bluuebunny/crossref_metadata_2025_split huggingface dataset:
Schizosaccharomyces pombe
Hst4 Functions in DNA Damage Response by Regulating Histone H3 K56 Acetylation
Authors: Haldar Devyani , Kamakaka Rohinton T. 
Published: March 2008

ABSTRACT

The packaging of eukaryotic DNA into chromatin is likely to be crucial for the maintenance of genomic integrity. Histone acetylation and deacetylation, which alter chromatin accessibility, have been implicated in DNA damage tolerance. Here we show that
Schizosaccharomyces pombe
Hst4, a homolog of histone deacetylase Sir2, participates in S-phase-specific DNA damage tolerance. Hst4 was essential for the survival of cells exposed to the genotoxic agent methyl methanesulfonate (MMS) as well as for cells lacking components of the DNA damage checkpoint pathway. It was required for the deacetylation of histone H3 core domain residue lysine 56, since a strain with a point mutation of its catalytic domain was unable to deacetylate this residue in vivo. Hst4 regulated the acetylation of H3 K56 and was itself cell cycle regulated. We also show that MMS treatment resulted in increased acetylation of histone H3 lysine 56 in wild-type cells and
hst4
Δ mutants had constitutively elevated levels of histone H3 K56 acetylation. Interestingly, the level of expression of Hst4 decreased upon MMS treatment, suggesting that the cell regulates access to the site of DNA damage by changing the level of this protein. Furthermore, we find that the phenotypes of both K56Q and K56R mutants of histone H3 were similar to those of
hst4
Δ mutants, suggesting that proper regulation of histone acetylation is important for DNA integrity. We propose that Hst4 is a deacetylase involved in the restoration of chromatin structure following the S phase of cell cycle and DNA damage response.
Ultrastructural Characterization of the Prokaryotic Symbiosis in “Chlorochromatium aggregatum”
Authors: Wanner Gerhard , Vogl Kajetan , Overmann Jörg 
Published: March 2008

ABSTRACTThe phototrophic consortium “Chlorochromatium aggregatum” currently represents the most highly developed interspecific association of bacteria and consists of green sulfur bacteria, so-called epibionts, surrounding a central, motile, chemotrophic bacterium. In order to identify subcellular structures characteristic of this symbiosis, consortia were studied by a combination of high-resolution analytical scanning electron microscopy, transmission electron microscopy, and three-dimensional reconstruction and image analyses. Epibionts are interconnected and to a lesser extent are also connected with the central bacterium, by electron-dense, hair-like filaments. In addition, numerous periplasmic tubules extend from the outer membrane of the central bacterium and are in direct contact with the outer membrane of the epibionts. In each epibiont cell, the attachment site to the central bacterium is characterized by the absence of chlorosomes and an additional 17-nm-thick layer (epibiont contact layer [ECL]) attached to the inner side of the cytoplasmic membrane. The ECL is only occasionally observed in pure cultures of the epibiont, where it occurs in about 10 to 20% of the free-living cells. A striking feature of the central bacterium is the presence of one or two hexagonally packed flat crystals (central bacterium crystal [CBC]) per cell. The CBC reaches 1 μm in length, is 35 nm thick, and consists of bilayers of subunits with a spacing of 9 nm. A detailed model for consortia is presented, summarizing our conclusions regarding (i) cohesion of the cells, (ii) common periplasmic space between the central bacterium and the epibiont, (iii) ECL as a symbiosis-specific structure, and (iv) formation of the interior paracrystalline structures, central bacterium membrane layer, and CBC.
Evidence that AphB, Essential for the Virulence of
Vibrio vulnificus
, Is a Global Regulator
Authors: Jeong Hee Gon , Choi Sang Ho 
Published: March 2008

ABSTRACT

The
Vibrio vulnificus aphB
mutant was significantly less virulent than the wild type and was impaired in motility and adherence to host cells. Microarray analysis revealed that AphB of
V. vulnificus
(AphB

Vv

) influences the expression of over 10% of the
V. vulnificus
genome. The combined results indicated that AphB

Vv

is a global regulator contributing to the pathogenesis of
V. vulnificus
.
Fine-Tuning of Galactoglucan Biosynthesis in
Sinorhizobium meliloti
by Differential WggR (ExpG)-, PhoB-, and MucR-Dependent Regulation of Two Promoters
Authors: Bahlawane Christelle , Baumgarth Birgit , Serrania Javier , Rüberg Silvia , Becker Anke 
Published: March 2008

