bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-Function Analysis of Immunity Proteins of Pediocin-Like Bacteriocins: C-Terminal Parts of Immunity Proteins Are Involved in Specific Recognition of Cognate Bacteriocins
Authors: Johnsen Line , Fimland Gunnar , Mantzilas Dimitris , Nissen-Meyer Jon 
Published: May 2004

ABSTRACT

The immunity proteins of pediocin-like bacteriocins show a high degree of specificity with respect to the pediocin-like bacteriocin they recognize and confer immunity to. The aim of this study was to identify regions of the immunity proteins that are involved in this specific recognition. Six different hybrid immunity proteins were constructed from three different pediocin-like bacteriocin immunity proteins that have similar sequences but confer resistance to different bacteriocins. These hybrid immunity proteins were then tested for their ability to confer immunity to various pediocin-like bacteriocins. The specificities of the hybrid immunity proteins proved to be similar to those of the immunity proteins from which the C-terminal halves were derived, thus revealing that the C-terminal half of immunity proteins for pediocin-like bacteriocins contains a domain that is involved in specific recognition of the bacteriocins they confer immunity to. Moreover, the results also revealed that the effectiveness of an immunity protein is strain dependent and that its functionality thus depends in part on interplay with strain-dependent factors. To further investigate the structure-function relationship of these immunity proteins, the enterocin A and leucocin A immunity proteins (EntA-im and LeuA-im) were purified to homogeneity and structurally analyzed under various conditions by Circular dichroism (CD) spectroscopy. The results revealed that both immunity proteins are α-helical and well structured in an aqueous environment, the denaturing temperature being 78.5°C for EntA-im and 58.0°C for LeuA-im. The CD spectra also revealed that there was no further increase in the structuring or α-helical content when the immunity proteins were exposed to dodecylphosphocholine micelles or dioleoyl-
l
-α-phosphatidyl-
dl
-glycerol (DOPG) liposomes, indicating that the immunity proteins, in contrast to the bacteriocins, do not interact extensively with membranes. They may nevertheless be loosely associated with the membrane, possibly as peripheral membrane proteins, thus enabling them to interact with their cognate bacteriocin.
Regulation of Fumonisin Biosynthesis inFusarium verticillioidesby a Zinc Binuclear Cluster-Type Gene,ZFR1
Authors: Flaherty Joseph E. , Woloshuk Charles P. 
Published: May 2004

ABSTRACTFusarium verticillioides, a pathogen of maize, produces a class of mycotoxins called fumonisins in infected kernels. In this study, a candidate regulatory gene,ZFR1, was identified in an expressed sequence tag library enriched for transcripts expressed byF. verticillioidesduring fumonisin B1(FB1) biosynthesis.ZFR1deletion mutants exhibited normal growth and development on maize kernels, but fumonisin production was reduced to less than 10% of that of the wild-type strain.ZFR1encodes a putative protein of 705 amino acids with sequence similarity to the Zn(II)2Cys6 binuclear cluster family that are regulators of both primary and secondary metabolism in fungi. Expression ofZFR1in colonized germ and degermed kernel tissues correlated with FB1levels. Overexpression ofZFR1inzfr1mutants restored FB1production to wild-type levels; however, FB1was not restored in anfcc1(FusariumC-type cyclin) mutant by overexpression ofZFR1. The results of this study indicate thatZFR1is a positive regulator of FB1biosynthesis inF. verticillioidesand suggest thatFCC1is required forZFR1function.
Heat Shock Protein-Mediated Resistance to High Hydrostatic Pressure in
Escherichia coli
Authors: Aertsen Abram , Vanoirbeek Kristof , De Spiegeleer Philipp , Sermon Jan , Hauben Kristel , Farewell Anne , Nyström Thomas , Michiels Chris W. 
Published: May 2004

