bluuebunny/crossref_metadata_2025_split huggingface dataset:
MtrR Modulates
rpoH
Expression and Levels of Antimicrobial Resistance in
Neisseria gonorrhoeae
Authors: Folster Jason P. , Johnson Paul J. T. , Jackson Lydgia , Dhulipali Vijaya , Dyer David W. , Shafer William M. 
Published: November 2008

ABSTRACT

The MtrR transcriptional-regulatory protein is known to repress transcription of the
mtrCDE
operon, which encodes a multidrug efflux pump possessed by
Neisseria gonorrhoeae
that is important in the ability of gonococci to resist certain hydrophobic antibiotics, detergents, dyes, and host-derived antimicrobials. In order to determine whether MtrR can exert regulatory action on other gonococcal genes, we performed a whole-genome microarray analysis using total RNA extracted from actively growing broth cultures of isogenic MtrR-positive and MtrR-negative gonococci. We determined that, at a minimum, 69 genes are directly or indirectly subject to MtrR control, with 47 being MtrR repressed and 22 being MtrR activated.
rpoH
, which encodes the general stress response sigma factor RpoH (sigma 32), was found by DNA-binding studies to be directly repressed by MtrR, as it was found to bind to a DNA sequence upstream of
rpoH
that included sites within the
rpoH
promoter. MtrR also repressed the expression of certain RpoH-regulated genes, but this regulation was likely indirect and a reflection of MtrR control of
rpoH
expression. Inducible expression of MtrR was found to repress
rpoH
expression and to increase gonococcal susceptibility to hydrogen peroxide (H
2
O
2
) and an antibiotic (erythromycin) recognized by the MtrC-MtrD-MtrE efflux pump system. We propose that, apart from its ability to control the expression of the
mtrCDE
-encoded efflux pump operon and, as a consequence, levels of gonococcal resistance to host antimicrobials (e.g., antimicrobial peptides) recognized by the efflux pump, the ability of MtrR to regulate the expression levels of
rpoH
and RpoH-regulated genes also modulates levels of gonococcal susceptibility to H
2
O
2
.
Expression and Physiological Relevance of
Agrobacterium tumefaciens
Phosphatidylcholine Biosynthesis Genes
Authors: Klüsener Sonja , Aktas Meriyem , Thormann Kai M. , Wessel Mirja , Narberhaus Franz 
Published: November 2008

ABSTRACT

Phosphatidylcholine (PC), or lecithin, is the major phospholipid in eukaryotic membranes, whereas only 10% of all bacteria are predicted to synthesize PC. In
Rhizobiaceae
, including the phytopathogenic bacterium
Agrobacterium tumefaciens
, PC is essential for the establishment of a successful host-microbe interaction.
A. tumefaciens
produces PC via two alternative pathways, the methylation pathway and the Pcs pathway. The responsible genes,
pmtA
(coding for a phospholipid
N
-methyltransferase) and
pcs
(coding for a PC synthase), are located on the circular chromosome of
A. tumefaciens
C58. Recombinant expression of
pmtA
and
pcs
in
Escherichia coli
revealed that the individual proteins carry out the annotated enzyme functions. Both genes and a putative ABC transporter operon downstream of PC are constitutively expressed in
A. tumefaciens
. The amount of PC in
A. tumefaciens
membranes reaches around 23% of total membrane lipids. We show that PC is distributed in both the inner and outer membranes. Loss of PC results in reduced motility and increased biofilm formation, two processes known to be involved in virulence. Our work documents the critical importance of membrane lipid homeostasis for diverse cellular processes in
A. tumefaciens
.
A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera
Authors: Deloger Marc , El Karoui Meriem , Petit Marie-Agnès 
Published: November 2008

ABSTRACT
The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.
The
Anaplasma phagocytophilum
PleC Histidine Kinase and PleD Diguanylate Cyclase Two-Component System and Role of Cyclic Di-GMP in Host Cell Infection
Authors: Lai Tzung-Huei , Kumagai Yumi , Hyodo Mamoru , Hayakawa Yoshihiro , Rikihisa Yasuko 
Published: November 2008

