bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hyperthermophilic Thermotoga Species Differ with Respect to Specific Carbohydrate Transporters and Glycoside Hydrolases
Authors: Frock Andrew D. , Gray Steven R. , Kelly Robert M. 
Published: January 2012

ABSTRACT

Four hyperthermophilic members of the bacterial genus
Thermotoga
(
T. maritima
,
T. neapolitana
,
T. petrophila
, and
Thermotoga
sp. strain RQ2) share a core genome of 1,470 open reading frames (ORFs), or about 75% of their genomes. Nonetheless, each species exhibited certain distinguishing features during growth on simple and complex carbohydrates that correlated with genomic inventories of specific ABC sugar transporters and glycoside hydrolases. These differences were consistent with transcriptomic analysis based on a multispecies cDNA microarray. Growth on a mixture of six pentoses and hexoses showed no significant utilization of galactose or mannose by any of the four species.
T. maritima
and
T. neapolitana
exhibited similar monosaccharide utilization profiles, with a strong preference for glucose and xylose over fructose and arabinose.
Thermotoga
sp. strain RQ2 also used glucose and xylose, but was the only species to utilize fructose to any extent, consistent with a phosphotransferase system (PTS) specific for this sugar encoded in its genome.
T. petrophila
used glucose to a significantly lesser extent than the other species. In fact, the XylR regulon was triggered by growth on glucose for
T. petrophila
, which was attributed to the absence of a glucose transporter (XylE2F2K2), otherwise present in the other
Thermotoga
species. This suggested that
T. petrophila
acquires glucose through the XylE1F1K1 transporter, which primarily serves to transport xylose in the other three
Thermotoga
species. The results here show that subtle differences exist among the hyperthermophilic
Thermotogales
with respect to carbohydrate utilization, which supports their designation as separate species.
Response of Fatty Acid Synthesis Genes to the Binding of Human Salivary Amylase by Streptococcus gordonii
Authors: Nikitkova Anna E. , Haase Elaine M. , Vickerman M. Margaret , Gill Steven R. , Scannapieco Frank A. 
Published: January 2012

ABSTRACT

Streptococcus gordonii
, an important primary colonizer of dental plaque biofilm, specifically binds to salivary amylase via the surface-associated amylase-binding protein A (AbpA). We hypothesized that a function of amylase binding to
S. gordonii
may be to modulate the expression of chromosomal genes, which could influence bacterial survival and persistence in the oral cavity. Gene expression profiling by microarray analysis was performed to detect genes in
S. gordonii
strain CH1 that were differentially expressed in response to the binding of purified human salivary amylase versus exposure to purified heat-denatured amylase. Selected genes found to be differentially expressed were validated by quantitative reverse transcription-PCR (qRT-PCR). Five genes from the fatty acid synthesis (FAS) cluster were highly (10- to 35-fold) upregulated in
S. gordonii
CH1 cells treated with native amylase relative to those treated with denatured amylase. An
abpA
-deficient strain of
S. gordonii
exposed to amylase failed to show a response in FAS gene expression similar to that observed in the parental strain. Predicted phenotypic effects of amylase binding to
S. gordonii
strain CH1 (associated with increased expression of FAS genes, leading to changes in fatty acid synthesis) were noted; these included increased bacterial growth, survival at low pH, and resistance to triclosan. These changes were not observed in the amylase-exposed
abpA
-deficient strain, suggesting a role for AbpA in the amylase-induced phenotype. These results provide evidence that the binding of salivary amylase elicits a differential gene response in
S. gordonii
, resulting in a phenotypic adjustment that is potentially advantageous for bacterial survival in the oral environment.
Wide Distribution of Closely Related, Antibiotic-Producing Arthrobacter Strains throughout the Arctic Ocean
Authors: Wietz Matthias , Månsson Maria , Bowman Jeff S. , Blom Nikolaj , Ng Yin , Gram Lone 
Published: January 2012

ABSTRACT

We isolated 16 antibiotic-producing bacterial strains throughout the central Arctic Ocean, including seven
Arthrobacter
spp. with almost identical 16S rRNA gene sequences. These strains were numerically rare, as revealed using 454 pyrosequencing libraries.
Arthrobacter
spp. produced arthrobacilins A to C under different culture conditions, but other, unidentified compounds likely contributed to their antibiotic activity.
Evidence of Two Functionally Distinct Ornithine Decarboxylation Systems in Lactic Acid Bacteria
Authors: Romano Andrea , Trip Hein , Lonvaud-Funel Aline , Lolkema Juke S. , Lucas Patrick M. 
Published: January 2012