ABSTRACT

A random library of
Escherichia coli
MG1655 genomic fragments fused to a promoterless green fluorescent protein (GFP) gene was constructed and screened by differential fluorescence induction for promoters that are induced after exposure to a sublethal high hydrostatic pressure stress. This screening yielded three promoters of genes belonging to the heat shock regulon (
dnaK
,
lon
,
clpPX
), suggesting a role for heat shock proteins in protection against, and/or repair of, damage caused by high pressure. Several further observations provide additional support for this hypothesis: (i) the expression of
rpoH
, encoding the heat shock-specific sigma factor σ
32
, was also induced by high pressure; (ii) heat shock rendered
E. coli
significantly more resistant to subsequent high-pressure inactivation, and this heat shock-induced pressure resistance followed the same time course as the induction of heat shock genes; (iii) basal expression levels of GFP from heat shock promoters, and expression of several heat shock proteins as determined by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins extracted from pulse-labeled cells, was increased in three previously isolated pressure-resistant mutants of
E. coli
compared to wild-type levels.
Bacterial Communities Associated with Flowering Plants of the Ni Hyperaccumulator
Thlaspi goesingense
Authors: Idris Rughia , Trifonova Radoslava , Puschenreiter Markus , Wenzel Walter W. , Sessitsch Angela 
Published: May 2004

ABSTRACT

Thlaspi goesingense
is able to hyperaccumulate extremely high concentrations of Ni when grown in ultramafic soils. Recently it has been shown that rhizosphere bacteria may increase the heavy metal concentrations in hyperaccumulator plants significantly, whereas the role of endophytes has not been investigated yet. In this study the rhizosphere and shoot-associated (endophytic) bacteria colonizing
T. goesingense
were characterized in detail by using both cultivation and cultivation-independent techniques. Bacteria were identified by 16S rRNA sequence analysis, and isolates were further characterized regarding characteristics that may be relevant for a beneficial plant-microbe interaction—Ni tolerance, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and siderophore production. In the rhizosphere a high percentage of bacteria belonging to the
Holophaga/Acidobacterium
division and
α-Proteobacteria
were found. In addition, high-G+C gram-positive bacteria,
Verrucomicrobia
, and microbes of the
Cytophaga/Flexibacter/Bacteroides
division colonized the rhizosphere. The community structure of shoot-associated bacteria was highly different. The majority of clones affiliated with the
Proteobacteria
, but also bacteria belonging to the
Cytophaga/Flexibacter/Bacteroides
division, the
Holophaga/Acidobacterium
division, and the low-G+C gram-positive bacteria, were frequently found. A high number of highly related
Sphingomonas
16S rRNA gene sequences were detected, which were also obtained by the cultivation of endophytes. Rhizosphere isolates belonged mainly to the genera
Methylobacterium, Rhodococcus
, and
Okibacterium
, whereas the majority of endophytes showed high levels of similarity to
Methylobacterium mesophilicum
. Additionally,
Sphingomonas
spp. were abundant. Isolates were resistant to Ni concentrations between 5 and 12 mM; however, endophytes generally tolerated higher Ni levels than rhizosphere bacteria. Almost all bacteria were able to produce siderophores. Various strains, particularly endophytes, were able to grow on ACC as the sole nitrogen source.
Detection of Enteric Viruses in Shellfish from the Norwegian Coast
Authors: Myrmel M. , Berg E. M. M. , Rimstad E. , Grinde B. 
Published: May 2004

ABSTRACT

Common blue mussels (
Mytilus edulis
), horse mussels (
Modiolus modiolus
), and flat oysters (
Ostrea edulis
) obtained from various harvesting and commercial production sites along the Norwegian coast were screened for the presence of norovirus by a real-time reverse transcription (RT)-nested PCR assay and for possible indicators of fecal contamination, i.e., for F-specific RNA bacteriophages (F-RNA phages) by plaque assay and for human adenoviruses and human circoviruses by nested PCR assay. The aims were to obtain relevant information for assessing the risk of transmission of enteric viruses by shellfish and to investigate the potential of various indicator viruses in routine screening. Noroviruses were detected in 6.8% of the samples, and the indicators were detected in 23.8% (F-RNA phages), 18.6% (adenoviruses), and 8.0% (circoviruses) of the samples. A seasonal variation was observed, with the exception of circoviruses, with more positive samples in the winter. A positive correlation was found between F-RNA phages and noroviruses. However, F-RNA phages were present in only 43% of the norovirus-positive samples. The results show that mussels from the Norwegian coast can constitute a risk of infection with enteric viruses and that routine testing of samples may be justified. Advantages and disadvantages of various options for screening are discussed.
Detection of EnterotoxigenicClostridium perfringensType A Isolates in American Retail Foods
Authors: Wen Qiyi , McClane Bruce A. 
Published: May 2004

