bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of the
Streptococcus mutans irvA
Gene in GbpC-Independent, Dextran-Dependent Aggregation and Biofilm Formation
Authors: Zhu Min , Ajdić Dragana , Liu Yuan , Lynch David , Merritt Justin , Banas Jeffrey A. 
Published: September 2009

ABSTRACT

Dextran-dependent aggregation (DDAG) of
Streptococcus mutans
is an in vitro phenomenon that is believed to represent a property of the organism that is beneficial for sucrose-dependent biofilm development. GbpC, a cell surface glucan-binding protein, is responsible for DDAG in
S. mutans
when cultured under defined stressful conditions. Recent reports have described a putative transcriptional regulator gene,
irvA
, located just upstream of
gbpC
, that is normally repressed by the product of an adjacent gene,
irvR
. When repression of
irvA
is relieved, there is a resulting increase in the expression of GbpC and decreases in competence and synthesis of the antibiotic mutacin I. This study examined the role of
irvA
in DDAG and biofilm formation by engineering strains that overexpressed
irvA
(IrvA+) on an extrachromosomal plasmid. The IrvA+ strain displayed large aggregation particles that did not require stressful growth conditions. A novel finding was that overexpression of
irvA
in a
gbpC
mutant background retained a measure of DDAG, albeit very small aggregation particles. Biofilms formed by the IrvA+ strain in the parental background possessed larger-than-normal microcolonies. In a
gbpC
mutant background, the overexpression of
irvA
reversed the fragile biofilm phenotype normally associated with loss of GbpC. Real-time PCR and Northern blot analyses found that expression of
gbpC
did not change significantly in the IrvA+ strain but expression of
spaP
, encoding the major surface adhesin P1, increased significantly. Inactivation of
spaP
eliminated the small-particle DDAG. The results suggest that IrvA promotes DDAG not only by GbpC, but also via an increase in P1.
Molecular Characterization of Potential Nitrogen Fixation by Anaerobic Methane-Oxidizing Archaea in the Methane Seep Sediments at the Number 8 Kumano Knoll in the Kumano Basin, Offshore of Japan
Authors: Miyazaki Junichi , Higa Ryosaku , Toki Tomohiro , Ashi Juichiro , Tsunogai Urumu , Nunoura Takuro , Imachi Hiroyuki , Takai Ken 
Published: September 2009

ABSTRACTThe potential for microbial nitrogen fixation in the anoxic methane seep sediments in a mud volcano, the number 8 Kumano Knoll, was characterized by molecular phylogenetic analyses. A total of 111 of thenifH(a gene coding a nitrogen fixation enzyme, Fe protein) clones were obtained from different depths of the core sediments, and the phylogenetic analysis of the clones indicated the genetic diversity ofnifHgenes. The predominant group detected (methane seep group 2), representing 74% of clonal abundance, was phylogenetically related to thenifHsequences obtained from theMethanosarcinaspecies but was most closely related to thenifHsequences potentially derived from the anoxic methanotrophic archaea (ANME-2 archaea). The recovery of thenifgene clusters including thenifHsequences of the methane seep group 2 and the subsequent reverse transcription-PCR detection of thenifDandnifHgenes strongly suggested that the genetic components of the gene clusters would be operative for the in situ assimilation of molecular nitrogen (N2) by the host microorganisms. DNA-based quantitative PCR of the archaeal 16S rRNA gene, the group-specificmcrA(a gene encoding the methyl-coenzyme M reductase α subunit) gene, and thenifDandnifHgenes demonstrated the similar distribution patterns of the archaeal 16S rRNA gene, themcrAgroups c-d and e, and thenifDandnifHgenes through the core sediments. These results supported the idea that the anoxic methanotrophic archaea ANME-2c could be the microorganisms hosting thenifgene clusters and could play an important role in not only the in situ carbon (methane) cycle but also the nitrogen cycle in subseafloor sediments.
Effect of Carbohydrate Composition in Barley and Oat Cultivars on Microbial Ecophysiology and Proliferation of
Salmonella enterica
in an In Vitro Model of the Porcine Gastrointestinal Tract
Authors: Pieper Robert , Bindelle Jérôme , Rossnagel Brian , Van Kessel Andrew , Leterme Pascal 
Published: September 2009

