bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adhesive Activity of the
Haemophilus
Cryptic Genospecies Cha Autotransporter Is Modulated by Variation in Tandem Peptide Repeats
Authors: Sheets Amanda J. , St. Geme Joseph W. 
Published: October 2010

ABSTRACT

The
Haemophilus
cryptic genospecies is an important cause of maternal genital tract and neonatal systemic infections and initiates infection by colonizing the genital or respiratory epithelium. In recent work, we identified a unique
Haemophilus
cryptic genospecies protein called Cha, which mediates efficient adherence to genital and respiratory epithelia. The Cha adhesin belongs to the trimeric autotransporter family and contains an N-terminal signal peptide, an internal passenger domain that harbors adhesive activity, and a C-terminal membrane anchor domain. The passenger domain in Cha contains clusters of YadA-like head domains and neck motifs as well as a series of tandem 28-amino-acid peptide repeats. In the current study, we report that variation in peptide repeat number gradually modulates Cha adhesive activity, associated with a direct effect on the length of Cha fibers on the bacterial cell surface. The N-terminal 404 residues of the Cha passenger domain mediate binding to host cells and also facilitate bacterial aggregation through intermolecular Cha-Cha binding. As the tandem peptide repeats expand, the Cha fiber becomes longer and Cha adherence activity decreases. The expansion and contraction of peptide repeats represent a novel mechanism for modulating adhesive capacity, potentially balancing the need of the organism to colonize the genital and respiratory tracts with the ability to attach to alternative substrates, disperse within the host, or evade the host immune system.
A Small Protein Required for the Switch from σ
F
to σ
G
during Sporulation in
Bacillus subtilis
Authors: Camp Amy H. , Wang Anna F. , Losick Richard 
Published: October 2010

ABSTRACT

A cascade of alternative sigma factors governs the program of developmental gene expression during sporulation in
Bacillus subtilis
. Little is known, however, about how the early-acting sigma factors are inactivated and replaced by the later-acting factors. Here we identify a small protein, Fin (formerly known as YabK), that is required for efficient switching from σ
F
- to σ
G
-directed gene expression in the forespore compartment of the developing sporangium. The
fin
gene, which is conserved among
Bacillus
species and species of related genera, is transcribed in the forespore under the control of both σ
F
and σ
G
. Cells mutant for
fin
are unable to fully deactivate σ
F
and, conversely, are unable to fully activate σ
G
. Consistent with their deficiency in σ
G
-directed gene expression,
fin
cells are arrested in large numbers following the engulfment stage of sporulation, ultimately forming 50-fold fewer heat-resistant spores than the wild type. Based in part on the similarity of Fin to the anti-σ
G
factor CsfB (also called Gin), we speculate that Fin is an anti-σ
F
factor which, by disabling σ
F
, promotes the switch to late developmental gene expression in the forespore.
Activation of the SoxR Regulon in
Streptomyces coelicolor
by the Extracellular Form of the Pigmented Antibiotic Actinorhodin
Authors: Shin Jung-Ho , Singh Atul K. , Cheon Dong-Joo , Roe Jung-Hye 
Published: October 2010

