bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Riboswitch Regulates a Thiamine Pyrophosphate ABC Transporter of the Oral Spirochete Treponema denticola
Authors: Bian Jiang , Shen Hongwu , Tu Youbin , Yu Aiming , Li Chunhao 
Published: May 2011

ABSTRACT

Thiamine pyrophosphate (TPP), a biologically active form of thiamine (vitamin B
1
), is an essential cofactor in all living systems. Microorganisms either synthesize TPP via
de novo
biosynthesis pathways or uptake exogenous thiamine from the environment via specific transporters. The oral spirochete
Treponema denticola
is an important pathogen that is associated with human periodontal diseases. It lacks a
de novo
TPP biosynthesis pathway and needs exogenous TPP for growth, suggesting that it may obtain exogenous TPP via a thiamine transporter. In this study, we identified a gene cluster that encodes a TPP ABC transporter which consists of a TPP-binding protein (TDE0143), a transmembrane permease (TDE0144), and a cytosolic ATPase (TDE0145). Transcriptional and translational analyses showed that the genes encoding these three proteins are cotranscribed and form an operon (

tbpABC
Td

) that is initiated by a σ
70
-like promoter. The expression level of this operon is negatively regulated by exogenous TPP and is mediated by a TPP-sensing riboswitch (Td

thi-

box
). Genetic and biochemical studies revealed that the
TDE0143
deletion mutant (
T. denticola
Δ
tbpA
) had a decreased ability to transport exogenous TPP, and the mutant failed to grow when exogenous TPP was insufficient. These results taken together indicate that the

tbpABC
Td

operon encodes an ABC transporter that is required for the uptake of exogenous TPP and that the expression of this operon is regulated by a TPP-binding riboswitch via a feedback inhibition mechanism.
Genomes of Three Methylotrophs from a Single Niche Reveal the Genetic and Metabolic Divergence of the Methylophilaceae
Authors: Lapidus Alla , Clum Alicia , LaButti Kurt , Kaluzhnaya Marina G. , Lim Sujung , Beck David A. C. , Glavina del Rio Tijana , Nolan Matt , Mavromatis Konstantinos , Huntemann Marcel , Lucas Susan , Lidstrom Mary E. , Ivanova Natalia , Chistoserdova Ludmila 
Published: May 2011

ABSTRACT

The genomes of three representatives of the family
Methylophilaceae
,
Methylotenera mobilis
JLW8,
Methylotenera versatilis
301, and
Methylovorus glucosetrophus
SIP3-4, all isolated from a single study site, Lake Washington in Seattle, WA, were completely sequenced. These were compared to each other and to the previously published genomes of
Methylobacillus flagellatus
KT and an unclassified
Methylophilales
strain, HTCC2181. Comparative analysis revealed that the core genome of
Methylophilaceae
may be as small as approximately 600 genes, while the pangenome may be as large as approximately 6,000 genes. Significant divergence between the genomes in terms of both gene content and gene and protein conservation was uncovered, including the varied presence of certain genes involved in methylotrophy. Overall, our data demonstrate that metabolic potentials can vary significantly between different species of
Methylophilaceae
, including organisms inhabiting the very same environment. These data suggest that genetic divergence among the members of this family may be responsible for their specialized and nonredundant functions in C
1
cycling, which in turn suggests means for their successful coexistence in their specific ecological niches.
Using Single-Nucleotide Polymorphisms To Discriminate Disease-Associated from Carried Genomes of Neisseria meningitidis
Authors: Katz Lee S. , Sharma Nitya V. , Harcourt Brian H. , Thomas Jennifer Dolan , Wang Xin , Mayer Leonard W. , Jordan I. King 
Published: May 2011

