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Shankar M, Mohapatra SS, Biswas S, Biswas I. Gene Regulation by the LiaSR Two-Component System in Streptococcus mutans. PLoS One 2015; 10:e0128083. [PMID: 26020679 PMCID: PMC4447274 DOI: 10.1371/journal.pone.0128083] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/23/2015] [Indexed: 12/22/2022] Open
Abstract
The LiaSR two-component signal transduction system regulates cellular responses to several environmental stresses, including those that induce cell envelope damages. Downstream regulons of the LiaSR system have been implicated in tolerance to acid, antibiotics and detergents. In the dental pathogen Streptococcus mutans, the LiaSR system is necessary for tolerance against acid, antibiotics, and cell wall damaging stresses during growth in the oral cavity. To understand the molecular mechanisms by which LiaSR regulates gene expression, we created a mutant LiaR in which the conserved aspartic acid residue (the phosphorylation site), was changed to alanine residue (D58A). As expected, the LiaR-D58A variant was unable to acquire the phosphate group and bind to target promoters. We also noted that the predicted LiaR-binding motif upstream of the lia operon does not appear to be well conserved. Consistent with this observation, we found that LiaR was unable to bind to the promoter region of lia; however, we showed that LiaR was able to bind to the promoters of SMU.753, SMU.2084 and SMU.1727. Based on sequence analysis and DNA binding studies we proposed a new 25-bp conserved motif essential for LiaR binding. Introducing alterations at fully conserved positions in the 25-bp motif affected LiaR binding, and the binding was dependent on the combination of positions that were altered. By scanning the S. mutans genome for the occurrence of the newly defined LiaR binding motif, we identified the promoter of hrcA (encoding a key regulator of the heat shock response) that contains a LiaR binding motif, and we showed that hrcA is negatively regulated by the LiaSR system. Taken together our results suggest a putative role of the LiaSR system in heat shock responses of S. mutans.
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Affiliation(s)
- Manoharan Shankar
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Saswat S. Mohapatra
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Saswati Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- * E-mail:
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152
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Zhang S, Wang J, Xu W, Liu Y, Wang W, Wu K, Wang Z, Zhang X. Antibacterial effects of Traditional Chinese Medicine monomers against Streptococcus pneumoniae via inhibiting pneumococcal histidine kinase (VicK). Front Microbiol 2015; 6:479. [PMID: 26042111 PMCID: PMC4438233 DOI: 10.3389/fmicb.2015.00479] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/30/2015] [Indexed: 01/28/2023] Open
Abstract
Two-component systems (TCSs) have the potential to be an effective target of the antimicrobials, and thus received much attention in recent years. VicK/VicR is one of TCSs in Streptococcus pneumoniae (S. pneumoniae), which is essential for pneumococcal survival. We have previously obtained several Traditional Chinese Medicine monomers using a computer-based screening. In this study, either alone or in combination with penicillin, their antimicrobial activities were evaluated based on in vivo and in vitro assays. The results showed that the MICs of 5'-(Methylthio)-5'-deoxyadenosine, octanal 2, 4-dinitrophenylhydrazone, deoxyshikonin, kavahin, and dodecyl gallate against S. pneumoniae were 37.1, 38.5, 17, 68.5, and 21 μg/mL, respectively. Time-killing assays showed that these compounds elicited bactericidal effects against S. pneumoniae D39 strain, which led to a 6-log reduction in CFU after exposure to compounds at four times of the MIC for 24 h. The five compounds inhibited the growth of Streptococcus pyogenes, Streptococcus mitis, Streptococcus mutans or Streptococcus pseudopneumoniae, meanwhile, deoxyshikonin and dodecyl gallate displayed strong inhibitory activities against Staphylococcus aureus. These compounds showed no obvious cytotoxicity effects on Vero cells. Survival time of the mice infected by S. pneumoniae strains was prolonged by the treatment with the compounds. Importantly, all of the five compounds exerted antimicrobial effects against multidrug-resistant clinical strains of S. pneumoniae. Moreover, even at sub-MIC concentration, they inhibited cell division and biofilm formation. The five compounds all have enhancement effect on penicillin. Deoxyshikonin and dodecyl gallate showed significantly synergic antimicrobial activity with penicillin in vivo and in vitro, and effectively reduced nasopharyngeal and lung colonization caused by different penicillin-resistant pneumococcal serotypes. In addition, the two compounds also showed synergic antimicrobial activity with erythromycin and tetracycline. Taken together, our results suggest that these novel VicK inhibitors may be promising compounds against the pneumococcus, including penicillin-resistant strains.
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Affiliation(s)
- Shuai Zhang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing, China
| | - Jianmin Wang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing, China
| | - Wenchun Xu
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing, China
| | - Yusi Liu
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing, China
| | - Wei Wang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing, China
| | - Kaifeng Wu
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing, China
| | - Zhe Wang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing, China
| | - Xuemei Zhang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing, China
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153
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Development and validation of a high-throughput cell-based screen to identify activators of a bacterial two-component signal transduction system. Antimicrob Agents Chemother 2015; 59:3789-99. [PMID: 25870061 DOI: 10.1128/aac.00236-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/05/2015] [Indexed: 01/16/2023] Open
Abstract
CpxRA is a two-component signal transduction system (2CSTS) found in many drug-resistant Gram-negative bacteria. In response to periplasmic stress, CpxA autophosphorylates and donates a phosphoryl group to its cognate response regulator, CpxR. Phosphorylated CpxR (CpxR-P) upregulates genes involved in membrane repair and downregulates multiple genes that encode virulence factors, which are trafficked across the cell membrane. Mutants that constitutively activate CpxRA in Salmonella enterica serovar Typhimurium and Haemophilus ducreyi are avirulent in mice and humans, respectively. Thus, the activation of CpxRA has high potential as a novel antimicrobial/antivirulence strategy. Using a series of Escherichia coli strains containing a CpxR-P-responsive lacZ reporter and deletions in genes encoding CpxRA system components, we developed and validated a novel cell-based high-throughput screen (HTS) for CpxRA activators. A screen of 36,000 compounds yielded one hit compound that increased reporter activity in wild-type cells. This is the first report of a compound that activates, rather than inhibits, a 2CSTS. The activity profile of the compound against CpxRA pathway mutants in the presence of glucose suggested that the compound inhibits CpxA phosphatase activity. We confirmed that the compound induced the accumulation of CpxR-P in treated cells. Although the hit compound contained a nitro group, a derivative lacking this group retained activity in serum and had lower cytotoxicity than that of the initial hit. This HTS is amenable for the screening of larger libraries to find compounds that activate CpxRA by other mechanisms, and it could be adapted to find activators of other two-component systems.
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154
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Huang CL, Pu PH, Huang HJ, Sung HM, Liaw HJ, Chen YM, Chen CM, Huang MB, Osada N, Gojobori T, Pai TW, Chen YT, Hwang CC, Chiang TY. Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts. BMC Genomics 2015; 16:188. [PMID: 25879893 PMCID: PMC4372319 DOI: 10.1186/s12864-015-1369-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 02/20/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. RESULTS Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. CONCLUSION Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification.
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Affiliation(s)
- Chao-Li Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Pei-Hua Pu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Huang-Mo Sung
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Hung-Jiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Yi-Min Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Chien-Ming Chen
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 202, Taiwan.
| | - Ming-Ban Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Naoki Osada
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Yata, Japan.
| | - Takashi Gojobori
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Yata, Japan.
- Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 202, Taiwan.
| | - Yu-Tin Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Chi-Chuan Hwang
- Department of Engineering Science and Supercomputing Research Center, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
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155
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Dupré E, Herrou J, Lensink MF, Wintjens R, Vagin A, Lebedev A, Crosson S, Villeret V, Locht C, Antoine R, Jacob-Dubuisson F. Virulence regulation with Venus flytrap domains: structure and function of the periplasmic moiety of the sensor-kinase BvgS. PLoS Pathog 2015; 11:e1004700. [PMID: 25738876 PMCID: PMC4352136 DOI: 10.1371/journal.ppat.1004700] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/14/2015] [Indexed: 11/23/2022] Open
Abstract
Two-component systems (TCS) represent major signal-transduction pathways for adaptation to environmental conditions, and regulate many aspects of bacterial physiology. In the whooping cough agent Bordetella pertussis, the TCS BvgAS controls the virulence regulon, and is therefore critical for pathogenicity. BvgS is a prototypical TCS sensor-kinase with tandem periplasmic Venus flytrap (VFT) domains. VFT are bi-lobed domains that typically close around specific ligands using clamshell motions. We report the X-ray structure of the periplasmic moiety of BvgS, an intricate homodimer with a novel architecture. By combining site-directed mutagenesis, functional analyses and molecular modeling, we show that the conformation of the periplasmic moiety determines the state of BvgS activity. The intertwined structure of the periplasmic portion and the different conformation and dynamics of its mobile, membrane-distal VFT1 domains, and closed, membrane-proximal VFT2 domains, exert a conformational strain onto the transmembrane helices, which sets the cytoplasmic moiety in a kinase-on state by default corresponding to the virulent phase of the bacterium. Signaling the presence of negative signals perceived by the periplasmic domains implies a shift of BvgS to a distinct state of conformation and activity, corresponding to the avirulent phase. The response to negative modulation depends on the integrity of the periplasmic dimer, indicating that the shift to the kinase-off state implies a concerted conformational transition. This work lays the bases to understand virulence regulation in Bordetella. As homologous sensor-kinases control virulence features of diverse bacterial pathogens, the BvgS structure and mechanism may pave the way for new modes of targeted therapeutic interventions.
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Affiliation(s)
- Elian Dupré
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Julien Herrou
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Marc F. Lensink
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, University Lille North of France, Villeneuve d’Ascq, France
| | - René Wintjens
- Laboratory of Biopolymers and Supramolecular Nanomaterials, Université Libre de Bruxelles, Brussels, Belgium
| | - Alexey Vagin
- Structural Biology Laboratory, University of York, York, England, United Kingdom
| | - Andrey Lebedev
- Research Complex at Harwell, Science and Technology Facilities Council Rutherford Appleton Laboratory, Didcot, England, United Kingdom
| | - Sean Crosson
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Vincent Villeret
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, University Lille North of France, Villeneuve d’Ascq, France
| | - Camille Locht
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Rudy Antoine
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Françoise Jacob-Dubuisson
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
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156
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Wilke K, Francis S, Carlson EE. Inactivation of multiple bacterial histidine kinases by targeting the ATP-binding domain. ACS Chem Biol 2015; 10:328-35. [PMID: 25531939 PMCID: PMC4301073 DOI: 10.1021/cb5008019] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 12/19/2014] [Indexed: 01/14/2023]
Abstract
Antibacterial agents that exploit new targets will be required to combat the perpetual rise of bacterial resistance to current antibiotics. We are exploring the inhibition of histidine kinases, constituents of two-component systems. Two-component systems are the primary signaling pathways that bacteria utilize to respond to their environment. They are ubiquitous in bacteria and trigger various pathogenic mechanisms. To attenuate these signaling pathways, we sought to broadly target the histidine kinase family by focusing on their highly conserved ATP-binding domain. Development of a fluorescence polarization displacement assay facilitated high-throughput screening of ∼53 000 diverse small molecules for binding to the ATP-binding pocket. Of these compounds, nine inhibited the catalytic activity of two or more histidine kinases. These scaffolds could provide valuable starting points for the design of broadly effective HK inhibitors, global reduction of bacterial signaling, and ultimately, a class of antibiotics that function by a new mechanism of action.
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Affiliation(s)
- Kaelyn
E. Wilke
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Samson Francis
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Erin E. Carlson
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
- Department
of Molecular and Cellular Biochemistry, Indiana University, 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
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157
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Melander RJ, Melander C. Innovative strategies for combating biofilm-based infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 831:69-91. [PMID: 25384664 DOI: 10.1007/978-3-319-09782-4_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Roberta J Melander
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
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158
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Alliband A, Wang Z, Thacker C, English DS, Burns DH. Developing a targeting system for bacterial membranes: measuring receptor-phosphatidylglycerol interactions with1H NMR, ITC and fluorescence correlation spectroscopy. Org Biomol Chem 2015; 13:502-12. [DOI: 10.1039/c4ob01895h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the development of a potential targeting system for bacterial membranes containing phosphatidylglycerol.
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Affiliation(s)
| | - Zifan Wang
- Department of Chemistry
- Wichita State University
- Wichita
- USA
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159
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Parvege MM, Rahman M, Hossain MS. Genome-wide Analysis of Mycoplasma hominis for the Identification of Putative Therapeutic Targets. Drug Target Insights 2014; 8:51-62. [PMID: 25574133 PMCID: PMC4263438 DOI: 10.4137/dti.s19728] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 01/14/2023] Open
Abstract
Ever increasing propensity of antibiotic resistance among pathogenic bacteria raises the demand for the development of novel therapeutic agents to control this grave problem. Advances in the field of bioinformatics, genomics, and proteomics have greatly facilitated the discovery of alternative drugs by swift identification of new drug targets. In the present study, we employed comparative genomics and metabolic pathway analysis with an aim of identifying therapeutic targets in Mycoplasma hominis. Our study has revealed 40 annotated metabolic pathways, including five unique pathways of M. hominis. Our study also identified 179 essential proteins, including 59 proteins having no similarity with human proteins. Further filtering by molecular weight, subcellular localization, functional analysis, and protein network interaction, we identified 57 putative candidates for which new drugs can be developed. Druggability analysis for each of the identified targets has prioritized 16 proteins as suitable for potential drug development.
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Affiliation(s)
- Md Masud Parvege
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Monzilur Rahman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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160
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Njimona I, Yang R, Lamparter T. Temperature effects on bacterial phytochrome. PLoS One 2014; 9:e109794. [PMID: 25289638 PMCID: PMC4188573 DOI: 10.1371/journal.pone.0109794] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/12/2014] [Indexed: 02/01/2023] Open
Abstract
Bacteriophytochromes (BphPs) are light-sensing regulatory proteins encoded in photosynthetic and non-photosynthetic bacteria. This protein class incorporate bilin as their chromophore, with majority of them bearing a light- regulated His kinase or His kinase related module in the C-terminal. We studied the His kinase actives in the temperature range of 5°C to 40°C on two BphPs, Agp1 from Agrobacterium tumefaciens and Cph1 from cyanobacterium Synechocystis PCC 6803. As reported, the phosphorylation activities of the far red (FR) irradiated form of the holoprotein is stronger than that of the red (R) irradiated form in both phytochromes. We observed for the apoprotein and FR irradiated holoprotein of Agp1 an increase in the phosphorylation activities from 5°C to 25°C and a decrease from 25°C to 40°C. At 5°C the activities of the apoprotein were significantly lower than those of the FR irradiated holoprotein, which was opposite at 40°C. A similar temperature pattern was observed for Cph1, but the maximum of the apoprotein was at 20°C while the maximum of the FR irradiated holoprotein was at 10°C. At 40°C, prolonged R irradiation leads to an irreversible bleaching of Cph1, an effect which depends on the C-terminal His kinase module. A more prominent and reversible temperature effect on spectral properties of Agp1, mediated by the His kinase, has been reported before. His kinases in phytochromes could therefore share similar temperature characteristics. We also found that phytochrome B mutants of Arabidopsis have reduced hypocotyl growth at 37°C in darkness, suggesting that this phytochrome senses the temperature or mediates signal transduction of temperature effects.