ABSTRACT

Depending on the phosphate concentration encountered in the environment
Sinorhizobium meliloti
2011 synthesizes two different exopolysaccharides (EPS). Galactoglucan (EPS II) is produced under phosphate starvation but also in the presence of extra copies of the transcriptional regulator WggR (ExpG) or as a consequence of a mutation in
mucR
. The galactoglucan biosynthesis gene cluster contains the operons
wga
(
expA
),
wge
(
expE
),
wgd
(
expD
), and
wggR
(
expG
). Two promoters, differentially controlled by WggR, PhoB, and MucR, were identified upstream of each of these operons. The proximal promoters of the
wga
,
wge
, and
wgd
transcription units were constitutively active when separated from the upstream regulatory sequences. Promoter activity studies and the positions of predicted PhoB and WggR binding sites suggested that the proximal promoters are cooperatively induced by PhoB and WggR. MucR was shown to strongly inhibit the distal promoters and bound to the DNA in the vicinity of the distal transcription start sites. An additional inhibitory effect on the distal promoter of the structural galactoglucan biosynthesis genes was identified as a new feature of WggR in a
mucR
mutant. A regulatory model of the fine-tuning of galactoglucan production is proposed.
Opine-BasedAgrobacteriumCompetitiveness: Dual Expression Control of the Agrocinopine Catabolism (acc) Operon by Agrocinopines and Phosphate Levels
Authors: Kim H. Stanley , Yi Hyojeong , Myung Jaehee , Piper Kevin R. , Farrand Stephen K. 
Published: March 2008

ABSTRACTAgrobacterium tumefaciensstrain C58 can transform plant cells to produce and secrete the sugar-phosphate conjugate opines agrocinopines A and B. The bacterium then moves in response to the opines and utilizes them as exclusive sources of carbon, energy, and phosphate via the functions encoded by theaccoperon. These privileged opine-involved activities contribute to the formation of agrobacterial niches in the environment. We found that the expression of theaccoperon is induced by agrocinopines and also by limitation of phosphate. The main promoter is present in front of the first gene,accR, which codes for a repressor. This operon structure enables efficient repression when opine levels are low. The promoter contains two putative operators, one overlapping the −10 sequence and the other in the further upstream from it; two partly overlapped putativephoboxes between the two operators; and two consecutive transcription start sites. DNA fragments containing either of the operators bound purified repressor AccR in the absence of agrocinopines but not in the presence of the opines, demonstrating the on-off switch of the promoter. Induction of theaccoperon can occur under low-phosphate conditions in the absence of agrocinopines and further increases when the opines also are present. Such opine-phosphate dual regulatory system of the operon may ensure maximum utilization of agrocinopines when available and thereby increase the chances of agrobacterial survival in the highly competitive environment with limited general food sources.
Cold Shock Exoribonuclease R (VacB) Is Involved in
Aeromonas hydrophila
Pathogenesis
Authors: Erova Tatiana E. , Kosykh Valeri G. , Fadl Amin A. , Sha Jian , Horneman Amy J. , Chopra Ashok K. 
Published: March 2008

ABSTRACT

In this study, we cloned and sequenced a virulence-associated gene (
vacB
) from a clinical isolate SSU of
Aeromonas
hydrophila
. We identified this gene based on our recently annotated genome sequence of the environmental isolate ATCC 7966
T
of
A. hydrophila
and the
vacB
gene of
Shigella flexneri
. The
A. hydrophila
VacB protein contained 798 amino acid residues, had a molecular mass of 90.5 kDa, and exhibited an exoribonuclease (RNase R) activity. The RNase R of
A. hydrophila
was a cold-shock protein and was required for bacterial growth at low temperature. The
vacB
isogenic mutant, which we developed by homologous recombination using marker exchange mutagenesis, was unable to grow at 4°C. In contrast, the wild-type (WT)
A. hydrophila
exhibited significant growth at this low temperature. Importantly, the
vacB
mutant was not defective in growth at 37°C. The
vacB
mutant also exhibited reduced motility, and these growth and motility phenotype defects were restored after complementation of the
vacB
mutant. The
A. hydrophila
RNase R-lacking strain was found to be less virulent in a mouse lethality model (70% survival) when given by the intraperitoneal route at as two 50% lethal doses (LD
50
). On the other hand, the WT and complemented strains of
A. hydrophila
caused 80 to 90% of the mice to succumb to infection at the same LD
50
dose. Overall, this is the first report demonstrating the role of RNase R in modulating the expression of
A. hydrophila
virulence.
Catalytic Mechanism of Cyclic Di-GMP-Specific Phosphodiesterase: a Study of the EAL Domain-Containing RocR fromPseudomonas aeruginosa
Authors: Rao Feng , Yang Ye , Qi Yaning , Liang Zhao-Xun 
Published: March 2008

