bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple Promoter Inversions Generate Surface Antigenic Variation in
Mycoplasma penetrans
Authors: Horino Atsuko , Sasaki Yuko , Sasaki Tsuguo , Kenri Tsuyoshi 
Published: December 2002

ABSTRACT

Mycoplasma penetrans
is a newly identified species of the genus
Mycoplasma
. It was first isolated from a urine sample from a human immunodeficiency virus (HIV)-infected patient.
M. penetrans
changes its surface antigen profile with high frequency. The changes originate from ON↔OFF phase variations of the P35 family of surface membrane lipoproteins. The P35 family lipoproteins are major antigens recognized by the human immune system during
M. penetrans
infection and are encoded by the
mpl
genes. Phase variations of P35 family lipoproteins occur at the transcriptional level of
mpl
genes; however, the precise genetic mechanisms are unknown. In this study, the molecular mechanisms of surface antigen profile change in
M. penetrans
were investigated. The focus was on the 46-kDa protein that is present in
M. penetrans
strain HF-2 but not in the type strain, GTU. The 46-kDa protein was the product of a previously reported
mpl
gene, pepIMP13, with an amino-terminal sequence identical to that of the P35 family lipoproteins. Nucleotide sequencing analysis of the pepIMP13 gene region revealed that the promoter-containing 135-bp DNA of this gene had the structure of an invertible element that functioned as a switch for gene expression. In addition, all of the
mpl
genes of
M. penetrans
HF-2 were identified using the whole-genome sequence data that has recently become available for this bacterium. There are at least 38
mpl
genes in the
M. penetrans
HF-2 genome. Interestingly, most of these
mpl
genes possess invertible promoter-like sequences, similar to those of the pepIMP13 gene promoter. A model for the generation of surface antigenic variation by multiple promoter inversions is proposed.
The Global Transcriptional Response ofBacillus subtilisto Peroxide Stress Is Coordinated by Three Transcription Factors
Authors: Helmann John D. , Wu Ming Fang Winston , Gaballa Ahmed , Kobel Phil A. , Morshedi Maud M. , Fawcett Paul , Paddon Chris 
Published: December 2002

ABSTRACTBacillus subtilisexhibits a complex adaptive response to low levels of peroxides. We used global transcriptional profiling to monitor the magnitude and kinetics of changes in the mRNA population after exposure to either hydrogen peroxide (H2O2) ortert-butyl peroxide (t-buOOH). The peroxide stimulons could be largely accounted for by three regulons controlled by the PerR, σB, and OhrR transcription factors. Three members of the PerR regulon (katA,mrgA, andzosA) were strongly induced by H2O2and weakly induced by t-buOOH. The remaining members of the PerR regulon were only modestly up-regulated by peroxide treatment. Overall, the magnitude of peroxide induction of PerR regulon genes corresponded well with the extent of derepression in aperRmutant strain. The σBregulon was activated by 58 μM H2O2but not by 8 μM H2O2and was strongly activated by either t-buOOH or, in a control experiment,tert-butyl alcohol. Apart from the σBregulon there was a single gene,ohrA, that was strongly and rapidly induced by t-buOOH exposure. This gene, controlled by the peroxide-sensing repressor OhrR, was not induced by any of the other conditions tested.
The Crystal Structure of the Phosphorylation Domain in PhoP Reveals a Functional Tandem Association Mediated by an Asymmetric Interface
Authors: Birck Catherine , Chen Yinghua , Hulett F. Marion , Samama Jean-Pierre 
Published: December 2002

ABSTRACTPhoP fromBacillus subtilisbelongs to the OmpR subfamily of response regulators. It regulates the transcription of several operons and participates in a signal transduction network that controls adaptation of the bacteria to phosphate deficiency. The receiver domains of two members of this subfamily, PhoB fromEscherichia coliand DrrD fromThermotoga maritima, have been structurally characterized. These modules have similar overall folds but display remarkable differences in the conformation of the β4-α4 and α4 regions. The crystal structure of the receiver domain of PhoP (PhoPN) described in this paper illustrates yet another geometry in this region. Another major issue of the structure determination is the dimeric state of the protein and the novel mode of association between receiver domains. The protein-protein interface is provided by two different surfaces from each protomer, and the tandem unit formed through this asymmetric interface leaves free interaction surfaces. This design is well suited for further association of PhoP dimers to form oligomeric structures. The interprotein interface buries 970 Å2from solvent and mostly involves interactions between charged residues. As described in the accompanying paper, mutations of a single residue in one salt bridge shielded from solvent prevented dimerization of the unphosphorylated and phosphorylated response regulator and had drastic functional consequences. The three structurally documented members of the OmpR family (PhoB, DrrD, and PhoP) provide a framework to consider possible relationships between structural features and sequence signatures in critical regions of the receiver domains.
Residue R113 Is Essential for PhoP Dimerization and Function: a Residue Buried in the Asymmetric PhoP Dimer Interface Determined in the PhoPN Three-Dimensional Crystal Structure
Authors: Chen Yinghua , Birck Catherine , Samama Jean-Pierre , Hulett F. Marion 
Published: December 2002

