bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological Roles of the cyAbrB Transcriptional Regulator Pair Sll0822 and Sll0359 in Synechocystis sp. strain PCC 6803
Authors: Yamauchi Yuki , Kaniya Yuki , Kaneko Yasuko , Hihara Yukako 
Published: June 2011

ABSTRACT

All known cyanobacterial genomes possess multiple copies of genes encoding AbrB-like transcriptional regulators, known as cyAbrBs, which are distinct from those conserved among other bacterial species. In this study, we addressed the physiological roles of Sll0822 and Sll0359, the two cyAbrBs in
Synechocystis
sp. strain PCC 6803, under nonstress conditions (20 μmol of photons m
−2
s
−1
in ambient CO
2
). When the sll0822 gene was disrupted, the expression levels of nitrogen-related genes such as
urtA
,
amt1
, and
glnB
significantly decreased compared with those in the wild-type cells. Possibly due to the increase of the cellular carbon/nitrogen ratio in the sll0822-disrupted cells, a decrease in pigment contents, downregulation of carbon-uptake related genes, and aberrant accumulation of glycogen took place. Moreover, the mutant exhibited the decrease in the expression level of cytokinesis-related genes such as
ftsZ
and
ftsQ
, resulting in the defect in cell division and significant increase in cell size. The pleiotrophic phenotype of the mutant was efficiently suppressed by the introduction of Sll0822 and also partially suppressed by the introduction of Sll0359. When His-tagged cyAbrBs were purified from overexpression strains, Sll0359 and Sll0822 were copurified with each other. The cyAbrBs in
Synechocystis
sp. strain PCC 6803 seem to interact with each other and regulate carbon and nitrogen metabolism as well as the cell division process under nonstress conditions.
Novel Insights into the Regulation of LexA in the Cyanobacterium Synechocystis sp. Strain PCC 6803
Authors: Oliveira Paulo , Lindblad Peter 
Published: June 2011

ABSTRACT

The transcription factor LexA in the cyanobacterium
Synechocystis
sp. strain PCC 6803 has been shown to regulate genes that are not directly involved in DNA repair but instead in several different metabolic pathways. However, the signal transduction pathways remain largely uncharacterized. The present work gives novel insights into the regulation of LexA in this unicellular cyanobacterium. A combination of Northern and Western blotting, using specific antibodies against the cyanobacterial LexA, was employed to show that this transcription regulator is under posttranscriptional control, in addition to the classical and already-described transcriptional regulation. Moreover, detailed two-dimensional (2D) electrophoresis analyses of the protein revealed that LexA undergoes posttranslational modifications. Finally, a fully segregated LexA::GFP (green fluorescent protein) fusion-modified strain was produced to image LexA's spatial distribution in live cells. The fusion protein retains DNA binding capabilities, and the GFP fluorescence indicates that LexA is localized in the innermost region of the cytoplasm, decorating the DNA in an evenly distributed pattern. The implications of these findings for the overall role of LexA in
Synechocystis
sp. strain PCC 6803 are further discussed.
Identification and Characterization of a Novel Serine Protease, VvpS, That Contains Two Functional Domains and Is Essential for Autolysis of Vibrio vulnificus
Authors: Lim Moon Sub , Kim Jeong-A , Lim Jong Gyu , Kim Byoung Sik , Jeong Kwang Cheol , Lee Kyu-Ho , Choi Sang Ho 
Published: June 2011