ABSTRACTBiogenic amines are low-molecular-weight organic bases whose presence in food can result in health problems. The biosynthesis of biogenic amines in fermented foods mostly proceeds through amino acid decarboxylation carried out by lactic acid bacteria (LAB), but not all systems leading to biogenic amine production by LAB have been thoroughly characterized. Here, putative ornithine decarboxylation pathways consisting of a putative ornithine decarboxylase and an amino acid transporter were identified in LAB by strain collection screening and database searches. The decarboxylases were produced in heterologous hosts and purified and characterizedin vitro, whereas transporters were heterologously expressed inLactococcus lactisand functionally characterizedin vivo. Amino acid decarboxylation by whole cells of the original hosts was determined as well. We concluded that two distinct types of ornithine decarboxylation systems exist in LAB. One is composed of an ornithine decarboxylase coupled to an ornithine/putrescine transmembrane exchanger. Their combined activities results in the extracellular release of putrescine. This typical amino acid decarboxylation system is present in only a few LAB strains and may contribute to metabolic energy production and/or pH homeostasis. The second system is widespread among LAB. It is composed of a decarboxylase active on ornithine andl-2,4-diaminobutyric acid (DABA) and a transporter that mediates unidirectional transport of ornithine into the cytoplasm. Diamines that result from this second system are retained within the cytosol.
Characterization of the ELPhiS Prophage from Salmonella enterica Serovar Enteritidis Strain LK5
Authors: Hanna L. Farris , Matthews T. David , Dinsdale Elizabeth A. , Hasty David , Edwards Robert A. 
Published: January 2012

ABSTRACT

Phages are a primary driving force behind the evolution of bacterial pathogens by transferring a variety of virulence genes into their hosts. Similar to other bacterial genomes, the
Salmonella enterica
serovar Enteritidis LK5 genome contains several regions that are homologous to phages. Although genomic analysis demonstrated the presence of prophages, it was unable to confirm which phage elements within the genome were viable. Genetic markers were used to tag one of the prophages in the genome to allow monitoring of phage induction. Commonly used laboratory strains of
Salmonella
were resistant to phage infection, and therefore a rapid screen was developed to identify susceptible hosts. This approach showed that a genetically tagged prophage, ELPhiS (Enteritidis lysogenic phage S), was capable of infecting
Salmonella
serovars that are diverse in host range and virulence and has the potential to laterally transfer genes between these serovars via lysogenic conversion. The rapid screen approach is adaptable to any system with a large collection of isolates and may be used to test the viability of prophages found by sequencing the genomes of various bacterial pathogens.
Fine-Tuned Transcriptional Regulation of Malate Operons in Enterococcus faecalis
Authors: Mortera Pablo , Espariz Martín , Suárez Cristian , Repizo Guillermo , Deutscher Josef , Alarcón Sergio , Blancato Víctor , Magni Christian 
Published: January 2012

ABSTRACT

In
Enterococcus faecalis
, the
mae
locus is constituted by two putative divergent operons,
maePE
and
maeKR
. The first operon encodes a putative H
+
/malate symporter (MaeP) and a malic enzyme (MaeE) previously shown to be essential for malate utilization in this bacterium. The
maeKR
operon encodes two putative proteins with significant similarity to two-component systems involved in sensing malate and activating its assimilation in bacteria. Our transcriptional and genetic assays showed that
maePE
and
maeKR
are induced in response to malate by the response regulator MaeR. In addition, we observed that both operons were partially repressed in the presence of glucose. Accordingly, the cometabolism of this sugar and malate was detected. The binding of the complex formed by CcpA and its corepressor P-Ser-HPr to a
cre
site located in the
mae
region was demonstrated
in vitro
and explains the carbon catabolite repression (CCR) observed for the
maePE
operon. However, our results also provide evidence for a CcpA-independent CCR mechanism regulating the expression of both operons. Finally, a biomass increment of 40 or 75% was observed compared to the biomass of cells grown only on glucose or malate, respectively. Cells cometabolizing both carbon sources exhibit a higher rate of glucose consumption and a lower rate of malate utilization. The growth improvement achieved by
E. faecalis
during glucose-malate cometabolism might explain why this microorganism employs different regulatory systems to tightly control the assimilation of both carbon sources.
Development and Validation of a Predictive Model for the Growth of Vibrio vulnificus in Postharvest Shellstock Oysters
Authors: DaSilva Ligia , Parveen Salina , DePaola Angelo , Bowers John , Brohawn Kathy , Tamplin Mark L. 
Published: January 2012

