as part of an apparent polycistronic transcript of ∼5.6 kb, together with a putative chromatin remodeling protein homologous toSaccharomyces cerevisiae, CHD1. Recombinant Sam1, when expressed inEscherichia coli, showed functional enzyme activity. Immunoprecipitation and confocal immunofluorescence analysis using an antipeptide antibody showed that this enzyme is expressed inP. murina. Thus,Pneumocystis, like other organisms, can synthesize its own AdoMet and may not depend on its host for the supply of this important molecule.
Aspergillus
Mycoviruses Are Targets and Suppressors of RNA Silencing
Authors: Hammond T. M. , Andrewski M. D. , Roossinck M. J. , Keller N. P. 
Published: December 2007

ABSTRACT

RNA silencing can function as a virus defense mechanism in a diverse range of eukaryotes, and many viruses are capable of suppressing the silencing machinery targeting them. However, the extent to which this occurs between fungal RNA silencing and mycoviruses is unclear. Here, three
Aspergillus
dsRNA mycoviruses were partially characterized, and their relationship to RNA silencing was investigated.
Aspergillus
virus 1816 is related to
Agaricus bisporus
white button mushroom virus 1 and suppresses RNA silencing through a mechanism that alters the level of small interfering RNA.
Aspergillus
virus 178 is related to RNA virus L1 of
Gremmeniella abietina
and does not appear to affect RNA silencing. The third virus investigated,
Aspergillus
virus 341, is distantly related to
Sphaeropsis sapinea
RNA virus 2. Detection of mycovirus-derived siRNA from this mycovirus demonstrates that it is targeted for degradation by the
Aspergillu
s RNA silencing machinery. Thus, our results indicate that
Aspergillus
mycoviruses are both targets and suppressors of RNA silencing. In addition, they suggest that the morphological and physiological changes associated with some mycoviruses could be a result of their antagonistic relationship with RNA silencing.
Global Transcriptional Profile of
Mycobacterium tuberculosis
during THP-1 Human Macrophage Infection
Authors: Fontán Patricia , Aris Virginie , Ghanny Saleena , Soteropoulos Patricia , Smith Issar 
Published: December 2007

ABSTRACT

During lung infection,
Mycobacterium tuberculosis
resides in macrophages and subverts the bactericidal mechanisms of these professional phagocytes. Comprehension of this host-pathogen relationship is fundamental for the development of new therapies to cure and prevent tuberculosis. In this work, we analyzed the transcriptional profile of
M. tuberculosis
infecting human macrophage-like THP-1 cells in order to identify putative bacterial pathogenic factors that can be relevant for the intracellular survival of
M. tuberculosis.
We compared the gene expression profile of
M. tuberculosis
H37Rv after 4 h and 24 h of infection of human macrophage-like THP-1 cells with the gene expression profile of the strain growing exponentially in broth cultures. We found 585 genes expressed differentially by intracellular
M. tuberculosis
. An analysis of the gene expression profile of
M. tuberculosis
inside THP-1 cells suggests the perturbation of the cell envelope as a major intracellular stress inside THP-1 macrophages.
NF-κB Activation during AcuteHelicobacter pyloriInfection in Mice
Authors: Ferrero Richard L. , Avé Patrick , Ndiaye Delphine , Bambou Jean-Christophe , Huerre Michel R. , Philpott Dana J. , Mémet Sylvie 
Published: December 2007

ABSTRACTNuclear factor κB (NF-κB) plays a key regulatory role in host cell responses toHelicobacter pyloriinfection in humans. Although mice are routinely used as a model to studyH. pyloripathogenesis, the role of NF-κB in murine cell responses to helicobacters has not been studied in detail. We thus investigated the abilities of differentHelicobacterisolates to induce NF-κB-dependent responses in murine gastric epithelial cells (GECs) and in transgenic mice harboring an NF-κB-responsivelacZreporter gene.H. pyloriandHelicobacter felisstrains up-regulated the synthesis in mouse GECs of the NF-κB-dependent chemokines KC (CXCL1) and MIP-2 (CXCL2). These responses werecagpathogenicity island (cagPAI) independent and could be abolished by pretreatment with a pharmacological inhibitor of NF-κB. Consistent with the in vitro data, experimentalHelicobacterinfection of transgenic mice resulted in increased numbers of GECs with nuclear β-galactosidase activity, which is indicative of specific NF-κB activation. The numbers of β-galactosidase-positive cells in mice were significantly increased at day 1 postinoculation with wild-typeH. pyloristrains harboring or not harboring a functionalcagPAI, compared to naive animals (P= 0.007 andP= 0.04, respectively). Strikingly, however, no differences were observed in the levels of gastric NF-κB activation at day 1 postinoculation withH. felisor at day 30 or 135 postinoculation withH. pylori. This work demonstrates for the first time the induction of NF-κB activation within gastric mucosal cells during acuteH. pyloriinfection. Furthermore, the data suggest that helicobacters may be able to regulate NF-κB signaling during chronic infection.
Novel Class of Mutations of
pilS
Mutants, Encoding Plasmid R64 Type IV Prepilin: Interface of PilS-PilV Interactions
Authors: Shimoda Eriko , Muto Tatsuya , Horiuchi Takayuki , Furuya Nobuhisa , Komano Teruya 
Published: December 2007

