bluuebunny/crossref_metadata_2025_split huggingface dataset:
RsmC ofErwinia carotovorasubsp.carotovoraNegatively Controls Motility, Extracellular Protein Production, and Virulence by Binding FlhD and Modulating Transcriptional Activity of the Master Regulator, FlhDC
Authors: Chatterjee Asita , Cui Yaya , Chatterjee Arun K. 
Published: May 2009

ABSTRACTRsmC and FlhDC are global regulators controlling extracellular proteins/enzymes,rsmBRNA, motility, and virulence ofErwinia carotovorasubsp.carotovora. FlhDC, the master regulator of flagellar genes, controls these traits by positively regulatinggacA,fliA, andrsmCand negatively regulatinghexA. RsmC, on the other hand, is a negative regulator of extracellular proteins/enzymes, motility, and virulence since the deficiency of RsmC in FlhDC+strain results in overproduction of extracellular proteins/enzymes, hypermotility, and hypervirulence. These phenotypes are abolished in an RsmC−FlhDC−double mutant. We show that RsmC interferes with FlhDC action. Indeed, the expression of all three targets (i.e.,gacA,rsmC, andfliA) positively regulated inE.carotovorasubsp.carotovoraby FlhDC is inhibited by RsmC. RsmC also partly relieves the inhibition ofhexAexpression by FlhDC. The results of yeast two-hybrid analysis revealed that RsmC binds FlhD and FlhDC, but not FlhC. We propose that binding of RsmC with FlhD/FlhDC interferes with its regulatory functions and that RsmC acts as an anti-FlhD4FlhC2factor. We document here for the first time that RsmC interferes with activation offliAand motility in several members of theEnterobacteriaceaefamily. The extent ofE.carotovorasubsp.carotovoraRsmC-mediated inhibition of FlhDC-dependent expression offliAand motility varies depending upon enterobacterial species. The data presented here support the idea that differences in structural features in enterobacterial FlhD are responsible for differential susceptibility toE.carotovorasubsp.carotovoraRsmC action.
Survival of Pathogenic Mycobacteria in Macrophages Is Mediated through Autophosphorylation of Protein Kinase G
Authors: Scherr Nicole , Müller Philipp , Perisa Damir , Combaluzier Benoît , Jenö Paul , Pieters Jean 
Published: May 2009

ABSTRACT
Pathogenic mycobacteria survive within macrophages through the inhibition of phagosome-lysosome fusion. A crucial factor for avoiding lysosomal degradation is the mycobacterial serine/threonine protein kinase G (PknG). PknG is released into the macrophage cytosol upon mycobacterial infection, suggesting that PknG might exert its activity by interfering with host signaling cascades, but the mode of action of PknG remains unknown. Here, we show that PknG undergoes autophosphorylation on threonine residues located at the N terminus. In contrast to all other mycobacterial kinases investigated thus far, autophosphorylation of PknG was not involved in the regulation of its kinase activity. However, autophosphorylation was crucial for the capacity of PknG to promote mycobacterial survival within macrophages. These results will contribute to a better understanding of the virulence mechanisms of pathogenic mycobacteria and may help to design improved inhibitors of PknG to be developed as antimycobacterial compounds.
Activation of the Promoter of the Fengycin Synthetase Operon by the UP Element
Authors: Ke Wan-Ju , Chang Ban-Yang , Lin Tsuey-Pin , Liu Shih-Tung 
Published: May 2009

ABSTRACTBacillus subtilisF29-3 produces an antifungal peptidic antibiotic that is synthesized nonribosomally by fengycin synthetases. Our previous work established that the promoter of the fengycin synthetase operon is located 86 nucleotides upstream of the translational initiation codon offenC. This investigation involved transcriptional fusions with a DNA fragment that contains the region between positions −105 and +80 and determined that deleting the region between positions −55 and −42 reduces the promoter activity by 64.5%. Transcriptional fusions in theB. subtilisDB2 chromosome also indicated that mutating the sequence markedly reduces the promoter activity. An in vitro transcription analysis confirmed that the transcription is inefficient when the sequence in this region is mutated. Electrophoretic mobility shift and footprinting analyses demonstrated that the C-terminal domain of the RNA polymerase α subunit binds to the region between positions −55 and −39. These results indicated that the sequence is an UP element. Finally, this UP element is critical for the production of fengycin, since mutating the UP sequence in the chromosome ofB. subtilisF29-3 reduces the transcription of thefenoperon by 85% and prevents the cells from producing enough fengycin to suppress the germination ofPaecilomyces variotiispores on agar plates.
The Oligopeptide Transport System Is Essential for the Development of Natural Competence inStreptococcus thermophilusStrain LMD-9
Authors: Gardan Rozenn , Besset Colette , Guillot Alain , Gitton Christophe , Monnet Véronique 
Published: May 2009