ABSTRACT

Postharvest growth of
Vibrio vulnificus
in oysters can increase risk of human infection. Unfortunately, limited information is available regarding
V. vulnificus
growth and survival patterns over a wide range of storage temperatures in oysters harvested from different estuaries and in different oyster species. In this study, we developed a predictive model for
V. vulnificus
growth in Eastern oysters (
Crassostrea virginica
) harvested from Chesapeake Bay, MD, over a temperature range of 5 to 30°C and then validated the model against
V. vulnificus
growth rates (GRs) in Eastern and Asian oysters (
Crassostrea ariakensis
) harvested from Mobile Bay, AL, and Chesapeake Bay, VA, respectively. In the model development studies,
V. vulnificus
was slowly inactivated at 5 and 10°C with average GRs of −0.0045 and −0.0043 log most probable number (MPN)/h, respectively. Estimated average growth rates at 15, 20, 25, and 30°C were 0.022, 0.042, 0.087, and 0.093 log MPN/h, respectively. With respect to Eastern oysters, bias (
B
f
) and accuracy (
A
f
) factors for model-dependent and -independent data were 1.02 and 1.25 and 1.67 and 1.98, respectively. For Asian oysters,
B
f
and
A
f
were 0.29 and 3.40. Residual variations in growth rate about the fitted model were not explained by season, region, water temperature, or salinity at harvest. Growth rate estimates for Chesapeake Bay and Mobile Bay oysters stored at 25 and 30°C showed relatively high variability and were lower than Food and Agricultural Organization (FAO)/WHO
V. vulnificus
quantitative risk assessment model predictions. The model provides an improved tool for designing and implementing food safety plans that minimize the risk associated with
V. vulnificus
in oysters.
Marked Genomic Diversity of Norovirus Genogroup I Strains in a Waterborne Outbreak
Authors: Nenonen Nancy P. , Hannoun Charles , Larsson Charlotte U. , Bergström Tomas 
Published: January 2012

ABSTRACT

Marked norovirus (NoV) diversity was detected in patient samples from a large community outbreak of gastroenteritis with waterborne epidemiology affecting approximately 2,400 people. NoV was detected in 33 of 50 patient samples examined by group-specific real-time reverse transcription-PCR. NoV genotype I (GI) strains predominated in 31 patients, with mixed GI infections occurring in 5 of these patients. Sequence analysis of RNA-dependent polymerase-N/S capsid-coding regions (∼900 nucleotides in length) confirmed the dominance of the GI strains (
n
= 36). Strains of NoV GI.4 (
n
= 21) and GI.7 (
n
= 9) were identified, but six strains required full capsid amino acid analyses (530 to 550 amino acids) based on control sequencing of cloned amplicons before the virus genotype could be determined. Three strains were assigned to a new NoV GI genotype, proposed as GI.9, based on capsid amino acid analyses showing 26% dissimilarity from the established genotypes GI.1 to GI.8. Three other strains grouped in a sub-branch of GI.3 with 13 to 15% amino acid dissimilarity to GI.3 GenBank reference strains. Phylogenetic analysis (2.1 kb) of 10 representative strains confirmed these genotype clusters. Strains of NoV GII.4 (
n
= 1), NoV GII.6 (
n
= 2), sapovirus GII.2 (
n
= 1), rotavirus (
n
= 3), adenovirus (
n
= 1), and
Campylobacter
spp. (
n
= 2) were detected as single infections or as mixtures with NoV GI. Marked NoV GI diversity detected in patients was consistent with epidemiologic evidence of waterborne NoV infections, suggesting human fecal contamination of the water supply. Recognition of NoV diversity in a cluster of patients provided a useful warning marker of waterborne contamination in the Lilla Edet outbreak.
SulE, a Sulfonylurea Herbicide De-Esterification Esterase from Hansschlegelia zhihuaiae S113
Authors: Hang Bao-Jian , Hong Qing , Xie Xiang-Ting , Huang Xing , Wang Cheng-Hong , He Jian , Li Shun-Peng 
Published: January 2012