ABSTRACT

Little is known about the molecular mechanism for autolysis of Gram-negative bacteria. In the present study, we identified the
vvpS
gene encoding a serine protease, VvpS, from
Vibrio vulnificus
, a Gram-negative food-borne pathogen. The amino acid sequence predicted that VvpS consists of two functional domains, an N-terminal protease catalytic domain (PCD) and a C-terminal carbohydrate binding domain (CBD). A null mutation of
vvpS
significantly enhanced viability during stationary phase, as measured by enumerating CFU and differentially staining viable cells. The
vvpS
mutant reduced the release of cytoplasmic β-galactosidase and high-molecular-weight extracellular chromosomal DNA into the culture supernatants, indicating that VvpS contributes to the autolysis of
V. vulnificus
during stationary phase. VvpS is secreted via a type II secretion system (T2SS), and it exerts its effects on autolysis through intracellular accumulation during stationary phase. Consistent with this, a disruption of the T2SS accelerated intracellular accumulation of VvpS and thereby the autolysis of
V. vulnificus
. VvpS also showed peptidoglycan-hydrolyzing activity, indicating that the autolysis of
V. vulnificus
is attributed to the self-digestion of the cell wall by VvpS. The functions of the VvpS domains were assessed by C-terminal deletion analysis and demonstrated that the PCD indeed possesses a proteolytic activity and that the CBD is required for hydrolyzing peptidoglycan effectively. Finally, the
vvpS
mutant exhibited reduced virulence in the infection of mice. In conclusion, VvpS is a serine protease with a modular structure and plays an essential role in the autolysis and pathogenesis of
V. vulnificus
.
Regulation of Flagellum Number by FliA and FlgM and Role in Biofilm Formation by Rhodobacter sphaeroides
Authors: Wilkinson David A. , Chacko Sarah J. , Vénien-Bryan Catherine , Wadhams George H. , Armitage Judith P. 
Published: June 2011

ABSTRACT

The FlgM secretion checkpoint plays a crucial role in coordinating bacterial flagellar assembly. Here we identify a new role for FlgM and FliA as part of a complex regulatory network which controls flagellum number and is essential for efficient swimming and biofilm formation in the monotrichous bacterium
Rhodobacter sphaeroides
.
Acinetobacter baumannii RecA Protein in Repair of DNA Damage, Antimicrobial Resistance, General Stress Response, and Virulence
Authors: Aranda Jesús , Bardina Carlota , Beceiro Alejandro , Rumbo Soraya , Cabral Maria P. , Barbé Jordi , Bou Germán 
Published: June 2011

ABSTRACT

RecA is the major enzyme involved in homologous recombination and plays a central role in SOS mutagenesis. In
Acinetobacter
spp., including
Acinetobacter baumannii
, a multidrug-resistant bacterium responsible for nosocomial infections worldwide, DNA repair responses differ in many ways from those of other bacterial species. In this work, the function of
A. baumannii
RecA was examined by constructing a
recA
mutant. Alteration of this single gene had a pleiotropic effect, showing the involvement of RecA in DNA damage repair and consequently in cellular protection against stresses induced by DNA damaging agents, several classes of antibiotics, and oxidative agents. In addition, the absence of RecA decreased survival in response to both heat shock and desiccation. Virulence assays
in vitro
(with macrophages) and
in vivo
(using a mouse model) similarly implicated RecA in the pathogenicity of
A. baumannii
. Thus, the data strongly suggest a protective role for RecA in the bacterium and indicate that inactivation of the protein can contribute to a combined therapeutic approach to controlling
A. baumannii
infections.
Identification of an Anchor Residue for CheA-CheY Interactions in the Chemotaxis System of Escherichia coli
Authors: Thakor Hemang , Nicholas Sarah , Porter Ian M. , Hand Nicole , Stewart Richard C. 
Published: June 2011