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Affiliation(s)
- Ibrahim Njimona
- Karlsruhe Institute of Technology KIT, Botanical Institute, Karlsruhe, Germany
| | - Rui Yang
- Karlsruhe Institute of Technology KIT, Botanical Institute, Karlsruhe, Germany
| | - Tilman Lamparter
- Karlsruhe Institute of Technology KIT, Botanical Institute, Karlsruhe, Germany
- * E-mail:
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161
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Alkali metals in addition to acidic pH activate the EvgS histidine kinase sensor in Escherichia coli. J Bacteriol 2014; 196:3140-9. [PMID: 24957621 DOI: 10.1128/jb.01742-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Two-component signal transduction systems (TCSs) in bacteria perceive environmental stress and transmit the information via phosphorelay to adjust multiple cellular functions for adaptation. The EvgS/EvgA system is a TCS that confers acid resistance to Escherichia coli cells. Activation of the EvgS sensor initiates a cascade of transcription factors, EvgA, YdeO, and GadE, which induce the expression of a large group of acid resistance genes. We searched for signals activating EvgS and found that a high concentration of alkali metals (Na(+), K(+)) in addition to low pH was essential for the activation. EvgS is a histidine kinase, with a large periplasmic sensor region consisting of two tandem PBPb (bacterial periplasmic solute-binding protein) domains at its N terminus. The periplasmic sensor region of EvgS was necessary for EvgS activation, and Leu152, located within the first PBPb domain, was involved in the activation. Furthermore, chimeras of EvgS and PhoQ histidine kinases suggested that alkali metals were perceived at the periplasmic sensor region, whereas the cytoplasmic linker domain, connecting the transmembrane region and the histidine kinase domain, was required for low-pH perception.
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162
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Dual-site phosphorylation of the control of virulence regulator impacts group a streptococcal global gene expression and pathogenesis. PLoS Pathog 2014; 10:e1004088. [PMID: 24788524 PMCID: PMC4006921 DOI: 10.1371/journal.ppat.1004088] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 03/10/2014] [Indexed: 11/20/2022] Open
Abstract
Phosphorylation relays are a major mechanism by which bacteria alter transcription in response to environmental signals, but understanding of the functional consequences of bacterial response regulator phosphorylation is limited. We sought to characterize how phosphorylation of the control of virulence regulator (CovR) protein from the major human pathogen group A Streptococcus (GAS) influences GAS global gene expression and pathogenesis. CovR mainly serves to repress GAS virulence factor-encoding genes and has been shown to homodimerize following phosphorylation on aspartate-53 (D53) in vitro. We discovered that CovR is phosphorylated in vivo and that such phosphorylation is partially heat-stable, suggesting additional phosphorylation at non-aspartate residues. Using mass spectroscopy along with targeted mutagenesis, we identified threonine-65 (T65) as an additional CovR phosphorylation site under control of the serine/threonine kinase (Stk). Phosphorylation on T65, as mimicked by the recombinant CovR T65E variant, abolished in vitro CovR D53 phosphorylation. Similarly, isoallelic GAS strains that were either unable to be phosphorylated at D53 (CovR-D53A) or had functional constitutive phosphorylation at T65 (CovR-T65E) had essentially an identical gene repression profile to each other and to a CovR-inactivated strain. However, the CovR-D53A and CovR-T65E isoallelic strains retained the ability to positively influence gene expression that was abolished in the CovR-inactivated strain. Consistent with these observations, the CovR-D53A and CovR-T65E strains were hypervirulent compared to the CovR-inactivated strain in a mouse model of invasive GAS disease. Surprisingly, an isoalleic strain unable to be phosphorylated at CovR T65 (CovR-T65A) was hypervirulent compared to the wild-type strain, as auto-regulation of covR gene expression resulted in lower covR gene transcript and CovR protein levels in the CovR-T65A strain. Taken together, these data establish that CovR is phosphorylated in vivo and elucidate how the complex interplay between CovR D53 activating phosphorylation, T65 inhibiting phosphorylation, and auto-regulation impacts streptococcal host-pathogen interaction. Group A Streptococcus (GAS) causes a variety of human diseases ranging from mild throat infections to deadly invasive infections. The capacity of GAS to cause infections at such diverse locations is dependent on its ability to precisely control the production of a broad variety of virulence factors. The control of virulence regulator (CovR) is a master regulator of GAS genes encoding virulence factors. It is known that CovR can be phosphorylated on aspartate-53 in vitro and that such phosphorylation increases its regulatory activity, but what additional factors influence CovR-mediated gene expression have not been established. Herein we show for the first time that CovR is phosphorylated in vivo and that phosphorylation of CovR on threonine-65 by the threonine/serine kinase Stk prevents aspartate-53 phosphorylation, thereby decreasing CovR regulatory activity. Further, while CovR-mediated gene repression is highly dependent on aspartate-53 phosphorylation, CovR-mediated gene activation proceeds via a phosphorylation-independent mechanism. Modifications in CovR phosphorylation sites significantly affected the expression of GAS virulence factors during infection and markedly altered the ability of GAS to cause disease in mice. These data establish that multiple inter-related pathways converge to influence CovR phosphorylation, thereby providing new insight into the complex regulatory network used by GAS during infection.
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163
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Abstract
Inhibitors of bacterial histidine kinases that globally deactivate bacterial signaling may offer a new offensive against antibiotic resistance.
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Affiliation(s)
- Kaelyn E Wilke
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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164
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Cerqueira GM, Kostoulias X, Khoo C, Aibinu I, Qu Y, Traven A, Peleg AY. A global virulence regulator in Acinetobacter baumannii and its control of the phenylacetic acid catabolic pathway. J Infect Dis 2014; 210:46-55. [PMID: 24431277 DOI: 10.1093/infdis/jiu024] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Acinetobacter baumannii is one of the most notorious hospital-acquired pathogens, and novel treatment strategies are desperately required. Two-component regulatory systems represent potential therapeutic targets as they mediate microorganism adaptation to changing environments, often control virulence, and are specific to bacteria. Here we describe the first global virulence regulator in A. baumannii. METHODS AND RESULTS Using transcriptional profiling and functional assays of a deletion mutant in the A. baumannii sensor kinase gene, A1S_0574 (termed as gacS), we show that this sensor kinase regulates key virulence characteristics, including pili synthesis, biofilms, and motility, resulting in virulence attenuation in a mammalian septicemia model. Notably, we also identified that GacS regulates an operon novel to A. baumannii (paa operon), which is responsible for the metabolism of aromatic compounds. Deletion of paaE (A1S_1340) confirmed the role of this operon in A. baumannii virulence. Finally, we identified the cognate response regulator (A1S_0236) for GacS and confirmed their interaction. A1S_0236 was shown to regulate 75% of the GacS transcriptome and the same virulence phenotypes. Overexpression of A1S_0236 restored virulence in the gacS mutant. CONCLUSIONS Our study characterizes a global virulence regulator, which may provide an alternate therapeutic target, in one of the most troublesome hospital-acquired pathogens.
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165
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Fothergill JL, Winstanley C, James CE. Novel therapeutic strategies to counterPseudomonas aeruginosainfections. Expert Rev Anti Infect Ther 2014; 10:219-35. [DOI: 10.1586/eri.11.168] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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166
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Dhiman A, Bhatnagar S, Kulshreshtha P, Bhatnagar R. Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis. FEBS Open Bio 2014; 4:65-76. [PMID: 24490131 PMCID: PMC3907690 DOI: 10.1016/j.fob.2013.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/24/2013] [Accepted: 12/24/2013] [Indexed: 12/20/2022] Open
Abstract
Two-component signal transduction systems (TCS), consisting of a sensor histidine protein kinase and its cognate response regulator, are an important mode of environmental sensing in bacteria. Additionally, they have been found to regulate virulence determinants in several pathogens. Bacillus anthracis, the causative agent of anthrax and a bioterrorism agent, harbours 41 pairs of TCS. However, their role in its pathogenicity has remained largely unexplored. Here, we show that WalRK of B. anthracis forms a functional TCS which exhibits some species-specific functions. Biochemical studies showed that domain variants of WalK, the histidine kinase, exhibit classical properties of autophosphorylation and phosphotransfer to its cognate response regulator WalR. Interestingly, these domain variants also show phosphatase activity towards phosphorylated WalR, thereby making WalK a bifunctional histidine kinase/phosphatase. An in silico regulon determination approach, using a consensus binding sequence from Bacillus subtilis, provided a list of 30 genes that could form a putative WalR regulon in B. anthracis. Further, electrophoretic mobility shift assay was used to show direct binding of purified WalR to the upstream regions of three putative regulon candidates, an S-layer protein EA1, a cell division ABC transporter FtsE and a sporulation histidine kinase KinB3. Our work lends insight into the species-specific functions and mode of action of B. anthracis WalRK. WalRK forms a functional TCS in B. anthracis, expressed throughout the growth phase. WalK variants exhibit autophosphorylation and phosphotransfer to WalR. WalKc variants also show phosphatase activity towards phosphorylated WalR. A potential WalR regulon in B. anthracis was predicted in silico. DNA binding ability was demonstrated for WalR.