ABSTRACT

The influence of the carbohydrate (CHO) composition of cereal cultivars on microbial ecophysiology was studied using an in vitro model of the porcine gastrointestinal tract. Ten hull-less barley cultivars, six barley cultivars with hulls, six oat cultivars, and six oat groats that differed in β-glucan, nonstarch polysaccharide (NSP), and starch contents and starch type were hydrolyzed enzymatically and incubated for 72 h with pig feces. Fermentation kinetics were modeled, and microbial compositions and short-chain fatty acid (SCFA) profiles were analyzed using terminal restriction fragment length polymorphism and gas chromatography. Cluster analysis and canonical ordination revealed different effects on fermentation and microbial ecology depending on the type of CHO and cultivar. First, in cultivars of barley with hulls and oats, the cellulose and insoluble NSP contents (i) increased
Ruminococcus flavefaciens
-like and
Clostridium xylanolyticum
-like phylotypes, (ii) increased acetate production, and (iii) decreased fermentation activity. Second, in hull-less barley cultivars the β-glucan, amylose, amylopectin, crude protein, and soluble NSP contents determined the microbial community composition and activity as follows: (i) the amylose contents of the hull-less barley varieties increased the butyrate production and the abundance of
Clostridium
butyricum
-like phylotypes, (ii) the β-glucan content determined the total amounts of SCFA, and (iii) the amylopectin and starch contents affected the abundance of
Clostridium
ramosum
-like phylotypes, members of
Clostridium
cluster XIVa, and
Bacteroides
-like bacteria. Finally, the effect of CHO on proliferation of
Salmonella enterica
in the model was determined.
Salmonella
cell counts were not affected, but the relative proportion of
Salmonella
decreased with hull-less barley cultivars and increased with oat cultivars as revealed by quantitative PCR. Our results shed light on the complex interactions of cereal CHO with intestinal bacterial ecophysiology and the possible impact on host health.
Comparison of Bacterioneuston and Bacterioplankton Dynamics during a Phytoplankton Bloom in a Fjord Mesocosm
Authors: Cunliffe Michael , Whiteley Andrew S. , Newbold Lindsay , Oliver Anna , Schäfer Hendrik , Murrell J. Colin 
Published: September 2009

ABSTRACT

The bacterioneuston is the community of
Bacteria
present in surface microlayers, the thin surface film that forms the interface between aquatic environments and the atmosphere. In this study we compared bacterial cell abundances and bacterial community structures of the bacterioneuston and the bacterioplankton (from the subsurface water column) during a phytoplankton bloom mesocosm experiment. Bacterial cell abundance, determined by flow cytometry, followed a typical bacterioplankton response to a phytoplankton bloom, with
Synechococcus
and high-nucleic acid content (HNA) bacterial cell numbers initially falling, probably due to selective protist grazing. Subsequently HNA and low-nucleic acid content bacterial cells increased in abundance, but
Synechococcus
cells did not. There was no significant difference between bacterioneuston and bacterioplankton cell abundances during the experiment. Conversely, distinct and consistent differences between the bacterioneuston and the bacterioplankton community structures were observed. This was monitored simultaneously by
Bacteria
16S rRNA gene terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis. The conserved patterns of community structure observed in all of the mesocosms indicate that the bacterioneuston is distinctive and nonrandom.
Impact of Host Developmental Age on the Transcriptome of the Symbiotic Bacterium
Buchnera aphidicola
in the Pea Aphid (
Acyrthosiphon pisum
)
Authors: Bermingham John , Rabatel Andréane , Calevro Federica , Viñuelas José , Febvay Gérard , Charles Hubert , Douglas Angela , Wilkinson Tom 
Published: September 2009

ABSTRACT

Of the 617 genes from
Buchnera aphidicola
, the obligate bacterial symbiont of the pea aphid, 23% were differentially expressed in embryos compared to adults. Genes involved in flagellar apparatus and riboflavin synthesis exhibited particularly robust upregulation in embryos, suggesting functional differences between the symbiosis in the adult and embryo insect.
Population Structure of the Lyme Borreliosis Spirochete
Borrelia burgdorferi
in the Western Black-Legged Tick (
Ixodes pacificus
) in Northern California
Authors: Girard Yvette A. , Travinsky Bridgit , Schotthoefer Anna , Fedorova Natalia , Eisen Rebecca J. , Eisen Lars , Barbour Alan G. , Lane Robert S. 
Published: September 2009