ABSTRACT

De-esterification is an important degradation or detoxification mechanism of sulfonylurea herbicide in microbes and plants. However, the biochemical and molecular mechanisms of sulfonylurea herbicide de-esterification are still unknown. In this study, a novel esterase gene,
sulE
, responsible for sulfonylurea herbicide de-esterification, was cloned from
Hansschlegelia zhihuaiae
S113. The gene contained an open reading frame of 1,194 bp, and a putative signal peptide at the N terminal was identified with a predicted cleavage site between Ala37 and Glu38, resulting in a 361-residue mature protein. SulE minus the signal peptide was synthesized in
Escherichia coli
BL21 and purified to homogeneity. SulE catalyzed the de-esterification of a variety of sulfonylurea herbicides that gave rise to the corresponding herbicidally inactive parent acid and exhibited the highest catalytic efficiency toward thifensulfuron-methyl. SulE was a dimer without the requirement of a cofactor. The activity of the enzyme was completely inhibited by Ag
+
, Cd
2+
, Zn
2+
, methamidophos, and sodium dodecyl sulfate. A
sulE
-disrupted mutant strain, Δ
sulE
, was constructed by insertion mutation. Δ
sulE
lost the de-esterification ability and was more sensitive to the herbicides than the wild type of strain S113, suggesting that
sulE
played a vital role in the sulfonylurea herbicide resistance of the strain. The transfer of
sulE
into
Saccharomyces cerevisiae
BY4741 conferred on it the ability to de-esterify sulfonylurea herbicides and increased its resistance to the herbicides. This study has provided an excellent candidate for the mechanistic study of sulfonylurea herbicide metabolism and detoxification through de-esterification, construction of sulfonylurea herbicide-resistant transgenic crops, and bioremediation of sulfonylurea herbicide-contaminated environments.
Transcriptional Responses of Escherichia coli K-12 and O157:H7 Associated with Lettuce Leaves
Authors: Fink Ryan C. , Black Elaine P. , Hou Zhe , Sugawara Masayuki , Sadowsky Michael J. , Diez-Gonzalez Francisco 
Published: January 2012

ABSTRACT

An increasing number of outbreaks of gastroenteritis recently caused by
Escherichia coli
O157:H7 have been linked to the consumption of leafy green vegetables. Although it is known that
E. coli
survives and grows in the phyllosphere of lettuce plants, the molecular mechanisms by which this bacterium associates with plants are largely unknown. The goal of this study was to identify
E. coli
genes relevant to its interaction, survival, or attachment to lettuce leaf surfaces, comparing
E. coli
K-12, a model system, and
E. coli
O157:H7, a pathogen associated with a large number of outbreaks. Using microarrays, we found that upon interaction with intact leaves, 10.1% and 8.7% of the 3,798 shared genes were differentially expressed in K-12 and O157:H7, respectively, whereas 3.1% changed transcript levels in both. The largest group of genes downregulated consisted of those involved in energy metabolism, including
tnaA
(33-fold change), encoding a tryptophanase that converts tryptophan into indole. Genes involved in biofilm modulation (
bhsA
and
ybiM
) and curli production (
csgA
and
csgB
) were significantly upregulated in
E. coli
K-12 and O157:H7. Both
csgA
and
bhsA
(
ycfR
) mutants were impaired in the long-term colonization of the leaf surface, but only
csgA
mutants had diminished ability in short-term attachment experiments. Our data suggested that the interaction of
E. coli
K-12 and O157:H7 with undamaged lettuce leaves likely is initiated via attachment to the leaf surface using curli fibers, a downward shift in their metabolism, and the suppression of biofilm formation.
Comparison of the Prevalences and Antimicrobial Resistances of Escherichia coli Isolates from Different Retail Meats in the United States, 2002 to 2008
Authors: Zhao S. , Blickenstaff K. , Bodeis-Jones S. , Gaines S. A. , Tong E. , McDermott P. F. 
Published: January 2012