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Affiliation(s)
- Alisha Dhiman
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi 110078, India
| | - Parul Kulshreshtha
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rakesh Bhatnagar
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
- Corresponding author. Tel.: +91 1126704079/1126742040; fax: +91 1126742040.
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167
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Lou YC, Wang I, Rajasekaran M, Kao YF, Ho MR, Hsu STD, Chou SH, Wu SH, Chen C. Solution structure and tandem DNA recognition of the C-terminal effector domain of PmrA from Klebsiella pneumoniae. Nucleic Acids Res 2013; 42:4080-93. [PMID: 24371275 PMCID: PMC3973317 DOI: 10.1093/nar/gkt1345] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Klebsiella pneumoniae PmrA is a polymyxin-resistance-associated response regulator. The C-terminal effector/DNA-binding domain of PmrA (PmrAC) recognizes tandem imperfect repeat sequences on the promoters of genes to induce antimicrobial peptide resistance after phosphorylation and dimerization of its N-terminal receiver domain (PmrAN). However, structural information concerning how phosphorylation of the response regulator enhances DNA recognition remains elusive. To gain insights, we determined the nuclear magnetic resonance solution structure of PmrAC and characterized the interactions between PmrAC or BeF3(-)-activated full-length PmrA (PmrAF) and two DNA sequences from the pbgP promoter of K. pneumoniae. We showed that PmrAC binds to the PmrA box, which was verified to contain two half-sites, 5'-CTTAAT-3' and 5'-CCTAAG-3', in a head-to-tail fashion with much stronger affinity to the first than the second site without cooperativity. The structural basis for the PmrAC-DNA complex was investigated using HADDOCK docking and confirmed by paramagnetic relaxation enhancement. Unlike PmrAC, PmrAF recognizes the two sites simultaneously and specifically. In the PmrAF-DNA complex, PmrAN may maintain an activated homodimeric conformation analogous to that in the free form and the interactions between two PmrAC molecules aid in bending and binding of the DNA duplex for transcription activation.
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Affiliation(s)
- Yuan-Chao Lou
- Institute of Biomedical Sciences, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Institute of Biochemistry and Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
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168
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Wang L, Quan C, Liu B, Wang J, Xiong W, Zhao P, Fan S. Functional reconstitution of Staphylococcus aureus truncated AgrC histidine kinase in a model membrane system. PLoS One 2013; 8:e80400. [PMID: 24303011 PMCID: PMC3841183 DOI: 10.1371/journal.pone.0080400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022] Open
Abstract
The integral membrane protein AgrC is a histidine kinase whose sensor domains interact with an autoinducing peptide, resulting in a series of downstream responses. In this study, truncated AgrCTM5-6C and AgrCTM5-6C-GFP with GFP as a reporter gene were produced using a bacterial system. Purified AgrCTM5-6C and AgrCTM5-6C-GFP were reconstituted into liposomes by a detergent-mediated method. To achieve high-yield protein incorporation, we investigated the effect of different detergents on protein reconstitution efficiency. The highest incorporation was found with N,N-dimethyldode-cylamine N-oxide during complete liposome solubilization, which resulted in a yield of 85±5%. The COOH-terminus of the protein AgrCTM5-6C was almost exclusively oriented towards the inside of the vesicles. AgrCTM5-6C in proteoliposomes exhibited approximately a 6-fold increase in constitutive activity compared with AgrCTM5-6C in detergent micelles. The reconstitution of AgrCTM5-6C or AgrCTM5-6C-GFP was characterized using dynamic light scattering, fluorescence microscopy, and transmission electron microscopy. Based on the results, the optimal conditions for protein incorporation were defined. These findings contribute to the study of membrane protein structure and function in vitro using a reconstitution system.
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Affiliation(s)
- Lina Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Chunshan Quan
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
- * E-mail:
| | - Baoquan Liu
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
| | - Jianfeng Wang
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
| | - Wen Xiong
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
| | - Pengchao Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Shengdi Fan
- Department of Life Science, Dalian Nationalities University, Dalian, China
- The State Ethnic Affairs Commission-Ministry of Education, Dalian, China
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169
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Wojnowska M, Yan J, Sivalingam GN, Cryar A, Gor J, Thalassinos K, Djordjevic S. Autophosphorylation activity of a soluble hexameric histidine kinase correlates with the shift in protein conformational equilibrium. ACTA ACUST UNITED AC 2013; 20:1411-20. [PMID: 24210218 PMCID: PMC3899027 DOI: 10.1016/j.chembiol.2013.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 09/10/2013] [Accepted: 09/20/2013] [Indexed: 01/28/2023]
Abstract
In a commonly accepted model, in response to stimuli, bacterial histidine kinases undergo a conformational transition between an active and inactive form. Structural information on histidine kinases is limited. By using ion mobility-mass spectrometry (IM-MS), we demonstrate an exchange between two conformational populations of histidine kinase ExsG that are linked to different levels of kinase activity. ExsG is an atypical signaling protein that incorporates an uncommon histidine kinase catalytic core at the C terminus preceded by an N-terminal “receiver domain” that is normally associated with the response regulator proteins in two-component signal transduction systems. IM-MS analysis and enzymatic assays indicate that phosphorylation of the ExsG receiver domain stabilizes the “compact” form of the protein and inhibits kinase core activity; in contrast, nucleotide binding required for kinase activity is associated with the more open conformation of ExsG. Conformational states of a histidine kinase demonstrated with IM-MS Phosphorylation of an N-terminal regulatory domain stabilizes compact conformation Conformational states are correlated with kinase activity
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Affiliation(s)
- Marta Wojnowska
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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170
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Njoroge JW, Sperandio V. Interference with Bacterial Cell-to-Cell Chemical Signaling in Development of New Anti-Infectives. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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171
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Blackledge MS, Worthington RJ, Melander C. Biologically inspired strategies for combating bacterial biofilms. Curr Opin Pharmacol 2013; 13:699-706. [PMID: 23871261 PMCID: PMC3795836 DOI: 10.1016/j.coph.2013.07.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/11/2013] [Accepted: 07/01/2013] [Indexed: 01/07/2023]
Abstract
Infections caused by bacterial biofilms are a significant global health problem, causing considerable patient morbidity and mortality and contributing to the economic burden of infectious disease. This review describes diverse strategies to combat bacterial biofilms, focusing firstly on small molecule interference with bacterial communication and signaling pathways, including quorum sensing and two-component signal transduction systems. Secondly we discuss enzymatic approaches to the degradation of extracellular matrix components to effect biofilm dispersal. Both of these approaches are based upon non-microbicidal mechanisms of action, and thereby do not place a direct evolutionary pressure on the bacteria to develop resistance. Such approaches have the potential to, in combination with conventional antibiotics, play an important role in the eradication of biofilm based bacterial infections.