ABSTRACT

Factors potentially contributing to the lower incidence of Lyme borreliosis (LB) in the far-western than in the northeastern United States include tick host-seeking behavior resulting in fewer human tick encounters, lower densities of
Borrelia burgdorferi
-infected vector ticks in peridomestic environments, and genetic variation among
B. burgdorferi
spirochetes to which humans are exposed. We determined the population structure of
B. burgdorferi
in over 200 infected nymphs of the primary bridging vector to humans,
Ixodes pacificus
, collected in Mendocino County, CA. This was accomplished by sequence typing the spirochete lipoprotein
ospC
and the 16S-23S rRNA intergenic spacer (IGS). Thirteen
ospC
alleles belonging to 12 genotypes were found in California, and the two most abundant,
ospC
genotypes H3 and E3, have not been detected in ticks in the Northeast. The most prevalent
ospC
and IGS biallelic profile in the population, found in about 22% of ticks, was a new
B. burgdorferi
strain defined by
ospC
genotype H3. Eight of the most common
ospC
genotypes in the northeastern United States, including genotypes I and K that are associated with disseminated human infections, were absent in Mendocino County nymphs.
ospC
H3 was associated with hardwood-dominated habitats where western gray squirrels, the reservoir host, are commonly infected with LB spirochetes. The differences in
B. burgdorferi
population structure in California ticks compared to the Northeast emphasize the need for a greater understanding of the genetic diversity of spirochetes infecting California LB patients.
Gene Cloning, Protein Characterization, and Alteration of Product Selectivity for the Trehalulose Hydrolase and Trehalulose Synthase from “
Pseudomonas mesoacidophila
” MX-45
Authors: Watzlawick Hildegard , Mattes Ralf 
Published: September 2009

ABSTRACT

The naturally occurring structural isomer of sucrose, trehalulose, is produced by sucrose isomerase (SI). Screening of chromosomal DNA from “
Pseudomonas mesoacidophila
” MX-45 with an SI-specific probe facilitated the cloning of two adjacent gene homologs,
mutA
and
mutB
. Both genes were expressed separately in
E
scherichia
c
oli
, and their enzyme products were characterized. MutA hydrolyzed the substrates trehalulose, isomaltulose, and sucrose into glucose and fructose. Due to its highest activity on trehalulose, MutA was referred to as trehalulase.
m
utB
encodes the SI (trehalulose synthase) and catalyzes the isomerization of sucrose to mainly trehalulose. From Northern blot analysis it is apparent that the
mutB
gene is not transcribed as part of an operon and was transcriptionally upregulated when
P. mesoacidophila
MX-45 cells were grown in sucrose medium, whereas under investigated conditions no transcript for
mut
A
was detected. Mutants of
mutB
were created by a random mutagenesis approach in order to alter the product specificity of MutB. Two types of mutants have emerged, one type that prefers the hydrolytic reaction on sucrose and another type that still acts as an SI but with a significant shift in the product from trehalulose to isomaltulose. The hydrolytic character of MutB R311C was demonstrated through its higher catalytic efficiency for glucose production over trehalulose production. MutB D442N favored the transfer reaction, with an isomer preference for isomaltulose.
Deformed Wing Virus Implicated in Overwintering Honeybee Colony Losses
Authors: Highfield Andrea C. , El Nagar Aliya , Mackinder Luke C. M. , Noël Laure M.-L. J. , Hall Matthew J. , Martin Stephen J. , Schroeder Declan C. 
Published: September 2009

ABSTRACT

The worldwide decline in honeybee colonies during the past 50 years has often been linked to the spread of the parasitic mite
Varroa destructor
and its interaction with certain honeybee viruses. Recently in the United States, dramatic honeybee losses (colony collapse disorder) have been reported; however, there remains no clear explanation for these colony losses, with parasitic mites, viruses, bacteria, and fungal diseases all being proposed as possible candidates. Common characteristics that most failing colonies share is a lack of overt disease symptoms and the disappearance of workers from what appears to be normally functioning colonies. In this study, we used quantitative PCR to monitor the presence of three honeybee viruses, deformed wing virus (DWV), acute bee paralysis virus (ABPV), and black queen cell virus (BQCV), during a 1-year period in 15 asymptomatic, varroa mite-positive honeybee colonies in Southern England, and 3 asymptomatic colonies confirmed to be varroa mite free. All colonies with varroa mites underwent control treatments to ensure that mite populations remained low throughout the study. Despite this, multiple virus infections were detected, yet a significant correlation was observed only between DWV viral load and overwintering colony losses. The long-held view has been that DWV is relatively harmless to the overall health status of honeybee colonies unless it is in association with severe varroa mite infestations. Our findings suggest that DWV can potentially act independently of varroa mites to bring about colony losses. Therefore, DWV may be a major factor in overwintering colony losses.
Suggestive Evidence for Darwinian Selection against Asparagine-Linked Glycans of Plasmodium falciparum and Toxoplasma gondii
Authors: Bushkin G. Guy , Ratner Daniel M. , Cui Jike , Banerjee Sulagna , Duraisingh Manoj T. , Jennings Cameron V. , Dvorin Jeffrey D. , Gubbels Marc-Jan , Robertson Seth D. , Steffen Martin , O'Keefe Barry R. , Robbins Phillips W. , Samuelson John 
Published: September 2009