ABSTRACT

Transfer of a phosphoryl group from autophosphorylated CheA (P-CheA) to CheY is an important step in the bacterial chemotaxis signal transduction pathway. This reaction involves CheY (i) binding to the P2 domain of P-CheA and then (ii) acquiring the phosphoryl group from the P1 domain. Crystal structures indicated numerous side chain interactions at the CheY-P2 binding interface. To investigate the individual contributions of the P2 side chains involved in these contacts, we analyzed the effects of eight alanine substitution mutations on CheA-CheY binding interactions. An F214A substitution in P2 caused ∼1,000-fold reduction in CheA-CheY binding affinity, while Ala substitutions at other P2 positions had small effects (E171A, E178A, and I216A) or no detectable effects (H181A, D202A, D207A, and C213A) on binding affinity. These results are discussed in relation to previous
in silico
predictions of hot-spot and anchor positions at the CheA-CheY interface. We also investigated the consequences of these mutations for chemotaxis signal transduction in living cells. CheA(F214A) was defective in mediating localization of CheY-YFP to the large clusters of signaling proteins that form at the poles of
Escherichia coli
cells, while the other CheA variants did not differ from wild-type (wt) CheA (CheA
wt
) in this regard. In our set of mutants, only CheA(F214A) exhibited a markedly diminished ability to support chemotaxis in motility agar assays. Surprisingly, however, in FRET assays that monitored receptor-regulated production of phospho-CheY, CheA(F214A) (and each of the other Ala substitution mutants) performed just as well as CheA
wt
. Overall, our findings indicate that F214 serves as an anchor residue at the CheA-CheY interface and makes an important contribution to the binding energy
in vitro
and
in vivo
; however, loss of this contribution does not have a large negative effect on the overall ability of the signaling pathway to modulate P-CheY levels in response to chemoattractants.
Characterization of the Self-Cleaving Effector Protein NopE1 of Bradyrhizobium japonicum
Authors: Schirrmeister Jana , Friedrich Lars , Wenzel Mandy , Hoppe Markus , Wolf Christine , Göttfert Michael , Zehner Susanne 
Published: June 2011

ABSTRACT

NopE1 is a type III-secreted protein of the symbiont
Bradyrhizobium japonicum
which is expressed in nodules.
In vitro
it exhibits self-cleavage in a duplicated domain of unknown function (DUF1521) but only in the presence of calcium. Here we show that either domain is self-sufficient for cleavage. An exchange of the aspartic acid residue at the cleavage site with asparagine prevented cleavage; however, cleavage was still observed with glutamic acid at the same position, indicating that a negative charge at the cleavage site is sufficient. Close to each cleavage site, an EF-hand-like motif is present. A replacement of one of the conserved aspartic acid residues with alanine prevented cleavage at the neighboring site. Except for EDTA, none of several protease inhibitors blocked cleavage, suggesting that a known protease-like mechanism is not involved in the reaction. In line with this, the reaction takes place within a broad pH and temperature range. Interestingly, magnesium, manganese, and several other divalent cations did not induce cleavage, indicating a highly specific calcium-binding site. Based on results obtained by blue-native gel electrophoresis, it is likely that the uncleaved protein forms a dimer and that the fragments of the cleaved protein oligomerize. A database search reveals that the DUF1521 domain is present in proteins encoded by
Burkholderia phytofirmans
PsNJ (a plant growth-promoting betaproteobacterium) and
Vibrio coralliilyticus
ATCC BAA450 (a pathogenic gammaproteobacterium). Obviously, this domain is more widespread in proteobacteria, and it might contribute to the interaction with hosts.
Wall Teichoic Acid-Dependent Adsorption of Staphylococcal Siphovirus and Myovirus
Authors: Xia Guoqing , Corrigan Rebecca M. , Winstel Volker , Goerke Christiane , Gründling Angelika , Peschel Andreas 
Published: June 2011

ABSTRACT

The molecular interactions between staphylococcal phages and host cell surfaces are poorly understood. Employing
Staphylococcus aureus
teichoic acid mutants, we demonstrate that wall teichoic acid (WTA), but not lipoteichoic acid, serves as a receptor for staphylococcal siphovirus and myovirus, while only the siphovirus requires glycosylated WTA.
Structure of the Flagellar Motor Protein Complex PomAB: Implications for the Torque-Generating Conformation
Authors: Yonekura Koji , Maki-Yonekura Saori , Homma Michio 
Published: June 2011