ABSTRACT

Escherichia coli
isolates were recovered from the National Antimicrobial Resistance Monitoring System retail meat program and examined for antimicrobial susceptibility. Retail meat samples (
n
= 11,921) from four U.S. states collected during 2002 to 2008, consisting of 2,988 chicken breast, 2,942 ground turkey, 2,991 ground beef, and 3,000 pork chop samples, were analyzed. A total of 8,286
E. coli
isolates were recovered. The greatest numbers of samples contaminated with the organism were chicken (83.5%) and turkey (82.0%), followed by beef (68.9%) and pork (44.0%). Resistance was most common to tetracycline (50.3%), followed by streptomycin (34.6%), sulfamethoxazole-sulfisoxazole (31.6%), ampicillin (22.5%), gentamicin (18.6%), kanamycin (8.4%), amoxicillin-clavulanic acid (6.4%), and cefoxitin (5.2%). Less than 5% of the isolates had resistance to trimethoprim, ceftriaxone, ceftiofur, nalidixic acid, chloramphenicol, and ciprofloxacin. All isolates were susceptible to amikacin. Compared to beef and pork isolates, the poultry meat isolates had a greater percentage of resistance to all tested drugs, with the exception of chloramphenicol, to which pork isolates had the most resistance. More than half of the turkey isolates (56%) were resistant to multidrugs (≥3 classes) compared to 38.9% of chicken, 17.3% of pork, and 9.3% of beef isolates. The
bla
CMY
gene was present in all ceftriaxone- and ceftiofur-resistant isolates. The
cmlA
,
flo
,
and catI
genes were present in 45%, 43%, and 40% of chloramphenicol-resistant isolates, respectively. Most nalidixic acid-resistant isolates (98.5%) had a
gyrA
mutation in S83 or D87 or both, whereas only 6.7% had a
parC
mutation in either S80 or E84. The results showed that
E. coli
was commonly present in the retail meats, and antimicrobial resistance profiles differed according to the animal origin of the isolates.
Relationship between Yield Components and Partial Resistance to Lecanicillium fungicola in the Button Mushroom, Agaricus bisporus, Assessed by Quantitative Trait Locus Mapping
Authors: Foulongne-Oriol Marie , Rodier Anne , Savoie Jean-Michel 
Published: January 2012

ABSTRACTDry bubble, caused byLecanicillium fungicola, is one of the most detrimental diseases affecting button mushroom cultivation. In a previous study, we demonstrated that breeding for resistance to this pathogen is quite challenging due to its quantitative inheritance. A second-generation hybrid progeny derived from an intervarietal cross between a wild strain and a commercial cultivar was characterized forL. fungicolaresistance under artificial inoculation in three independent experiments. Analysis of quantitative trait loci (QTL) was used to determine the locations, numbers, and effects of genomic regions associated with dry-bubble resistance. Four traits related to resistance were analyzed. Two to four QTL were detected per trait, depending on the experiment. Two genomic regions, on linkage group X (LGX) and LGVIII, were consistently detected in the three experiments. The genomic region on LGX was detected for three of the four variables studied. The total phenotypic variance accounted for by all QTL ranged from 19.3% to 42.1% over all traits in all experiments. For most of the QTL, the favorable allele for resistance came from the wild parent, but for some QTL, the allele that contributed to a higher level of resistance was carried by the cultivar. Comparative mapping with QTL for yield-related traits revealed five colocations between resistance and yield component loci, suggesting that the resistance results from both genetic factors and fitness expression. The consequences for mushroom breeding programs are discussed.
The Septin AspB in Aspergillus nidulans Forms Bars and Filaments and Plays Roles in Growth Emergence and Conidiation
Authors: Hernández-Rodríguez Yainitza , Hastings Susan , Momany Michelle 
Published: January 2012

ABSTRACTIn yeast, septins form rings at the mother-bud neck and function as diffusion barriers. In animals, septins form filaments that can colocalize with other cytoskeletal elements. In the filamentous fungusAspergillus nidulansthere are five septin genes,aspA(an ortholog ofSaccharomyces cerevisiae CDC11),aspB(an ortholog ofS. cerevisiae CDC3),aspC(an ortholog ofS. cerevisiae CDC12),aspD(an ortholog ofS. cerevisiae CDC10), andaspE(found only in filamentous fungi). TheaspBgene was previously reported to be the most highly expressedAspergillus nidulansseptin and to be essential. Using improved gene targeting techniques, we found that deletion ofaspBis not lethal but results in delayed septation, increased emergence of germ tubes and branches, and greatly reduced conidiation. We also found that AspB-green fluorescent protein (GFP) localizes as rings and collars at septa, branches, and emerging layers of the conidiophore and as bars and filaments in conidia and hyphae. Bars are found in dormant and isotropically expanding conidia and in subapical nongrowing regions of hyphae and display fast movements. Filaments form as the germ tube emerges, localize to hyphal and branch tips, and display slower movements. All visible AspB-GFP structures are retained inΔaspDand lost inΔaspAandΔaspCstrains. Interestingly, in theΔaspEmutant, AspB-GFP rings, bars, and filaments are visible in early growth, but AspB-GFP rods and filaments disappear after septum formation. AspE orthologs are only found in filamentous fungi, suggesting that this class of septins might be required for stability of septin bars and filaments in highly polar cells.