ABSTRACTCurrently there is only limited understanding of the reservoirs forClostridium perfringenstype A food poisoning. A recent survey (Y.-T. Lin and R. Labbe, Appl. Environ. Microbiol.69:1642-1646, 2003) of non-outbreak American retail foods did not identify the presence of a singleC. perfringensisolate carrying the enterotoxin gene (cpe) necessary for causing food poisoning. The present study revisited this issue, using revised methodology and food sampling strategies. In our survey,cpe-positiveC. perfringensisolates were detected in ∼1.4% of ∼900 surveyed non-outbreak American retail foods. Interestingly, those enterotoxigenic isolates in non-outbreak foods appear indistinguishable fromC. perfringensisolates known to cause food poisoning outbreaks: i.e., the enterotoxigenic retail food isolates all carry a chromosomalcpegene, are classified as type A, and exhibit exceptional heat resistance. Collectively, these findings indicate that some American foods are contaminated, at the time of retail purchase, withC. perfringensisolates having full potential to cause food poisoning. Furthermore, demonstrating that type A isolates carrying a chromosomalcpegene are the enterotoxigenic isolates most commonly present in foods helps to explain why these isolates (rather than type A isolates carrying a plasmidcpegene orcpe-positive type C or D isolates) are strongly associated with food poisoning outbreaks. Finally, since type A chromosomalcpeisolates present in the surveyed raw foods exhibited strong heat resistance, it appears that exceptional heat resistance is not a survivor trait selected for by cooking but is instead an intrinsic trait possessed by many type A chromosomalcpeisolates.
Responses of Active Bacterial and Fungal Communities in Soils under Winter Wheat to Different Fertilizer and Pesticide Regimens
Authors: Girvan Martina S. , Bullimore Juliet , Ball Andrew S. , Pretty Jules N. , Osborn A. Mark 
Published: May 2004

ABSTRACT
The composition of the active microbial (bacterial and fungal) soil community in an arable wheat field subjected to different management practices was examined at five times during a 1-year period. Field sections were fertilized either at good agricultural practice (GAP) levels or at reduced levels (0.5× GAP) and were inoculated with vesicular arbuscular mycorrhizae (VAM) at the same time. Field subsections were treated either with or without pesticides. Changes in the active microbial communities were investigated by denaturing gradient gel electrophoresis analysis of reverse transcription-PCR-amplified 16S and 18S rRNA. Microbial community structure was primarily determined by season, and the seasonal trends were similar for the fungal and bacterial components. Between-sample microbial heterogeneity decreased under a mature crop in the summer but increased following harvesting and plowing. Although similar overall trends were seen for the two microbial components, sample variability was greater for the fungal community than for the bacterial community. The greatest management effects were due to GAP fertilization, which caused increases in the bacterial numbers in the total and culturable communities. Microbial biomass similarly increased. GAP fertilization also caused large shifts in both the active bacterial community structure and the active fungal community structure and additionally resulted in a decrease in the heterogeneity of the active bacterial community. Pesticide addition did not significantly affect bacterial numbers or heterogeneity, but it led to major shifts in the active soil bacterial community structure. PCR primers specific for Glomales 25S rRNA genes were used to monitor the VAM population following inoculation. Glomales were detected initially only in VAM-inoculated field sections but were subsequently detected in noninoculated field sections as the season progressed. After plowing, the level of Glomales was reduced in noninoculated field sections but remained high in VAM-inoculated field sections. Inoculation of VAM correlated with elevated soil phosphate and carbon levels.
Behavior of an
Aeromonas hydrophila aroA
Live Vaccine in Water Microcosms
Authors: Vivas José , Carracedo Begoña , Riaño Jorge , Razquin Blanca E. , López-Fierro Pilar , Acosta Félix , Naharro Germán , Villena Alberto J. 
Published: May 2004