ABSTRACT

Neisseria meningitidis
is one of the main agents of bacterial meningitis, causing substantial morbidity and mortality worldwide. However, most of the time
N. meningitidis
is carried as a commensal not associated with invasive disease. The genomic basis of the difference between disease-associated and carried isolates of
N. meningitidis
may provide critical insight into mechanisms of virulence, yet it has remained elusive. Here, we have taken a comparative genomics approach to interrogate the difference between disease-associated and carried isolates of
N. meningitidis
at the level of individual nucleotide variations (i.e., single nucleotide polymorphisms [SNPs]). We aligned complete genome sequences of 8 disease-associated and 4 carried isolates of
N. meningitidis
to search for SNPs that show mutually exclusive patterns of variation between the two groups. We found 63 SNPs that distinguish the 8 disease-associated genomes from the 4 carried genomes of
N. meningitidis
, which is far more than can be expected by chance alone given the level of nucleotide variation among the genomes. The putative list of SNPs that discriminate between disease-associated and carriage genomes may be expected to change with increased sampling or changes in the identities of the isolates being compared. Nevertheless, we show that these discriminating SNPs are more likely to reflect phenotypic differences than shared evolutionary history. Discriminating SNPs were mapped to genes, and the functions of the genes were evaluated for possible connections to virulence mechanisms. A number of overrepresented functional categories related to virulence were uncovered among SNP-associated genes, including genes related to the category “symbiosis, encompassing mutualism through parasitism.”
Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements
Authors: Chan Cheong Xin , Beiko Robert G. , Ragan Mark A. 
Published: May 2011

ABSTRACT

The widespread presence of antibiotic resistance and virulence among
Staphylococcus
isolates has been attributed in part to lateral genetic transfer (LGT), but little is known about the broader extent of LGT within this genus. Here we report the first systematic study of the modularity of genetic transfer among 13
Staphylococcus
genomes covering four distinct named species. Using a topology-based phylogenetic approach, we found, among 1,354 sets of homologous genes examined, strong evidence of LGT in 368 (27.1%) gene sets, and weaker evidence in another 259 (19.1%). Within-gene and whole-gene transfer contribute almost equally to the topological discordance of these gene sets against a reference phylogeny. Comparing genetic transfer in single-copy and in multicopy gene sets, we observed a higher frequency of LGT in the latter, and a substantial functional bias in cases of whole-gene transfer (little such bias was observed in cases of fragmentary genetic transfer). We found evidence that lateral transfer, particularly of entire genes, impacts not only functions related to antibiotic, drug, and heavy-metal resistance, as well as membrane transport, but also core informational and metabolic functions not associated with mobile elements. Although patterns of sequence similarity support the cohesion of recognized species, LGT within
S. aureus
appears frequently to disrupt clonal complexes. Our results demonstrate that LGT and gene duplication play important parts in functional innovation in staphylococcal genomes.
Role of High-Fidelity Escherichia coli DNA Polymerase I in Replication Bypass of a Deoxyadenosine DNA-Peptide Cross-Link
Authors: Yamanaka Kinrin , Minko Irina G. , Finkel Steven E. , Goodman Myron F. , Lloyd R. Stephen 
Published: May 2011

ABSTRACT

Reaction of bifunctional electrophiles with DNA in the presence of peptides can result in DNA-peptide cross-links. In particular, the linkage can be formed in the major groove of DNA via the exocyclic amino group of adenine (
N
6
-dA). We previously demonstrated that an A family human polymerase, Pol ν, can efficiently and accurately synthesize DNA past
N
6
-dA-linked peptides. Based on these results, we hypothesized that another member of that family,
Escherichia coli
polymerase I (Pol I), may also be able to bypass these large major groove DNA lesions. To test this, oligodeoxynucleotides containing a site-specific
N
6
-dA dodecylpeptide cross-link were created and utilized for
in vitro
DNA replication assays using
E. coli
DNA polymerases. The results showed that Pol I and Pol II could efficiently and accurately bypass this adduct, while Pol III replicase, Pol IV, and Pol V were strongly inhibited. In addition, cellular studies were conducted using
E. coli
strains that were either wild type or deficient in all three DNA damage-inducible polymerases, i.e., Pol II, Pol IV, and Pol V. When single-stranded DNA vectors containing a site-specific
N
6
-dA dodecylpeptide cross-link were replicated in these strains, the efficiencies of replication were comparable, and in both strains, intracellular bypass of the lesion occurred in an error-free manner. Collectively, these findings demonstrate that despite its constrained active site, Pol I can catalyze DNA synthesis past
N
6
-dA-linked peptide cross-links and is likely to play an essential role in cellular bypass of large major groove DNA lesions.
Functional Organization of MobB, a Small Protein Required for Efficient Conjugal Transfer of Plasmid R1162
Authors: Meyer Richard 
Published: May 2011