ABSTRACT

Anaplasma phagocytophilum
, the etiologic agent of human granulocytic anaplasmosis (HGA), has genes predicted to encode three sensor kinases, one of which is annotated PleC, and three response regulators, one of which is PleD. Prior to this study, the roles of PleC and PleD in the obligatory intracellular parasitism of
A. phagocytophilum
and their biochemical activities were unknown. The present study illustrates the relevance of these factors by demonstrating that both
pleC
and
pleD
were expressed in an HGA patient. During
A. phagocytophilum
development in human promyelocytic HL-60 cells, PleC and PleD were synchronously upregulated at the exponential growth stage and downregulated prior to extracellular release. A recombinant PleC kinase domain (rPleCHKD) has histidine kinase activity; no activity was observed when the conserved site of phosphorylation was replaced with alanine. A recombinant PleD (rPleD) has autokinase activity using phosphorylated rPleCHKD as the phosphoryl donor but not with two other recombinant histidine kinases. rPleCHKD could not serve as the phosphoryl donor for a mutant rPleD (with a conserved aspartic acid, the site of phosphorylation, replaced by alanine) or two other
A. phagocytophilum
recombinant response regulators. rPleD had diguanylate cyclase activity to generate cyclic (c) di-GMP from GTP in vitro. UV cross-linking of
A. phagocytophilum
lysate with c-di-[
32
P]GMP detected an ∼47-kDa endogenous protein, presumably c-di-GMP downstream receptor. A new hydrophobic c-di-GMP derivative, 2′-
O
-di(tert-butyldimethylsilyl)-c-di-GMP, inhibited
A. phagocytophilum
infection in HL-60 cells. Our results suggest that the two-component PleC-PleD system is a diguanylate cyclase and that a c-di-GMP-receptor complex regulates
A. phagocytophilum
intracellular infection.
The pH-Responsive Regulon of HP0244 (FlgS), the Cytoplasmic Histidine Kinase of
Helicobacter pylori
Authors: Wen Yi , Feng Jing , Scott David R. , Marcus Elizabeth A , Sachs George 
Published: November 2008

ABSTRACT

Helicobacter pylori
colonizes the acidic gastric environment, in contrast to all other neutralophiles, whose acid resistance and tolerance responses allow only gastric transit. This acid adaptation is dependent on regulation of gene expression in response to pH changes in the periplasm and cytoplasm. The cytoplasmic histidine kinase, HP0244, which until now was thought only to regulate flagellar gene expression via its cognate response regulator, HP0703, was found to generate a response to declining medium pH. Although not required for survival at pH 4.5, HP0244 is required for survival at pH 2.5 with 10 mM urea after 30 min. Transcriptional profiling of a HP0244 deletion mutant grown at pH 7.4 confirmed the contribution of HP0244 to σ
54
activation via HP0703 to coordinate flagellar biosynthesis by a pH-independent regulon that includes 14 flagellar genes. Microarray analysis of cells grown at pH 4.5 without urea revealed an additional 22 genes, including 4 acid acclimation genes (
ureA
,
ureB
,
ureI
, and
amiE
) that are positively regulated by HP0244. Additionally, 86 differentially expressed genes, including 3 acid acclimation genes (
ureF
,
rocF
[arginase], and
ansB
[asparaginase]), were found in cells grown at pH 2.5 with 30 mM urea. Hence, HP0244 has, in addition to the pH-independent flagellar regulon, a pH-dependent regulon, which allows adaptation to a wider range of environmental acid conditions. An acid survival study using an HP0703 mutant and an electrophoretic mobility shift assay with in vitro-phosphorylated HP0703 showed that HP0703 does not contribute to acid survival and does not bind to the promoter regions of several genes in the HP0244 pH-dependent regulon, suggesting that there is a pathway outside the HP0703 regulon which transduces the acid-responsive signal sensed by HP0244.
DegU and Spo0A Jointly Control Transcription of Two Loci Required for Complex Colony Development byBacillus subtilis
Authors: Verhamme Daniel T. , Murray Ewan J. , Stanley-Wall Nicola R. 
Published: November 2008