ABSTRACT

The bacterial flagellar motor is driven by an ion flux through a channel called MotAB in
Escherichia coli
or
Salmonella
and PomAB in
Vibrio alginolyticus
. PomAB is composed of two transmembrane (TM) components, PomA and PomB, and converts a sodium ion flux to rotation of the flagellum. Its homolog, MotAB, utilizes protons instead of sodium ions. PomB/MotB has a peptidoglycan (PG)-binding motif in the periplasmic domain, allowing it to function as the stator by being anchored to the PG layer. To generate torque, PomAB/MotAB is thought to undergo a conformational change triggered by the ion flux and to interact directly with FliG, a component of the rotor. Here, we present the first three-dimensional structure of this torque-generating stator unit analyzed by electron microscopy. The structure of PomAB revealed two arm domains, which contain the PG-binding site, connected to a large base made of the TM and cytoplasmic domains. The arms lean downward to the membrane surface, likely representing a “plugged” conformation, which would prevent ions leaking through the channel. We propose a model for how PomAB units are placed around the flagellar basal body to function as torque generators.
Residues in a Conserved α-Helical Segment Are Required for Cleavage but Not Secretion of an Escherichia coli Serine Protease Autotransporter Passenger Domain
Authors: Dautin Nathalie , Bernstein Harris D. 
Published: June 2011

ABSTRACT

Autotransporters are a superfamily of virulence factors produced by Gram-negative bacteria that are comprised of an N-terminal extracellular domain (passenger domain) and a C-terminal β barrel domain (β domain) that resides in the outer membrane (OM). The β domain promotes the translocation of the passenger domain across the OM by an unknown mechanism. Available evidence indicates that an α-helical segment that spans the passenger domain-β domain junction is embedded inside the β domain at an early stage of assembly. Following its secretion, the passenger domain of the
s
erine
p
rotease
a
uto
t
ransporters of the

E

nterobacteriaceae
(SPATEs) and the pertactin family of
Bordetella pertussis
autotransporters is released from the β domain through an intrabarrel autoproteolytic cleavage of the α-helical segment. Although the mutation of conserved residues that surround the cleavage site has been reported to impair both the translocation and cleavage of the passenger domain of a SPATE called Tsh, we show here that the mutation of the same residues in another SPATE (EspP) affects only passenger domain cleavage. Our results strongly suggest that the conserved residues are required to position the α-helical segment for the cleavage reaction and are not required to promote passenger domain secretion.
Complete Genome Sequence of the Anaerobic, Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LF
Authors: Zhao Baisuo , Mesbah Noha M. , Dalin Eileen , Goodwin Lynne , Nolan Matt , Pitluck Sam , Chertkov Olga , Brettin Thomas S. , Han James , Larimer Frank W. , Land Miriam L. , Hauser Loren , Kyrpides Nikolaos , Wiegel Juergen 
Published: June 2011

ABSTRACT

The genome of the anaerobic halophilic alkalithermophile
Natranaerobius thermophilus
consists of one 3,165,557-bp chromosome and two plasmids (17,207 bp and 8,689 bp). The present study is the first to report the completely sequenced genome of an anaerobic polyextremophile and genes associated with roles in regulation of intracellular osmotic pressure, pH homeostasis, and growth at elevated temperatures.
Genome Sequence of the Mercury-Methylating and Pleomorphic Desulfovibrio africanus Strain Walvis Bay
Authors: Brown Steven D. , Wall Judy D. , Kucken Amy M. , Gilmour Cynthia C. , Podar Mircea , Brandt Craig C. , Teshima Hazuki , Detter John C. , Han Cliff S. , Land Miriam L. , Lucas Susan , Han James , Pennacchio Len , Nolan Matt , Pitluck Sam , Woyke Tanja , Goodwin Lynne , Palumbo Anthony V. , Elias Dwayne A. 
Published: June 2011

ABSTRACT

Desulfovibrio africanus
strain Walvis Bay is an anaerobic sulfate-reducing bacterium capable of producing methylmercury (MeHg), a potent human neurotoxin. The mechanism of methylation by this and other organisms is unknown. We present the 4.2-Mb genome sequence to provide further insight into microbial mercury methylation and sulfate-reducing bacteria.
Genome Sequence of the Repetitive-Sequence-Rich Mycoplasma fermentans Strain M64
Authors: Shu Hung-Wei , Liu Tze-Tze , Chan Huang-I , Liu Yen-Ming , Wu Keh-Ming , Shu Hung-Yu , Tsai Shih-Feng , Hsiao Kwang-Jen , Hu Wensi S. , Ng Wailap Victor 
Published: June 2011