ABSTRACT

The redox-sensitive transcription factor SoxR in enteric bacteria senses and regulates the cellular response to superoxide and nitric oxide. In other bacterial groups, however, it may respond to redox-active small molecules, as demonstrated for pyocyanin sensing in pseudomonads. The antibiotic-producing soil bacterium
Streptomyces coelicolor
contains a gene for an SoxR homologue (SCO1697) whose DNA recognition helix is identical to that of
Escherichia coli
SoxR. Using the
E. coli
SoxR binding sequence, we predicted five candidate genes of the SoxR regulon and demonstrated that SoxR binds to their promoter regions and activates their expression concurrently with the production of the blue antibiotic actinorhodin (a benzoisochromanequinone). These genes encode a probable NADPH-dependent flavin reductase (SCO2478), an NADPH-dependent quinone reductase (SCO4266), an ABC transporter (SCO7008), a monooxygenase (SCO1909), and a hypothetical protein (SCO1178). Addition of actinorhodin to exponentially growing cells activated the expression of SoxR target genes in an SoxR-dependent manner. The secreted γ-actinorhodin was over 10-fold more effective in activation than the intracellular form of actinorhodin, suggesting that SoxR is specified to respond more to exogenous signals than to intracellular metabolites. The
ΔsoxR
mutant was not compromised in resistance against oxidants but was slow in forming aerial mycelium on R2YE medium with reduced sporulation, and its production of actinorhodin and undecylprodigiosin was lowered by about 50% and 30%, respectively, compared to that of the wild type. These results support the proposal that SoxR senses redox-active molecules, such as actinorhodin in
S. coelicolor
, and induces a protective function against them. It also functions to ensure that cells undergo optimal differentiation and secondary metabolite production.
Inactivation of the RluD Pseudouridine Synthase Has Minimal Effects on Growth and Ribosome Function in Wild-TypeEscherichia coliandSalmonella enterica
Authors: O'Connor Michael , Gregory Steven T. 
Published: October 2010

ABSTRACTTheEscherichia coli rluDgene encodes a pseudouridine synthase responsible for the pseudouridine (Ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23S rRNA. It has been reported that deletion ofrluDin K-12 strains ofE. coliis associated with extremely slow growth, increased readthrough of stop codons, and defects in 50S ribosomal subunit assembly and 30S-50S subunit association. Suppressor mutations in theprfBandprfCgenes encoding release factor 2 (RF2) and RF3 that restore the wild type-growth rate and also correct the ribosomal defects have now been isolated. These suppressors link helix 69 Ψ residues with the termination phase of protein synthesis. However, further genetic analysis reported here also reveals that the slow growth and other defects associated with inactivation ofrluDinE. coliK-12 strains are due to a defective RF2 protein, with a threonine at position 246, which is present in all K-12 strains. This is in contrast to the more typical alanine found at this position in most bacterial RF2s, including those of otherE. colistrains. Inactivation ofrluDinE. colistrains containing theprfBallele fromE. coliB or inSalmonella enterica, both carrying an RF2 with Ala246, has negligible effects on growth, termination, or ribosome function. The results indicate that, in contrast to those in wild bacteria, termination functions inE. coliK-12 strains carrying a partially defective RF2 protein are especially susceptible to perturbation of ribosome-RF interactions, such as that caused by loss of h69 Ψ modifications.
Orientation of SecA and SecB in Complex, Derived from Disulfide Cross-Linking
Authors: Suo Yuying , Hardy Simon J. S. , Randall Linda L. 
Published: October 2010

ABSTRACT

SecA is the ATPase that acts as the motor for protein export in the general secretory, or Sec, system of
Escherichia coli
. The tetrameric cytoplasmic chaperone SecB binds to precursors of exported proteins before they can become stably folded and delivers them to SecA. During this delivery step, SecB binds to SecA. The complex between SecA and SecB that is maximally active in translocation contains two protomers of SecA bound to a tetramer of SecB. The aminoacyl residues on each protein that are involved in binding the other have previously been identified by site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy; however, that study provided no information concerning the relative orientation of the proteins within the complex. Here we used our extensive collection of single-cysteine variants of the two proteins and subjected pairwise combinations of SecA and SecB to brief oxidation to identify residues in close proximity. These data were used to generate a model for the orientation of the two proteins within the complex.
Distinct Roles of Multiple NDH-1 Complexes in the Cyanobacterial Electron Transport Network as Revealed by Kinetic Analysis of P700
+
Reduction in Various
ndh
-Deficient Mutants of
Synechocystis
sp. Strain PCC6803
Authors: Bernát Gábor , Appel Jens , Ogawa Teruo , Rögner Matthias 
Published: October 2010