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Affiliation(s)
- Meghan S. Blackledge
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Christian Melander
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
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172
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Dangel A, Ackermann N, Abdel-Hadi O, Maier R, Önder K, Francois P, Müller CW, Pané-Farré J, Engelmann S, Schrenzel J, Heesemann J, Lindermayr C. A de novo-designed antimicrobial peptide with activity against multiresistant Staphylococcus aureus acting on RsbW kinase. FASEB J 2013; 27:4476-88. [PMID: 23901070 DOI: 10.1096/fj.13-234575] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antimicrobial peptides are a promising complement to common antibiotics, development of resistance to which is a growing problem. Here we present a de novo-designed peptide, SP1-1 (RKKRLKLLKRLL-NH2), with antimicrobial activity against multiresistant Staphylococcus aureus (minimal inhibitory concentration: 6.25 μM). Elucidation of the mode of action of this peptide revealed a strong interaction with RsbW kinase (Kd: 6.01±2.73 nM), a serine kinase negatively regulating the activity of the transcription factor σB (SigB). SP1-1 binding and functional modulation of RsbW were shown in vitro by a combination of biochemical, molecular, and biophysical methods, which were further genetically evidenced in vivo by analysis of S. aureus ΔsigB deletion mutants. Intracellular localization of the peptide was demonstrated using nanometer-scaled secondary ion mass spectrometry. Moreover, microarray analysis revealed that transcription of numerous genes, involved in cell wall and amino acid metabolism, transport mechanisms, virulence, and pigmentation, is affected. Interestingly, several WalR binding motif containing genes are induced by SP1-1. In sum, the designed peptide SP1-1 seems to have multiple modes of action, including inhibition of a kinase, and therefore might contribute to the development of new antibacterial compounds, giving bacterial kinase inhibition a closer inspection.
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Affiliation(s)
- Alexandra Dangel
- 1Helmholtz Zentrum Munich, Landstrasse, München-Neuherberg, D-85764 Germany.
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173
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Yeo KJ, Han YH, Eo Y, Cheong HK. Expression, purification, crystallization and preliminary X-ray analysis of the extracellular sensory domain of DraK histidine kinase from Streptomyces coelicolor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:909-11. [PMID: 23908041 DOI: 10.1107/s1744309113018769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 07/06/2013] [Indexed: 11/10/2022]
Abstract
The bacterium Streptomyces coelicolor produces useful antibiotics from its secondary metabolites. DraK is a sensory histidine kinase involved in the differential regulation of antibiotics in S. coelicolor through the DraR/DraK two-component system. Here, the extracellular sensory domain of DraK was overexpressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method. The crystal diffracted to 2.2 Å resolution and belonged to space group C222₁, with unit-cell parameters a = 41.91, b = 174.50, c = 145.25 Å, α = β = γ = 90°.
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Affiliation(s)
- Kwon Joo Yeo
- Division of Magnetic Resonance, Korea Basic Science Institute, 16 Yeongudanji-Ro, Ochang, Chungbuk 363-883, Republic of Korea
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174
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Small-molecule inhibition of bacterial two-component systems to combat antibiotic resistance and virulence. Future Med Chem 2013; 5:1265-84. [DOI: 10.4155/fmc.13.58] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Infections caused by multidrug-resistant bacteria are a considerable and increasing global problem. The development of new antibiotics is not keeping pace with the rapid evolution of resistance to almost all clinically available drugs, and novel strategies are required to fight bacterial infections. One such strategy is the control of pathogenic behaviors, as opposed to simply killing bacteria. Bacterial two-component system (TCS) signal transduction pathways control many pathogenic bacterial behaviors, such as virulence, biofilm formation and antibiotic resistance and are, therefore, an attractive target for the development of new drugs. This review presents an overview of TCS that are potential targets for such a strategy, describes small-molecules inhibitors of TCS identified to date and discusses assays for the identification of novel inhibitors. The future perspective for the identification and use of inhibitors of TCS to potentially provide new therapeutic options for the treatment of drug-resistant bacterial infections is discussed.
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175
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Histidine phosphotransfer proteins in fungal two-component signal transduction pathways. EUKARYOTIC CELL 2013; 12:1052-60. [PMID: 23771905 DOI: 10.1128/ec.00083-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The histidine phosphotransfer (HPt) protein Ypd1 is an important participant in the Saccharomyces cerevisiae multistep two-component signal transduction pathway and, unlike the expanded histidine kinase gene family, is encoded by a single gene in nearly all model and pathogenic fungi. Ypd1 is essential for viability in both S. cerevisiae and in Cryptococcus neoformans. These and other aspects of Ypd1 biology, combined with the availability of structural and mutational data in S. cerevisiae, suggest that the essential interactions between Ypd1 and response regulator domains would be a good target for antifungal drug development. The goal of this minireview is to summarize the wealth of data on S. cerevisiae Ypd1 and to consider the potential benefits of conducting related studies in pathogenic fungi.
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176
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Kim J, Park W. Identification and characterization of genes regulated by AqsR, a LuxR-type regulator in Acinetobacter oleivorans DR1. Appl Microbiol Biotechnol 2013; 97:6967-78. [DOI: 10.1007/s00253-013-5006-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 05/09/2013] [Accepted: 05/17/2013] [Indexed: 12/25/2022]
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177
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Igarashi M, Watanabe T, Hashida T, Umekita M, Hatano M, Yanagida Y, Kino H, Kimura T, Kinoshita N, Inoue K, Sawa R, Nishimura Y, Utsumi R, Nomoto A. Waldiomycin, a novel WalK-histidine kinase inhibitor from Streptomyces sp. MK844-mF10. J Antibiot (Tokyo) 2013; 66:459-64. [DOI: 10.1038/ja.2013.33] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 02/13/2013] [Accepted: 02/19/2013] [Indexed: 11/09/2022]
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178
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Kostakioti M, Hadjifrangiskou M, Hultgren SJ. Bacterial biofilms: development, dispersal, and therapeutic strategies in the dawn of the postantibiotic era. Cold Spring Harb Perspect Med 2013; 3:a010306. [PMID: 23545571 DOI: 10.1101/cshperspect.a010306] [Citation(s) in RCA: 518] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Biofilm formation constitutes an alternative lifestyle in which microorganisms adopt a multicellular behavior that facilitates and/or prolongs survival in diverse environmental niches. Biofilms form on biotic and abiotic surfaces both in the environment and in the healthcare setting. In hospital wards, the formation of biofilms on vents and medical equipment enables pathogens to persist as reservoirs that can readily spread to patients. Inside the host, biofilms allow pathogens to subvert innate immune defenses and are thus associated with long-term persistence. Here we provide a general review of the steps leading to biofilm formation on surfaces and within eukaryotic cells, highlighting several medically important pathogens, and discuss recent advances on novel strategies aimed at biofilm prevention and/or dissolution.
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Affiliation(s)
- Maria Kostakioti
- Department of Molecular Microbiology and Microbial Pathogenesis, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110-1010, USA
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179
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Abstract
β-Lactam antibiotics are one of the most important antibiotic classes but are plagued by problems of resistance, and the development of new β-lactam antibiotics through side-chain modification of existing β-lactam classes is not keeping pace with resistance development. In this JOCSynopsis, we summarize small molecule strategies to overcome resistance to β-lactam antibiotics. These approaches include the development of β-lactamase inhibitors and compounds that interfere with the ability of the bacteria to sense an antibiotic threat and activate their resistance mechanisms.
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Affiliation(s)
- Roberta J Worthington
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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180
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Role of the PAS sensor domains in the Bacillus subtilis sporulation kinase KinA. J Bacteriol 2013; 195:2349-58. [PMID: 23504013 DOI: 10.1128/jb.00096-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Histidine kinases are sophisticated molecular sensors that are used by bacteria to detect and respond to a multitude of environmental signals. KinA is the major histidine kinase required for initiation of sporulation upon nutrient deprivation in Bacillus subtilis. KinA has a large N-terminal region (residues 1 to 382) that is uniquely composed of three tandem Per-ARNT-Sim (PAS) domains that have been proposed to constitute a sensor module. To further enhance our understanding of this "sensor" region, we defined the boundaries that give rise to the minimal autonomously folded PAS domains and analyzed their homo- and heteroassociation properties using analytical ultracentrifugation, nuclear magnetic resonance (NMR) spectroscopy, and multiangle laser light scattering. We show that PAS(A) self-associates very weakly, while PAS(C) is primarily a monomer. In contrast, PAS(B) forms a stable dimer (K(d) [dissociation constant] of <10 nM), and it appears to be the main N-terminal determinant of KinA dimerization. Analysis of KinA mutants deficient for one or more PAS domains revealed a critical role for PAS(B), but not PAS(A), in autophosphorylation of KinA. Our findings suggest that dimerization of PAS(B) is important for keeping the catalytic domain of KinA in a functional conformation. We use this information to propose a model for the structure of the N-terminal sensor module of KinA.