ABSTRACT

The type IV pili of plasmid R64 belonging to the type IVB group are required only for liquid mating. They consist of the major and minor components PilS pilin and PilV adhesin, respectively. PilS pilin is first synthesized as a 22-kDa prepilin from the
pilS
gene and is then processed to a 19-kDa mature pilin by PilU prepilin peptidase. In a previous genetic analysis, we identified four classes of the
pilS
mutants (T. Horiuchi and T. Komano, J. Bacteriol.
180:
4613-4620, 1998). The products of the class I
pilS
mutants were not processed by prepilin peptidase; the products of the class II mutants were not secreted; in the class III mutants type IV pili with reduced activities in liquid mating were produced; and in the class IV mutants type IV pili with normal activities were produced. Here, we describe a novel class, class V, of
pilS
mutants. Mutations in the
pilS
gene at Gly-56 or Tyr-57 produced type IV pili lacking PilV adhesin, which were inactive in liquid mating. Residues 56 and 57 of PilS pilin are suggested to function as an interface of PilS-PilV interactions.
Analysis of Genetic Relatedness of
Haemophilus influenzae
Isolates by Multilocus Sequence Typing
Authors: Erwin Alice L. , Sandstedt Sara A. , Bonthuis Paul J. , Geelhood Jennifer L. , Nelson Kevin L. , Unrath William C. T. , Diggle Mathew A. , Theodore Mary J. , Pleatman Cynthia R. , Mothershed Elizabeth A. , Sacchi Claudio T. , Mayer Leonard W. , Gilsdorf Janet R. , Smith Arnold L. 
Published: December 2007

ABSTRACT

The gram-negative bacterium
Haemophilus influenzae
is a human-restricted commensal of the nasopharynx that can also be associated with disease. The majority of
H. influenzae
respiratory isolates lack the genes for capsule production and are nontypeable (NTHI). Whereas encapsulated strains are known to belong to serotype-specific phylogenetic groups, the structure of the NTHI population has not been previously described. A total of 656
H. influenzae
strains, including 322 NTHI strains, have been typed by multilocus sequence typing and found to have 359 sequence types (ST). We performed maximum-parsimony analysis of the 359 sequences and calculated the majority-rule consensus of 4,545 resulting equally most parsimonious trees. Eleven clades were identified, consisting of six or more ST on a branch that was present in 100% of trees. Two additional clades were defined by branches present in 91% and 82% of trees, respectively. Of these 13 clades, 8 consisted predominantly of NTHI strains, three were serotype specific, and 2 contained distinct NTHI-specific and serotype-specific clusters of strains. Sixty percent of NTHI strains have ST within one of the 13 clades, and eBURST analysis identified an additional phylogenetic group that contained 20% of NTHI strains. There was concordant clustering of certain metabolic reactions and putative virulence loci but not of disease source or geographic origin. We conclude that well-defined phylogenetic groups of NTHI strains exist and that these groups differ in genetic content. These observations will provide a framework for further study of the effect of genetic diversity on the interaction of NTHI with the host.
Chemotaxis of
Escherichia coli
to Pyrimidines: a New Role for the Signal Transducer Tap
Authors: Liu Xianxian , Parales Rebecca E. 
Published: December 2007

ABSTRACT

Escherichia coli
exhibits chemotactic responses to sugars, amino acids, and dipeptides, and the responses are mediated by methyl-accepting chemotaxis proteins (MCPs). Using capillary assays, we demonstrated that
Escherichia coli
RP437 is attracted to the pyrimidines thymine and uracil and the response was constitutively expressed under all tested growth conditions. All MCP mutants lacking the MCP Tap protein showed no response to pyrimidines, suggesting that Tap, which is known to mediate dipeptide chemotaxis, is required for pyrimidine chemotaxis. In order to confirm the role of Tap in pyrimidine chemotaxis, we constructed chimeric chemoreceptors (Tapsr and Tsrap), in which the periplasmic and cytoplasmic domains of Tap and Tsr were switched. When Tapsr and Tsrap were individually expressed in an
E. coli
strain lacking all four native MCPs, Tapsr mediated chemotaxis toward pyrimidines and dipeptides, but Tsrap did not complement the chemotaxis defect. The addition of the C-terminal 19 amino acids from Tsr to the C terminus of Tsrap resulted in a functional chemoreceptor that mediated chemotaxis to serine but not pyrimidines or dipeptides. These results indicate that the periplasmic domain of Tap is responsible for detecting pyrimidines and the Tsr signaling domain confers on Tapsr the ability to mediate efficient chemotaxis. A mutant lacking dipeptide binding protein (DBP) was wild type for pyrimidine taxis, indicating that DBP, which is the primary chemoreceptor for dipeptides, is not responsible for detecting pyrimidines. It is not yet known whether Tap detects pyrimidines directly or via an additional chemoreceptor protein.
Additional In Vitro and In Vivo Evidence for SecA Functioning as Dimers in the Membrane: Dissociation into Monomers Is Not Essential for Protein Translocation in
Escherichia coli
Authors: Wang Hongyun , Na Bing , Yang Hsiuchin , Tai Phang C. 
Published: December 2007