ABSTRACT
MobB is a small (molecular weight = 15,097) protein encoded by the broad-host-range plasmid R1162 and is required for its efficient transfer by conjugation. The C-terminal half of the protein contains a membrane domain essential for transfer. This region can be replaced by a putative membrane domain from another, unrelated protein, and thus is likely to function independently from the rest of MobB. The other, functionally active region of MobB, identified by mutagenesis, is at the N-terminal end. One mutation affecting this region inhibits replication, suggesting that this part of the protein is contacting and sequestering the relaxase-linked primase. The overall organization reflects a multimeric and bipolar organization, with molecules of MobB anchored in the membrane at one end and engaging the relaxase at the other. This arrangement could increase the transfer frequency by raising the probability of contact between the relaxase and the membrane-embedded, coupling protein for type IV secretion.
Genome Sequence of Lactococcus garvieae 21881, Isolated in a Case of Human Septicemia
Authors: Aguado-Urda Mónica , López-Campos Guillermo H. , Blanco M. Mar , Fernández-Garayzábal José F. , Cutuli M. Teresa , Aspiroz Carmen , López-Alonso Victoria , Gibello Alicia 
Published: May 2011

ABSTRACT

Lactococcus garvieae
is a Gram-positive bacterium considered an important opportunistic emerging human pathogen and also a well-recognized fish pathogen. Here, we present the draft genome sequence of
Lactococcus garvieae
strain 21881 (2,164,557 bp, with a G+C content of 37.9%), which represents the first report of a genome sequence on
Lactococcus garvieae
.
Functional Characterization of Seven γ-Glutamylpolyamine Synthetase Genes and the
bauRABCD
Locus for Polyamine and β-Alanine Utilization in Pseudomonas aeruginosa PAO1
Authors: Yao Xiangyu , He Weiqing , Lu Chung-Dar 
Published: May 2011

ABSTRACT

Pseudomonas aeruginosa
and many other bacteria can utilize biogenic polyamines, including diaminopropane (DAP), putrescine (Put), cadaverine (Cad), and spermidine (Spd), as carbon and/or nitrogen sources. Transcriptome analysis in response to exogenous Put and Spd led to the identification of a list of genes encoding putative enzymes for the catabolism of polyamines. Among them,
pauA1
to
pauA6
,
pauB1
to
pauB4
,
pauC
, and
pauD1
and
pauD2
(
p
oly
a
mine
u
tilization) encode enzymes homologous to
Escherichia coli
PuuABCD of the γ-glutamylation pathway in converting Put into GABA. A series of unmarked
pauA
mutants was constructed for growth phenotype analysis. The results revealed that it requires specific combinations of
pauA
knockouts to abolish utilization of different polyamines and support the importance of γ-glutamylation for polyamine catabolism in
P. aeruginosa
. Another finding was that the list of Spd-inducible genes overlaps almost completely with that of Put-inducible ones except the
pauA3B2
operon and the
bauABCD
operon (
β
-
a
lanine
u
tilization). Mutation analysis led to the conclusion that
pauA3B2
participate in catabolism of DAP, which is related to the aminopropyl moiety of Spd, and that
bauABCD
are essential for growth on β-alanine derived from DAP (or Spd) catabolism via the γ-glutamylation pathway. Measurements of the
pauA3-lacZ
and
bauA-lacZ
expression indicated that these two promoters were differentially induced by Spd, DAP, and β-alanine but showed no apparent response to Put, Cad, and GABA. Induction of the
pauA3
and
bauA
promoters was abolished in the
bauR
mutant. The recombinant BauR protein was purified to demonstrate its interactions with the
pauA3
and
bauA
regulatory regions
in vitro
. In summary, the present study support that the γ-glutamylation pathway for polyamine utilization is evolutionarily conserved in
E. coli
and
Pseudomonas
spp. and is further expanded in
Pseudomonas
to accommodate a more diverse metabolic capacity in this group of microorganisms.
Quorum Sensing in Chromobacterium violaceum: DNA Recognition and Gene Regulation by the CviR Receptor
Authors: Stauff Devin L. , Bassler Bonnie L. 
Published: May 2011