ABSTRACT

Genetically modified auxotrophic mutants of different fish pathogens have been used as live vaccines in laboratory experiments, but the behavior of the strains after release into aquatic ecosystems has not been characterized. We previously constructed and characterized an
aroA
mutant of
Aeromonas hydrophila
and studied the protection afforded by this mutant as a live vaccine in rainbow trout. In this work, we describe the survival of this strain in aquatic microcosms prepared from fish water tanks. The
aroA
mutant disappeared rapidly in nonfiltered, nonautoclaved fish tank water, declining below detection levels after 15 days, suggesting an inhibitory effect of the autochthonous microflora of the water. When the
aroA
strain was used to inoculate sterilized water, its culturability was lower than that of wild-type strain
A. hydrophila
AG2; after long periods of incubation,
aroA
cells were able to enter a viable but nonculturable state. Entry into this nonculturable state was accompanied by changes in the cell morphology from rods to spheres, but the cells appeared to remain potentially viable, as assessed by the preservation of cell membrane integrity. Supplementation of the culture medium with sodium pyruvate favored the culturability and resuscitation of the two
A. hydrophila
strains at low temperatures (6 and 16°C). These results contribute to a better understanding of the behavior of the
aroA
strain in natural environments and suggest that the inactivation of the
aroA
gene may be beneficial for the safety of this live vaccine for aquacultures.
Modification of Spatial Distribution of 2,4-Dichlorophenoxyacetic Acid Degrader Microhabitats during Growth in Soil Columns
Authors: Pallud C. , Dechesne A. , Gaudet J. P. , Debouzie D. , Grundmann G. L. 
Published: May 2004

ABSTRACTBacterial processes in soil, including biodegradation, require contact between bacteria and substrates. Knowledge of the three-dimensional spatial distribution of bacteria at the microscale is necessary to understand and predict such processes. Using a soil microsampling strategy combined with a mathematical spatial analysis, we studied the spatial distribution of 2,4-dichlorophenoxyacetic acid (2,4-D) degrader microhabitats as a function of 2,4-D degrader abundance. Soil columns that allowed natural flow were percolated with 2,4-D to increase the 2,4-D degrader abundance. Hundreds of soil microsamples (minimum diameter, 125 μm) were collected and transferred to culture medium to check for the presence of 2,4-D degraders. Spatial distributions of bacterial microhabitats were characterized by determining the average size of colonized soil patches and the average number of patches per gram of soil. The spatial distribution of 2,4-D degrader microhabitats was not affected by water flow, but there was an overall increase in colonized patch sizes after 2,4-D amendment; colonized microsamples were dispersed in the soil at low 2,4-D degrader densities and clustered in patches that were more than 0.5 mm in diameter at higher densities. During growth, spreading of 2,4-D degraders within the soil and an increase in 2,4-D degradation were observed. We hypothesized that spreading of the bacteria increased the probability of encounters with 2,4-D and resulted in better interception of the degradable substrate. This work showed that characterization of bacterial microscale spatial distribution is relevant to microbial ecology studies. It improved quantitative bacterial microhabitat description and suggested that sporadic movement of cells occurs. Furthermore, it offered perspectives for linking microbial function to the soil physicochemical environment.
Increased ATPase Activity Is Responsible for Acid Sensitivity of Nisin-Resistant
Listeria monocytogenes
ATCC 700302
Authors: McEntire Jennifer Cleveland , Carman George M. , Montville Thomas J. 
Published: May 2004

ABSTRACT

The growth of the foodborne pathogen
Listeria monocytogenes
can be controlled by nisin, an antimicrobial peptide. A spontaneous mutant of
L. monocytogenes
shows both resistance to nisin and increased acid sensitivity compared to the wild type. Changes in the cell membrane correlated with nisin resistance, but the mechanism for acid sensitivity appears unrelated. When hydrochloric or lactic acid is added to cultures, intracellular ATP levels drop significantly in the mutant (
P
< 0.01) compared to the results seen with the wild type. Characterization of the F
0
F
1
ATPase, which hydrolyzes ATP to pump protons from the cell cytoplasm, shows that the enzyme is more active in the mutant than in the wild type. These data support a model in which the increased activity of the mutant ATPase upon acid addition depletes the cells' supply of ATP, resulting in cell death.
Transformation of Verapamil byCunninghamella blakesleeana
Authors: Sun Lu , Huang Hai-Hua , Liu Lei , Zhong Da-Fang 
Published: May 2004

