bluuebunny/crossref_metadata_2025_split huggingface dataset:
The
Helicobacter pylori
GroES Cochaperonin HspA Functions as a Specialized Nickel Chaperone and Sequestration Protein through Its Unique C-Terminal Extension
Authors: Schauer Kristine , Muller Cécile , Carrière Marie , Labigne Agnès , Cavazza Christine , De Reuse Hilde 
Published: January 2010

ABSTRACT

The transition metal nickel plays a central role in the human gastric pathogen
Helicobacter pylori
because it is required for two enzymes indispensable for colonization, the nickel metalloenzyme urease and [NiFe] hydrogenase. To sustain nickel availability for these metalloenzymes while providing protection from the metal's harmful effects,
H. pylori
is equipped with several specific nickel-binding proteins. Among these,
H. pylori
possesses a particular chaperone, HspA, that is a homolog of the highly conserved and essential bacterial heat shock protein GroES. HspA contains a unique His-rich C-terminal extension and was demonstrated to bind nickel
in vitro
. To investigate the function of this extension in
H. pylori
, we constructed mutants carrying either a complete deletion or point mutations in critical residues of this domain. All mutants presented a decreased intracellular nickel content measured by inductively coupled plasma mass spectrometry (ICP-MS) and reduced nickel tolerance. While urease activity was unaffected in the mutants, [NiFe] hydrogenase activity was significantly diminished when the C-terminal extension of HspA was mutated. We conclude that
H. pylori
HspA is involved in intracellular nickel sequestration and detoxification and plays a novel role as a specialized nickel chaperone involved in nickel-dependent maturation of hydrogenase.
DsrR, a Novel IscA-Like Protein Lacking Iron- and Fe-S-Binding Functions, Involved in the Regulation of Sulfur Oxidation inAllochromatium vinosum
Authors: Grimm Frauke , Cort John R. , Dahl Christiane 
Published: January 2010

ABSTRACTIn the purple sulfur bacteriumAllochromatium vinosum, the reverse-acting dissimilatory sulfite reductase (DsrAB) is the key enzyme responsible for the oxidation of intracellular sulfur globules. The genesdsrABare the first and the genedsrRis the penultimate of the 15 genes of thedsroperon inA. vinosum. Genes homologous todsrRoccur in a number of other environmentally important sulfur-oxidizing bacteria utilizing Dsr proteins. DsrR exhibits sequence similarities to A-type scaffolds, like IscA, that partake in the maturation of protein-bound iron-sulfur clusters. We used nuclear magnetic resonance (NMR) spectroscopy to solve the solution structure of DsrR and to show that the protein is indeed structurally highly similar to A-type scaffolds. However, DsrR does not retain the Fe-S- or the iron-binding ability of these proteins, which is due to the lack of all three highly conserved cysteine residues of IscA-like scaffolds. Taken together, these findings suggest a common function for DsrR and IscA-like proteins different from direct participation in iron-sulfur cluster maturation. AnA. vinosumΔdsrRdeletion strain showed a significantly reduced sulfur oxidation rate that was fully restored upon complementation withdsrRintrans. Immunoblot analyses revealed a reduced level of DsrE and DsrL in the ΔdsrRstrain. These proteins are absolutely essential for sulfur oxidation. Transcriptional and translational gene fusion experiments suggested the participation of DsrR in the posttranscriptional control of thedsroperon, similar to the alternative function of cyanobacterial IscA as part of the sense and/or response cascade set into action upon iron limitation.
The Three RelE Homologs of
Mycobacterium tuberculosis
Have Individual, Drug-Specific Effects on Bacterial Antibiotic Tolerance
Authors: Singh Ramandeep , Barry Clifton E. , Boshoff Helena I. M. 
Published: January 2010

