bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and Quantification of Superoxide Formed within the Periplasm ofEscherichia coli
Authors: Korshunov Sergei , Imlay James A. 
Published: August 2006

ABSTRACTMany gram-negative bacteria harbor a copper/zinc-containing superoxide dismutase (CuZnSOD) in their periplasms. In pathogenic bacteria, one role of this enzyme may be to protect periplasmic biomolecules from superoxide that is released by host phagocytic cells. However, the enzyme is also present in many nonpathogens and/or free-living bacteria, includingEscherichia coli. In this study we were able to detect superoxide being released into the medium from growing cultures ofE. coli. Exponential-phase cells do not normally synthesize CuZnSOD, which is specifically induced in stationary phase. However, the engineered expression of CuZnSOD in growing cells eliminated superoxide release, confirming that this superoxide was formed within the periplasm. The rate of periplasmic superoxide production was surprisingly high and approximated the estimated rate of cytoplasmic superoxide formation when both were normalized to the volume of the compartment. The rate increased in proportion to oxygen concentration, suggesting that the superoxide is generated by the adventitious oxidation of an electron carrier. Mutations that eliminated menaquinone synthesis eradicated the superoxide formation, while mutations in genes encoding respiratory complexes affected it only insofar as they are likely to affect the redox state of menaquinone. We infer that the adventitious autoxidation of dihydromenaquinone in the cytoplasmic membrane releases a steady flux of superoxide into the periplasm ofE. coli. This endogenous superoxide may create oxidative stress in that compartment and be a primary substrate of CuZnSOD.
Essential Role of Flavohemoglobin in Long-Term Anaerobic Survival of
Bacillus subtilis
Authors: Nakano Michiko M. 
Published: August 2006

ABSTRACT

A
Bacillus subtilis
culture incubated anaerobically in nitrate-containing medium lost viability during the first 3 days but recovered thereafter. A flavohemoglobin mutant showed very poor survival under these conditions unless the cells were prevented from carrying out nitrate respiration.
Independent Control of Replication Initiation of the Two
Vibrio cholerae
Chromosomes by DnaA and RctB
Authors: Duigou Stéphane , Knudsen Kristine G. , Skovgaard Ole , Egan Elizabeth S. , Løbner-Olesen Anders , Waldor Matthew K. 
Published: August 2006

ABSTRACT

Although the two
Vibrio cholerae
chromosomes initiate replication in a coordinated fashion, we show here that each chromosome appears to have a specific replication initiator. DnaA overproduction promoted overinitiation of chromosome I and not chromosome II. In contrast, overproduction of RctB, a protein that binds to the origin of replication of chromosome II, promoted overinitiation of chromosome II and not chromosome I.
Proline Betaine Uptake in
Sinorhizobium meliloti
: Characterization of Prb, an Opp-Like ABC Transporter Regulated by both Proline Betaine and Salinity Stress
Authors: Alloing Geneviève , Travers Isabelle , Sagot Brice , Le Rudulier Daniel , Dupont Laurence 
Published: August 2006

ABSTRACT

Sinorhizobium meliloti
uses proline betaine (PB) as an osmoprotectant when osmotically stressed and as an energy source in low-osmolarity environments. To fulfill this dual function, two separate PB transporters, BetS and Hut, that contribute to PB uptake at high and low osmolarity, respectively, have been previously identified. Here, we characterized a novel transport system that mediates the uptake of PB at both high and low osmolarities. Sequence analysis of Tn
5-luxAB
chromosomal insertions from several PB-inducible mutants has revealed the presence of a four-gene locus encoding the components of an ABC transporter, Prb, which belongs to the oligopeptide permease (Opp) family. Surprisingly,
prb
mutants were impaired in their ability to transport PB, and oligopeptides were not shown to be competitors for PB uptake. Further analysis of Prb specificity has shown its ability to take up other quaternary ammonium compounds such as choline and, to a lesser extent, glycine betaine. Interestingly, salt stress and PB were found to control
prb
expression in a positive and synergistic way and to increase Prb transport activity. At low osmolarity, Prb is largely implicated in PB uptake by stationary-phase cells, likely to provide PB as a source of carbon and nitrogen. Furthermore, at high osmolarity, the analysis of
prb
and
betS
single and double mutants demonstrated that Prb, together with BetS, is a key system for protection by PB.
The Highly Efficient Translation Initiation Region from the
Escherichia coli rpsA
Gene Lacks a Shine-Dalgarno Element
Authors: Skorski Patricia , Leroy Prune , Fayet Olivier , Dreyfus Marc , Hermann-Le Denmat Sylvie 
Published: August 2006