ABSTRACT

The bacterial pathogen
Chromobacterium violaceum
uses a LuxIR-type quorum-sensing system to detect and respond to changes in cell population density. CviI synthesizes the autoinducer C
10
-homoserine lactone (C
10
-HSL), and CviR is a cytoplasmic DNA binding transcription factor that activates gene expression following binding to C
10
-HSL. A number of behaviors are controlled by quorum sensing in
C. violaceum
. However, few genes have been shown to be directly controlled by CviR, in part because the DNA motif bound by CviR is not well characterized. Here, we define the DNA sequence required for promoter recognition by CviR. Using
in vivo
data generated from a library of point mutations in a CviR-regulated promoter, we find that CviR binds to a palindrome with the ideal sequence CTGNCCNNNNGGNCAG. We constructed a position weight matrix using these
in vivo
data and scanned the
C. violaceum
genome to predict CviR binding sites. We measured direct activation of the identified promoters by CviR and found that CviR controls the expression of the promoter for a chitinase, a type VI secretion-related gene, a transcriptional regulator gene, a guanine deaminase gene, and
cviI
. Indeed, regulation of
cviI
expression by CviR generates a canonical quorum-sensing positive-feedback loop.
Complete Genome Sequence of Melissococcus plutonius ATCC 35311
Authors: Okumura Kayo , Arai Rie , Okura Masatoshi , Kirikae Teruo , Takamatsu Daisuke , Osaki Makoto , Miyoshi-Akiyama Tohru 
Published: May 2011

ABSTRACT

We report the first completely annotated genome sequence of
Melissococcus plutonius
ATCC 35311.
M. plutonius
is a one-genus, one-species bacterium and the etiological agent of European foulbrood of the honeybee. The genome sequence will provide new insights into the molecular mechanisms underlying its pathogenicity.
Quantitative Analysis of Spatial-Temporal Correlations during Germination of Spores of Bacillus Species
Authors: Zhang Jinqiao , Garner Will , Setlow Peter , Yu Ji 
Published: May 2011

ABSTRACT

Bacteria of
Bacillus
species sporulate upon starvation, and the resultant dormant spores germinate when the environment appears likely to allow the resumption of vegetative growth. Normally, the rates of germination of individual spores in populations are very heterogeneous, and the current work has investigated whether spore-to-spore communication enhances the synchronicity of germination. In order to do this work, time-lapse optical images of thousands of individual spores were captured during germination, and an image analysis algorithm was developed to do the following: (i) measure the positions and germination rates of many thousands of individual spores and (ii) compute pairwise correlations of their germination. This analysis showed that an individual spore's germination rate was dependent on its distance from other spores, especially at short distances. Thus, spores that were within a few micrometers exhibited an increased synchronicity in germination, suggesting that there is a mechanism for short-range communication between such spores during germination. However, two molecules known to be germinants that are released during germination,
l
-alanine and the 1:1 chelate of Ca
2+
and dipicolinic acid, did not mediate spore-to-spore communication during germination.
Complete Genome Sequence of Lactobacillus buchneri NRRL B-30929, a Novel Strain from a Commercial Ethanol Plant
Authors: Liu Siqing , Leathers Timothy D. , Copeland Alex , Chertkov Olga , Goodwin Lynne , Mills David A. 
Published: May 2011