ABSTRACTWe are interested in asparagine-linked glycans (N-glycans) ofPlasmodium falciparumandToxoplasma gondii, because their N-glycan structures have been controversial and because we hypothesize that there might be selection against N-glycans in nucleus-encoded proteins that must pass through the endoplasmic reticulum (ER) prior to threading into the apicoplast. In support of our hypothesis, we observed the following. First, in protists with apicoplasts, there is extensive secondary loss of Alg enzymes that make lipid-linked precursors to N-glycans.Theileriamakes no N-glycans, andPlasmodiummakes a severely truncated N-glycan precursor composed of one or two GlcNAc residues. Second, secreted proteins ofToxoplasma, which uses its own 10-sugar precursor (Glc3Man5GlcNAc2) and the host 14-sugar precursor (Glc3Man9GlcNAc2) to make N-glycans, have very few sites for N glycosylation, and there is additional selection against N-glycan sites in its apicoplast-targeted proteins. Third, while the GlcNAc-bindingGriffonia simplicifolialectin II labels ER, rhoptries, and surface of plasmodia, there is no apicoplast labeling. Similarly, the antiretroviral lectin cyanovirin-N, which binds to N-glycans ofToxoplasma, labels ER and rhoptries, but there is no apicoplast labeling. We conclude that possible selection against N-glycans in protists with apicoplasts occurs by eliminating N-glycans (Theileria), reducing their length (Plasmodium), or reducing the number of N-glycan sites (Toxoplasma). In addition, occupation of N-glycan sites is markedly reduced in apicoplast proteins versus some secretory proteins in bothPlasmodiumandToxoplasma.
Mapping of the
Saccharomyces cerevisiae
Oxa1-Mitochondrial Ribosome Interface and Identification of MrpL40, a Ribosomal Protein in Close Proximity to Oxa1 and Critical for Oxidative Phosphorylation Complex Assembly
Authors: Jia Lixia , Kaur Jasvinder , Stuart Rosemary A. 
Published: September 2009

ABSTRACT

The Oxa1 protein plays a central role in facilitating the cotranslational insertion of the nascent polypeptide chains into the mitochondrial inner membrane. Mitochondrially encoded proteins are synthesized on matrix-localized ribosomes which are tethered to the inner membrane and in physical association with the Oxa1 protein. In the present study we used a chemical cross-linking approach to map the
Saccharomyces cerevisiae
Oxa1-ribosome interface, and we demonstrate here a close association of Oxa1 and the large ribosomal subunit protein, MrpL40. Evidence to indicate that a close physical and functional relationship exists between MrpL40 and another large ribosomal protein, the Mrp20/L23 protein, is also provided. MrpL40 shares sequence features with the bacterial ribosomal protein L24, which like Mrp20/L23 is known to be located adjacent to the ribosomal polypeptide exit site. We propose therefore that MrpL40 represents the
Saccharomyces cerevisiae
L24 homolog. MrpL40, like many mitochondrial ribosomal proteins, contains a C-terminal extension region that bears no similarity to the bacterial counterpart. We show that this C-terminal mitochondria-specific region is important for MrpL40's ability to support the synthesis of the correct complement of mitochondrially encoded proteins and their subsequent assembly into oxidative phosphorylation complexes.
A Point Mutation in the Sensor Histidine Kinase SaeS of
Staphylococcus aureus
Strain Newman Alters the Response to Biocide Exposure
Authors: Schäfer Daniel , Lâm Thiên-Trí , Geiger Tobias , Mainiero Markus , Engelmann Susanne , Hussain Muzaffar , Bosserhoff Armin , Frosch Matthias , Bischoff Markus , Wolz Christiane , Reidl Joachim , Sinha Bhanu 
Published: September 2009