ABSTRACT

The translational initiation region (TIR) of the
Escherichia coli rpsA
gene, which encodes ribosomal protein S1, shows a number of unusual features. It extends far upstream (to position −91) of the initiator AUG, it lacks a canonical Shine-Dalgarno sequence (SD) element, and it can fold into three successive hairpins (I, II, and III) that are essential for high translational activity. Two conserved GGA trinucleotides, present in the loops of hairpins I and II, have been proposed to form a discontinuous SD. Here, we have tested this hypothesis with the “specialized ribosome” approach. Depending upon the constructs used, translation initiation was decreased three- to sevenfold upon changing the conserved GGA to CCU. However, although chemical probing showed that the mutated trinucleotides were accessible, no restoration was observed when the ribosome anti-SD was symmetrically changed from CCUCC to GGAGG. When the same change was introduced in the SD from a conventional TIR as a control, activity was stimulated. This result suggests that the GGA trinucleotides do not form a discontinuous SD. Others hypotheses that may account for their role are discussed. Curiously, we also find that, when expressed at moderate level (30 to 40% of total ribosomes), specialized ribosomes are only twofold disadvantaged over normal ribosomes for the translation of bulk cellular mRNAs. These findings suggest that, under these conditions, the SD-anti-SD interaction plays a significant but not essential role for the synthesis of bulk cellular proteins.
Type III Pilus of Corynebacteria: Pilus Length Is Determined by the Level of Its Major Pilin Subunit
Authors: Swierczynski Arlene , Ton-That Hung 
Published: August 2006

ABSTRACT

Multiple pilus gene clusters have been identified in several gram-positive bacterial genomes sequenced to date, including the
Actinomycetales
, clostridia, streptococci, and corynebacteria. The genome of
Corynebacterium diphtheriae
contains three pilus gene clusters, two of which have been previously characterized. Here, we report the characterization of the third pilus encoded by the
spaHIG
cluster. By using electron microscopy and biochemical analysis, we demonstrate that SpaH forms the pilus shaft, while SpaI decorates the structure and SpaG is largely located at the pilus tip. The assembly of the SpaHIG pilus requires a specific sortase located within the
spaHIG
pilus gene cluster. Deletion of genes specific for the synthesis and polymerization of the other two pilus types does not affect the SpaHIG pilus. Moreover, SpaH but not SpaI or SpaG is essential for the formation of the filament. When expressed under the control of an inducible promoter, the amount of the SpaH pilin regulates pilus length; no pili are assembled from an SpaH precursor that has an alanine in place of the conserved lysine of the SpaH pilin motif. Thus, the
spaHIG
pilus gene cluster encodes a pilus structure that is independently assembled and antigenically distinct from other pili of
C. diphtheriae
. We incorporate these findings in a model of sortase-mediated pilus assembly that may be applicable to many gram-positive pathogens.
Genetic Evidence for an Interaction of the UbiG
O
-Methyltransferase with UbiX in
Escherichia coli
Coenzyme Q Biosynthesis
Authors: Gulmezian Melissa , Zhang Haitao , Javor George T. , Clarke Catherine F. 
Published: August 2006

ABSTRACT

IS16 is a thiol-sensitive, Q-deficient mutant strain of
Escherichia coli.
Here, we show that IS16 harbors a mutation in the
ubiG
gene encoding a methyltransferase required for two O-methylation steps of Q biosynthesis. Complementation of IS16 with either
ubiG
or
ubiX
K-12
reverses this phenotype, suggesting that UbiX may interact with UbiG.
The Blue-Light Receptor YtvA Acts in the Environmental Stress Signaling Pathway of
Bacillus subtilis
Authors: Gaidenko Tatiana A. , Kim Tae-Jong , Weigel Andrea L. , Brody Margaret S. , Price Chester W. 
Published: August 2006