ABSTRACT

In
Escherichia coli
, expression of the RelE and HipA toxins in the absence of their cognate antitoxins has been associated with generating multidrug-tolerant “persisters.” Here we show that unlike persisters of
E. coli
, persisters of
Mycobacterium tuberculosis
selected with one drug do not acquire cross-resistance to other classes of drugs.
M. tuberculosis
has three homologs of RelE arranged in operons with their apparent antitoxins. Each toxin individually arrests growth of both
M. tuberculosis
and
E. coli
, an effect that is neutralized by coexpression of the cognate antitoxin. Overexpression or deletion of each of the RelE toxins had a toxin- and drug-specific effect on the proportion of bacilli surviving antibiotic killing. All three toxins were upregulated
in vivo
, but none of the deletions affected survival during murine infection. RelE2 overexpression increased bacterial survival rates in the presence of rifampin
in vitro
, while deletion significantly decreased survival rates. Strikingly, deletion of this toxin had no discernible effect on the level of persisters seen in rifampin-treated mice. Our results suggest that,
in vivo
, RelE-generated persisters are unlikely to play a significant role in the generation of bacilli that survive in the face of multidrug therapy or in the generation of multidrug-resistant
M. tuberculosis
.
TnpR Encoded by an IS
Ppu12
Isoform Regulates Transposition of Two Different IS
L3
-Like Insertion Sequences in
Pseudomonas stutzeri
after Conjugative Interaction
Authors: Christie-Oleza J. A. , Nogales B. , Lalucat J. , Bosch R. 
Published: January 2010

ABSTRACT

Pseudomonas stutzeri
AN10 has two IS
L3
-like insertion sequences (ISs). One of them has been recently described as IS
Pst9
. In this study we show that the second IS, situated 4.5 kb upstream of IS
Pst9
, is an isoform of IS
Ppu12
from
Pseudomonas putida
mt-2. Although both IS
L3
-like ISs are flanked by nearly identical (21/24 conserved residues) inverted repeats (IRs) and harbor similar transposases (93% amino acid identity), they differ in their accompanying genes. As described for IS
Pst9
, the isoform of IS
Ppu12
also transposes by a conservative mechanism, forms circular double-stranded DNA (dsDNA) transposition intermediates, and is induced by interaction with the conjugative strain
Escherichia coli
S17-1λ

pir

(conjugative interaction) but not with the nonconjugative
E. coli
DH5α. In fact, we demonstrate that IS
Pst9
transposition after conjugative interaction occurs only when IS
Ppu12
is present, indicating that IS
Ppu12
is upregulating transposition of both ISs under such conditions. We also demonstrate that this conjugative interaction-mediated induction of IS
Ppu12
is not exclusive to the
P. stutzeri
AN10 strain but is a more general phenomenon, at least in
Pseudomonas
. Mutation of TnpR, a MerR-like transcriptional regulator present in IS
Ppu12
but not in IS
Pst9
, reduced the transcription of
tnpA
(IS
Ppu12
transposase-encoding gene) and decreased formation of circular dsDNA transposition intermediates after conjugative interaction. Complementation of the TnpR mutant restored the phenotype. In addition, the presence of TnpR in an IS
Ppu12
-free genetic background did not induce IS
Pst9
after conjugative interaction. Thus, our results suggest that TnpR, after conjugative interaction, activates transcription of
tnpA
of IS
Ppu12
. Then, TnpA of IS
Ppu12
would bind to IRs of both ISs, IS
Ppu12
and IS
Pst9
, causing their transposition.
In
Helicobacter pylori
, LuxS Is a Key Enzyme in Cysteine Provision through a Reverse Transsulfuration Pathway
Authors: Doherty Neil C. , Shen Feifei , Halliday Nigel M. , Barrett David A. , Hardie Kim R. , Winzer Klaus , Atherton John C. 
Published: January 2010