ABSTRACTEAL domain proteins are the major phosphodiesterases for maintaining the cellular concentration of second-messenger cyclic di-GMP in bacteria. Given the pivotal roles of EAL domains in the regulation of many bacterial behaviors, the elucidation of their catalytic and regulatory mechanisms would contribute to the effort of deciphering the cyclic di-GMP signaling network. Here, we present data to show that RocR, an EAL domain protein that regulates the expression of virulence genes and biofilm formation inPseudomonas aeruginosaPAO-1, catalyzes the hydrolysis of cyclic di-GMP by using a general base-catalyzed mechanism with the assistance of Mg2+ion. In addition to the five essential residues involved in Mg2+binding, we propose that the essential residue E352functions as a general base catalyst assisting the deprotonation of Mg2+-coordinated water to generate the nucleophilic hydroxide ion. The mutation of other conserved residues caused various degree of changes in thekcatorKm, leading us to propose their roles in residue positioning and substrate binding. With functions assigned to the conserved groups in the active site, we discuss the molecular basis for the lack of activity of some characterized EAL domain proteins and the possibility of predicting the phosphodiesterase activities for the vast number of EAL domains in bacterial genomes in light of the catalytic mechanism.
Mutations in
pimE
Restore Lipoarabinomannan Synthesis and Growth in a
Mycobacterium smegmatis lpqW
Mutant
Authors: Crellin Paul K. , Kovacevic Svetozar , Martin Kirstee L. , Brammananth Rajini , Morita Yasu S. , Billman-Jacobe Helen , McConville Malcolm J. , Coppel Ross L. 
Published: March 2008

ABSTRACT

Lipoarabinomannans (LAMs) and phosphatidylinositol mannosides (PIMs) are abundant glycolipids in the cell walls of all corynebacteria and mycobacteria, including the devastating human pathogen
Mycobacterium tuberculosis
. We have recently shown that
M. smegmatis
mutants of the lipoprotein-encoding
lpqW
gene have a profound defect in LAM biosynthesis. When these mutants are cultured in complex medium, spontaneous bypass mutants consistently evolve in which LAM biosynthesis is restored at the expense of polar PIM synthesis. Here we show that restoration of LAM biosynthesis in the
lpqW
mutant results from secondary mutations in the
pimE
gene. PimE is a mannosyltransferase involved in converting AcPIM4, a proposed branch point intermediate in the PIM and LAM biosynthetic pathways, to more polar PIMs. Mutations in
pimE
arose due to insertion of the mobile genetic element ISMsm1 and independent point mutations that were clustered in predicted extracytoplasmic loops of this polytopic membrane protein. Our findings provide the first strong evidence that LpqW is required to channel intermediates such as AcPIM4 into LAM synthesis and that loss of PimE function results in the accumulation of AcPIM4, bypassing the need for LpqW. These data highlight new mechanisms regulating the biosynthetic pathways of these essential cell wall components.
Stabilization of pSW100 fromPantoea stewartiiby the F Conjugation System
Authors: Lin Mei-Hui , Liu Shih-Tung 
Published: March 2008

ABSTRACTPlasmid pSW100 is 1 of the 13 plasmids fromPantoea stewartiisubsp.stewartiiSW2 which has a replicon that resembles that of ColE1. This work uses a pSW100 derivative, pSW140K, to study how the pSW100 replicon is stably maintained in its hosts. Our results indicate that although pSW140K is stable inEscherichia coliHB101, the plasmid is rapidly lost in anotherE. colistrain, DH5α, indicating that the genetic background of anE. colistrain affects the stability of pSW140K. Mutagenesis ofE. coliHB101 with EZ::TN <DHFR-1> revealed that mutations intraC,traF,traG,traN, andtraV, which encode the components of the sex pilus assembly, reduce plasmid stability. Furthermore, this work identified that a 38-bp region located immediately upstream of the RNAII promoter is critical to the maintenance of plasmid stability inE. coliHB101. TraC binds to the region, and in addition, deleting the region destabilizes the plasmid. Furthermore, inserting this 38-bp fragment into a plasmid that contains the minimal replicon from pSW200 stabilizes the plasmid inE. coliHB101. Fluorescence in situ hybridization and immunofluorescence staining also revealed that derivatives of pSW100, pSW128A, and TraC are colocalized in cells, suggesting that pSW100 may use the sex pilus assembly as a partition apparatus to ensure the even distribution of the plasmid during cell division, which may thus maintain the plasmid's stability.
Proteins Found in a CikA Interaction Assay Link the Circadian Clock, Metabolism, and Cell Division in
Synechococcus elongatus
Authors: Mackey Shannon R. , Choi Jong-Soon , Kitayama Yohko , Iwasaki Hideo , Dong Guogang , Golden Susan S. 
Published: March 2008