ABSTRACT

The general stress response of the bacterium
Bacillus subtilis
is regulated by a partner-switching mechanism in which serine and threonine phosphorylation controls protein interactions in the stress-signaling pathway. The environmental branch of this pathway contains a family of five paralogous proteins that function as negative regulators. Here we present genetic evidence that a sixth paralog, YtvA, acts as a positive regulator in the same environmental signaling branch. We also present biochemical evidence that YtvA and at least three of the negative regulators can be isolated from cell extracts in a large environmental signaling complex. YtvA differs from these associated negative regulators by its flavin mononucleotide (FMN)-containing light-oxygen-voltage domain. Others have shown that this domain has the photochemistry expected for a blue-light sensor, with the covalent linkage of the FMN chromophore to cysteine 62 composing a critical part of the photocycle. Consistent with the view that light intensity modifies the output of the environmental signaling pathway, we found that cysteine 62 is required for YtvA to exert its positive regulatory role in the absence of other stress. Transcriptional analysis of the
ytvA
structural gene indicated that it provides the entry point for at least one additional environmental input, mediated by the Spx global regulator of disulfide stress. These results support a model in which the large signaling complex serves to integrate multiple environmental signals in order to modulate the general stress response.
Blue Light Activates the σ
B
-Dependent Stress Response of
Bacillus subtilis
via YtvA
Authors: Ávila-Pérez Marcela , Hellingwerf Klaas J. , Kort Remco 
Published: August 2006

ABSTRACT

Here we present evidence for a physiologically relevant light response mediated by the LOV domain-containing protein YtvA in the soil bacterium
Bacillus subtilis
. The loss and overproduction of YtvA abolish and enhance, respectively, the increase in σ
B
-controlled
ctc
promoter activity at moderate light intensities. These effects were absent in the dark and in red light but present under blue-light illumination. Thus, activation of the general stress response in
B. subtilis
is modulated by blue light.
Pseudomonas syringae
HrpJ Is a Type III Secreted Protein That Is Required for Plant Pathogenesis, Injection of Effectors, and Secretion of the HrpZ1 Harpin
Authors: Fu Zheng Qing , Guo Ming , Alfano James R. 
Published: August 2006

ABSTRACT

The bacterial plant pathogen
Pseudomonas syringae
requires a type III protein secretion system (TTSS) to cause disease. The
P. syringae
TTSS is encoded by the
hrp-hrc
gene cluster. One of the genes within this cluster,
hrpJ
, encodes a protein with weak similarity to YopN, a type III secreted protein from the animal pathogenic
Yersinia
species. Here, we show that HrpJ is secreted in culture and translocated into plant cells by the
P. syringae
pv. tomato DC3000 TTSS. A DC3000
hrpJ
mutant, UNL140, was greatly reduced in its ability to cause disease symptoms and multiply in
Arabidopsis thaliana
. UNL140 exhibited a reduced ability to elicit a hypersensitive response (HR) in nonhost tobacco plants. UNL140 was unable to elicit an AvrRpt2- or AvrB1-dependent HR in
A. thaliana
but maintained its ability to secrete AvrB1 in culture via the TTSS. Additionally, UNL140 was defective in its ability to translocate the effectors AvrPto1, HopB1, and AvrPtoB. Type III secretion assays showed that UNL140 secreted HrpA1 and AvrPto1 but was unable to secrete HrpZ1, a protein that is normally secreted in culture in relatively large amounts, into culture supernatants. Taken together, our data indicate that HrpJ is a type III secreted protein that is important for pathogenicity and the translocation of effectors into plant cells. Based on the failure of UNL140 to secrete HrpZ1, HrpJ may play a role in controlling type III secretion, and in its absence, specific accessory proteins, like HrpZ1, may not be extracellularly localized, resulting in disabled translocation of effectors into plant cells.
Transcriptional Profiling of the
Bacillus anthracis
Life Cycle In Vitro and an Implied Model for Regulation of Spore Formation
Authors: Bergman Nicholas H. , Anderson Erica C. , Swenson Ellen E. , Niemeyer Matthew M. , Miyoshi Amy D. , Hanna Philip C. 
Published: August 2006