ABSTRACT

In many bacteria, LuxS functions as a quorum-sensing molecule synthase. However, it also has a second, more central metabolic function in the activated methyl cycle (AMC), which generates the
S
-adenosylmethionine required by methyltransferases and recycles the product via methionine.
Helicobacter pylori
lacks an enzyme catalyzing homocysteine-to-methionine conversion, rendering the AMC incomplete and thus making any metabolic role of
H. pylori
LuxS (LuxS
Hp
) unclear. Interestingly,
luxS
Hp
is located next to genes annotated as
cysK
Hp
and
metB
Hp
, involved in other bacteria in cysteine and methionine metabolism. We showed that isogenic strains carrying mutations in
luxS
Hp
,
cysK
Hp
, and
metB
Hp
could not grow without added cysteine (whereas the wild type could), suggesting roles in cysteine synthesis. Growth of the Δ
luxS
Hp
mutant was restored by homocysteine or cystathionine and growth of the Δ
cysK
Hp
mutant by cystathionine only. The Δ
metB
Hp
mutant had an absolute requirement for cysteine. Metabolite analyses showed that
S
-ribosylhomocysteine accumulated in the Δ
luxS
Hp
mutant, homocysteine in the Δ
cysK
Hp
mutant, and cystathionine in the Δ
metB
Hp
mutant. This suggests that
S
-ribosylhomocysteine is converted by LuxS
Hp
to homocysteine (as in the classic AMC) and thence by CysK
Hp
to cystathionine and by MetB
Hp
to cysteine.
In silico
analysis suggested that
cysK-metB-luxS
were acquired by
H. pylori
from a Gram-positive source. We conclude that
cysK-metB-luxS
encode the capacity to generate cysteine from products of the incomplete AMC of
H. pylori
in a process of reverse transsulfuration. We recommend that the misnamed genes
cysK
Hp
and
metB
Hp
be renamed
mccA
(methionine-to-cysteine-conversion gene A) and
mccB
, respectively.
Tricarboxylic Acid Cycle-Dependent Synthesis of
Staphylococcus aureus
Type 5 and 8 Capsular Polysaccharides
Authors: Sadykov Marat R. , Mattes Theodoric A. , Luong Thanh T. , Zhu Yefei , Day Shandra R. , Sifri Costi D. , Lee Chia Y. , Somerville Greg A. 
Published: January 2010

ABSTRACT

Staphylococcus aureus
capsule synthesis requires the precursor
N
-acetyl-glucosamine; however, capsule is synthesized during post-exponential growth when the availability of
N
-acetyl-glucosamine is limited. Capsule biosynthesis also requires aerobic respiration, leading us to hypothesize that capsule synthesis requires tricarboxylic acid cycle intermediates. Consistent with this hypothesis,
S. aureus
tricarboxylic acid cycle mutants fail to make capsule.
The Chemoreceptor Dimer Is the Unit of Conformational Coupling and Transmembrane Signaling
Authors: Amin Divya N. , Hazelbauer Gerald L. 
Published: January 2010

ABSTRACTTransmembrane chemoreceptors are central components in bacterial chemotaxis. Receptors couple ligand binding and adaptational modification to receptor conformation in processes that create transmembrane signaling. Homodimers, the fundamental receptor structural units, associate in trimers and localize in patches of thousands. To what degree do conformational coupling and transmembrane signaling require higher-order interactions among dimers? To what degree are they altered by such interactions? To what degree are they inherent features of homodimers? We addressed these questions using nanodiscs to create membrane environments in which receptor dimers had few or no potential interaction partners. Receptors with many, few, or no interaction partners were tested for conformational changes and transmembrane signaling in response to ligand occupancy and adaptational modification. Conformation was assayed by measuring initial rates of receptor methylation, a parameter independent of receptor-receptor interactions. Coupling of ligand occupancy and adaptational modification to receptor conformation and thus to transmembrane signaling occurred with essentially the same sensitivity and magnitude in isolated dimers as for dimers with many neighbors. Thus, we conclude that the chemoreceptor dimer is the fundamental unit of conformational coupling and transmembrane signaling. This implies that in signaling complexes, coupling and transmembrane signaling occur through individual dimers and that changes between dimers in a receptor trimer or among trimer-based signaling complexes are subsequent steps in signaling.
Complete Genome Sequence ofListeria seeligeri, a Nonpathogenic Member of the GenusListeria
Authors: Steinweg Christiane , Kuenne Carsten T. , Billion André , Mraheil Mobarak A. , Domann Eugen , Ghai Rohit , Barbuddhe Sukhadeo B. , Kärst Uwe , Goesmann Alexander , Pühler Alfred , Weisshaar Bernd , Wehland Jürgen , Lampidis Robert , Kreft Jürgen , Goebel Werner , Chakraborty Trinad , Hain Torsten 
Published: January 2010