ABSTRACTBacillus subtilisPhoP is a member of the OmpR/PhoB family of response regulators that is directly required for transcriptional activation or repression of Pho regulon genes in conditions under which Piis growth limiting. Characterization of the PhoP protein has established that phosphorylation of the protein is not essential for PhoP dimerization or DNA binding but is essential for transcriptional regulation of Pho regulon genes. DNA footprinting studies of PhoP-regulated promoters showed that there was cooperative binding between PhoP dimers at PhoP-activated promoters and/or extensive PhoP oligomerization 3′ of PhoP-binding consensus repeats in PhoP-repressed promoters. The crystal structure of PhoPN described in the accompanying paper revealed that the dimer interface between two PhoP monomers involves nonidentical surfaces such that each monomer in a dimer retains a second surface that is available for further oligomerization. A salt bridge between R113 on one monomer and D60 on another monomer was judged to be of major importance in the protein-protein interaction. We describe the consequences of mutation of the PhoP R113 codon to a glutamate or alanine codon and mutation of the PhoP D60 codon to a lysine codon. In vivo expression of either PhoPR113E, PhoPR113A, or PhoPD60Kresulted in a Pho-negative phenotype. In vitro analysis showed that PhoPR113Ewas phosphorylated by PhoR (the cognate histidine kinase) but was unable to dimerize. Monomeric PhoPR113E∼P was deficient in DNA binding, contributing to the PhoPR113Ein vivo Pho-negative phenotype. While previous studies emphasized that phosphorylation was essential for PhoP function, data reported here indicate that phosphorylation is not sufficient as PhoP dimerization or oligomerization is also essential. Our data support the physiological relevance of the residues of the asymmetric dimer interface in PhoP dimerization and function.
LuxS-Based Signaling inStreptococcus gordonii: Autoinducer 2 Controls Carbohydrate Metabolism and Biofilm Formation withPorphyromonas gingivalis
Authors: McNab Roderick , Ford Suzannah K. , El-Sabaeny Azza , Barbieri Bruno , Cook Guy S. , Lamont Richard J. 
Published: December 2002

ABSTRACTCommunication based on autoinducer 2 (AI-2) is widespread among gram-negative and gram-positive bacteria, and the AI-2 pathway can control the expression of genes involved in a variety of metabolic pathways and pathogenic mechanisms. In the present study, we identifiedluxS, a gene responsible for the synthesis of AI-2, inStreptococcus gordonii, a major component of the dental plaque biofilm.S. gordoniiconditioned medium induced bioluminescence in an AI-2 reporter strain ofVibrio harveyi. An isogenic mutant ofS. gordonii, generated by insertional inactivation of theluxSgene, was unaffected in growth and in its ability to form biofilms on polystyrene surfaces. In contrast, the mutant strain failed to induce bioluminescence inV. harveyiand was unable to form a mixed species biofilm with a LuxS-null strain of the periodontal pathogenPorphyromonas gingivalis. Complementation of theluxSmutation inS. gordoniirestored normal biofilm formation with theluxS-deficientP. gingivalis. Differential display PCR demonstrated that the inactivation ofS. gordonii luxSdownregulated the expression of a number of genes, includinggtfG, encoding glucosyltransferase;fruA, encoding extracellular exo-β-d-fructosidase; andlacDencoding tagatose 1,6-diphosphate aldolase. However,S. gordoniicell surface expression of SspA and SspB proteins, previously implicated in mediating adhesion betweenS. gordoniiandP. gingivalis, was unaffected by inactivation ofluxS. The results suggest thatS. gordoniiproduces an AI-2-like signaling molecule that regulates aspects of carbohydrate metabolism in the organism. Furthermore, LuxS-dependent intercellular communication is essential for biofilm formation between nongrowing cells ofP. gingivalisandS. gordonii.
Regulation of the
Escherichia coli rrnB
P2 Promoter
Authors: Murray Heath D. , Appleman J. Alex , Gourse Richard L. 
Published: December 2002