ABSTRACT

Lactobacillus buchneri
strain NRRL B-30929 was a contaminant obtained from a commercial ethanol fermentation. This facultative anaerobe is unique because of its rapid growth on xylose and simultaneous fermentation of xylose and glucose. The strain utilizes a broad range of carbohydrate substrates and possesses a high tolerance to ethanol and other stresses, making it an attractive candidate for bioconversion of biomass substrates to various bioproducts. The genome sequence of NRRL B-30929 will provide insight into the unique properties of this lactic acid bacterium.
Complete Genome Sequence of Bordetella pertussis CS, a Chinese Pertussis Vaccine Strain
Authors: Zhang Shumin , Xu Yinghua , Zhou Zhemin , Wang Shaojing , Yang Ruifu , Wang Junzhi , Wang Lei 
Published: May 2011

ABSTRACT

Bordetella pertussis
is the causative agent of pertussis. Here, we report the genome sequence of
Bordetella pertussis
strain CS, isolated from an infant patient in Beijing and widely used as a vaccine strain for production of an acellular pertussis vaccine in China.
Phosphorylation of Spo0A by the Histidine Kinase KinD Requires the Lipoprotein Med in Bacillus subtilis
Authors: Banse Allison V. , Hobbs Errett C. , Losick Richard 
Published: May 2011

ABSTRACT

The response regulatory protein Spo0A of
Bacillus subtilis
is activated by phosphorylation by multiple histidine kinases via a multicomponent phosphorelay. Here we present evidence that the activity of one of the kinases, KinD, depends on the lipoprotein Med, a mutant of which has been known to cause a cannibalism phenotype. We show that the absence of Med impaired and the overproduction of Med stimulated the transcription of two operons (
sdp
and
skf
) involved in cannibalism whose transcription is known to depend on Spo0A in its phosphorylated state (Spo0A∼P). Further, these effects of Med were dependent on KinD but not on kinases KinA, KinB, and KinC. Additionally, we show that deletion or overproduction of Med impaired or enhanced, respectively, biofilm formation and that these effects, too, depended specifically on KinD. Finally, we report that overproduction of Med bypassed the dominant negative effect on transcription of
sdp
of a truncated KinD retaining the transmembrane segments but lacking the kinase domain. We propose that Med directly or indirectly interacts with KinD in the cytoplasmic membrane and that this interaction is required for KinD-dependent phosphorylation of Spo0A.
Genome Sequence of Pseudomonas sp. Strain S9, an Extracellular Arylsulfatase-Producing Bacterium Isolated from Mangrove Soil
Authors: Long Mengxian , Ruan Lingwei , Yu Ziniu , Xu Xun 
Published: May 2011

ABSTRACT

Pseudomonas
sp. strain S9 was originally isolated from mangrove soil in Xiamen, China. It is an aerobic bacterium which shows extracellular arylsulfatase activity. Here, we describe the 4.8-Mb draft genome sequence of
Pseudomonas
sp. S9, which exhibits novel cysteine-type sulfatases.
Complete Genome Sequence of the Universal Killer Salmonella enterica Serovar Typhimurium UK-1 (ATCC 68169)
Authors: Luo Yingqin , Kong Qingke , Yang Jiseon , Golden Greg , Wanda Soo-Young , Jensen Roderick V. , Ernst Peter B. , Curtiss Roy 
Published: May 2011

ABSTRACT

The
Salmonella enterica
serovar Typhimurium strain UK-1 exhibits the highest invasion and virulence attributes among the most frequently studied strains.
S.
Typhimurium UK-1 has been used as the foundation for developing recombinant vaccines and has been used extensively on virulence and colonization studies in chickens and mice. We describe here the complete genome sequence of
S.
Typhimurium UK-1. Comparative genomics of
Salmonella
Typhimurium will provide insight into factors that determine virulence and invasion.
Genome Sequence of the Algicidal Bacterium Kordia algicida OT-1
Authors: Lee Hyun Sook , Kang Sung Gyun , Kwon Kae Kyoung , Lee Jung-Hyun , Kim Sang-Jin 
Published: May 2011

