bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precise Region and the Character of the Pathogenicity Island in Clinical
Vibrio parahaemolyticus
Strains
Authors: Sugiyama Tomohiko , Iida Tetsuya , Izutsu Kaori , Park Kwon-Sam , Honda Takeshi 
Published: December 2007

ABSTRACT

In this study, we determined the borders of the pathogenicity island in
V. parahaemolyticus
RIMD2210633 (Vp-PAI). Vp-PAI has features in common with Tn
7
and other related elements at both terminal ends. Our findings indicate that the mobile element with a transposase which contains the DDE motif may have been involved in Vp-PAI formation.
Mutation at Different Sites in the
Nostoc punctiforme cyaC
Gene, Encoding the Multiple-Domain Enzyme Adenylate Cyclase, Results in Different Levels of Infection of the Host Plant
Blasia pusilla
Authors: Chapman Karen E. , Duggan Paula S. , Billington Natalie A. , Adams David G. 
Published: December 2007

ABSTRACT

The filamentous cyanobacterium
Nostoc punctiforme
forms symbioses with plants. Disruption of the catalytic domain of the
N. punctiforme
adenylate cyclase (CyaC) significantly increased symbiotic competence, whereas reduced infectivity was observed in a mutant with a disruption close to the N terminus of CyaC. The total cellular cyclic AMP levels were significantly reduced in both mutants.
Localization and Interactions of Teichoic Acid Synthetic Enzymes inBacillus subtilis
Authors: Formstone Alex , Carballido-López Rut , Noirot Philippe , Errington Jeffery , Scheffers Dirk-Jan 
Published: December 2007

ABSTRACTThe thick wall of gram-positive bacteria is a polymer meshwork composed predominantly of peptidoglycan (PG) and teichoic acids, both of which have a critical function in maintenance of the structural integrity and the shape of the cell. InBacillus subtilis168 the major teichoic acid is covalently coupled to PG and is known as wall teichoic acid (WTA). Recently, PG insertion/degradation over the lateral wall has been shown to occur in a helical pattern. However, the spatial organization of WTA assembly and its relationship with cell shape and PG assembly are largely unknown. We have characterized the localization of green fluorescent protein fusions to proteins involved in several steps of WTA synthesis inB. subtilis: TagB, -F, -G, -H, and -O. All of these localized similarly to the inner side of the cytoplasmic membrane, in a pattern strikingly similar to that displayed by probes of nascent PG. Helix-like localization patterns are often attributable to the morphogenic cytoskeletal proteins of the MreB family. However, localization of the Tag proteins did not appear to be substantially affected by single disruption of any of the three MreB homologues ofB. subtilis. Bacterial and yeast two-hybrid experiments revealed a complex network of interactions involving TagA, -B, -E, -F, -G, -H, and -O and the cell shape determinants MreC and MreD (encoded by themreBCDoperon and presumably involved in the spatial organization of PG synthesis). Taken together, our results suggest that, inB. subtilisat least, the synthesis and export of WTA precursors are mediated by a large multienzyme complex that may be associated with the PG-synthesizing machinery.
Role of Accessory DNA Polymerases in DNA Replication in
Escherichia coli
: Analysis of the
dnaX36
Mutator Mutant
Authors: Gawel Damian , Pham Phuong T. , Fijalkowska Iwona J. , Jonczyk Piotr , Schaaper Roel M. 
Published: December 2007

ABSTRACT

The
dnaX36
(TS) mutant of
Escherichia coli
confers a distinct mutator phenotype characterized by enhancement of transversion base substitutions and certain (−1) frameshift mutations. Here, we have further investigated the possible mechanism(s) underlying this mutator effect, focusing in particular on the role of the various
E. coli
DNA polymerases. The
dnaX
gene encodes the τ subunit of DNA polymerase III (Pol III) holoenzyme, the enzyme responsible for replication of the bacterial chromosome. The
dnaX36
defect resides in the C-terminal domain V of τ, essential for interaction of τ with the α (polymerase) subunit, suggesting that the mutator phenotype is caused by an impaired or altered α-τ interaction. We previously proposed that the mutator activity results from aberrant processing of terminal mismatches created by Pol III insertion errors. The present results, including lack of interaction of
dnaX
36 with
mutM, mutY
, and
recA
defects, support our assumption that
dnaX36
-mediated mutations originate as errors of replication rather than DNA damage-related events. Second, an important role is described for DNA Pol II and Pol IV in preventing and producing, respectively, the mutations. In the system used, a high fraction of the mutations is dependent on the action of Pol IV in a (
dinB
) gene dosage-dependent manner. However, an even larger but opposing role is deduced for Pol II, revealing Pol II to be a major editor of Pol III mediated replication errors. Overall, the results provide insight into the interplay of the various DNA polymerases, and of τ subunit, in securing a high fidelity of replication.
Glycerate 2-Kinase of
Thermotoga maritima
and Genomic Reconstruction of Related Metabolic Pathways
Authors: Yang Chen , Rodionov Dmitry A. , Rodionova Irina A. , Li Xiaoqing , Osterman Andrei L. 
Published: December 2007