ABSTRACT

Mycoplasma fermentans
is a microorganism commonly found in the genitourinary and respiratory tracts of healthy individuals and AIDS patients. The complete genome of the repetitive-sequence-rich
M. fermentans
strain M64 is reported here. Comparative genomics analysis revealed dramatic differences in genome size between this strain and the recently completely sequenced JER strain.
Microbial Ecology of the Dark Ocean above, at, and below the Seafloor
Authors: Orcutt Beth N. , Sylvan Jason B. , Knab Nina J. , Edwards Katrina J. 
Published: June 2011

SUMMARYThe majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.
Does hormone replacement therapy cause breast cancer? An application of causal principles to three studies: Table 1
Authors: Shapiro Samuel , Farmer Richard D T , Mueck Alfred O , Seaman Helen , Stevenson John C 
Published: June 2011

BackgroundBased principally on findings in three studies, the Collaborative Reanalysis (CR), the Women's Health Initiative (WHI), and the Million Women Study (MWS), it is claimed that combined hormone replacement therapy (HRT) with estrogen plus progestogen is now an established cause of breast cancer. For unopposed estrogen therapy the evidence in the three studies is conflicting: the CR and MWS have reported increased risks in estrogen users, while the WHI has not. The authors have previously reviewed the findings in the CR (Part 1).ObjectiveTo evaluate the evidence for causality in the WHI studies.MethodsUsing generally accepted causal criteria, in this paper (Part 2) the authors evaluate the findings in the WHI for estrogen plus progestogen; in a related paper (Part 3) the authors evaluate the findings for unopposed estrogen. An evaluation of the MWS (Part 4), and of trends in breast cancer incidence following publication of the WHI findings in 2002 (Part 5) will follow.ResultsFor estrogen plus progestogen the findings did not adequately satisfy the criteria of bias, confounding, statistical stability and strength of association, duration-response, internal consistency, external consistency or biological plausibility.ConclusionHRT with estrogen plus progestogen may or may not increase the risk of breast cancer, but the WHI did not establish that it does.
Does hormone replacement therapy cause breast cancer? An application of causal principles to three studies
Authors: Shapiro Samuel , Farmer Richard D T , Mueck Alfred O , Seaman Helen , Stevenson John C 
Published: June 2011

BackgroundStudies from the Women's Health Initiative have reported an increased risk of breast cancer in users of estrogen plus progestogen. Among users of estrogen alone an increased risk was not observed.Objective To evaluate the evidence for unopposed estrogen.MethodsIn a related article (Part 2) the authors apply generally accepted causal criteria to the findings for estrogen plus progestogen. Here (Part 3) the authors apply the criteria to the findings for unopposed estrogen, as reported in a clinical trial, and in combined data from the trial and an observational study.ResultsIn the clinical trial, after 7.1 years of follow-up the relative risk (RR) of invasive breast cancer for women assigned to estrogen was 0.77 in an ‘intention-to-treat’ analysis (95% CI 0.59–1.01) and 0.67 (95% CI 0.47–0.97) in an ‘as treated’ analysis; after 10.7 years the risk reduction persisted. Time order was correctly specified; detection bias was minimal; in the ‘as treated’ analysis confounding was unlikely; duration-response and internal consistency could be evaluated only to a limited extent because of scanty data; the findings were discordant with increased risks observed in the Collaborative Reanalysis and the Million Women Study; biological plausibility could not be assessed.In the combined analysis, among women who had previously used estrogen soon after the menopause there was no clear evidence of either a reduction or an increase in the risk of breast cancer among women assigned to estrogen during the trial, or among women who were using estrogen in the observational study when follow-up commenced. The combined analysis did not satisfy the criteria of time order, bias, confounding, statistical stability and strength of association, duration-response, and internal consistency; biological plausibility could not be assessed.ConclusionsThe evidence from the clinical trial suggests that unopposed estrogen does not increase the risk of breast cancer, and may even reduce it. The latter possibility, however, is based on statistically borderline evidence.