ABSTRACT

Diverse organisms time their cellular activities to occur at distinct phases of Earth's solar day, not through the direct regulation of these processes by light and darkness but rather through the use of an internal biological (circadian) clock that is synchronized with the external cycle. Input pathways serve as mechanisms to transduce external cues to a circadian oscillator to maintain synchrony between this internal oscillation and the environment. The circadian input pathway in the cyanobacterium
Synechococcus elongatus
PCC 7942 requires the kinase CikA. A
cikA
null mutant exhibits a short circadian period, the inability to reset its clock in response to pulses of darkness, and a defect in cell division. Although CikA is copurified with the Kai proteins that constitute the circadian central oscillator, no direct interaction between CikA and either KaiA, KaiB, or KaiC has been demonstrated. Here, we identify four proteins that may help connect CikA with the oscillator. Phenotypic analyses of null and overexpression alleles demonstrate that these proteins are involved in at least one of the functions—circadian period regulation, phase resetting, and cell division—attributed to CikA. Predictions based on sequence similarity suggest that these proteins function through protein phosphorylation, iron-sulfur cluster biosynthesis, and redox regulation. Collectively, these results suggest a model for circadian input that incorporates proteins that link the circadian clock, metabolism, and cell division.
Concerted Action of Lactate Oxidase and Pyruvate Oxidase in Aerobic Growth of
Streptococcus pneumoniae
: Role of Lactate as an Energy Source
Authors: Taniai Hiroaki , Iida Ken-ichiro , Seki Masanori , Saito Mitsumasa , Shiota Susumu , Nakayama Hiroaki , Yoshida Shin-ichi 
Published: March 2008

ABSTRACT

Streptococcus pneumoniae
was shown to possess lactate oxidase in addition to well-documented pyruvate oxidase. The activities of both H
2
O
2
-forming oxidases in wild-type cultures were detectable even in the early exponential phase of growth and attained the highest levels in the early stationary phase. For each of these oxidases, a defective mutant was constructed and compared to the parent regarding the dynamics of pyruvate and lactate in aerobic cultures. The results obtained indicated that the energy-yielding metabolism in the wild type could be best described by the following scheme. (i) As long as glucose is available, approximately one-fourth of the pyruvate formed is converted to acetate by the sequential action of pyruvate oxidase and acetate kinase with acquisition of additional ATP; (ii) the rest of the pyruvate is reduced by lactate dehydrogenase to form lactate, with partial achievement of redox balance; (iii) the lactate is oxidized by lactate oxidase back to pyruvate, which is converted to acetate as described above; and (iv) the sequential reactions mentioned above continue to occur as long as lactate is present. As predicted by this model, exogenously added lactate was shown to increase the final growth yield in the presence of both oxidases.
The Virulence Regulator Sae ofStaphylococcus aureus:Promoter Activities and Response to Phagocytosis-Related Signals
Authors: Geiger Tobias , Goerke Christiane , Mainiero Markus , Kraus Dirk , Wolz Christiane 
Published: March 2008