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181
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PacC and pH-dependent transcriptome of the mycotrophic fungus Trichoderma virens. BMC Genomics 2013; 14:138. [PMID: 23445374 PMCID: PMC3618310 DOI: 10.1186/1471-2164-14-138] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 02/23/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND In fungi, environmental pH is an important signal for development, and successful host colonization depends on homeostasis. Surprisingly, little is known regarding the role of pH in fungal-fungal interactions. Species of Trichoderma grow as soil saprobes but many are primarily mycotrophic, using other fungi as hosts. Therefore, Trichoderma spp. are studied for their potential in biocontrol of plant diseases. Particularly in alkaline soil, pH is a critical limiting factor for these biofungicides, whose optimal growth pH is 4-6. Gaining an understanding of pH adaptability is an important step in broadening the activity spectrum of these economically important fungi. RESULTS We studied the pH-responsive transcription factor PacC by gene knockout and by introduction of a constitutively active allele (pacCc). ΔpacC mutants exhibited reduced growth at alkaline pH, while pacCc strains grew poorly at acidic pH. In plate confrontation assays ΔpacC mutants showed decreased ability to compete with the plant pathogens Rhizoctonia solani and Sclerotium rolfsii. The pacCc strain exhibited an overgrowth of R. solani that was comparable to the wild type, but was unable to overgrow S. rolfsii. To identify genes whose expression is dependent on pH and pacC, we designed oligonucleotide microarrays from the transcript models of the T. virens genome, and compared the transcriptomes of wild type and mutant cultures exposed to high or low pH. Transcript levels from several functional classes were dependent on pacC, on pH, or on both. Furthermore, the expression of a set of pacC-dependent genes was increased in the constitutively-active pacCc strain, and was pH-independent in some, but not all cases. CONCLUSIONS PacC is important for biocontrol-related antagonism of other fungi by T. virens. As much as 5% of the transcriptome is pH-dependent, and of these genes, some 25% depend on pacC. Secondary metabolite biosynthesis and ion transport are among the relevant gene classes. We suggest that ΔpacC mutants may have lost their full biocontrol potential due to their inability to adapt to alkaline pH, to perceive ambient pH, or both. The results raise the novel possibility of genetically manipulating Trichoderma in order to improve adaptability and biocontrol at alkaline pH.
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Wang C, Sang J, Wang J, Su M, Downey JS, Wu Q, Wang S, Cai Y, Xu X, Wu J, Senadheera DB, Cvitkovitch DG, Chen L, Goodman SD, Han A. Mechanistic insights revealed by the crystal structure of a histidine kinase with signal transducer and sensor domains. PLoS Biol 2013; 11:e1001493. [PMID: 23468592 PMCID: PMC3582566 DOI: 10.1371/journal.pbio.1001493] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 01/14/2013] [Indexed: 02/02/2023] Open
Abstract
A crystal structure reveals an elegant mechanistic switch whereby helical bending and catalytic domain rotation allow self-activation of a histidine kinase during a bacterial stress response. Two-component systems (TCSs) are important for the adaptation and survival of bacteria and fungi under stress conditions. A TCS is often composed of a membrane-bound sensor histidine kinase (SK) and a response regulator (RR), which are relayed through sequential phosphorylation steps. However, the mechanism for how an SK is switched on in response to environmental stimuli remains obscure. Here, we report the crystal structure of a complete cytoplasmic portion of an SK, VicK from Streptococcus mutans. The overall structure of VicK is a long-rod dimer that anchors four connected domains: HAMP, Per-ARNT-SIM (PAS), DHp, and catalytic and ATP binding domain (CA). The HAMP, a signal transducer, and the PAS domain, major sensor, adopt canonical folds with dyad symmetry. In contrast, the dimer of the DHp and CA domains is asymmetric because of different helical bends in the DHp domain and spatial positions of the CA domains. Moreover, a conserved proline, which is adjacent to the phosphoryl acceptor histidine, contributes to helical bending, which is essential for the autokinase and phosphatase activities. Together, the elegant architecture of VicK with a signal transducer and sensor domain suggests a model where DHp helical bending and a CA swing movement are likely coordinated for autokinase activation. Two-component signal transduction systems (TCSs) are promising targets for new antimicrobial research because they help bacteria and fungi adapt and survive. One of the main components of TCSs is a sensor histidine kinase (SK), which relays extracellular signals to intracellular pathways. Despite intensive research, a full-length structure of an SK has yet to be solved. In this study, we report the first crystal structure of the complete cytoplasmic region of VicK, an important SK in the tooth decay pathogen S. mutans. VicK is composed of several domains (HAMP, PAS, DHp, and catalytic and ATP binding domain [CA]) in addition to a short transmembrane domain. We find that the dimeric VicK protein has an elegant rod-shaped structure with the domains linearly connected like beads on a string. The structure suggests that VicK kinase activates itself by helical bending of the DHp domain and coordinated swinging around of the catalytic CA domain to engage with the target histidine. Structure-based mutagenesis experiments also helped us to identify key residues that are required for VicK's opposing phosphatase activity. Our studies of the multi-modular VicK protein suggest a sequential kinase activation model that may involve helical bending of the DHp domain and repositioning of the CA domains.
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Affiliation(s)
- Chen Wang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Jiayan Sang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Jiawei Wang
- Department of Biology and Technology, Tsinghua University, Beijing, China
| | - Mingyan Su
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Jennifer S. Downey
- Division of Biomedical Science, Herman Ostrow School of Dentistry of University of Southern California, Los Angeles, California, United States of America
| | - Qinggan Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Shida Wang
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Xiaozheng Xu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Jun Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Dilani B. Senadheera
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Dennis G. Cvitkovitch
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Lin Chen
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Steven D. Goodman
- Division of Biomedical Science, Herman Ostrow School of Dentistry of University of Southern California, Los Angeles, California, United States of America
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
- * E-mail:
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Martinez MA, Das K, Saikolappan S, Materon LA, Dhandayuthapani S. A serine/threonine phosphatase encoded by MG_207 of Mycoplasma genitalium is critical for its virulence. BMC Microbiol 2013; 13:44. [PMID: 23432936 PMCID: PMC3639085 DOI: 10.1186/1471-2180-13-44] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/19/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Bacterial signal transduction systems like two component system (TCS) and Serine/Threonine kinase (STK) and Serine/Threonine phosphatase (STP) play important roles in the virulence and pathogenesis of bacterial pathogens. Mycoplasma genitalium, a mollicute that causes the urogenital diseases urethritis and cervicitis in men and women, respectively, is a pathogen which lacks TCS but possesses STK/STP. In this study, we investigated the biochemical and virulence properties of an STP protein encoded by the gene MG_207 of this species. RESULTS We overexpressed MG207 in Escherichia coli overexpression system as a recombinant His10MG207 protein and purified it with affinity chromatography. This recombinant protein readily hydrolyzed the substrate p-nitrophenyl phosphate (pNPP) in a dose-dependent manner. Additional studies using synthetic peptides as substrates revealed that the recombinant protein was able to hydrolyze the threonine phosphate. Further, a transposon insertion mutant strain of M. genitalium (TIM207) that lacks the protein MG207 showed differentially phosphorylated proteins when compared to the wild type G37 strain. Mass spectrometry revealed that some of the key proteins differentially phosphorylated in TIM207 strain were putative cytoskeletal protein encoded by the gene MG_328 and pyruvate dehydrogenase E1 α chain encoded by the gene MG_274. In addition, TIM207 was noticed to be less cytotoxic to HeLa cells and this correlated with the production of less hydrogen peroxide by this strain. This strain was also less efficient in inducing the differentiation of THP-1 cell line as compared to wild type M. genitalium. CONCLUSIONS The results of the study suggest that MG207 is an important signaling protein of M. genitalium and its presence may be crucial for the virulence of this species.