ABSTRACTWe report the complete and annotated genome sequence of the nonpathogenicListeria seeligeriSLCC3954 serovar 1/2b type strain harboring the smallest completely sequenced genome of the genusListeria.
Positions of Trp Codons in the Leader Peptide-Coding Region of the
at
Operon Influence Anti-Trap Synthesis and
trp
Operon Expression in
Bacillus licheniformis
Authors: Levitin Anastasia , Yanofsky Charles 
Published: January 2010

ABSTRACT

Tryptophan, phenylalanine, tyrosine, and several other metabolites are all synthesized from a common precursor, chorismic acid. Since tryptophan is a product of an energetically expensive biosynthetic pathway, bacteria have developed sensing mechanisms to downregulate synthesis of the enzymes of tryptophan formation when synthesis of the amino acid is not needed. In
Bacillus subtilis
and some other Gram-positive bacteria,
trp
operon expression is regulated by two proteins, TRAP (the tryptophan-activated RNA binding protein) and AT (the anti-TRAP protein). TRAP is activated by bound tryptophan, and AT synthesis is increased upon accumulation of uncharged tRNA
Trp
. Tryptophan-activated TRAP binds to
trp
operon leader RNA, generating a terminator structure that promotes transcription termination. AT binds to tryptophan-activated TRAP, inhibiting its RNA binding ability. In
B. subtilis
, AT synthesis is upregulated both transcriptionally and translationally in response to the accumulation of uncharged tRNA
Trp
. In this paper, we focus on explaining the differences in organization and regulatory functions of the
at
operon's leader peptide-coding region,
rtpLP
, of
B. subtilis
and
Bacillus licheniformis
. Our objective was to correlate the greater growth sensitivity of
B. licheniformis
to tryptophan starvation with the spacing of the three Trp codons in its
at
operon leader peptide-coding region. Our findings suggest that the Trp codon location in
rtpLP
of
B. licheniformis
is designed to allow a mild charged-tRNA
Trp
deficiency to expose the Shine-Dalgarno sequence and start codon for the AT protein, leading to increased AT synthesis.
Two Alternative Pathways for the Synthesis of the Rare Compatible Solute Mannosylglucosylglycerate inPetrotoga mobilis
Authors: Fernandes Chantal , Mendes Vitor , Costa Joana , Empadinhas Nuno , Jorge Carla , Lamosa Pedro , Santos Helena , da Costa Milton S. 
Published: January 2010