ABSTRACT

Members of a novel glycerate-2-kinase (GK-II) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the GarK (GK-I) family. The recently reported three-dimensional structure of GK-II from
Thermotoga maritima
(TM1585; PDB code 2b8n) revealed a new fold distinct from other known kinase families. Here, we verified the enzymatic activity of TM1585, assessed its kinetic characteristics, and used directed mutagenesis to confirm the essential role of the two active-site residues Lys-47 and Arg-325. The main objective of this study was to apply comparative genomics for the reconstruction of metabolic pathways associated with GK-II in all bacteria and, in particular, in
T. maritima
. Comparative analyses of ∼400 bacterial genomes revealed a remarkable variety of pathways that lead to GK-II-driven utilization of glycerate via a glycolysis/gluconeogenesis route. In the case of
T. maritima
, a three-step serine degradation pathway was inferred based on the tentative identification of two additional enzymes, serine-pyruvate aminotransferase and hydroxypyruvate reductase (TM1400 and TM1401, respectively), that convert serine to glycerate via hydroxypyruvate. Both enzymatic activities were experimentally verified, and the entire pathway was validated by its in vitro reconstitution.
A Common Virulence Plasmid in Biotype 2
Vibrio vulnificus
and Its Dissemination Aided by a Conjugal Plasmid
Authors: Lee Chung-Te , Amaro Carmen , Wu Keh-Ming , Valiente Esmeralda , Chang Yi-Feng , Tsai Shih-Feng , Chang Chuan-Hsiung , Hor Lien-I 
Published: December 2007

ABSTRACT

Strains of
Vibrio vulnificus
, a marine bacterial species pathogenic for humans and eels, are divided into three biotypes, and those virulent for eels are classified as biotype 2. All biotype 2 strains possess one or more plasmids, which have been shown to harbor the biotype 2-specific DNA sequences. In this study we determined the DNA sequences of three biotype 2 plasmids: pR99 (68.4 kbp) in strain CECT4999 and pC4602-1 (56.6 kb) and pC4602-2 (66.9 kb) in strain CECT4602. Plasmid pC4602-2 showed 92% sequence identity with pR99. Curing of pR99 from strain CECT4999 resulted in loss of resistance to eel serum and virulence for eels but had no effect on the virulence for mice, an animal model, and resistance to human serum. Plasmids pC4602-2 and pR99 could be transferred to the plasmid-cured strain by conjugation in the presence of pC4602-1, which was self-transmissible, and acquisition of pC4602-2 restored the virulence of the cured strain for eels. Therefore, both pR99 and pC4602-2 were virulence plasmids for eels but not mice. A gene in pR99, which encoded a novel protein and had an equivalent in pC4602-2, was further shown to be essential, but not sufficient, for the resistance to eel serum and virulence for eels. There was evidence showing that pC4602-2 may form a cointegrate with pC4602-1. An investigation of six other biotype 2 strains for the presence of various plasmid markers revealed that they all harbored the virulence plasmid and four of them possessed the conjugal plasmid in addition.
Genetic Evidence for the Actin Homolog Gene
mreBH
and the Bacitracin Resistance Gene
bcrC
as Targets of the Alternative Sigma Factor SigI of
Bacillus subtilis
Authors: Tseng Chi-Ling , Shaw Gwo-Chyuan 
Published: December 2007