ABSTRACTThe two-component system SaeRS ofStaphylococcus aureusis closely involved in the regulation of major virulence factors. However, little is known about the signals leading tosaeRSactivation. A total of four overlapping transcripts (T1 to T4) from three different transcription starting points are expressed in thesaeoperon. We used a β-galactosidase reporter assay to characterize the putative promoter regions within thesaeRSupstream region. The main transcript T2 is probably generated by endoribonucleolytic processing of the T1 transcript. Only two distinct promoter elements (P1 and P3) could be detected within thesaeRSupstream region. The P3 promoter, upstream ofsaeRS, generates the T3 transcript, includes acis-acting enhancer element and is repressed bysaeRS. The most distal P1 promoter is strongly autoregulated, activated byagr, and repressed by sigma factor B. In strain Newman a mutation within the histidine kinase SaeS leads to a constitutively activatedsaesystem. Evaluation of different external signals revealed that the P1 promoter in strain ISP479R and strain UAMS-1 is inhibited by low pH and high NaCl concentrations but activated by hydrogen peroxide. The most prominent induction of P1 was observed at subinhibitory concentrations of α-defensins in variousS. aureusstrains, with the exception of strain ISP479R and strain COL. P1 was not activated by the antimicrobial peptides LL37 and daptomycin. In summary, the results indicate that the sensor molecule SaeS is activated by alteration within the membrane allowing the pathogen to react to phagocytosis related effector molecules.
Regulation of theBacillus subtilis yciCGene and Insights into the DNA-Binding Specificity of the Zinc-Sensing Metalloregulator Zur
Authors: Gabriel Scott E. , Miyagi Faith , Gaballa Ahmed , Helmann John D. 
Published: March 2008

ABSTRACTTheBacillus subtilisZur protein regulates zinc homeostasis by repressing at least 10 genes in response to zinc sufficiency. One of these genes,yciC, encodes an abundant protein postulated to function as a metallochaperone. Here, we used a genetic approach to identify thecis-acting elements andtrans-acting factors contributing to the tight repression ofyciC. Initial studies led to the identification of onlytrans-acting mutations, and, when the selection was repeated using a transposon library, all recovered mutants contained insertionally inactivatedzur. Using azurmerodiploid strain, we obtained twocis-acting mutations that contained large deletions in theyciCregulatory region. We demonstrate that theyciCregulatory region contains two functional Zur boxes: a primary site (C2) overlapping a σApromoter ∼200 bp upstream ofyciCand a second site near the translational start point (C1). Zur binds to both of these sites to mediate strong, zinc-dependent repression ofyciC. Deletion studies indicate that either Zur box is sufficient for repression, although repression by Zur bound to C2 is more efficient. Binding studies demonstrate that both sites bind Zur with high affinity. Sequence alignment of these and previously described Zur boxes suggest that Zur recognizes a more extended operator than other Fur family members. We used synthetic oligonucleotides to identify bases critical for DNA binding by Zur. Unlike Fur and PerR, which bind efficiently to sequences containing a core 7-1-7 repeat element, Zur requires a 9-1-9 inverted repeat for high-affinity binding.
The GTPase CpgA Is Implicated in the Deposition of the Peptidoglycan Sacculus in
Bacillus subtilis
Authors: Absalon Cédric , Hamze Kassem , Blanot Didier , Frehel Claude , Carballido-Lopez Rut , Holland Barry I. , van Heijenoort Jean , Séror Simone J. 
Published: March 2008

ABSTRACT

Depletion of the
Bacillus subtilis
GTPase CpgA produces abnormal cell shapes, nonuniform deposition of cell wall, and five- to sixfold accumulation of peptidoglycan precursors. Nevertheless, the inherent structure of the cell wall appeared mostly unchanged. The results are consistent with CpgA being involved in coordinating normal peptidoglycan deposition.
Four weeks’ corticosteroid inhalation does not augment maximal power output in endurance athletes
Authors: Kuipers H , Hullenaar G A C Van’t , Pluim B M , Overbeek S E , De Hon O , Van Breda E J , Van Loon L C 
Published: March 2008

Objective:To assess possible ergogenic properties of corticosteroid administration.Design:A balanced, double-blind, placebo-controlled design was used.Participants:28 well-trained cyclists and rowers.Intervention:4 weeks’ daily inhalation of 800 μg budesonide or placebo.Main outcome measurements:The subjects performed three incremental cycle ergometer tests until exhaustion, before and after 2 and 4 weeks of placebo or budesonide administration, to measure maximal power output (Wmax). Once a week they filled in a profile of mood state (POMS) questionnaire.Results:There was no significant difference in Wmaxbetween the placebo (376 (SD 25) W) and the corticosteroid group (375 (36) W) during the preintervention test, and there were no significant changes in either group after 2 and 4 weeks of intervention. No effect of the intervention on mood state was found.Conclusion:4 weeks of corticosteroid or placebo inhalation in healthy, well-trained athletes did not affect maximal power output or mood state. Hence no ergogenic properties of 4 weeks’ corticosteroid administration could be demonstrated, which corroborates previous studies of short-term corticosteroid administration.