ABSTRACT

The life cycle of
Bacillus anthracis
includes both vegetative and endospore morphologies which alternate based on nutrient availability, and there is considerable evidence indicating that the ability of this organism to cause anthrax depends on its ability to progress through this life cycle in a regulated manner. Here we report the use of a custom
B. anthracis
GeneChip in defining the gene expression patterns that occur throughout the entire life cycle in vitro. Nearly 5,000 genes were expressed in five distinct waves of transcription as the bacteria progressed from germination through sporulation, and we identified a specific set of functions represented within each wave. We also used these data to define the temporal expression of the spore proteome, and in doing so we have demonstrated that much of the spore's protein content is not synthesized de novo during sporulation but rather is packaged from preexisting stocks. We explored several potential mechanisms by which the cell could control which proteins are packaged into the developing spore, and our analyses were most consistent with a model in which
B. anthracis
regulates the composition of the spore proteome based on protein stability. This study is by far the most comprehensive survey yet of the
B. anthracis
life cycle and serves as a useful resource in defining the growth-phase-dependent expression patterns of each gene. Additionally, the data and accompanying bioinformatics analyses suggest a model for sporulation that has broad implications for
B. anthracis
biology and offer new possibilities for microbial forensics and detection.
The RgpB C-Terminal Domain Has a Role in Attachment of RgpB to the Outer Membrane and Belongs to a Novel C-Terminal-Domain Family Found in
Porphyromonas gingivalis
Authors: Seers Christine A. , Slakeski Nada , Veith Paul D. , Nikolof Todd , Chen Yu-Yen , Dashper Stuart G. , Reynolds Eric C. 
Published: August 2006

ABSTRACT

Porphyromonas gingivalis
produces outer membrane-attached proteins that include the virulence-associated proteinases RgpA and RgpB (Arg-gingipains) and Kgp (Lys-gingipain). We analyzed the
P. gingivalis
outer membrane proteome and identified numerous proteins with C-terminal domains similar in sequence to those of RgpB, RgpA, and Kgp, indicating that these domains may have a common function. Using RgpB as a model to investigate the role of the C-terminal domain, we expressed RgpB as a full-length zymogen (recombinant RgpB [rRgpB]), with a catalytic Cys244Ala mutation [rRgpB(C244A)], or with the C-terminal 72 amino acids deleted (rRgpB435) in an Arg-gingipain
P. gingivalis
mutant (YH522AB) and an Arg- and Lys-gingipain mutant (YH522KAB). rRgpB was catalytically active and located predominantly attached to the outer membrane of both background strains. rRgpB(C244A) was inactive and outer membrane attached, with a typical attachment profile for both background strains according to sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but in YH522KAB, the prodomain was not removed. Thus, in vivo, RgpB export and membrane attachment are independent of the proteolytic activity of RgpA, RgpB, or Kgp. However, for maturation involving proteolytic processing of RgpB, the proteolytic activity of RgpB, RgpA, or Kgp is required. The C-terminally-truncated rRgpB435 was not attached to the outer membrane and was located as largely inactive, discrete 71-kDa and 48-kDa isoforms in the culture supernatant and the periplasm. These results suggest that the C-terminal domain is essential for outer membrane attachment and may be involved in a coordinated process of export and attachment to the cell surface.
Residues Involved in FecR Binding Are Localized on One Side of the FecA Signaling Domain in
Escherichia coli
Authors: Breidenstein Elena , Mahren Susanne , Braun Volkmar 
Published: August 2006

ABSTRACT

Ferric citrate transport in
Escherichia coli
involves proteins encoded by the
fec
genes, including the transport and signaling protein FecA and the signal transducing protein FecR. Randomly isolated FecA point mutants showed a reduced interaction with FecR and a reduced transcription initiation of the ferric citrate transport genes. The mutations were localized on one side of the FecA signaling domain, which might form the interface to FecR. Some of the mutants showed strongly reduced iron transport rates, which suggests that the signaling domain affects the structure of the FecA transporter domain.
Two Genes Encoding New Carotenoid-Modifying Enzymes in the Green Sulfur Bacterium
Chlorobium tepidum
Authors: Maresca Julia A. , Bryant Donald A. 
Published: August 2006

