bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathway and Evolutionary Implications of Diphenylamine Biodegradation by
Burkholderia
sp. Strain JS667
Authors: Shin Kwanghee A. , Spain Jim C. 
Published: February 2009

ABSTRACT

Diphenylamine (DPA) is a common contaminant at munitions-contaminated sites as well as at aniline manufacturing sites. Little is known about the biodegradation of the compound, and bacteria able to use DPA as the growth substrate have not been reported.
Burkholderia
sp. strain JS667 and
Ralstonia
sp. strain JS668 were isolated by selective enrichment from DPA-contaminated sediment. The isolates grew aerobically with DPA as the sole carbon, nitrogen, and energy source. During induction of DPA degradation, stoichiometric amounts of aniline accumulated and then disappeared, which suggested that aniline is on the DPA degradation pathway. Genes encoding the enzymes that catalyze the initial steps in DPA degradation were cloned from the genomic DNA of strain JS667. The
Escherichia coli
clone catalyzed stoichiometric transformation of DPA to aniline and catechol. Transposon mutagenesis, the sequence similarity of putative open reading frames to those of well-characterized dioxygenases, and
18
O
2
experiments support the conclusion that the initial reaction in DPA degradation is catalyzed by a multicomponent ring-hydroxylating dioxygenase. DPA is converted to aniline and catechol via dioxygenation at the 1,2 position of the aromatic ring and spontaneous rearomatization. Aniline and catechol are further biodegraded by the well-established aniline degradation pathway. Genes that encode the complete aniline degradation pathway were found 12 kb downstream of the genes that encode the initial dioxygenase. Expression of the relevant dioxygenases was confirmed by reverse transcription-PCR analysis. Both the sequence similarity and the gene organization suggest that the DPA degradation pathway evolved recently by the recruitment of two gene clusters that encode the DPA dioxygenase and aniline degradation pathway.
Chimeric Genomes of Natural Hybrids of
Saccharomyces cerevisiae
and
Saccharomyces kudriavzevii
Authors: Belloch Carmela , Pérez-Torrado Roberto , González Sara S. , Pérez-Ortín José E. , García-Martínez José , Querol Amparo , Barrio Eladio 
Published: February 2009

ABSTRACT

Recently, a new type of hybrid resulting from the hybridization between
Saccharomyces cerevisiae
and
Saccharomyces kudriavzevii
was described. These strains exhibit physiological properties of potential biotechnological interest. A preliminary characterization of these hybrids showed a trend to reduce the
S. kudriavzevii
fraction of the hybrid genome. We characterized the genomic constitution of several wine
S. cerevisiae
×
S. kudriavzevii
strains by using a combined approach based on the restriction fragment length polymorphism analysis of gene regions, comparative genome hybridizations with
S. cerevisiae
DNA arrays, ploidy analysis, and gene dose determination by quantitative real-time PCR. The high similarity in the genome structures of the
S. cerevisiae
×
S. kudriavzevii
hybrids under study indicates that they originated from a single hybridization event. After hybridization, the hybrid genome underwent extensive chromosomal rearrangements, including chromosome losses and the generation of chimeric chromosomes by the nonreciprocal recombination between homeologous chromosomes. These nonreciprocal recombinations between homeologous chromosomes occurred in highly conserved regions, such as Ty long terminal repeats (LTRs), rRNA regions, and conserved protein-coding genes. This study supports the hypothesis that chimeric chromosomes may have been generated by a mechanism similar to the recombination-mediated chromosome loss acting during meiosis in
Saccharomyces
hybrids. As a result of the selective processes acting during fermentation, hybrid genomes maintained the
S. cerevisiae
genome but reduced the
S. kudriavzevii
fraction.
Microbial Mineral Weathering for Nutrient Acquisition Releases Arsenic
Authors: Mailloux Brian J. , Alexandrova Ekaterina , Keimowitz Alison R. , Wovkulich Karen , Freyer Greg A. , Herron Michael , Stolz John F. , Kenna Timothy C. , Pichler Thomas , Polizzotto Matthew L. , Dong Hailiang , Bishop Michael , Knappett Peter S. K. 
Published: February 2009