ABSTRACTA filamentous fungus,Cunninghamella blakesleeanaAS 3.153, was used as a microbial model of mammalian metabolism to transform verapamil, a calcium channel antagonist. The metabolites of verapamil were separated and assayed by the liquid chromatography-ion trap mass spectrometry method. After 96 h of incubation, nearly 93% of the original drug was metabolized to 23 metabolites. Five major metabolites were isolated by semipreparative high-performance liquid chromatography and were identified by proton nuclear magnetic resonance and electrospray mass spectrometry. Other metabolites were characterized according to their chromatographic behavior and mass spectral data. The major metabolic pathways of verapamil transformation by the fungus were N dealkylation, O demethylation, and sulfate conjugation. The phase I metabolites of verapamil (introduction of a functional group) byC. blakesleeanaparalleled those in mammals; therefore,C. blakesleeanacould be a useful tool for generating the mammalian phase I metabolites of verapamil.
Evaluation of a
Clostridium perfringens
Predictive Model, Developed under Isothermal Conditions in Broth, To Predict Growth in Ground Beef during Cooling
Authors: Smith Sarah , Schaffner Donald W. 
Published: May 2004

ABSTRACT

Proper temperature control is essential in minimizing
Clostridium perfringens
germination, growth, and toxin production. The U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) offers two options for the cooling of meat products: follow a standard time-temperature schedule or validate that alternative cooling regimens result in no more than a 1-log
10
CFU/g increase of
C. perfringens
and no growth of
Clostridium botulinum
. A mathematical model developed by Juneja et al. (Food Microbiol.
16:
335-349, 1999) may be helpful in determining if the
C. perfringens
performance standard has been achieved, but this model has not been extensively validated. The objective of this study was to validate the Juneja 1999 model in ground beef under a variety of changing temperature and temperature abuse situations. The Juneja 1999 model consistently underpredicted growth of
C. perfringens
during exponential cooling of ground beef. The model also underpredicted growth of
C. perfringens
in ground beef cooled at two different rates. The results presented here show generally good agreement with published data on the growth of
C. perfringens
in similar products. The model error may be due to faster-than-expected exponential growth rates in ground beef during cooling or an error in the mathematical formulation of the model.
Lack of Protective Osmolytes Limits Final Cell Density and Volumetric Productivity of Ethanologenic
Escherichia coli
KO11 during Xylose Fermentation
Authors: Underwood S. A. , Buszko M. L. , Shanmugam K. T. , Ingram L. O. 
Published: May 2004

ABSTRACT

Limited cell growth and the resulting low volumetric productivity of ethanologenic
Escherichia coli
KO11 in mineral salts medium containing xylose have been attributed to inadequate partitioning of carbon skeletons into the synthesis of glutamate and other products derived from the citrate arm of the anaerobic tricarboxylic acid pathway. The results of nuclear magnetic resonance investigations of intracellular osmolytes under different growth conditions coupled with those of studies using genetically modified strains have confirmed and extended this hypothesis. During anaerobic growth in mineral salts medium containing 9% xylose (600 mM) and 1% corn steep liquor, proline was the only abundant osmolyte (71.9 nmol ml
−1
optical density at 550 nm [OD
550
] unit
−1
), and growth was limited. Under aerobic conditions in the same medium, twice the cell mass was produced, and cells contained a mixture of osmolytes: glutamate (17.0 nmol ml
−1
OD
550
unit
−1
), trehalose (9.9 nmol ml
−1
OD
550
unit
−1
), and betaine (19.8 nmol ml
−1
OD
550
unit
−1
). Two independent genetic modifications of
E. coli
KO11 (functional expression of
Bacillus subtilis citZ
encoding NADH-insensitive citrate synthase; deletion of
ackA
encoding acetate kinase) and the addition of a metabolite, such as glutamate (11 mM) or acetate (24 mM), as a supplement each increased the intracellular glutamate pool during fermentation, doubled cell growth, and increased volumetric productivity. This apparent requirement for a larger glutamate pool for increased growth and volumetric productivity was completely eliminated by the addition of a protective osmolyte (2 mM betaine or 0.25 mM dimethylsulfoniopropionate), consistent with adaptation to osmotic stress rather than relief of a specific biosynthetic requirement.