ABSTRACT

Staphylococcus aureus
reacts to changing environmental conditions such as heat, pH, and chemicals through global regulators such as the
sae
(
S. aureus
exoprotein expression) two-component signaling system. Subinhibitory concentrations of some antibiotics were shown to increase virulence factor expression. Here, we investigated the
S. aureus
stress response to sublethal concentrations of a commonly used biocide (Perform), by real-time quantitative PCR (qRT-PCR), promoter activity assay, sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, and a flow cytometric invasion assay. Perform, acting through the production of reactive oxygen species, generally downregulated expression of extracellular proteins in strains 6850, COL, ISP479C but upregulated these proteins in strain Newman. Upregulated proteins were
sae
dependent. The Perform component SDS, but not paraquat (another oxygen donor), mimicked the biocide effect. Eap (extracellular adherence protein) was most prominently augmented. Upregulation of
eap
and
sae
was confirmed by qRT-PCR. Promoter activity of
sae
P1 was increased by Perform and SDS. Both substances enhanced cellular invasiveness, by 2.5-fold and 3.2-fold, respectively. Increased invasiveness was dependent on Eap and the
sae
system, whereas
agr
,
sarA
,
sigB
, and fibronectin-binding proteins had no major effect in strain Newman. This unique response pattern was due to a point mutation in SaeS (the sensor histidine kinase), as demonstrated by allele swapping. Newman
saePQRS
ISP479C
behaved like ISP479C, whereas
saePQRS
Newman
rendered ISP479C equally responsive as Newman. Taken together, the findings indicate that a point mutation in SaeS of strain Newman was responsible for increased expression of Eap upon exposure to sublethal Perform and SDS concentrations, leading to increased Eap-dependent cellular invasiveness. This may be important for understanding the regulation of virulence in
S. aureus
.
LuxS-Based Quorum Sensing Does Not Affect the Ability ofSalmonella entericaSerovar Typhimurium To Express the SPI-1 Type 3 Secretion System, Induce Membrane Ruffles, or Invade Epithelial Cells
Authors: Perrett Charlotte A. , Karavolos Michail H. , Humphrey Suzanne , Mastroeni Pietro , Martinez-Argudo Isabel , Spencer Hannah , Bulmer David , Winzer Klaus , McGhie Emma , Koronakis Vassilis , Williams Paul , Khan C. M. Anjam , Jepson Mark A. 
Published: September 2009

ABSTRACTBacterial species can communicate by producing and sensing small autoinducer molecules by a process known as quorum sensing.Salmonella entericaproduces autoinducer 2 (AI-2) via theluxSsynthase gene, which is used by some bacterial pathogens to coordinate virulence gene expression with population density. We investigated whether theluxSgene might affect the ability ofSalmonella entericaserovar Typhimurium to invade epithelial cells. No differences were found between the wild-type strain ofS. Typhimurium, SL1344, and its isogenicluxSmutant with respect to the number and morphology of the membrane ruffles induced or their ability to invade epithelial cells. The dynamics of the ruffling process were also similar in the wild-type strain (SL1344) and theluxSmutant. Furthermore, comparing the Salmonella pathogenicityisland 1 (SPI-1) type 3 secretion profiles of wild-type SL1344 and theluxSmutant by Western blotting and measuring the expression of a single-copy green fluorescent protein fusion to theprgH(an essential SPI-1 gene) promoter indicated that SPI-1 expression and activity are similar in the wild-type SL1344 andluxSmutant. Genetic deletion ofluxSdid not alter the virulence ofS. Typhimurium in the mouse model, and therefore, it appears thatluxSdoes not play a significant role in regulating invasion ofSalmonellain vitro or in vivo.
The Catalase-Peroxidase KatG Is Required for Virulence of
Xanthomonas campestris
pv. campestris in a Host Plant by Providing Protection against Low Levels of H
2
O
2
Authors: Jittawuttipoka Thichakorn , Buranajitpakorn Sarinya , Vattanaviboon Paiboon , Mongkolsuk Skorn 
Published: September 2009

ABSTRACT

Xanthomonas campestris
pv. campestris
katG
encodes a catalase-peroxidase that has a role in protecting the bacterium against micromolar concentrations of H
2
O
2
. A knockout mutation in
katG
that causes loss of catalase-peroxidase activity correlates with increased susceptibility to H
2
O
2
and a superoxide generator and is avirulent in a plant model system.
katG
expression is induced by oxidants in an OxyR-dependent manner.