ABSTRACT

Tens of millions of people in Southeast Asia drink groundwater contaminated with naturally occurring arsenic. How arsenic is released from the sediment into the water remains poorly understood. Here, we show in laboratory experiments that phosphate-limited cells of
Burkholderia fungorum
mobilize ancillary arsenic from apatite. We hypothesize that arsenic mobilization is a by-product of mineral weathering for nutrient acquisition. The released arsenic does not undergo a redox transformation but appears to be solubilized from the apatite mineral lattice during weathering. Analysis of apatite from the source area in the Himalayan basin indicates the presence of elevated levels of arsenic, with an average concentration of 210 mg/kg. The rate of arsenic release is independent of the initial dissolved arsenic concentration and occurs at phosphate levels observed in Bangladesh aquifers. We also demonstrate the presence of the microbial phenotype that releases arsenic from apatite in Bangladesh aquifer sediments and groundwater. These results suggest that microbial mineral weathering for nutrient acquisition could be an important mechanism for arsenic mobilization.
Cellulase Production from Spent Lignocellulose Hydrolysates by Recombinant
Aspergillus niger
Authors: Alriksson Björn , Rose Shaunita H. , van Zyl Willem H. , Sjöde Anders , Nilvebrant Nils-Olof , Jönsson Leif J. 
Published: February 2009

ABSTRACT

A recombinant
Aspergillus niger
strain expressing the
Hypocrea jecorina
endoglucanase Cel7B was grown on spent hydrolysates (stillage) from sugarcane bagasse and spruce wood. The spent hydrolysates served as excellent growth media for the Cel7B-producing strain,
A. niger
D15[
egI
], which displayed higher endoglucanase activities in the spent hydrolysates than in standard medium with a comparable monosaccharide content (e.g., 2,100 nkat/ml in spent bagasse hydrolysate compared to 480 nkat/ml in standard glucose-based medium). In addition,
A. niger
D15[
egI
] was also able to consume or convert other lignocellulose-derived compounds, such as acetic acid, furan aldehydes, and phenolic compounds, which are recognized as inhibitors of yeast during ethanolic fermentation. The results indicate that enzymes can be produced from the stillage stream as a high-value coproduct in second-generation bioethanol plants in a way that also facilitates recirculation of process water.
Climate and Tick Seasonality Are Predictors of
Borrelia burgdorferi
Genotype Distribution
Authors: Gatewood Anne G. , Liebman Kelly A. , Vourc'h Gwenaël , Bunikis Jonas , Hamer Sarah A. , Cortinas Roberto , Melton Forrest , Cislo Paul , Kitron Uriel , Tsao Jean , Barbour Alan G. , Fish Durland , Diuk-Wasser Maria A. 
Published: February 2009

ABSTRACT

The blacklegged tick,
Ixodes scapularis
, is of significant public health importance as a vector of
Borrelia burgdorferi
, the agent of Lyme borreliosis. The timing of seasonal activity of each immature
I. scapularis
life stage relative to the next is critical for the maintenance of
B. burgdorferi
because larvae must feed after an infected nymph to efficiently acquire the infection from reservoir hosts. Recent studies have shown that some strains of
B. burgdorferi
do not persist in the primary reservoir host for more than a few weeks, thereby shortening the window of opportunity between nymphal and larval feeding that sustains their enzootic maintenance. We tested the hypothesis that climate is predictive of geographic variation in the seasonal activity of
I. scapularis
, which in turn differentially influences the distribution of
B. burgdorferi
genotypes within the geographic range of
I. scapularis
. We analyzed the relationships between climate, seasonal activity of
I. scapularis
, and
B. burgdorferi
genotype frequency in 30 geographically diverse sites in the northeastern and midwestern United States. We found that the magnitude of the difference between summer and winter daily temperature maximums was positively correlated with the degree of seasonal synchrony of the two immature stages of
I. scapularis
. Genotyping revealed an enrichment of 16S-23S rRNA intergenic spacer restriction fragment length polymorphism sequence type 1 strains relative to others at sites with lower seasonal synchrony. We conclude that climate-associated variability in the timing of
I. scapularis
host seeking contributes to geographic heterogeneities in the frequencies of
B. burgdorferi
genotypes, with potential consequences for Lyme borreliosis morbidity.
Coculture Fermentations ofBifidobacteriumSpecies andBacteroides thetaiotaomicronReveal a Mechanistic Insight into the Prebiotic Effect of Inulin-Type Fructans
Authors: Falony Gwen , Calmeyn Thomas , Leroy Frédéric , De Vuyst Luc 
Published: February 2009