ABSTRACTIn gram-positive bacteria, oligopeptide transport systems, called Opp or Ami, play a role in nutrition but are also involved in the internalization of signaling peptides that take part in the functioning of quorum-sensing pathways. Our objective was to reveal functions that are controlled by Ami via quorum-sensing mechanisms inStreptococcus thermophilus, a nonpathogenic bacterium widely used in dairy technology in association with other bacteria. Using a label-free proteomic approach combining one-dimensional electrophoresis with liquid chromatography-tandem mass spectrometry analysis, we compared the proteome of theS. thermophilusLMD-9 to that of a mutant deleted for the subunits C, D, and E of theamioperon. Both strains were grown in a chemically defined medium (CDM) without peptides. We focused our attention on proteins that were no more detected in theamideletion mutant. In addition to the three subunits of the Ami transporter, 17 proteins fulfilled this criterion and, among them, 7 were similar to proteins that have been identified as essential for transformation inS. pneumoniae. These results led us to find a condition of growth, the early exponential state in CDM, that allows natural transformation inS. thermophilusLMD-9 to turn on spontaneously. Cells were not competent in M17 rich medium. Furthermore, we demonstrated that the Ami transporter controls the triggering of the competence state through the control of the transcription ofcomX, itself controlling the transcription of late competence genes. We also showed that one of the two oligopeptide-binding proteins of strain LMD-9 plays the predominant role in the control of competence.
Transcription Activity of IndividualrrnOperons inBacillus subtilisMutants Deficient in (p)ppGpp Synthetase Genes,relA,yjbM, andywaC
Authors: Natori Yousuke , Tagami Kazumi , Murakami Kana , Yoshida Sawako , Tanigawa Osamu , Moh Yoonsuh , Masuda Kenta , Wada Tetsuya , Suzuki Shota , Nanamiya Hideaki , Tozawa Yuzuru , Kawamura Fujio 
Published: May 2009

ABSTRACTInBacillus subtilisa null mutation of therelAgene, whose gene product is involved in the synthesis and/or hydrolysis of (p)ppGpp, causes a growth defect that can be suppressed by mutation(s) ofyjbMand/orywaCcoding for small (p)ppGpp synthetases. All 35 suppressor mutations newly isolated were classified into two groups, eitheryjbMorywaC, by mapping and sequencing their mutations, suggesting that there are no (p)ppGpp synthetases other than RelA, YjbM, and YwaC inB. subtilis. In order to understand better the relation between RelA and rRNA synthesis, we studied in therelAmutant the transcriptional regulation of seven rRNA operons (rrnO, -A, -J, -I, -E, -D, or -B) individually after integration of a promoter- and terminatorlesscatgene. We identified the transcriptional start sites of eachrrnoperon (a G) and found that transcription of allrrnoperons from their P1 promoters was drastically reduced in therelAmutant while this was almost completely restored in therelA yjbM ywaCtriple mutant. Taken together with previous results showing that the intracellular GTP concentration was reduced in therelAmutant while it was restored in the triple mutant, it seems likely that continuous (p)ppGpp synthesis by YjbM and/or YwaC at a basal level causes a decrease in the amounts of intracellular GTP.
Genome Sequencing and Comparative Analysis ofKlebsiella pneumoniaeNTUH-K2044, a Strain Causing Liver Abscess and Meningitis
Authors: Wu Keh-Ming , Li Ling-Hui , Yan Jing-Jou , Tsao Nina , Liao Tsai-Lien , Tsai Hui-Chi , Fung Chang-Phone , Chen Hsiang-Ju , Liu Yen-Ming , Wang Jin-Tung , Fang Chi-Tai , Chang Shan-Chwen , Shu Hung-Yu , Liu Tze-Tze , Chen Ying-Tsong , Shiau Yih-Ru , Lauderdale Tsai-Ling , Su Ih-Jen , Kirby Ralph , Tsai Shih-Feng 
Published: May 2009