ABSTRACTBiofilm formation is an example of a multicellular process which depends on cooperative behavior and differentiation within a bacterial population. Our findings indicate that there is a complex feedback loop that maintains the stoichiometry of the extracellular matrix and other proteins required for complex colony development byBacillus subtilis. Analysis of the transcriptional regulation of two DegU-activated genes that are required for complex colony development byB. subtilisrevealed additional involvement of global regulators that are central to controlling biofilm formation. Activation of transcription from both theyvcAandyuaBpromoters requires DegU∼phosphate, but transcription is inhibited by direct AbrB binding to the promoter regions. Inhibition of transcription by AbrB is relieved when Spo0A∼phosphate is generated due to its known role in inhibitingabrBexpression. Deletion of SinR, a key coordinator of motility and biofilm formation, enhanced transcription from both loci; however, no evidence of a direct interaction with SinR for either theyvcAoryuaBpromoter regions was observed. The enhanced transcription in thesinRmutant background was subsequently demonstrated to be dependent on biosynthesis of the polysaccharide component that forms the major constituent of theB. subtilisbiofilm matrix. Together, these findings indicate that a genetic network dependent on activation of both DegU and Spo0A controls complex colony development byB. subtilis.
Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes
Authors: Novichkov Pavel S. , Wolf Yuri I. , Dubchak Inna , Koonin Eugene V. 
Published: November 2008

ABSTRACTIn order to explore microevolutionary trends in bacteria and archaea, we constructed a data set of 41 alignable tight genome clusters (ATGCs). We show that the ratio of the medians of nonsynonymous to synonymous substitution rates (dN/dS) that is used as a measure of the purifying selection pressure on protein sequences is a stable characteristic of the ATGCs. In agreement with previous findings, parasitic bacteria, notwithstanding the sometimes dramatic genome shrinkage caused by gene loss, are typically subjected to relatively weak purifying selection, presumably owing to relatively small effective population sizes and frequent bottlenecks. However, no evidence of genome streamlining caused by strong selective pressure was found in any of the ATGCs. On the contrary, a significant positive correlation between the genome size, as well as gene size, and selective pressure was observed, although a variety of free-living prokaryotes with very close selective pressures span nearly the entire range of genome sizes. In addition, we examined the connections between the sequence evolution rate and other genomic features. Although gene order changes much faster than protein sequences during the evolution of prokaryotes, a strong positive correlation was observed between the “rearrangement distance” and the amino acid distance, suggesting that at least some of the events leading to genome rearrangement are subjected to the same type of selective constraints as the evolution of amino acid sequences.
The LuxR Family Quorum-Sensing Activator MrtR Requires Its Cognate Autoinducer for Dimerization and Activation but Not for Protein Folding
Authors: Yang Menghua , Giel Jennifer L. , Cai Tao , Zhong Zengtao , Zhu Jun 
Published: November 2008

ABSTRACT

MrtR, a LuxR homolog in
Mesorhizobium tianshanense
, is important for symbiosis. We found that MrtR requires its cognate
N
-acylhomoserine lactone for forming dimers, binding to a single DNA site and activating the downstream promoter. However, MrtR is able to fold independently of its ligand.
Relaxed Specificity of the
Bacillus subtilis
TatAdCd Translocase in Tat-Dependent Protein Secretion
Authors: Eijlander Robyn T. , Jongbloed Jan D. H. , Kuipers Oscar P. 
Published: November 2008

ABSTRACT

Protein translocation via the twin arginine translocation (TAT) pathway is characterized by the translocation of prefolded proteins across the hydrophobic lipid bilayer of the membrane. In
Bacillus subtilis
, two different Tat translocases are involved in this process, and both display different substrate specificities: PhoD is secreted via TatAdCd, whereas YwbN is secreted via TatAyCy. It was previously assumed that both TatAy and TatCy are essential for the translocation of the YwbN precursor. Through complementation studies, we now show that TatAy can be functionally replaced by TatAd when the latter is offered to the cells in excess amounts. Moreover, under conditions of overproduction, TatAdCd, in contrast to TatAyCy, shows an increased tolerance toward the acceptance of various Tat-dependent proteins.
Maximal Efficiency of Coupling between ATP Hydrolysis and Translocation of Polypeptides Mediated by SecB Requires Two Protomers of SecA
Authors: Mao Chunfeng , Hardy Simon J. S. , Randall Linda L. 
Published: November 2008