ABSTRACTFour bifidobacteria, each representing a cluster of strains with specific inulin-type-fructan degradation capacities, were grown in coculture fermentations withBacteroides thetaiotaomicronLMG 11262, a strain able to metabolize both oligofructose and inulin. In a medium for colon bacteria with inulin as the sole added energy source, the ability of the bifidobacteria to compete for this substrate reflected phenotypical variation.Bifidobacterium breveYakult, a strain that was not able to degrade oligofructose or inulin, was outcompeted byB. thetaiotaomicronLMG 11262.Bifidobacterium adolescentisLMG 10734, a strain that could degrade oligofructose (displaying a preferential breakdown mechanism) but that did not grow on inulin, managed to become competitive when oligofructose and short fractions of inulin started to accumulate in the fermentation medium.Bifidobacterium angulatumLMG 11039T, a strain that was previously shown to degrade all oligofructose fractions simultaneously and to be able to partially break down inulin, was competitive from the beginning of the fermentation, consuming short fractions of inulin from the moment they appeared.Bifidobacterium longumLMG 11047, representing a cluster of bifidobacteria that shared both high fructose consumption and oligofructose degradation rates and were able to perform partial breakdown of inulin, was the dominating strain in a coculture withB. thetaiotaomicronLMG 11262. These observations indicate that distinct subgroups within the large-intestinalBifidobacteriumpopulation will be stimulated by different groups of prebiotic inulin-type fructans, a variation that could be reflected in differences concerning their health-promoting effects.
Effect of Substrate Concentration on Carbon Isotope Fractionation during Acetoclastic Methanogenesis by
Methanosarcina barkeri
and
M. acetivorans
and in Rice Field Soil
Authors: Goevert Dennis , Conrad Ralf 
Published: February 2009

ABSTRACT

Methanosarcina
is the only acetate-consuming genus of methanogenic archaea other than
Methanosaeta
and thus is important in methanogenic environments for the formation of the greenhouse gases methane and carbon dioxide. However, little is known about isotopic discrimination during acetoclastic CH
4
production. Therefore, we studied two species of the
Methanosarcinaceae
family,
Methanosarcina barkeri
and
Methanosarcina acetivorans
, and a methanogenic rice field soil amended with acetate. The values of the isotope enrichment factor (ε) associated with consumption of total acetate (ε
ac
), consumption of acetate-methyl (ε
ac-methyl
) and production of CH
4
(ε
CH4
) were an ε
ac
of −30.5‰, an ε
ac-methyl
of −25.6‰, and an ε
CH4
of −27.4‰ for
M. barkeri
and an ε
ac
of −35.3‰, an ε
ac-methyl
of −24.8‰, and an ε
CH4
of −23.8‰ for
M. acetivorans
. Terminal restriction fragment length polymorphism of archaeal 16S rRNA genes indicated that acetoclastic methanogenic populations in rice field soil were dominated by
Methanosarcina
spp. Isotope fractionation determined during acetoclastic methanogenesis in rice field soil resulted in an ε
ac
of −18.7‰, an ε
ac-methyl
of −16.9‰, and an ε
CH4
of −20.8‰. However, in rice field soil as well as in the pure cultures, values of ε
ac
and ε
ac-methyl
decreased as acetate concentrations decreased, eventually approaching zero. Thus, isotope fractionation of acetate carbon was apparently affected by substrate concentration. The ε values determined in pure cultures were consistent with those in rice field soil if the concentration of acetate was taken into account.
CodY in
Staphylococcus aureus
: a Regulatory Link between Metabolism and Virulence Gene Expression
Authors: Pohl Konstanze , Francois Patrice , Stenz Ludwig , Schlink Frank , Geiger Tobias , Herbert Silvia , Goerke Christiane , Schrenzel Jacques , Wolz Christiane 
Published: February 2009

ABSTRACT

The repressor CodY is reported to inhibit metabolic genes mainly involved in nitrogen metabolism. We analyzed
codY
mutants from three unrelated
Staphylococcus aureus
strains (Newman, UAMS-1, and RN1HG). The mutants grew more slowly than their parent strains in a chemically defined medium. However, only
codY
mutants were able to grow in medium lacking threonine. An excess of isoleucine resulted in growth inhibition in the wild type but not in the
codY
mutants, indicating that isoleucine plays a role in CodY-dependent repression. Prototypic CodY-repressed genes including the virulence regulator
agr
are repressed after up-shift with isoleucine. The CodY-dependent repression of
agr
is consistent with the concomitant influence of CodY on typical
agr
-regulated genes such as
cap
,
spa
,
fnbA
, and
coa
. However, some of these virulence genes (e.g.,
cap
,
fnbA
, and
spa
) were also regulated by CodY in an
agr-
negative background. Microarray analysis revealed that the large majority of CodY-repressed genes were involved in amino acid metabolism; CodY-activated genes were mainly involved in nucleotide metabolism or virulence. In summary, CodY in
S. aureus
not only acts as a repressor for genes involved in nitrogen metabolism but also contributes to virulence gene regulation by supporting as well as substituting for
agr
function.
The LiaFSR System Regulates the Cell Envelope Stress Response inStreptococcus mutans
Authors: Suntharalingam Prashanth , Senadheera M. D. , Mair Richard W. , Lévesque Céline M. , Cvitkovitch Dennis G. 
Published: February 2009