ABSTRACT

The seven rRNA operons in
Escherichia coli
each contain two promoters,
rrn
P1 and
rrn
P2. Most previous studies have focused on the
rrn
P1 promoters. Here we report a systematic analysis of the activity and regulation of the
rrnB
P2 promoter in order to define the intrinsic properties of
rrn
P2 promoters and to understand better their contributions to rRNA synthesis when they are in their natural setting downstream of
rrn
P1 promoters. In contrast to the conclusions reached in some previous studies, we find that
rrnB
P2 is regulated: it displays clear responses to amino acid availability (stringent control), rRNA gene dose (feedback control), and changes in growth rate (growth rate-dependent control). Stringent control of
rrnB
P2 requires the alarmone ppGpp, but growth rate-dependent control of
rrnB
P2 does not require ppGpp. The
rrnB
P2 core promoter sequence (−37 to +7) is sufficient to serve as the target for growth rate-dependent regulation.
Common Extracellular Sensory Domains in Transmembrane Receptors for Diverse Signal Transduction Pathways inBacteriaandArchaea
Authors: Zhulin Igor B. , Nikolskaya Anastasia N. , Galperin Michael Y. 
Published: December 2002

ABSTRACTTransmembrane receptors in microorganisms, such as sensory histidine kinases and methyl-accepting chemotaxis proteins, are molecular devices for monitoring environmental changes. We report here that sensory domain sharing is widespread among different classes of transmembrane receptors. We have identified two novel conserved extracellular sensory domains, named CHASE2 and CHASE3, that are found in at least four classes of transmembrane receptors: histidine kinases, adenylate cyclases, predicted diguanylate cyclases, and either serine/threonine protein kinases (CHASE2) or methyl-accepting chemotaxis proteins (CHASE3). Three other extracellular sensory domains were shared by at least two different classes of transmembrane receptors: histidine kinases and either diguanylate cyclases, adenylate cyclases, or phosphodiesterases. These observations suggest that microorganisms use similar conserved domains to sense similar environmental signals and transmit this information via different signal transduction pathways to different regulatory circuits: transcriptional regulation (histidine kinases), chemotaxis (methyl-accepting proteins), catabolite repression (adenylate cyclases), and modulation of enzyme activity (diguanylate cyclases and phosphodiesterases). The variety of signaling pathways using the CHASE-type domains indicates that these domains sense some critically important extracellular signals.
Evolutionary History of
hrgA
, Which Replaces the Restriction Gene
hpy
IIIR in the
hpy
III Locus of
Helicobacter pylori
Authors: Ando T. , Aras R. A. , Kusugami K. , Blaser M. J. , Wassenaar T. M. 
Published: December 2002

ABSTRACT

A recently identified
Helicobacter pylori
gene,
hrgA
, was previously reported to be present in 70 (33%) of 208 strains examined (T. Ando, T. M. Wassenaar, R. M. Peek, R. A. Aras, A. I. Tschumi, L.-J. Van Doorn, K. Kusugami, and M. J. Blaser, Cancer Res.
62:
2385-2389, 2002). Sequence analysis of nine such strains indicated that in each strain
hrgA
replaced
hpy
IIIR, which encodes a restriction endonuclease and which, together with the gene for its cognate methyltransferase, constitutes the
hpy
III locus. As a consequence of either the
hrgA
insertion or independent mutations,
hpy
IIIM function was lost in 11 (5%) of the 208 strains examined, rendering chromosomal DNA sensitive to
Mbo
I digestion. The evolutionary history of the locus containing either
hpy
III or
hrgA
was reconstructed. By homologous recombination involving flanking sequences,
hrgA
and
hpy
IIIR can replace one another in the
hpy
III locus, and there is simultaneous replacement of several flanking genes. These findings, combined with the
hpy
IM
/iceA2
locus discovered previously, suggest that the two most strongly conserved methylase genes of
H. pylori
,
hpy
IIIM and
hpy
IM, are both preceded by alternative genes that compete for presence at their loci.
A Previously Unrecognized Step in Pentachlorophenol Degradation in
Sphingobium chlorophenolicum
Is Catalyzed by Tetrachlorobenzoquinone Reductase (PcpD)
Authors: Dai MingHua , Rogers Julie Bull , Warner Joseph R. , Copley Shelley D. 
Published: December 2002