ABSTRACT

Kordia algicida
OT-1 is an algicidal bacterium against the bloom-forming microalgae. The genome sequence of
K. algicida
revealed a number of interesting features, including the degradation of macromolecules, the biosynthesis of carotenoid pigment and secondary metabolites, and the capacity for gliding motility, which might facilitate the understanding of algicidal mechanisms.
Complete Genome Sequence of
Pusillimonas
sp. T7-7, a Cold-Tolerant Diesel Oil-Degrading Bacterium Isolated from the Bohai Sea in China
Authors: Cao Boyang , Ma Ting , Ren Yan , Ren Yi , Li Guoqiang , Li Ping , Guo Xi , Ding Peng , Feng Lu 
Published: May 2011

ABSTRACT

Pusillimonas
sp. T7-7 is a diesel oil-degrading cold-tolerant bacterium isolated from the benthal mud of a petroleum-contaminated site in Bohai Sea, China. We present here the complete genome sequence of T7-7. Genome analysis revealed many features of typical marine bacteria, including the absence of intact sugar metabolic pathways, the presence of glyoxylate and gluconeogenesis pathways, and the abilities for nitrate assimilation and denitrification, as well as sulfate reduction and sulfite oxidation. The presence of novel genes for the degradation of diesel oils was suggested.
Draft Genome Sequence of Bacteroides vulgatus PC510, a Strain Isolated from Human Feces
Authors: Cuív Páraic Ó , Klaassens Eline S. , Durkin A. Scott , Harkins Derek M. , Foster Les , McCorrison Jamison , Torralba Manolito , Nelson Karen E. , Morrison Mark 
Published: May 2011

ABSTRACT

Although
Bacteroides vulgatus
is one of the most prevalent microorganisms in the human gastrointestinal tract, little is known about the genetic potential of this species. Here, we describe the annotated draft genome sequence of
B. vulgatus
PC510 isolated from human feces.
Genome Sequence of Rhodobacter sphaeroides Strain WS8N
Authors: Porter Steven L. , Wilkinson David A. , Byles Elaine D. , Wadhams George H. , Taylor Stephen , Saunders Nigel J. , Armitage Judith P. 
Published: May 2011

ABSTRACT

Rhodobacter sphaeroides
is a metabolically diverse photosynthetic alphaproteobacterium found ubiquitously in soil and freshwater habitats. Here we present the annotated genome sequence of
R. sphaeroides
WS8N.
Genome Sequences of the Zoonotic Pathogens Chlamydia psittaci 6BC and Cal10
Authors: Grinblat-Huse Valerie , Drabek Elliott F. , Creasy Heather Huot , Daugherty Sean C. , Jones Kristine M. , Santana-Cruz Ivette , Tallon Luke J. , Read Timothy D. , Hatch Thomas P. , Bavoil Patrik , Myers Garry S. A. 
Published: May 2011

ABSTRACT

Chlamydia psittaci
is a highly prevalent avian pathogen and the cause of a potentially lethal zoonosis, causing life-threatening pneumonia in humans. We report the genome sequences of
C. psittaci
6BC, the prototype strain of the species, and
C. psittaci
Cal10, a widely used laboratory strain.
Genome Sequence of the Vertebrate Gut Symbiont Lactobacillus reuteri ATCC 53608
Authors: Heavens Darren , Tailford Louise E. , Crossman Lisa , Jeffers Faye , MacKenzie Donald A. , Caccamo Mario , Juge Nathalie 
Published: May 2011

ABSTRACT

Lactobacillus reuteri
, inhabiting the gastrointestinal tracts of a range of vertebrates, is a true symbiont with effects established as beneficial to the host. Here we describe the draft genome of
L. reuteri
ATCC 53608, isolated from a pig. The genome sequence provides important insights into the evolutionary changes underlying host specialization.