ABSTRACTMaintaining cell envelope integrity is critical for bacterial survival, including bacteria living in a complex and dynamic environment such as the human oral cavity.Streptococcus mutans, a major etiological agent of dental caries, uses two-component signal transduction systems (TCSTSs) to monitor and respond to various environmental stimuli. Previous studies have shown that the LiaSR TCSTS inS. mutansregulates virulence traits such as acid tolerance and biofilm formation. Although not examined in streptococci, homologs of LiaSR are widely disseminated inFirmicutesand function as part of the cell envelope stress response network. We describe hereliaSRand its upstreamliaFgene in the cell envelope stress tolerance ofS. mutansstrain UA159. Transcriptional analysis establishedliaSRas part of the pentacistronicliaFSR-ppiB-pnpBoperon. A survey of cell envelope antimicrobials revealed that mutants deficient in one or all of theliaFSRgenes were susceptible to Lipid II cycle interfering antibiotics and to chemicals that perturbed the cell membrane integrity. These compounds inducedliaRtranscription in a concentration-dependent manner. Notably, under bacitracin stress conditions, the LiaFSR signaling system was shown to induce transcription of several genes involved in membrane protein synthesis, peptidoglycan biosynthesis, envelope chaperone/proteases, and transcriptional regulators. In the absence of an inducer such as bacitracin, LiaF repressed LiaR-regulated expression, whereas supplementing cultures with bacitracin resulted in derepression ofliaSR. While LiaF appears to be an integral component of the LiaSR signaling cascade, taken collectively, we report a novel role for LiaFSR in sensing cell envelope stress and preserving envelope integrity inS. mutans.
Mqo, a Tricarboxylic Acid Cycle Enzyme, Is Required for Virulence of
Pseudomonas syringae
pv. tomato Strain DC3000 on
Arabidopsis thaliana
Authors: Mellgren Eve M. , Kloek Andrew P. , Kunkel Barbara N. 
Published: February 2009

ABSTRACT

Plant pathogenic bacteria, such as
Pseudomonas syringae
pv. tomato strain DC3000, the causative agent of tomato bacterial speck disease, grow to high levels in the apoplastic space between plant cells. Colonization of plant tissue requires expression of virulence factors that modify the apoplast to make it more suitable for pathogen growth or facilitate adaptation of the bacteria to the apoplastic environment. To identify new virulence factors involved in these processes, DC3000 Tn
5
transposon insertion mutants with reduced virulence on
Arabidopsis thaliana
were identified. In one of these mutants, the Tn
5
insertion disrupted the malate:quinone oxidoreductase gene (
mqo
), which encodes an enzyme of the tricarboxylic acid cycle.
mqo
mutants do not grow to wild-type levels in plant tissue at early time points during infection. Further, plants infected with
mqo
mutants develop significantly reduced disease symptoms, even when the growth of the
mqo
mutant reaches wild-type levels at late stages of infection. Mutants lacking
mqo
function grow more slowly in culture than wild-type bacteria when dicarboxylates are the only available carbon source. To explore whether dicarboxylates are important for growth of DC3000 in the apoplast, we disrupted the
dctA1
dicarboxylate transporter gene. DC3000 mutants lacking
dctA1
do not grow to wild-type levels in planta, indicating that transport and utilization of dicarboxylates are important for virulence of DC3000. Thus,
mqo
may be required by DC3000 to meet nutritional requirements in the apoplast and may provide insight into the mechanisms underlying the important, but poorly understood process of adaptation to the host environment.
Chemotaxis to Pyrimidines and Identification of a Cytosine Chemoreceptor in
Pseudomonas putida
Authors: Liu Xianxian , Wood Piper L. , Parales Juanito V. , Parales Rebecca E. 
Published: February 2009