ABSTRACT

The green sulfur bacterium
Chlorobium tepidum
produces chlorobactene as its primary carotenoid. Small amounts of chlorobactene are hydroxylated by the enzyme CrtC and then glucosylated and acylated to produce chlorobactene glucoside laurate. The genes encoding the enzymes responsible for these modifications of chlorobactene, CT1987, and CT0967, have been identified by comparative genomics, and these genes were insertionally inactivated in
C. tepidum
to verify their predicted function. The gene encoding chlorobactene glucosyltransferase (CT1987) has been named
cruC
, and the gene encoding chlorobactene lauroyltransferase (CT0967) has been named
cruD
. Homologs of these genes are found in the genomes of all sequenced green sulfur bacteria and filamentous anoxygenic phototrophs as well as in the genomes of several nonphotosynthetic bacteria that produce similarly modified carotenoids. The other bacteria in which these genes are found are not closely related to green sulfur bacteria or to one another. This suggests that the ability to synthesize modified carotenoids has been a frequently transferred trait.
ADVANCED COOLING TECHNOLOGIES FOR MICROPROCESSORS
Authors: KENNY THOMAS W. , GOODSON KENNETH E. , SANTIAGO JUAN G. , WANG EVELYN , KOO JAE-MO , JIANG LINAN , POP ERIC , SINHA SANJIV , ZHANG LIAN , FOGG DAVID , YAO SHUHUAI , FLYNN ROGER , CHANG CHING-HSIANG , HIDROVO CARLOS H. 
Published: August 2006

Recent trends in processor power for the next generation devices point clearly to significant increase in processor heat dissipation over the coming years. In the desktop system design space, the tendency has been to minimize system enclosure size while maximizing performance, which in turn leads to high power densities in future generation systems. The current thermal solutions used today consist of advanced heat sink designs and heat pipe designs with forced air cooling to cool high power processors. However, these techniques are already reaching their limits to handle high heat flux, and there is a strong need for development of more efficient cooling systems which are scalable to handle the high heat flux generated by the future products. To meet this challenge, there has been research in academia and in industry to explore alternative methods for extracting heat from high-density power sources in electronic systems. This talk will discuss the issues surrounding device cooling, from the transistor level to the system level, and describe system-level solutions being developed for desktop computer applications developed in our group at Stanford University.
Health Psychology: Psychological Adjustment to Chronic Disease
Authors: Stanton Annette L. , Revenson Tracey A. , Tennen Howard 
Published: August 2006

Abstract Chronic diseases carry important psychological and social consequences that demand significant psychological adjustment. The literature is providing increasingly nuanced conceptualizations of adjustment, demonstrating that the experience of chronic disease necessitates adaptation in multiple life domains. Heterogeneity in adjustment is apparent between individuals and across the course of the disease trajectory. Focusing on cancer, cardiovascular disease, and rheumatic diseases, we review longitudinal investigations of distal (socioeconomic variables, culture/ethnicity, and gender-related processes) and proximal (interpersonal relationships, personality attributes, cognitive appraisals, and coping processes) risk and protective factors for adjustment across time. We observe that the past decade has seen a surge in research that is longitudinal in design, involves adequately characterized samples of sufficient size, and includes statistical control for initial values on dependent variables. A progressively convincing characterization of risk and protective factors for favorable adjustment to chronic illness has emerged. We identify critical issues for future research.
Ostracism
Authors: Williams Kipling D. 
Published: August 2006

Abstract In this review, I examine the social psychological research on ostracism, social exclusion, and rejection. Being ignored, excluded, and/or rejected signals a threat for which reflexive detection in the form of pain and distress is adaptive for survival. Brief ostracism episodes result in sadness and anger and threaten fundamental needs. Individuals then act to fortify or replenish their thwarted need or needs. Behavioral consequences appear to be split into two general categories: attempts to fortify relational needs (belonging, self-esteem, shared understanding, and trust), which lead generally to prosocial thoughts and behaviors, or attempts to fortify efficacy/existence needs of control and recognition that may be dealt with most efficiently through antisocial thoughts and behaviors. Available research on chronic exposure to ostracism appears to deplete coping resources, resulting in depression and helplessness.