ABSTRACT

While methyl viologen had only a small effect on P700
+
rereduction kinetics after far-red pulses in KCN-treated wild-type
Synechocystis
sp. strain PCC6803 and an NdhF3/NdhF4 (NdhF3/F4)-defective mutant, it involved a rather slow P700
+
rereduction in an NdhF1-defective mutant. This strongly indicates that (i) active electron flow from metabolites to plastoquinone is suppressed upon deletion of
ndhF1
and (ii) photosystem 1-mediated cyclic electron transport is dependent on NdhF3/F4-type NDH-1 complexes.
Characterization of the
Bacteroides
CTnDOT Regulatory Protein RteC
Authors: Park Jiyeon , Salyers Abigail A. 
Published: October 2010

ABSTRACT

Excision of the
Bacteroides
conjugative transposon CTnDOT is stimulated by tetracycline. It was shown previously that a gene,
rteC
, is necessary for tetracycline-stimulated transcriptional regulation of the
orf2c
operon, which contains the excision genes. The protein encoded by this gene, RteC, did not have primary amino acid sequence homology to any known proteins in the databases. Accordingly, we sought structural homologs of RteC. A three-dimensional structure prediction by Robetta suggested that RteC might have two domains and that the C-terminal domain might have a winged helix motif. Based on the Robetta prediction, the human transcriptional factors E2F-4 and DP2 were identified as the most likely structural homologs of RteC. We made alanine substitutions within the putative DNA binding helix 3 region of RteC. Assays of
orf2c
::
uidA
activation by alanine mutants indicated that residues 174, 175, 178, 180, and 184 in helix 3 might contact the upstream region of P
E
. The upstream region of
orf2c
contained two inverted-repeat half sites. Mutational analysis of these half sites showed that both half sites are important for activity. Thus, we have identified the DNA binding portion of RteC and the DNA site to which it binds.
X-Ray Structure and Site-Directed Mutagenesis Analysis of theEscherichia coliColicin M Immunity Protein
Authors: Gérard Fabien , Brooks Mark A. , Barreteau Hélène , Touzé Thierry , Graille Marc , Bouhss Ahmed , Blanot Didier , van Tilbeurgh Herman , Mengin-Lecreulx Dominique 
Published: October 2010

ABSTRACTColicin M (ColM), which is produced by someEscherichia colistrains to kill competitor strains from the same or related species, was recently shown to inhibit cell wall peptidoglycan biosynthesis through enzymatic degradation of its lipid II precursor. ColM-producing strains are protected from the toxin that they produce by coexpression of a specific immunity protein, named Cmi, whose mode of action still remains to be identified. We report here the resolution of the crystal structure of Cmi, which is composed of four β strands and four α helices. This rather compact structure revealed a disulfide bond between residues Cys31 and Cys107. Interestingly, these two cysteines and several other residues appeared to be conserved in the sequences of several proteins of unknown function belonging to the YebF family which exhibit 25 to 35% overall sequence similarity with Cmi. Site-directed mutagenesis was performed to assess the role of these residues in the ColM immunity-conferring activity of Cmi, which showed that the disulfide bond and residues from the C-terminal extremity of the protein were functionally essential. The involvement of DsbA oxidase in the formation of the Cmi disulfide bond is also demonstrated.
Catabolite Control Protein A Controls Hydrogen Peroxide Production and Cell Death inStreptococcus sanguinis
Authors: Zheng Lanyan , Chen Zhijun , Itzek Andreas , Ashby Michael , Kreth Jens 
Published: October 2010