ABSTRACT

SecA is the ATPase that provides energy for translocation of precursor polypeptides through the SecYEG translocon in
Escherichia coli
during protein export. We showed previously that when SecA receives the precursor from SecB, the ternary complex is fully active only when two protomers of SecA are bound. Here we used variants of SecA and of SecB that populate complexes containing two protomers of SecA to different degrees to examine both the hydrolysis of ATP and the translocation of polypeptides. We conclude that the low activity of the complexes with only one protomer is the result of a low efficiency of coupling between ATP hydrolysis and translocation.
A water-soluble carbon monoxide-releasing molecule (CORM-3) lowers intraocular pressure in rabbits
Authors: Stagni E , Privitera M G , Bucolo C , Leggio G M , Motterlini R , Drago F 
Published: November 2008

Background:Carbon monoxide-releasing molecules (CORMs) are a novel group of substances that are capable of modulating physiological functions via the liberation of CO.Aims:This study was undertaken to investigate the effects of CORM-3, a water-soluble CO-releasing agent, on two rabbit models of ocular hypertension.Methods:Ocular hypertension was induced by injecting α-chymotrypsin in the rabbit eye. The dose–response effect of CORM-3 on IOP was assessed by topical administration of the drug (0.001, 0.01, 0.1 and 1%). Ocular hypertension was also obtained by weekly subconjunctival injection of betamethasone, and animals were treated topically with CORM-3. A group of animals in both models was treated with the inactive form of the drug (iCORM-3).Results:CORM-3 induced a dose-dependent reduction in IOP in rabbits treated with α-chymotrypsin. A similar reduction in IOP was observed in rabbits with betamethasone-induced ocular hypertension treated with the drug. Treatment with the iCORM-3 had no effect on IOP in both models.Conclusions:Treatment with CORM-3 is associated with a reduction in IOP in two different rabbit models of ocular hypertension. These results support previous findings on the effect of haem oxygenase-derived CO on IOP and suggest a direct involvement of CO system in the regulation of ocular pressure probably through the modulation of aqueous humour dynamics.
Rapid detection and quantification of Propionibacteriaceae
Authors: Goldschmidt P , Ferreira C Costa , Degorge S , Benallaoua D , Boutboul S , Laroche L , Batellier L , Chaumeil C 
Published: November 2008

Background:Propionibacteriaceae (Propioni) are anaerobic bacteria associated with human and animal infections. Present-day methods of diagnosis for Propioni are unsatisfactory due to a lack of sensitivity of culture, time required for culture results (3 to 14 days) and difficulties in interpreting SYBR Green real-time PCR results. The goal of this work was to validate a new rapid and sensitive test for the diagnosis of Propioni infections (endophthalmitis, corneal ulcers and others).Material and methods:DNA was extracted using the MagNA Pure isolation kit (Roche), and bacterial detection and quantification were carried out with a set of original primers and probe (5′ATACGTAGGGTGCGAGCGTTGTCC; 5′TGGTGTTCCTCCTGATATCTGCGC and [Amino C6+JOE]-GATCGCGTCGGAAGTGTAATCTTGGGG-Black Hole Quencher). The PCR cycling programme consisted of one cycle at 95°C, 20 s and 45 cycles at 95°C, 3 s and 30 s at 60°C. DNA extraction yields were assessed in the same tube.Results:This test detects as few as 0.01 Equivalent PFU/μl Propioni in phosphate-buffered saline (PBS), aqueous humour, vitreous or cell suspensions. Propioni is detected as a single contaminant or mixed with other bacteria, fungi or human cells.Conclusion:The new real-time PCR is able to detect 0.01 Eq/CFU μl of Propioni suspended in PBS, vitreous, aqueous humour and human cells in less than 1.30 h.
New time-dependent approach to analyse the prognostic significance of immunohistochemical biomarkers in colon cancer and diffuse large B-cell lymphoma
Authors: Adams H , Tzankov A , Lugli A , Zlobec I 
Published: November 2008