ABSTRACT

The
Bacillus subtilis sigI
gene, which is a member of the class VI heat shock genes of the
B. subtilis
heat shock stimulon, encodes an alternative sigma factor whose regulon is poorly defined. In this study, by using a binary vector system, we showed that
B. subtilis
SigI could drive expression of a transcriptional fusion between the
sigI
regulatory region from
Bacillus licheniformis, Bacillus
sp. strain NRRL B-14911,
B. subtilis
, or
Bacillus thuringiensis
and the
xylE
reporter gene in
B. subtilis
. The transcriptional initiation sites of these fusions in
B. subtilis
were mapped by primer extension analyses. A putative consensus promoter sequence probably recognized by the
B. subtilis
SigI was thus deduced. Using a consensus sequence-based search procedure, we found putative σ
I
promoters preceding the actin homolog gene
mreBH
and the bacitracin resistance gene
bcrC
of
B. subtilis
. Overexpression of the
B. subtilis sigI
gene could specifically stimulate expression of both an
mreBH
promoter region-
bgaB
fusion and a
bcrC
promoter region-
bgaB
fusion. Expression of these two fusions at the
amyE
locus of the
B. subtilis
chromosome was heat inducible and SigI dependent as revealed by
sigI
gene disruption experiments. Primer extension analysis showed that the identified
mreBH
and
bcrC
transcriptional start sites were at appropriate distances from their σ
I
promoter elements. This further supports the notion that SigI can directly regulate
mreBH
and
bcrC
expression. Taken together, these results strongly suggest that
mreBH
and
bcrC
are new members of the SigI regulon.
Transcriptome Analysis of Sorbic Acid-Stressed
Bacillus subtilis
Reveals a Nutrient Limitation Response and Indicates Plasma Membrane Remodeling
Authors: Beek Alex Ter , Keijser Bart J. F. , Boorsma Andre , Zakrzewska Anna , Orij Rick , Smits Gertien J. , Brul Stanley 
Published: December 2007

ABSTRACT

The weak organic acid sorbic acid is a commonly used food preservative, as it inhibits the growth of bacteria, yeasts, and molds. We have used genome-wide transcriptional profiling of
Bacillus subtilis
cells during mild sorbic acid stress to reveal the growth-inhibitory activity of this preservative and to identify potential resistance mechanisms. Our analysis demonstrated that sorbic acid-stressed cells induce responses normally seen upon nutrient limitation. This is indicated by the strong derepression of the CcpA, CodY, and Fur regulon and the induction of tricarboxylic acid cycle genes, SigL- and SigH-mediated genes, and the stringent response. Intriguingly, these conditions did not lead to the activation of sporulation, competence, or the general stress response. The fatty acid biosynthesis (
fab
) genes and BkdR-regulated genes are upregulated, which may indicate plasma membrane remodeling. This was further supported by the reduced sensitivity toward the
fab
inhibitor cerulenin upon sorbic acid stress. We are the first to present a comprehensive analysis of the transcriptional response of
B. subtilis
to sorbic acid stress.
Distinct Roles for Two CYP226 Family Cytochromes P450 in Abietane Diterpenoid Catabolism by
Burkholderia xenovorans
LB400
Authors: Smith Daryl J. , Patrauchan Marianna A. , Florizone Christine , Eltis Lindsay D. , Mohn William W. 
Published: December 2007

ABSTRACT

The 80-kb
dit
cluster of
Burkholderia xenovorans
LB400 encodes the catabolism of abietane diterpenoids. This cluster includes
ditQ
and
ditU
, predicted to encode cytochromes P450 (P450s) belonging to the poorly characterized CYP226A subfamily. Using proteomics, we identified 16
dit
-encoded proteins that were significantly more abundant in LB400 cells grown on dehydroabietic acid (DhA) or abietic acid (AbA) than in succinate-grown cells. A key difference in the catabolism of DhA and AbA lies in the differential expression of the P450s; DitU was detected only in the AbA-grown cells, whereas DitQ was expressed both during growth on DhA and during growth on AbA. Analyses of insertion mutants showed that
ditQ
was required for growth on DhA,
ditU
was required for growth on AbA, and neither gene was required for growth on the central intermediate, 7-oxo-DhA. In cell suspension assays, patterns of substrate removal and metabolite accumulation confirmed the role of DitU in AbA transformation and the role of DitQ in DhA transformation. Spectral assays revealed that DitQ binds both DhA (dissociation constant, 0.98 ± 0.01 μM) and palustric acid. Finally, DitQ transformed DhA to 7-hydroxy-DhA in vitro. These results demonstrate the distinct roles of the P450s DitQ and DitU in the transformation of DhA and AbA, respectively, to 7-oxo-DhA in a convergent degradation pathway.
Staphylococcus aureusCodY Negatively Regulates Virulence Gene Expression
Authors: Majerczyk Charlotte D. , Sadykov Marat R. , Luong Thanh T. , Lee Chia , Somerville Greg A. , Sonenshein Abraham L. 
Published: December 2007