ABSTRACTStreptococcus sanguinisis a commensal oral bacterium producing hydrogen peroxide (H2O2) that is dependent on pyruvate oxidase (Spx) activity. In addition to its well-known role in bacterial antagonism during interspecies competition, H2O2causes cell death in about 10% of theS. sanguinispopulation. As a consequence of H2O2-induced cell death, largely intact chromosomal DNA is released into the environment. This extracellular DNA (eDNA) contributes to the self-aggregation phenotype under aerobic conditions. To further investigate the regulation ofspxgene expression, we assessed the role of catabolite control protein A (CcpA) inspxexpression control. We report here that CcpA repressesspxexpression. An isogenic ΔccpAmutant showed elevatedspxexpression, increased Spx abundance, and H2O2production, whereas the wild type did not respond with alteredspxexpression in the presence of glucose and other carbohydrates. Since H2O2is directly involved in the release of eDNA and bacterial cell death, the presented data suggest that CcpA is a central control element in this important developmental process inS. sanguinis.
Pseudomonas aeruginosaMucD Regulates the Alginate Pathway through Activation of MucA Degradation via MucP Proteolytic Activity
Authors: Damron F. Heath , Yu Hongwei D. 
Published: October 2010

ABSTRACTAlginate overproduction inPseudomonas aeruginosacan be caused by the proteolysis of the anti-sigma factor MucA regulated by the AlgW protease. Here, we show that inactivation of MucD, an HtrA/DegP homolog and alginate regulator, can bypass AlgW, leading to an atypical proteolysis of MucA that is dependent on the MucP protease.
Regulation of Horizontal Gene Transfer in
Bacillus subtilis
by Activation of a Conserved Site-Specific Protease
Authors: Bose Baundauna , Grossman Alan D. 
Published: October 2010

ABSTRACT

The mobile genetic element ICE
Bs1
is an integrative and conjugative element (a conjugative transposon) found in
Bacillus subtilis
. The RecA-dependent SOS response and the RapI-PhrI cell sensory system activate ICE
Bs1
gene expression by stimulating cleavage of ImmR, the ICE
Bs1
immunity repressor, by the protease ImmA. We found that increasing the amount of wild-type ImmA
in vivo
caused partial derepression of ICE
Bs1
gene expression. However, during RapI-mediated derepression of ICE
Bs1
gene expression, ImmA levels did not detectably increase, indicating that RapI likely activates the protease ImmA by increasing its specific activity. We also isolated and characterized mutations in
immA
(
immA

h

) that cause partial derepression of ICE
Bs1
gene expression in the absence of inducing signals. We obtained two types of
immA

h

mutations: one type caused increased amounts of the mutant proteins
in vivo
but no detectable effect on specific activity
in vitro
; the other type had no detectable effect on the amount of the mutant protein
in vivo
but caused increased specific activity of the protein (as measured
in vitro
). Together, these findings indicate that derepression of ICE
Bs1
gene expression is likely caused by an increase in the specific activity of ImmA. Homologs of ImmA and ImmR are found in many mobile genetic elements, so the mechanisms that regulate ImmA-mediated cleavage of ImmR may be widely conserved.
Complete Genome Sequence of the Probiotic
Lactobacillus plantarum
ST-III
Authors: Wang Yinyu , Chen Chen , Ai Lianzhong , Zhou Fangfang , Zhou Zhemin , Wang Lei , Zhang Hao , Chen Wei , Guo Benheng 
Published: October 2010

ABSTRACT

Lactobacillus plantarum
strain ST-III, a probiotic strain with several functions, was isolated from kimchi. Here we report the complete genome sequence of ST-III and compared it with two published
L. plantarum
genomes.
Complete Genome Sequence of
Cronobacter turicensis
LMG 23827, a Food-Borne Pathogen Causing Deaths in Neonates
Authors: Stephan Roger , Lehner Angelika , Tischler Patrick , Rattei Thomas 
Published: October 2010

ABSTRACT

Here, we report the complete and annotated genome sequence of
Cronobacter turicensis
, an opportunistic food-borne pathogen, which is known as a rare but important cause of life-threatening neonatal infections. Among all proteins of
C. turicensis
, 223 have been annotated as virulence- and disease-related proteins.
Complete Genome Sequence of
Bifidobacterium bifidum
S17
Authors: Zhurina Daria , Zomer Aldert , Gleinser Marita , Brancaccio Vincenco Francesco , Auchter Marc , Waidmann Mark S. , Westermann Christina , van Sinderen Douwe , Riedel Christian U. 
Published: October 2010