ABSTRACTNosocomial infections caused by antibiotic-resistantKlebsiella pneumoniaeare emerging as a major health problem worldwide, while community-acquiredK. pneumoniaeinfections present with a range of diverse clinical pictures in different geographic areas. In particular, an invasive form ofK. pneumoniaethat causes liver abscesses was first observed in Asia and then was found worldwide. We are interested in how differences in gene content of the same species result in different diseases. Thus, we sequenced the whole genome ofK. pneumoniaeNTUH-K2044, which was isolated from a patient with liver abscess and meningitis, and analyzed differences compared to strain MGH 78578, which was isolated from a patient with pneumonia. Six major types of differences were found in gene clusters that included an integrative and conjugative element, clusters involved in citrate fermentation, lipopolysaccharide synthesis, and capsular polysaccharide synthesis, phage-related insertions, and a cluster containing fimbria-related genes. We also conducted comparative genomic hybridization with 15K. pneumoniaeisolates obtained from community-acquired or nosocomial infections using tiling probes for the NTUH-K2044 genome. Hierarchical clustering revealed three major groups of genomic insertion-deletion patterns that correlate with the strains' clinical features, antimicrobial susceptibilities, and virulence phenotypes with mice. Here we report the whole-genome sequence ofK. pneumoniaeNTUH-K2044 and describe evidence showing significant genomic diversity and sequence acquisition amongK. pneumoniaepathogenic strains. Our findings support the hypothesis that these factors are responsible for the changes that have occurred in the disease profile over time.
Two Distinct Pathways for Metabolism of Theophylline and Caffeine Are Coexpressed in
Pseudomonas putida
CBB5
Authors: Yu Chi Li , Louie Tai Man , Summers Ryan , Kale Yogesh , Gopishetty Sridhar , Subramanian Mani 
Published: May 2009

ABSTRACT

Pseudomonas putida
CBB5 was isolated from soil by enrichment on caffeine. This strain used not only caffeine, theobromine, paraxanthine, and 7-methylxanthine as sole carbon and nitrogen sources but also theophylline and 3-methylxanthine. Analyses of metabolites in spent media and resting cell suspensions confirmed that CBB5 initially N demethylated theophylline via a hitherto unreported pathway to 1- and 3-methylxanthines. NAD(P)H-dependent conversion of theophylline to 1- and 3-methylxanthines was also detected in the crude cell extracts of theophylline-grown CBB5. 1-Methylxanthine and 3-methylxanthine were subsequently N demethylated to xanthine. CBB5 also oxidized theophylline and 1- and 3-methylxanthines to 1,3-dimethyluric acid and 1- and 3-methyluric acids, respectively. However, these methyluric acids were not metabolized further. A broad-substrate-range xanthine-oxidizing enzyme was responsible for the formation of these methyluric acids. In contrast, CBB5 metabolized caffeine to theobromine (major metabolite) and paraxanthine (minor metabolite). These dimethylxanthines were further N demethylated to xanthine via 7-methylxanthine. Theobromine-, paraxanthine-, and 7-methylxanthine-grown cells also metabolized all of the methylxanthines mentioned above via the same pathway. Thus, the theophylline and caffeine N-demethylation pathways converged at xanthine via different methylxanthine intermediates. Xanthine was eventually oxidized to uric acid. Enzymes involved in theophylline and caffeine degradation were coexpressed when CBB5 was grown on theophylline or on caffeine or its metabolites. However, 3-methylxanthine-grown CBB5 cells did not metabolize caffeine, whereas theophylline was metabolized at much reduced levels to only methyluric acids. To our knowledge, this is the first report of theophylline N demethylation and coexpression of distinct pathways for caffeine and theophylline degradation in bacteria.
Complete Genome Sequence ofAggregatibacter(Haemophilus)aphrophilusNJ8700
Authors: Di Bonaventura Maria Pia , DeSalle Rob , Pop Mihai , Nagarajan Niranjan , Figurski David H. , Fine Daniel H. , Kaplan Jeffrey B. , Planet Paul J. 
Published: May 2009

ABSTRACTWe report the finished and annotated genome sequence ofAggregatibacter aphrophilusstrain NJ8700, a strain isolated from the oral flora of a healthy individual, and discuss characteristics that may affect its dual roles in human health and disease. This strain has a rough appearance, and its genome contains genes encoding a type VI secretion system and several factors that may participate in host colonization.
Rapid Identification of Biothreat and Other Clinically Relevant Bacterial Species by Use of Universal PCR Coupled with High-Resolution Melting Analysis
Authors: Yang Samuel , Ramachandran Padmini , Rothman Richard , Hsieh Yu-Hsiang , Hardick Andrew , Won Helen , Kecojevic Aleksandar , Jackman Joany , Gaydos Charlotte 
Published: May 2009

ABSTRACT
A rapid assay for eubacterial species identification is described using high-resolution melt analysis to characterize PCR products. Unique melt profiles generated from multiple hypervariable regions of the 16S rRNA gene for 100 clinically relevant bacterial pathogens, including category A and B biothreat agents and their surrogates, allowed highly specific species identification.
Utilization of Immunoglobulin G Fc Receptors by Human Immunodeficiency Virus Type 1: a Specific Role for Antibodies against the Membrane-Proximal External Region of gp41
Authors: Perez Lautaro G. , Costa Matthew R. , Todd Christopher A. , Haynes Barton F. , Montefiori David C. 
Published: May 2009