ABSTRACTCodY is a global regulatory protein that was first discovered inBacillus subtilis, where it couples gene expression to changes in the pools of critical metabolites through its activation by GTP and branched-chain amino acids. Homologs of CodY can be found encoded in the genomes of nearly all low-G+C gram-positive bacteria, includingStaphylococcus aureus. The introduction of acodY-null mutation into twoS. aureusclinical isolates, SA564 and UAMS-1, through allelic replacement, resulted in the overexpression of several virulence genes. The mutant strains had higher levels of hemolytic activity toward rabbit erythrocytes in their culture fluid, produced more polysaccharide intercellular adhesin (PIA), and formed more robust biofilms than did their isogenic parent strains. These phenotypes were associated with derepressed levels of RNA for the hemolytic alpha-toxin (hla), the accessory gene regulator (agr) (RNAIIandRNAIII/hld), and the operon responsible for the production of PIA (icaADBC). These data suggest that CodY represses, either directly or indirectly, the synthesis of a number of virulence factors ofS. aureus.
The AraC-Like Transcriptional Regulator DhbR Is Required for Maximum Expression of the 2,3-Dihydroxybenzoic Acid Biosynthesis Genes inBrucella abortus2308 in Response to Iron Deprivation
Authors: Anderson Eric S. , Paulley James T. , Roop R. Martin 
Published: December 2007

ABSTRACTPhenotypic evaluation of isogenic mutants derived fromBrucella abortus2308 indicates that the AlcR homolog DhbR (2,3-dihydroxybenzoic acid [2,3-DHBA] biosynthesisregulator) modulates the expression of the genes involved in 2,3-DHBA production, employing 2,3-DHBA or brucebactin as a coinducer.
Reinvestigation of the Steady-State Kinetics and Physiological Function of the Soluble NiFe-Hydrogenase I of
Pyrococcus furiosus
Authors: van Haaster Daan J. , Silva Pedro J. , Hagedoorn Peter-Leon , Jongejan Jaap A. , Hagen Wilfred R. 
Published: December 2007

ABSTRACT

Pyrococcus furiosus
has two types of NiFe-hydrogenases: a heterotetrameric soluble hydrogenase and a multimeric transmembrane hydrogenase. Originally, the soluble hydrogenase was proposed to be a new type of H
2
evolution hydrogenase, because, in contrast to all of the then known NiFe-hydrogenases, the hydrogen production activity at 80°C was found to be higher than the hydrogen consumption activity and CO inhibition appeared to be absent. NADPH was proposed to be the electron donor. Later, it was found that the membrane-bound hydrogenase exhibits very high hydrogen production activity sufficient to explain cellular H
2
production levels, and this seems to eliminate the need for a soluble hydrogen production activity and therefore leave the soluble hydrogenase without a physiological function. Therefore, the steady-state kinetics of the soluble hydrogenase were reinvestigated. In contrast to previous reports, a low
K

m

for H
2
(∼20 μM) was found, which suggests a relatively high affinity for hydrogen. Also, the hydrogen consumption activity was 1 order of magnitude higher than the hydrogen production activity, and CO inhibition was significant (50% inhibition with 20 μM dissolved CO). Since the
K

m

for NADP
+
is ∼37 μM, we concluded that the soluble hydrogenase from
P. furiosus
is likely to function in the regeneration of NADPH and thus reuses the hydrogen produced by the membrane-bound hydrogenase in proton respiration.
The Intracellular Pathogen
Rhodococcus equi
Produces a Catecholate Siderophore Required for Saprophytic Growth
Authors: Miranda-CasoLuengo Raúl , Prescott John F. , Vázquez-Boland José A. , Meijer Wim G. 
Published: December 2007