Aims:Receiver operating characteristic (ROC) curve analysis is a well-established method to study the accuracies of biological markers. It may, however, be suboptimal for analysing outcomes over time, such as prognosis. Here, the clinical value of time-dependent ROC curve analysis for improving the identification of high-risk patients with colon cancers and diffuse large B-cell lymphomas (DLBCL) is explored.Methods:Using tissue microarrays, immunohistochemistry was performed on two matched sets (N = 469, each) of colon cancers (p53, CD8+tumour infiltrating lymphocytes (TILs), mammalian sterile-like 20 kinase 1 (MST1), mucin 2 (MUC2) and urokinase plasminogen activator receptor (uPAR)) and on 208 DLBCL (Bcl2, Bcl6, CD10, FOXP1 and Ki67). The area-under-the-curve (AUC)-over-time plots, cut-off scores for tumour marker positivity and Kaplan–Meier survival curves were analysed.Results:With the exception of uPAR, all markers were most accurate within the first 18 months following diagnosis. Expression of p53 (AUC = 0.75), uPAR (AUC = 0.64), Bcl2 (AUC = 0.58) and FOXp1 (AUC = 0.68) was linked to more aggressive tumours, while TILs (AUC = 0.38), MST1 (AUC = 0.39), MUC2 (AUC = 0.38), Bcl6 (AUC = 0.4), CD10 (AUC = 0.49) and Ki67 (AUC = 0.41) were predictive of improved survival. Cut-off scores for markers at their peak accuracies as well as survival time differences were reproducible between colon cancer groups. Only FOXp1 at its optimal cut-off of 60% had significant effects on survival in DLBCL (p = 0.019).Conclusions:Time-dependent ROC curve analysis is a novel tool for identifying potential immunohistochemical prognostic markers across varying follow-up times. Use of this tool could facilitate the identification of high-risk patients not only with colon cancer and DLBCL but with a range of other tumour types.
Induction of Both CD8+ and CD4+ T-Cell–Mediated Responses in Colorectal Cancer Patients by Colon Antigen-1
Authors: Maccalli Cristina , Di Cristanziano Veronica , Fodale Valentina , Corsi Domenico , D'Agostino Giuseppina , Petrangeli Valentina , Laurenti Luca , Guida Sofia , Mazzocchi Arabella , Arienti Flavio , Perrone Maria P. , Castelli Chiara , Rivoltini Licia , Zagonel Vittorina , Tartaglia Marco , Parmiani Giorgio , Belardelli Filippo 
Published: October 2008

AbstractPurpose: Colon antigen-1 (COA-1) was recently identified as a novel antigen of colorectal cancer encoded by the UBXD5 gene. Here, we evaluated whether a specific T-cell-mediated response directed against this molecule can occur in colorectal cancer patients.Experimental Design: Antigen- and tumor-specific immunologic responses of peripheral blood mononuclear cells (PBMC) stimulated in vitro with the MHC class II-associated immunogenic epitope of COA-1 (FSTFPPTLYQDDTLTLQAAG) were analyzed by IFN-γ ELISPOT assay.Results: COA-1-specific and tumor-reactive T lymphocytes were isolated from all (n = 7) HLA-DRβ1*0402+ or *1301+ colorectal cancer patients with progressive disease (Dukes' C and D) but not in patients (n = 4) with early-stage tumor (Dukes' A and B) and in healthy donors (n = 5), suggesting that the immune response against this antigen is associated with the progression of colorectal cancer. COA-1- and tumor-specific T lymphocytes displayed a CD3+CD4+CD69+CD45RA+ phenotype, compatible with the activated effector-type T-cell subset, and most of them exerted cytotoxic activity against HLA-matched and COA-1+ tumor cells. COA-1-specific T cells could also be isolated by in vitro stimulation of peripheral blood mononuclear cells with autologous dendritic cells loaded with tumor lysate, suggesting that this antigen can generate a dominant immunologic response against colorectal cancer cells. Notably, we could identify also COA-1-derived epitopes binding to HLA-A*0201 molecules that elicited antigen- and tumor-specific CD8+ T-cell-mediated responses in colorectal cancer patients.Conclusions: Both CD4+ and CD8+ T-cell responses against COA-1 can occur in colorectal cancer patients with metastatic disease, suggesting that this antigen is suitable for immunotherapeutic protocols of these patients.