ABSTRACT

Here, we report on the first completely annotated genome sequence of a
Bifidobacterium bifidum
strain.
B. bifidum
S17, isolated from feces of a breast-fed infant, was shown to strongly adhere to intestinal epithelial cells and has potent anti-inflammatory activity
in vitro
and
in vivo
. The genome sequence will provide new insights into the biology of this potential probiotic organism and allow for the characterization of the molecular mechanisms underlying its beneficial properties.
Complete Genome Sequence of the BacteriumKetogulonicigenium vulgareY25
Authors: Xiong Xiang-hua , Han Shuang , Wang Jian-hua , Jiang Ze-hui , Chen Wei , Jia Ning , Wei Hong-li , Cheng Hong , Yang Yan-xin , Zhu Bin , You Song , He Jian-yong , Hou Wei , Chen Meng-xia , Yu Chun-jie , Jiao Ying-hui , Zhang Wei-cai 
Published: October 2010

ABSTRACTKetogulonicigenium vulgareis characterized by the efficient production of 2KGA froml-sorbose.Ketogulonicigenium vulgareY25 is known as a 2-keto-l-gulonic acid-producing strain in the vitamin C industry. Here we report the finished, annotated genome sequence ofKetogulonicigenium vulgareY25.
dnaX36
Mutator of
Escherichia coli
: Effects of the τ Subunit of the DNA Polymerase III Holoenzyme on Chromosomal DNA Replication Fidelity
Authors: Gawel Damian , Jonczyk Piotr , Fijalkowska Iwona J. , Schaaper Roel M. 
Published: October 2010

ABSTRACT

The
Escherichia coli dnaX36
mutant displays a mutator effect, reflecting a fidelity function of the
dnaX
-encoded τ subunit of the DNA polymerase III (Pol III) holoenzyme. We have shown that this fidelity function (i) applies to both leading- and lagging-strand synthesis, (ii) is independent of Pol IV, and (iii) is limited by Pol II.
Complete Genome Sequence of Strain HTCC2503
T
of
Parvularcula bermudensis
, the Type Species of the Order “
Parvularculales
” in the Class
Alphaproteobacteria
Authors: Oh Hyun-Myung , Kang Ilnam , Vergin Kevin L. , Kang Dongmin , Rhee Kwang-Hyun , Giovannoni Stephen J. , Cho Jang-Cheon 
Published: October 2010

ABSTRACT

The order “
Parvularculales
” represents the seventh order in the class
Alphaproteobacteria. Parvularcula bermudensis
, the type species of the order, was isolated from the Sargasso Sea using dilution-to-extinction culturing. We present here the complete genome sequence of
Parvularcula bermudensis
HTCC2503
T
, which contains genes for carotenoid biosynthesis, dimethylsulfoniopropionate demethylase, and transduction-like gene transfer agents.
Complete Genome Sequence of Strain HTCC2170, a Novel Member of the Genus
Maribacter
in the Family
Flavobacteriaceae
Authors: Oh Hyun-Myung , Kang Ilnam , Yang Seung-Jo , Jang Yoonra , Vergin Kevin L. , Giovannoni Stephen J. , Cho Jang-Cheon 
Published: October 2010

ABSTRACT

Strain HTCC2170 was isolated from surface waters off the Oregon coast using dilution-to-extinction culturing. Here, we present the finished genome sequence of a marine bacterium,
Maribacter
sp. strain HTCC2170. Strain sp. HTCC2170 is predicted to be a facultatively aerobic chemoorganotroph that, based on genomic sequence analysis, is capable of macromolecule degradation and anaerobic respiration.
Complete Genome Sequence of
Corynebacterium pseudotuberculosis
I19, a Strain Isolated from a Cow in Israel with Bovine Mastitis
Authors: Silva Artur , Schneider Maria Paula C. , Cerdeira Louise , Barbosa Maria Silvanira , Ramos Rommel Thiago J. , Carneiro Adriana R. , Santos Rodrigo , Lima Marília , D'Afonseca Vivian , Almeida Sintia S. , Santos Anderson R. , Soares Siomar C. , Pinto Anne C. , Ali Amjad , Dorella Fernanda A. , Rocha Flavia , de Abreu Vinicius Augusto Carvalho , Trost Eva , Tauch Andreas , Shpigel Nahum , Miyoshi Anderson , Azevedo Vasco 
Published: October 2010