ABSTRACTThe compatible solute mannosylglucosylglycerate (MGG), recently identified inPetrotoga miotherma, also accumulates inPetrotoga mobilisin response to hyperosmotic conditions and supraoptimal growth temperatures. Two functionally connected genes encoding a glucosyl-3-phosphoglycerate synthase (GpgS) and an unknown glycosyltransferase (gene Pmob_1143), which we functionally characterized as a mannosylglucosyl-3-phosphoglycerate synthase and designated MggA, were identified in the genome ofPtg. mobilis. This enzyme used the product of GpgS, glucosyl-3-phosphoglycerate (GPG), as well as GDP-mannose to produce mannosylglucosyl-3-phosphoglycerate (MGPG), the phosphorylated precursor of MGG. The MGPG dephosphorylation was determined in cell extracts, and the native enzyme was partially purified and characterized. Surprisingly, a gene encoding a putative glucosylglycerate synthase (Ggs) was also identified in the genome ofPtg. mobilis, and an active Ggs capable of producing glucosylglycerate (GG) from ADP-glucose andd-glycerate was detected in cell extracts and the recombinant enzyme was characterized, as well. Since GG has never been identified in this organism nor was it a substrate for the MggA, we anticipated the existence of a nonphosphorylating pathway for MGG synthesis. We putatively identified the corresponding gene, whose product had some sequence homology with MggA, but it was not possible to recombinantly express a functional enzyme fromPtg. mobilis, which we named mannosylglucosylglycerate synthase (MggS). In turn, a homologous gene fromThermotoga maritimawas successfully expressed, and the synthesis of MGG was confirmed from GDP-mannose and GG. Based on the measurements of the relevant enzyme activities in cell extracts and on the functional characterization of the key enzymes, we propose two alternative pathways for the synthesis of the rare compatible solute MGG inPtg. mobilis.
Glycosylation of the Collagen Adhesin EmaA ofAggregatibacter actinomycetemcomitansIs Dependent upon the Lipopolysaccharide Biosynthetic Pathway
Authors: Tang Gaoyan , Mintz Keith P. 
Published: January 2010

ABSTRACTThe human oropharyngeal pathogenAggregatibacter actinomycetemcomitanssynthesizes multiple adhesins, including the nonfimbrial extracellular matrix protein adhesin A (EmaA). EmaA monomers trimerize to form antennae-like structures on the surface of the bacterium, which are required for collagen binding. Two forms of the protein have been identified, which are suggested to be linked with the type of O-polysaccharide (O-PS) of the lipopolysaccharide (LPS) synthesized (G. Tang et al., Microbiology 153:2447-2457, 2007). This association was investigated by generating individual mutants for a rhamnose sugar biosynthetic enzyme (rmlC; TDP-4-keto-6-deoxy-d-glucose 3,5-epimerase), the ATP binding cassette (ABC) sugar transport protein (wzt), and the O-antigen ligase (waaL). All three mutants produced reduced amounts of O-PS, and the EmaA monomers in these mutants displayed a change in their electrophoretic mobility and aggregation state, as observed in sodium dodecyl sulfate (SDS)-polyacrylamide gels. The modification of EmaA with O-PS sugars was suggested by lectin blots, using the fucose-specificLens culinarisagglutinin (LCA). Fucose is one of the glycan components of serotype b O-PS. ThermlCmutant strain expressing the modified EmaA protein demonstrated reduced collagen adhesion using anin vitrorabbit heart valve model, suggesting a role for the glycoconjugant in collagen binding. These data provide experimental evidence for the glycosylation of an oligomeric, coiled-coil adhesin and for the dependence of the posttranslational modification of EmaA on the LPS biosynthetic machinery inA. actinomycetemcomitans.
Two Regions of
Bacillus subtilis
Transcription Factor SpoIIID Allow a Monomer To Bind DNA
Authors: Himes Paul , McBryant Steven J. , Kroos Lee 
Published: January 2010