ABSTRACTReceptors (FcγRs) for the constant region of immunoglobulin G (IgG) are an important link between humoral immunity and cellular immunity. To help define the role of FcγRs in determining the fate of human immunodeficiency virus type 1 (HIV-1) immune complexes, cDNAs for the four major human Fcγ receptors (FcγRI, FcγRIIa, FcγRIIb, and FcγRIIIa) were stably expressed by lentiviral transduction in a cell line (TZM-bl) commonly used for standardized assessments of HIV-1 neutralization. Individual cell lines, each expressing a different FcγR, bound human IgG, as evidence that the physical properties of the receptors were preserved. In assays with a HIV-1 multisubtype panel, the neutralizing activities of two monoclonal antibodies (2F5 and 4E10) that target the membrane-proximal external region (MPER) of gp41 were potentiated by FcγRI and, to a lesser extent, by FcγRIIb. Moreover, the neutralizing activity of an HIV-1-positive plasma sample known to contain gp41 MPER-specific antibodies was potentiated by FcγRI. The neutralizing activities of monoclonal antibodies b12 and 2G12 and other HIV-1-positive plasma samples were rarely affected by any of the four FcγRs. Effects with gp41 MPER-specific antibodies were moderately stronger for IgG1 than for IgG3 and were ineffective for Fab. We conclude that FcγRI and FcγRIIb facilitate antibody-mediated neutralization of HIV-1 by a mechanism that is dependent on the Fc region, IgG subclass, and epitope specificity of antibody. The FcγR effects seen here suggests that the MPER of gp41 could have greater value for vaccines than previously recognized.
The Paramyxoviruses Simian Virus 5 and Mumps Virus Recruit Host Cell CD46 To Evade Complement-Mediated Neutralization
Authors: Johnson John B. , Grant Ken , Parks Griffith D. 
Published: May 2009

ABSTRACTThe complement system is a critical component of the innate immune response that all animal viruses must face during natural infections. Our previous results have shown that treatment of the paramyxovirus simian virus 5 (SV5) with human serum results in deposition of complement C3-derived polypeptides on virion particles. Here, we show that the virion-associated C3 component includes the inactive form iC3b, suggesting that SV5 may have mechanisms to evade the host complement system. Electron microscopy, gradient centrifugation, and Western blot analysis indicated that purified SV5 virions derived from human A549 cells contained CD46, a plasma membrane-expressed regulator of complement that acts as a cofactor for cleavage and inactivation of C3b into iC3b. In vitro cleavage assays with purified complement components showed that SV5 virions had C3b cofactor activity, resulting in specific factor I-mediated cleavage of C3b into inactive iC3b. SV5 particles generated in CHO cells, which do not express CD46, did not have cofactor activity. Conversely, virions derived from a CHO cell line that was engineered to overexpress human CD46 contained elevated levels of virion-associated CD46 and displayed enhanced C3b cofactor activity. In comparison with C3b, purified SV5 virions had very low cofactor activity against C4b, consistent with the known preference of CD46 for C3b versus C4b. Similar results were obtained for the closely related mumps virus (MuV), except that MuV particles derived from CHO-CD46 cells had higher C4b cofactor activity than SV5 virions. In neutralization assays with human serum, SV5 and MuV containing CD46 showed slower kinetics and more resistance to neutralization than SV5 and MuV that lacked CD46. Our results support a model in which the rubulaviruses SV5 and MuV incorporate cell surface complement inhibitors into progeny virions as a mechanism to limit complement-mediated neutralization.
Biotin-free systems provide stronger immunohistochemical signal in oestrogen receptor evaluation of breast cancer
Authors: Rocha R M , Miller K , Soares F , Schenka N , Vassallo J , Gobbi H 
Published: May 2009