ABSTRACT

We developed a high-throughput quantitative capillary assay and demonstrated that
Pseudomonas putida
strains F1 and PRS2000 were attracted to cytosine, but not thymine or uracil. In contrast,
Pseudomonas aeruginosa
PAO1 was not chemotactic to any pyrimidines. Chemotaxis assays with a mutant strain of F1 in which the putative methyl-accepting chemotaxis protein-encoding gene Pput_0623 was deleted revealed that this gene (designated
mcpC
) encodes a chemoreceptor for positive chemotaxis to cytosine.
P. putida
F1 also responded weakly to cytidine, uridine, and thymidine, but these responses were not mediated by
mcpC
. Complementation of the F1 Δ
mcpC
mutant XLF004 with the wild-type gene restored chemotaxis to cytosine. In addition, introduction of this gene into
P. aeruginosa
PAO1 conferred the ability to respond to cytosine. To our knowledge, this is the first report of a chemoreceptor for cytosine.
A Vitamin B12-Based System for Conditional Expression RevealsdksATo Be an Essential Gene inMyxococcus xanthus
Authors: García-Moreno Diana , Polanco María Carmen , Navarro-Avilés Gloria , Murillo Francisco J. , Padmanabhan S. , Elías-Arnanz Montserrat 
Published: February 2009

ABSTRACTMyxococcus xanthusis a prokaryotic model system for the study of multicellular development and the response to blue light. The previous analyses of these processes and the characterization of new genes would benefit from a robust system for controlled gene expression, which has been elusive so far for this bacterium. Here, we describe a system for conditional expression of genes inM. xanthusbased on our recent finding that vitamin B12and CarH, a MerR-type transcriptional repressor, together downregulate a photoinducible promoter. Using this system, we confirmed thatM. xanthus rpoN, encoding σ54, is an essential gene, as reported earlier. We then tested it withftsZanddksA. In most bacteria,ftsZis vital due to its role in cell division, whereas null mutants ofdksA, whose product regulates the stringent response via transcriptional control of rRNA and amino acid biosynthesis promoters, are viable but cause pleiotropic effects. As withrpoN, it was impossible to delete endogenousftsZordksAinM. xanthusexcept in a merodiploid background carrying another functional copy, which indicates that these are essential genes. B12-based conditional expression offtsZwas insufficient to provide the high intracellular FtsZ levels required. WithdksA, as withrpoN, cells were viable under permissive but not restrictive conditions, and depletion of DksA or σ54produced filamentous, aberrantly dividing cells.dksAthus joinsrpoNin a growing list of genes dispensable in many bacteria but essential inM. xanthus.
Phylogeography of
Francisella tularensis
: Global Expansion of a Highly Fit Clone
Authors: Vogler Amy J. , Birdsell Dawn , Price Lance B. , Bowers Jolene R. , Beckstrom-Sternberg Stephen M. , Auerbach Raymond K. , Beckstrom-Sternberg James S. , Johansson Anders , Clare Ashley , Buchhagen Jordan L. , Petersen Jeannine M. , Pearson Talima , Vaissaire Josée , Dempsey Michael P. , Foxall Paul , Engelthaler David M. , Wagner David M. , Keim Paul 
Published: February 2009

ABSTRACT

Francisella tularensis
contains several highly pathogenic subspecies, including
Francisella tularensis
subsp.
holarctica
, whose distribution is circumpolar in the northern hemisphere. The phylogeography of these subspecies and their subclades was examined using whole-genome single nucleotide polymorphism (SNP) analysis, high-density microarray SNP genotyping, and real-time-PCR-based canonical SNP (canSNP) assays. Almost 30,000 SNPs were identified among 13 whole genomes for phylogenetic analysis. We selected 1,655 SNPs to genotype 95 isolates on a high-density microarray platform. Finally, 23 clade- and subclade-specific canSNPs were identified and used to genotype 496 isolates to establish global geographic genetic patterns. We confirm previous findings concerning the four subspecies and two
Francisella tularensis
subsp.
tularensis
subpopulations and identify additional structure within these groups. We identify 11 subclades within
F. tularensis
subsp.
holarctica
, including a new, genetically distinct subclade that appears intermediate between Japanese
F. tularensis
subsp.
holarctica
isolates and the common
F. tularensis
subsp.
holarctica
isolates associated with the radiation event (the B radiation) wherein this subspecies spread throughout the northern hemisphere. Phylogenetic analyses suggest a North American origin for this B-radiation clade and multiple dispersal events between North America and Eurasia. These findings indicate a complex transmission history for
F. tularensis
subsp.
holarctica
.