ABSTRACT

Nutrient limitation causes
Bacillus subtilis
to develop into two different cell types, a mother cell and a spore. SpoIIID is a key regulator of transcription in the mother cell and positively or negatively regulates more than 100 genes, in many cases by binding to the promoter region. SpoIIID was predicted to have a helix-turn-helix motif for sequence-specific DNA binding, and a 10-bp consensus sequence was recognized in binding sites, but some strong binding sites were observed to contain more than one match to the consensus sequence, suggesting that SpoIIID might bind as a dimer or cooperatively as monomers. Here we show that SpoIIID binds with high affinity as a monomer to a single copy of its recognition sequence. Using charge reversal substitutions of residues likely to be exposed on the surface of SpoIIID and assays for transcriptional activation
in vivo
and for DNA binding
in vitro
, we identify two regions essential for DNA binding, the putative recognition helix of the predicted helix-turn-helix motif and a basic region near the C terminus. SpoIIID is unusual among prokaryotic DNA-binding proteins with a single helix-turn-helix motif in its ability to bind DNA monomerically with high affinity. We propose that the C-terminal basic region of SpoIIID makes additional contacts with DNA, analogous to the N-terminal arm of eukaryotic homeodomain proteins and the “wings” of winged-helix proteins, but structurally distinct. SpoIIID is highly conserved only among bacteria that form endospores, including several important human pathogens. The need to conserve biosynthetic capacity during endospore formation might have favored the evolution of a small transcription factor capable of high-affinity binding to DNA as a monomer, and this unusual mode of DNA binding could provide a target for drug design.
Genome Sequence of the Deep-Rooted
Yersinia pestis
Strain Angola Reveals New Insights into the Evolution and Pangenome of the Plague Bacterium
Authors: Eppinger Mark , Worsham Patricia L. , Nikolich Mikeljon P. , Riley David R. , Sebastian Yinong , Mou Sherry , Achtman Mark , Lindler Luther E. , Ravel Jacques 
Published: January 2010

ABSTRACT

To gain insights into the origin and genome evolution of the plague bacterium
Yersinia pestis
, we have sequenced the deep-rooted strain Angola, a virulent Pestoides isolate. Its ancient nature makes this atypical isolate of particular importance in understanding the evolution of plague pathogenicity. Its chromosome features a unique genetic make-up intermediate between modern
Y. pestis
isolates and its evolutionary ancestor,
Y. pseudotuberculosis
. Our genotypic and phenotypic analyses led us to conclude that Angola belongs to one of the most ancient
Y. pestis
lineages thus far sequenced. The mobilome carries the first reported chimeric plasmid combining the two species-specific virulence plasmids. Genomic findings were validated in virulence assays demonstrating that its pathogenic potential is distinct from modern
Y. pestis
isolates. Human infection with this particular isolate would not be diagnosed by the standard clinical tests, as Angola lacks the plasmid-borne capsule, and a possible emergence of this genotype raises major public health concerns. To assess the genomic plasticity in
Y. pestis
, we investigated the global gene reservoir and estimated the pangenome at 4,844 unique protein-coding genes. As shown by the genomic analysis of this evolutionary key isolate, we found that the genomic plasticity within
Y. pestis
clearly was not as limited as previously thought, which is strengthened by the detection of the largest number of isolate-specific single-nucleotide polymorphisms (SNPs) currently reported in the species. This study identified numerous novel genetic signatures, some of which seem to be intimately associated with plague virulence. These markers are valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies.
Role of apoptosis induced by Helicobacter pylori infection in the development of duodenal ulcer
Authors: Kohda K , Tanaka K , Aiba Y , Yasuda M , Miwa T , Koga Y 
Published: January 2010

BACKGROUNDHelicobacter pylori affects gastric epithelium integrity by acceleration of apoptosis. However, it remains unclear what product of the bacteria causes apoptosis, or whether or not the apoptosis is involved in the development of ulcers.AIMSTo elucidate the factor from H pylori that causes acceleration of apoptosis and the role of apoptosis in the development of duodenal ulcer in H pylori infection.PATIENTSFiveH pylori negative healthy volunteers, 47H pylori positive patients with duodenal ulcer, and 35 H pylori positive patients with gastric ulcer.METHODSAn endoscopic examination was carried out to diagnose ulcers and determine their clinical stage. To analyse apoptosis, a cell cycle analysis was performed using biopsy specimens.RESULTSThere was a significant correlation between the urease activity of theH pylori strain and the level of apoptosis induced by this bacterial strain. Moreover, in duodenal ulcer patients infected with H pylori, the patients with an active ulcer exhibited a significantly higher level of apoptosis than those with ulcers at both the healing and scarring stages.CONCLUSIONThese findings suggest that acceleration of apoptosis in the antral mucosa caused by the urease of H pylori plays a crucial role in the development of ulcers in the duodenum.