Aims:Biotin-free polymeric visualisation systems (BFPS) were compared with streptavidin–biotin systems (SABS) in the evaluation of immunoreactivity for oestrogen receptor (ER) in breast carcinomas.Methods:The antiestrogen antibody clone SP1 was employed in a tissue microarray containing 320 breast carcinomas. Eleven different detection systems were used: six second-generation BFPS (Advance, Novolink, SuperPicTure, PicTure Max, Super Sensitive non-biotin HRP and Mouse/Rabbit Polydetector HRP/DAB), one first-generation BFP (EnVision+), and four SABS (LSAB+, EasyPath, Super Sensitive and Mouse/Rabbit Immunodetector HRP/DAB). The slides were digitalised using a Mirax scanner and the resulting images were analysed by an automated method and by visual analysis using the Allred score system considering positive nuclear staining. Cytoplasm staining was also separately evaluated.Results:The BFPS Advance and Novolink showed the highest scores by visual analysis, and additionally detected two positive cases that were considered negative using the other detection systems. Likewise, these systems, together with the SAB LSAB+, showed higher staining intensity by the automated method. BFPS revealed no cytoplasm staining, in contrast to the SABS.Conclusions:The second-generation BFPS, especially Advance and Novolink, provided stronger and sharper nuclear immunohistochemical signals as compared with most SABS, with no non-specific cytoplasm staining. In a few instances, the second-generation BFPS systems showed discordant results in relation to SABS; therefore further studies correlating these findings to therapeutic responses are necessary. BFPS may represent a high-quality tool for research and clinical evaluation of ER in breast cancer.
Castration-Resistant Prostate Cancer: Locking Up the Molecular Escape Routes
Authors: Attar Ricardo M. , Takimoto Chris H. , Gottardis Marco M. 
Published: May 2009

Abstract
The understanding of the key role that androgens play on the normal and pathological physiology of the prostate guided the development of different therapies for the treatment of locally advanced or metastatic prostate cancer (PCa). These so-called androgen deprivation therapies include surgical or chemical castration, achieved by the administration of gonadotropin-releasing hormone analogs; inhibition of steroidogenic enzymes; and finally, blocking of the binding of androgens to their receptor (AR) by the use of antiandrogens. Despite an excellent initial response, in approximately 2 to 3 years, most of these patients will succumb to the castration resistant form of the disease. Remarkably, even in the presence of castration levels of circulating androgens, these tumors are still dependent on a functional AR, and several molecular mechanisms have been proposed to explain this phenomenon. These include: (1) gene amplification and increased expression of the AR mRNA and protein, (2) selection of mutations in the AR that confer broader ligand specificity, (3) changes in the ratios or expression between the AR and its coregulators, (4) increased expression of steroidogenic enzymes, and (5) up-regulation of cross-talk signal transduction pathways that can activate the AR in a ligand-independent manner. We will summarize how these molecular hypotheses are being tested in the clinic by the latest therapeutic modalities.
Nuclear Factor-κB-Mediated Transforming Growth Factor-β-Induced Expression of Vimentin Is an Independent Predictor of Biochemical Recurrence after Radical Prostatectomy
Authors: Zhang Qiang , Helfand Brian T. , Jang Thomas L. , Zhu Lihua J. , Chen Lin , Yang Ximing J. , Kozlowski James , Smith Norm , Kundu Shilajit D. , Yang Guangyu , Raji Adekunle A. , Javonovic Borko , Pins Michael , Lindholm Paul , Guo Yinglu , Catalona William J. , Lee Chung 
Published: May 2009

Abstract
Purpose: Transforming growth factor-β (TGF-β)-mediated epithelial-to-mesenchymal transition (EMT) has been shown to occur in some cancers; however, the pathway remains controversial and varies with different cancers. In addition, the mechanisms by which TGF-β and the EMT contribute to prostate cancer recurrence are largely unknown. In this study, we elucidated TGF-β-mediated EMT as a predictor of disease recurrence after therapy for prostate cancer, which has not been reported before.
Experimental Design: We analyzed TGF-β-induced EMT using nuclear factor-κB (NF-κB) as an intermediate mediator in prostate cancer cell lines. A total of 287 radical prostatectomy specimens were evaluated using immunohistochemistry in a high-throughput tissue microarray analysis. Levels of TGF-β signaling components and EMT-related factors were analyzed using specific antibodies. Results were expressed as the percentage of cancer cells that stained positive for a given antibody and were correlated with disease recurrence rates at a mean of 7 years following radical prostatectomy.
Results: In prostate cancer cell lines, TGF-β-induced EMT was mediated by NF-κB signaling. Blockade of NF-κB or TGF-β signaling resulted in abrogation of vimentin expression and inhibition of the invasive capability of these cells. There was high risk of biochemical recurrence associated with tumors that displayed high levels of expression of TGF-β1, vimentin, and NF-κB and low level of cytokeratin 18. This was particularly true for vimentin, which is independent of patients' Gleason score.
Conclusions: The detection of NF-κB-mediated TGF-β-induced EMT in primary tumors predicts disease recurrence in prostate cancer patients following radical prostatectomy. The changes in TGF-β signaling and EMT-related factors provide novel molecular markers that may predict prostate cancer outcomes following treatment.