ABSTRACT

This work reports the completion and annotation of the genome sequence of
Corynebacterium pseudotuberculosis
I19, isolated from an Israeli dairy cow with severe clinical mastitis. To present the whole-genome sequence, a
de novo
assembly approach using 33 million short (25-bp) mate-paired SOLiD reads only was applied. Furthermore, the automatic, functional, and manual annotations were attained with the use of several algorithms in a multistep process.
Complete Genome Sequence of a Carbon Monoxide-Utilizing Acetogen,
Eubacterium limosum
KIST612
Authors: Roh Hanseong , Ko Hyeok-Jin , Kim Daehee , Choi Dong Geon , Park Shinyoung , Kim Sujin , Chang In Seop , Choi In-Geol 
Published: October 2010

ABSTRACT

Eubacterium limosum
KIST612 is an anaerobic acetogenic bacterium that uses CO as the sole carbon/energy source and produces acetate, butyrate, and ethanol. To evaluate its potential as a syngas microbial catalyst, we have sequenced the complete 4.3-Mb genome of
E. limosum
KIST612.
Complete Genome Sequence of
Paenibacillus polymyxa
SC2, a Strain of Plant Growth-Promoting Rhizobacterium with Broad-Spectrum Antimicrobial Activity
Authors: Ma Mingchao , Wang Cuicui , Ding Yanqin , Li Li , Shen Delong , Jiang Xin , Guan Dawei , Cao Fengming , Chen Huijun , Feng Ruihua , Wang Xuan , Ge Yifan , Yao Liangtong , Bing Xiaohui , Yang Xiaohong , Li Jun , Du Binghai 
Published: October 2010

ABSTRACT

Paenibacillus polymyxa
SC2 is an important plant growth-promoting rhizobacterium (PGPR). Here, we report the complete genome sequence of
P. polymyxa
SC2. Multiple sets of functional genes have been found in the genome. As far as we know, this is the first complete genome sequence of
Paenibacillus polymyxa
.
Genome Sequence of
Oceanicaulis
sp. Strain HTCC2633, Isolated from the Western Sargasso Sea
Authors: Oh Hyun-Myung , Kang Ilnam , Vergin Kevin L. , Lee Kiyoung , Giovannoni Stephen J. , Cho Jang-Cheon 
Published: October 2010

ABSTRACT

The genus
Oceanicaulis
represents dimorphic rods that were originally isolated from a marine dinoflagellate. Here, we announce the genome sequence of
Oceanicaulis
sp. strain HTCC2633, isolated by dilution-to-extinction culturing from the Sargasso Sea. The genome information of strain HTCC2633 indicates a chemoorganotrophic way of life of this strain.
Genome Sequence of Strain HTCC2083, a Novel Member of the Marine Clade
Roseobacter
Authors: Kang Ilnam , Vergin Kevin L. , Oh Hyun-Myung , Choi Ahyoung , Giovannoni Stephen J. , Cho Jang-Cheon 
Published: October 2010

ABSTRACT

Strain HTCC2083 was isolated from Oregon seawater using dilution-to-extinction culturing and represents a novel member of the
Roseobacter
clade. The draft genome sequence of HTCC2083 is presented here. The genome is predicted to contain genes for aerobic anoxygenic phototrophy, sulfite-oxidizing chemolithotrophy, anapleurotic CO
2
fixation, carbon monoxide oxidation, and dimethylsulfoniopropionate (DMSP) utilization.