ABSTRACT

SecA is an essential component in the Sec-dependent protein translocation pathway and, together with ATP, provides the driving force for the transport of secretory proteins across the cytoplasmic membrane of
Escherichia coli
. Previous studies established that SecA undergoes monomer-dimer equilibrium in solution. However, the oligomeric state of functional SecA during the protein translocation process is controversial. In this study, we provide additional evidence that SecA functions as a dimer in the membrane by (i) demonstration of the capability of the presumably monomeric SecA derivative to be cross-linked as dimers in vitro and in vivo, (ii) complementation of the growth of a
secA
(Ts) mutant with another nonfunctional SecA or (iii) in vivo complementation and in vitro function of a genetically tandem SecA dimer that does not dissociate into monomers, and (iv) formation of similar ring-like structures by the tandem SecA dimer and SecA in the presence of lipid bilayers. We conclude that SecA functions as a dimer in the membrane and dissociation into monomers is not necessary during protein translocation.
Lipopolysaccharide O-Antigen Chain Length Regulation in
Pseudomonas aeruginosa
Serogroup O11 Strain PA103
Authors: Kintz Erica , Scarff Jennifer M. , DiGiandomenico Antonio , Goldberg Joanna B. 
Published: December 2007

ABSTRACT

The Wzz proteins are important for determining the length of the O-antigen side chain attached to lipopolysaccharide (LPS). Several bacteria, including
Pseudomonas aeruginosa
strain PAO1 (serogroup O5), produce two such proteins responsible for the preference of two different chain lengths on the surface. Our group has previously identified one
wzz
gene (
wzz1
) within the O-antigen locus of
P. aeruginosa
strain PA103 (serogroup O11). In this study we have identified the second
wzz
gene (
wzz2
), located in the same region of the genome and with 92% similarity to PAO1's
wzz2
gene. Mutations were generated in both
wzz
genes by interruption with antibiotic resistance cassettes, and the effects of these mutations were characterized. Wild-type PA103 prefers two O-antigen chain lengths, referred to as long and very long. The expression of the long O-antigen chain length was reduced in the
wzz1
mutant, indicating the Wzz1 protein is important for this chain length preference. The
wzz2
mutant, on the other hand, was missing O-antigens of the very long chain length, indicating the Wzz2 protein is responsible for the production of very long O-antigen. The effects of the
wzz
mutations on virulence were also investigated. In both serum sensitivity assays and a mouse pneumonia model of infection, the
wzz1
mutants exhibited greater defects in virulence compared to either wild-type PA103 or the
wzz2
mutant, indicating the long chain length plays a greater role during these infectious processes.
TheCampylobacter jejuniNADH:Ubiquinone Oxidoreductase (Complex I) Utilizes Flavodoxin Rather than NADH
Authors: Weerakoon Dilan R. , Olson Jonathan W. 
Published: December 2007

ABSTRACTCampylobacter jejuniencodes 12 of the 14 subunits that make up the respiratory enzyme NADH:ubiquinone oxidoreductase (also called complex I). The twonuogenes not present inC. jejuniencode the NADH dehydrogenase, and in their place in the operon are the novel genes designated Cj1575c and Cj1574c. A series of mutants was generated in which each of the 12nuogenes (homologues to known complex I subunits) was disrupted or deleted. Each of thenuomutants will not grow in amino acid-based medium unless supplemented with an alternative respiratory substrate such as formate. Unlike thenuogenes, Cj1574c is an essential gene and could not be disrupted unless an intact copy of the gene was provided at an unrelated site on the chromosome. Anuodeletion mutant can efficiently respire formate but is deficient in α-ketoglutarate respiratory activity compared to the wild type. InC. jejuni, α-ketoglutarate respiration is mediated by the enzyme 2-oxoglutarate:acceptor oxidoreductase; mutagenesis of this enzyme abolishes α-ketoglutarate-dependent O2uptake and fails to reduce the electron transport chain. The electron acceptor for 2-oxoglutarate:acceptor oxidoreductase was determined to be flavodoxin, which was also determined to be an essential protein inC. jejuni. A model is presented in which CJ1574 mediates electron flow into the respiratory transport chain from reduced flavodoxin and through complex I.