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Affiliation(s)
- Mario A Martinez
- Regional Academic Health Center and Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, Edinburg, TX 78541, USA
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Yeo KJ, Kim EH, Hwang E, Han YH, Eo Y, Kim HJ, Kwon O, Hong YS, Cheong C, Cheong HK. pH-dependent structural change of the extracellular sensor domain of the DraK histidine kinase from Streptomyces coelicolor. Biochem Biophys Res Commun 2013; 431:554-9. [DOI: 10.1016/j.bbrc.2013.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 01/07/2013] [Indexed: 10/27/2022]
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185
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Worthington RJ, Melander C. Combination approaches to combat multidrug-resistant bacteria. Trends Biotechnol 2013; 31:177-84. [PMID: 23333434 DOI: 10.1016/j.tibtech.2012.12.006] [Citation(s) in RCA: 405] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 12/19/2022]
Abstract
The increasing prevalence of infections caused by multidrug-resistant bacteria is a global health problem that has been exacerbated by the dearth of novel classes of antibiotics entering the clinic over the past 40 years. Herein, we describe recent developments toward combination therapies for the treatment of multidrug-resistant bacterial infections. These efforts include antibiotic-antibiotic combinations, and the development of adjuvants that either directly target resistance mechanisms such as the inhibition of β-lactamase enzymes, or indirectly target resistance by interfering with bacterial signaling pathways such as two-component systems (TCSs). We also discuss screening of libraries of previously approved drugs to identify nonobvious antimicrobial adjuvants.
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186
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Segal G. The Legionella pneumophila two-component regulatory systems that participate in the regulation of Icm/Dot effectors. Curr Top Microbiol Immunol 2013; 376:35-52. [PMID: 23918177 DOI: 10.1007/82_2013_346] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Legionella pneumophila, the causative agent of Legionnaires' disease, actively manipulates intracellular processes to establish a replication niche inside their host cells. The establishment of its replication niche requires a functional Icm/Dot type IV secretion system which translocates about 300 effector proteins into the host cells during infection. This enormous number of effectors should be coordinated at the level of gene expression, in order to be expressed and translocated at the correct time and appropriate amounts. One of the predominant ways in bacteria to regulate virulence gene expression is by the use of two-component systems (TCSs). To date, four TCSs have been shown to be involved in the regulation of Icm/Dot effector-encoding genes: The PmrAB and CpxRA TCSs that directly control, and the LetAS and LqsRS TCSs that indirectly control the level of expression of effector-encoding genes. According to our current knowledge, these four TCSs control the expression of about 70 effector-encoding genes. The regulation by different TCSs divides the effectors into groups of co-regulated effector-encoding genes that are probably co-expressed at a similar time during infection and might perform related functions. In addition, examples of interplay between these TCSs were already reported indicating that they form part of a regulatory network that orchestrates the expression of L. pneumophila effector-encoding genes during infection.
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Affiliation(s)
- Gil Segal
- The George S. Wise Faculty of Life Sciences, Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, 69978, Ramat-Aviv, Tel-Aviv, Israel,
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Thompson RJ, Bobay BG, Stowe SD, Olson AL, Peng L, Su Z, Actis LA, Melander C, Cavanagh J. Identification of BfmR, a response regulator involved in biofilm development, as a target for a 2-Aminoimidazole-based antibiofilm agent. Biochemistry 2012. [PMID: 23186243 DOI: 10.1021/bi3015289] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2-Aminoimidazoles (2AIs) have been documented to disrupt bacterial protection mechanisms, including biofilm formation and genetically encoded antibiotic resistance traits. Using Acinetobacter baumannii, we provide initial insight into the mechanism of action of a 2AI-based antibiofilm agent. Confocal microscopy confirmed that the 2AI is cell permeable, while pull-down assays identified BfmR, a response regulator that is the master controller of biofilm formation, as a target for this compound. Binding assays demonstrated specificity of the 2AI for response regulators, while computational docking provided models for 2AI-BfmR interactions. The 2AI compound studied here represents a unique small molecule scaffold that targets bacterial response regulators.
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Affiliation(s)
- Richele J Thompson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
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188
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Nielsen A, Mansson M, Wietz M, Varming AN, Phipps RK, Larsen TO, Gram L, Ingmer H. Nigribactin, a novel siderophore from Vibrio nigripulchritudo, modulates Staphylococcus aureus virulence gene expression. Mar Drugs 2012. [PMID: 23203279 PMCID: PMC3509537 DOI: 10.3390/md10112584] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Staphylococcus aureus is a serious human pathogen that employs a number of virulence factors as part of its pathogenesis. The purpose of the present study was to explore marine bacteria as a source of compounds that modulate virulence gene expression in S. aureus. During the global marine Galathea 3 expedition, a strain collection was established comprising bacteria that express antimicrobial activity against Vibrio anguillarum and/or Staphylococcus aureus. Within this collection we searched colony material, culture supernatants, and cell extracts for virulence modulating activity showing that 68 out of 83 marine bacteria (affiliated with the Vibrionaceae and Pseudoalteromonas sp.) influenced expression of S. aureus hla encoding α-hemolysin toxin and/or spa encoding Protein A. The isolate that upon initial screening showed the highest degree of interference (crude ethyl acetate extract) was a Vibrio nigripulchritudo. Extraction, purification and structural elucidation revealed a novel siderophore, designated nigribactin, which induces spa transcription. The effect of nigribactin on spa expression is likely to be independent from its siderophore activity, as another potent siderophore, enterobactin, failed to influence S. aureus virulence gene expression. This study shows that marine microorganisms produce compounds with potential use in therapeutic strategies targeting virulence rather than viability of human pathogens.
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Affiliation(s)
- Anita Nielsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark; (A.N.); (A.N.V.)
| | - Maria Mansson
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.M.); (R.K.P.); (T.O.L.)
| | - Matthias Wietz
- National Food Institute, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.W.); (L.G.)
- Scripps Institution of Oceanography, Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Anders N. Varming
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark; (A.N.); (A.N.V.)
| | - Richard K. Phipps
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.M.); (R.K.P.); (T.O.L.)
| | - Thomas O. Larsen
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.M.); (R.K.P.); (T.O.L.)
| | - Lone Gram
- National Food Institute, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.W.); (L.G.)
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark; (A.N.); (A.N.V.)
- Author to whom correspondence should be addressed; ; Tel.: +45-35332773; Fax: +45-35332755
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Current understanding of HOG-MAPK pathway in Aspergillus fumigatus. Mycopathologia 2012; 175:13-23. [PMID: 23161019 DOI: 10.1007/s11046-012-9600-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 11/04/2012] [Indexed: 10/27/2022]
Abstract
Aspergillus fumigatus is an important opportunistic fungal pathogen that causes lethal systemic invasive aspergillosis. It must be able to adapt to stress in the microenvironment during host invasion and systemic spread. The high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) signaling pathway is a key element that controls adaptation to environmental stress. It plays a critical role in the virulence of several fungal pathogens. In this review, we summarize the current knowledge about the functions of different components of the HOG-MAPK pathway in A. fumigatus through mutant analysis or inferences from the genome annotation, focusing on their roles in adaptation to stress, regulation of infection-related morphogenesis, and effect on virulence. We also briefly compare the functions of the HOG pathway in A. fumigatus with those in the model fungi Saccharomyces cerevisiae and Aspergillus nidulans as well as several other human and plant pathogens including Candida albicans, Cryptococcus neoformans, and Magnaporthe oryzae. The genes described in this review mainly include tcsB, fos1, skn7, sho1, pbs2, and sakA whose deletion mutants have already been established in A. fumigatus. Among them, fos1 has been considered a virulence factor in A. fumigatus, indicating that components of the HOG pathway may be suitable as targets for developing new fungicides. However, quite a few of the genes of this pathway, such as sskA (ssk1), sskB, steC, and downstream regulator genes, are not well characterized. System biology approaches may contribute to a more comprehensive understanding of HOG pathway functions with dynamic details.