ABSTRACT

The first step in the pentachlorophenol (PCP) degradation pathway in
Sphingobium chlorophenolicum
has been believed for more than a decade to be conversion of PCP to tetrachlorohydroquinone. We show here that PCP is actually converted to tetrachlorobenzoquinone, which is subsequently reduced to tetrachlorohydroquinone by PcpD, a protein that had previously been suggested to be a PCP hydroxylase reductase.
pcpD
is immediately downstream of
pcpB
, the gene encoding PCP hydroxylase (PCP monooxygenase). Expression of PcpD is induced in the presence of PCP. A mutant strain lacking functional PcpD has an impaired ability to remove PCP from the medium. In contrast, the mutant strain removes tetrachlorophenol from the medium at the same rate as does the wild-type strain. These data suggest that PcpD catalyzes a step necessary for degradation of PCP, but not for degradation of tetrachlorophenol. Based upon the known mechanisms of flavin monooxygenases such as PCP hydroxylase, hydroxylation of PCP should produce tetrachlorobenzoquinone, while hydroxylation of tetrachlorophenol should produce tetrachlorohydroquinone. Thus, we proposed and verified experimentally that PcpD is a tetrachlorobenzoquinone reductase that catalyzes the NADPH-dependent reduction of tetrachlorobenzoquinone to tetrachlorohydroquinone.
ThecobYGene of the ArchaeonHalobacteriumsp. Strain NRC-1 Is Required for De Novo Cobamide Synthesis
Authors: Woodson J. D. , Peck R. F. , Krebs M. P. , Escalante-Semerena J. C. 
Published: December 2002

ABSTRACTGenetic and nutritional analyses of mutants of the extremely halophilic archaeonHalobacteriumsp. strain NRC-1 showed that open reading frame (ORF) Vng1581C encodes a protein with nucleoside triphosphate:adenosylcobinamide-phosphate nucleotidyltransferase enzyme activity. This activity was previously associated with thecobYgene of the methanogenic archaeonMethanobacterium thermoautotrophicumstrain ΔH, but no evidence was obtained to demonstrate the direct involvement of this protein in cobamide biosynthesis in archaea. Computer analysis of theHalobacteriumsp. strain NRC-1 ORF Vng1581C gene and thecobYgene ofM. thermoautotrophicumstrain ΔH showed the primary amino acid sequence of the proteins encoded by these two genes to be 35% identical and 48% similar. A strain ofHalobacteriumsp. strain NRC-1 carrying a null allele of thecobYgene was auxotrophic for cobinamide-GDP, a known intermediate of the late steps of cobamide biosynthesis. The auxotrophic requirement for cobinamide-GDP was corrected when a wild-type allele ofcobYwas introduced into the mutant strain, demonstrating that the lack ofcobYfunction was solely responsible for the observed block in cobamide biosynthesis in this archaeon. The data also show thatHalobacteriumsp. strain NRC-1 possesses a high-affinity transport system for corrinoids and that this archaeon can synthesize cobamides de novo under aerobic growth conditions. To the best of our knowledge this is the first genetic and nutritional analysis of cobalamin biosynthetic mutants in archaea.
Interdomain Linkers of Homologous Response Regulators Determine Their Mechanism of Action
Authors: Walthers Don , Tran Van K. , Kenney Linda J. 
Published: December 2002

ABSTRACT
OmpR and PhoB are response regulators that contain an N-terminal phosphorylation domain and a C-terminal DNA binding effector domain connected by a flexible interdomain linker. Phosphorylation of the N terminus results in an increase in affinity for specific DNA and the subsequent regulation of gene expression. Despite their sequence and structural similarity, OmpR and PhoB employ different mechanisms to regulate their effector domains. Phosphorylation of OmpR in the N terminus stimulates the DNA binding affinity of the C terminus, whereas phosphorylation of the PhoB N terminus relieves inhibition of the C terminus, enabling it to bind to DNA. Chimeras between OmpR and PhoB containing either interdomain linker were constructed to explore the basis of the differences in their activation mechanisms. Our results indicate that effector domain regulation by either N terminus requires its cognate interdomain linker. In addition, our findings suggest that the isolated C terminus of OmpR is not sufficient for a productive interaction with RNA polymerase.
Quorum Sensing Controls Exopolysaccharide Production in
Sinorhizobium meliloti
Authors: Marketon Melanie M. , Glenn Sarah A. , Eberhard Anatol , González Juan E. 
Published: December 2002