ABSTRACT

Little is known about the iron acquisition systems of the soilborne facultative intracellular pathogen
Rhodococcus equi
. We previously reported that expression of
iupABC
, encoding a putative siderophore ABC transporter system, is iron regulated and required for growth at low iron concentrations. Here we show that disruption of
iupA
leads to the concomitant accumulation of catecholates and a chromophore with absorption maxima at 341 and 528 nm during growth under iron-replete conditions. In contrast, the wild-type strain produces these compounds only in iron-depleted medium. Disruption of
iupU
and
iupS
, encoding nonribosomal peptide synthetases, prevented growth of the corresponding
R. equi
SID1 and SID3 mutants at low iron concentrations. However, only
R. equi
SID3 did not produce the chromophore produced by the wild-type strain during growth at low iron concentrations. The phenotype of
R. equi
SID3, but not that of
R. equi
SID1, could be rescued by coculture with the wild type, allowing growth at low iron concentrations. This strongly suggests that the product of the
iupS
gene is responsible for the synthesis of a diffusible compound required for growth at low iron concentrations. Transcription of
iupU
was constitutive, but that of
iupS
was iron regulated, with an induction of 3 orders of magnitude during growth in iron-depleted compared to iron-replete medium. Neither mutant was attenuated in vivo in a mouse infection model, indicating that the
iupU
- and
iupS
-encoded iron acquisition systems are primarily involved in iron uptake during saprophytic life.
In Situ Growth Rates and Biofilm Development of
Pseudomonas aeruginosa
Populations in Chronic Lung Infections
Authors: Yang Lei , Haagensen Janus A. J. , Jelsbak Lars , Johansen Helle Krogh , Sternberg Claus , Høiby Niels , Molin Søren 
Published: December 2007

ABSTRACT

The growth dynamics of bacterial pathogens within infected hosts are a fundamental but poorly understood feature of most infections. We have focused on the in situ distribution and growth characteristics of two prevailing and transmissible
Pseudomonas aeruginosa
clones that have caused chronic lung infections in cystic fibrosis (CF) patients for more than 20 years. We used fluorescence in situ hybridization (FISH) directly on sputum specimens to examine the spatial distribution of the infecting
P. aeruginosa
cells. Mucoid variants were present in sputum as cell clusters surrounded by an extracellular matrix, whereas nonmucoid variants were present mainly as dispersed cells. To obtain estimates of the growth rates of
P. aeruginosa
in CF lungs, we used quantitative FISH to indirectly measure growth rates of bacteria in sputum samples (reflecting the in vivo lung conditions). The concentration of rRNA in bacteria isolated from sputa was measured and correlated with the rRNA contents of the same bacteria growing in vitro at defined rates. The results showed that most cells were actively growing with doubling times of between 100 and 200 min, with some growing even faster. Only a small stationary-phase subpopulation seemed to be present in sputa. This was found for both mucoid and nonmucoid variants despite their different organizations in sputum. The results suggest that the bacterial population may be confronted with selection forces that favor optimized growth activities. This scenario constitutes a new perspective on the adaptation and evolution of
P. aeruginosa
during chronic infections in CF patients in particular and on long-term infections in general.
Pseudomonas syringaeBetT Is a Low-Affinity Choline Transporter That Is Responsible for Superior Osmoprotection by Choline over Glycine Betaine
Authors: Chen Chiliang , Beattie Gwyn A. 
Published: December 2007

ABSTRACTThe plant pathogenPseudomonas syringaederives better osmoprotection from choline than from glycine betaine, unlike most bacteria that have been characterized. In this report, we identified a betaine/carnitine/choline family transporter (BCCT) inP. syringaepv. tomato strain DC3000 that mediates the transport of choline and acetylcholine. This transporter has a particularly low affinity (Kmof 876 μM) and high capacity (Vmaxof 80 nmol/min/mg of protein) for choline transport relative to other known BCCTs. Although BetT activity increased in response to hyperosmolarity, BetT mediated significant uptake under low-osmolarity conditions, suggesting a role in transport for both osmoprotection and catabolism. Growth studies with mutants deficient in BetT and other choline transporters demonstrated that BetT was responsible for the superior osmoprotection conferred toP. syringaeby choline over glycine betaine when these compounds were provided at high concentrations (>100 μM). These results suggest thatP. syringaehas evolved to survive in relatively choline-rich habitats, a prediction that is supported by the common association ofP. syringaewith plants and the widespread production of choline, but genus- and species-specific production of glycine betaine, by plants. Among the three putative BCCT family transporters inPseudomonas aeruginosaand six inPseudomonas putida, different transporters were predicted to function based on similarity toEscherichia coliBetT than toP. syringaeBetT. FunctionalP. putidaandP. aeruginosatransporters were identified, and their possession of a long C-terminal tail suggested an osmoregulatory function for this tail; this function was confirmed forP. syringaeBetT using deletion derivatives.