ABSTRACT

Sinorhizobium meliloti
is a soil bacterium capable of invading and establishing a symbiotic relationship with alfalfa plants. This invasion process requires the synthesis, by
S. meliloti
, of at least one of the two symbiotically important exopolysaccharides, succinoglycan and EPS II. We have previously shown that the
sinRI
locus of
S. meliloti
encodes a quorum-sensing system that plays a role in the symbiotic process. Here we show that the
sinRI
locus exerts one level of control through regulation of EPS II synthesis. Disruption of the autoinducer synthase gene,
sinI
, abolished EPS II production as well as the expression of several genes in the
exp
operon that are responsible for EPS II synthesis. This phenotype was complemented by the addition of acyl homoserine lactone (AHL) extracts from the wild-type strain but not from a
sinI
mutant, indicating that the
sinRI
-specified AHLs are required for
exp
gene expression. This was further confirmed by the observation that synthetic palmitoleyl homoserine lactone (C
16:1
-HL), one of the previously identified
sinRI
-specified AHLs, specifically restored
exp
gene expression. Most importantly, the absence of symbiotically active EPS II in a
sinI
mutant was confirmed in plant nodulation assays, emphasizing the role of quorum sensing in symbiosis.
The
stm4066
Gene Product of
Salmonella enterica
Serovar Typhimurium Has Aminoimidazole Riboside (AIRs) Kinase Activity and Allows AIRs To Satisfy the Thiamine Requirement of
pur
Mutant Strains
Authors: Dougherty Michael , Downs Diana M. 
Published: December 2002

ABSTRACT

In bacteria the biosynthetic pathways for purine mononucleotides and the hydroxymethyl pyrimidine moiety of thiamine share five reactions that result in the formation of aminoimidazole ribotide, the last metabolite common to both pathways. Here we describe the characterization of a
Salmonella enterica
mutant strain that has gained the ability to efficiently use exogenous aminoimidazole riboside (AIRs) as a source of thiamine. The lesion responsible for this phenotype is a null mutation in a transcriptional regulator of the GntR family (encoded by
stm4068
). Lack of this protein derepressed transcription of an associated operon (
stm4065-4067
) that encoded a predicted kinase. The
stm4066
gene product was purified and shown to have AIRs kinase activity in vitro. This activity was consistent with the model presented to explain the phenotype caused by the original mutation. This mutation provides a genetic means to isolate the synthesis of the hydroxymethyl pyrimidine moiety of thiamine from the pathway for purine mononucleotide biosynthesis and thus facilitate in vivo analyses.
Forespore-Specific Expression ofBacillus subtilis yqfS, Which Encodes Type IV Apurinic/Apyrimidinic Endonuclease, a Component of the Base Excision Repair Pathway
Authors: Urtiz-Estrada Norma , Salas-Pacheco José M. , Yasbin Ronald E. , Pedraza-Reyes Mario 
Published: December 2002

ABSTRACTThe temporal and spatial expression of theyqfSgene ofBacillus subtilis, which encodes a type IV apurinic/apyrimidinic endonuclease, was studied. A reporter gene fusion to theyqfSopening reading frame revealed that this gene is not transcribed during vegetative growth but is transcribed during the last steps of the sporulation process and is localized to the developing forespore compartment. In agreement with these results,yqfSmRNAs were mainly detected by both Northern blotting and reverse transcription-PCR, during the last steps of sporulation. The expression pattern of theyqfS-lacZ fusion suggested thatyqfSmay be an additional member of the EσGregulon. A primer extension product mapped the transcriptional start site ofyqfS, 54 to 55 bp upstream of translation start codon ofyqfS. Such an extension product was obtained from RNA samples of sporulating cells but not from those of vegetatively growing cells. Inspection of the nucleotide sequence lying upstream of the in vivo-mapped transcriptionalyqfSstart site revealed the presence of a sequence with good homology to promoters preceding genes of the σGregulon. AlthoughyqfSexpression was temporally regulated, neither oxidative damage (after either treatment with paraquat or hydrogen peroxide) nor mitomycin C treatment induced the transcription of this gene.