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Ünal CM, Singh B, Fleury C, Singh K, Chávez de Paz L, Svensäter G, Riesbeck K. QseC controls biofilm formation of non-typeable Haemophilus influenzae in addition to an AI-2-dependent mechanism. Int J Med Microbiol 2012; 302:261-9. [DOI: 10.1016/j.ijmm.2012.07.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 06/02/2012] [Accepted: 07/08/2012] [Indexed: 12/24/2022] Open
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Abstract
Bacterial biofilms are defined as a surface attached community of bacteria embedded in a matrix of extracellular polymeric substances that they have produced. When in the biofilm state, bacteria are more resistant to antibiotics and the host immune response than are their planktonic counterparts. Biofilms are increasingly recognized as being significant in human disease, accounting for 80% of bacterial infections in the body and diseases associated with bacterial biofilms include: lung infections of cystic fibrosis patients, colitis, urethritis, conjunctivitis, otitis, endocarditis and periodontitis. Additionally, biofilm infections of indwelling medical devices are of particular concern, as once the device is colonized infection is virtually impossible to eradicate. Given the prominence of biofilms in infectious diseases, there has been an increased effort toward the development of small molecules that will modulate bacterial biofilm development and maintenance. In this review, we highlight the development of small molecules that inhibit and/or disperse bacterial biofilms through non-microbicidal mechanisms. The review discuses the numerous approaches that have been applied to the discovery of lead small molecules that mediate biofilm development. These approaches are grouped into: (1) the identification and development of small molecules that target one of the bacterial signaling pathways involved in biofilm regulation, (2) chemical library screening for compounds with anti-biofilm activity, and (3) the identification of natural products that possess anti-biofilm activity, and the chemical manipulation of these natural products to obtain analogues with increased activity.
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Thanikkal EJ, Mangu JCK, Francis MS. Interactions of the CpxA sensor kinase and cognate CpxR response regulator from Yersinia pseudotuberculosis. BMC Res Notes 2012; 5:536. [PMID: 23013530 PMCID: PMC3517363 DOI: 10.1186/1756-0500-5-536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 09/22/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The CpxA sensor kinase-CpxR response regulator two-component regulatory system is a sentinel of bacterial envelope integrity. Integrating diverse signals, it can alter the expression of a wide array of components that serve to shield the envelope from damage and to promote bacterial survival. In bacterial pathogens such as Yersinia pseudotuberculosis, this also extends to pathogenesis. CpxR is thought to dimerize upon phosphorylation by the sensor kinase CpxA. This phosphorylation enables CpxR binding to specific DNA sequences where it acts on gene transcription. As Cpx pathway activation is dependent on protein-protein interactions, we performed an interaction analysis of CpxR and CpxA from Y. pseudotuberculosis. RESULTS CpxR full-length and truncated versions that either contained or lacked a putative internal linker were all assessed for their ability to homodimerize and interact with CpxA. Using an adenylate cyclase-based bacterial two hybrid approach, full-length CpxR readily engaged with CpxA. The CpxR N-terminus could also homodimerize with itself and with a full-length CpxR. A second homodimerization assay based upon the λcI repressor also demonstrated that the CpxR C-terminus could homodimerize. While the linker was not specifically required, it enhanced CpxR homodimerization. Mutagenesis of cpxR identified the aspartate at residue 51, putative N-terminal coiled-coil and C-terminal winged-helix-turn-helix domains as mediators of CpxR homodimerization. Scrutiny of CpxA full-length and truncated versions revealed that dimerization involved the N-terminus and an internal dimerization and histidine phosphotransfer domain. CONCLUSIONS This interaction analysis mapped regions of CpxR and CpxA that were responsible for interactions with self or with each other. When combined with other physiological and biochemical tests both hybrid-based assays can be useful in dissecting molecular contacts that may underpin Cpx pathway activation and repression.
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Affiliation(s)
- Edvin J Thanikkal
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
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Sivakumar D, Lahiri C, Chakravortty D. Computational studies on histidine kinase protein BaeS to target multidrug-resistant Salmonella. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0188-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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194
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Role of the Helicobacter pylori sensor kinase ArsS in protein trafficking and acid acclimation. J Bacteriol 2012; 194:5545-51. [PMID: 22865848 DOI: 10.1128/jb.01263-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori survives and grows at low pHs via acid acclimation mechanisms that enable periplasmic pH homeostasis. Important components include a cytoplasmic urease; a pH-gated urea channel, UreI; and periplasmic α-carbonic anhydrase. To allow the rapid adjustment of periplasmic pH, acid acclimation components are recruited to the inner membrane in acid. The ArsRS two-component system, in an acid-responsive manner, controls the transcription of the urease gene cluster and α-carbonic anhydrase. The aim of this study is to determine the role of ArsS in protein trafficking as a component of acid acclimation. H. pylori wild-type and ΔarsS bacteria were incubated at acidic and neutral pHs. Intact bacteria, purified membranes, and total protein were analyzed by Western blotting and urease activity measurements. The total urease activity level was decreased in the ΔarsS strain, but the acid activation of UreI was unaffected. A 30-min acid exposure increased the level and activity of urease proteins at the membrane in the wild type but not in the ΔarsS strain. The urease levels and activity of the ΔarsS strain after a 90-min acid exposure were similar to those of the wild type. ArsS, in addition to its role in urease gene transcription, is also involved in the recruitment of urease proteins to the inner membrane to augment acid acclimation during acute acid exposure. Urease membrane recruitment following prolonged acid exposure in the absence of ArsS was similar to that of the wild type, suggesting a compensatory mechanism, possibly regulated by FlgS, underscoring the importance of urease membrane recruitment and activation in periplasmic pH homeostasis.
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Liu J, Thanikkal EJ, Obi IR, Francis MS. Elevated CpxR~P levels repress the Ysc-Yop type III secretion system of Yersinia pseudotuberculosis. Res Microbiol 2012; 163:518-30. [PMID: 22842077 DOI: 10.1016/j.resmic.2012.07.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 07/18/2012] [Indexed: 10/28/2022]
Abstract
One way that Gram-negative bacteria respond to extracytoplasmic stress is through the CpxA-CpxR system. An activated CpxA sensor kinase phosphorylates the CpxR response regulator to instigate positive auto-amplification of Cpx pathway activation, as well as synthesis of various bacterial survival factors. In the absence of CpxA, human enteropathogenic Yersinia pseudotuberculosis accumulates high CpxR~P levels aided by the action of low molecular weight phosphodonors such as acetyl~P. Critically, these bacteria are also defective for plasmid-encoded Ysc-Yop-dependent type III synthesis and secretion, an essential determinant of virulence. Herein, we investigated whether elevated CpxR~P levels account for lost Ysc-Yop function. Decisively, reducing CpxR∼P in Yersinia defective for CpxA phosphatase activity - through incorporating second-site suppressor mutations in ackA-pta or cpxR - dramatically restored Ysc-Yop T3S function. Moreover, the repressive effect of accumulated CpxR∼P is a direct consequence of binding to the promoter regions of the T3S genes. Thus, Cpx pathway activation has two consequences in Yersinia; one, to maintain quality control in the bacterial envelope, and the second, to restrict ysc-yop gene expression to those occasions where it will have maximal effect.
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Affiliation(s)
- Junfa Liu
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
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Abstract
To exist in a wide range of environmental niches, bacteria must sense and respond to a variety of external signals. A primary means by which this occurs is through two-component signal transduction pathways, typically composed of a sensor histidine kinase that receives the input stimuli and then phosphorylates a response regulator that effects an appropriate change in cellular physiology. Histidine kinases and response regulators have an intrinsic modularity that separates signal input, phosphotransfer, and output response; this modularity has allowed bacteria to dramatically expand and diversify their signaling capabilities. Recent work has begun to reveal the molecular basis by which two-component proteins evolve. How and why do orthologous signaling proteins diverge? How do cells gain new pathways and recognize new signals? What changes are needed to insulate a new pathway from existing pathways? What constraints are there on gene duplication and lateral gene transfer? Here, we review progress made in answering these questions, highlighting how the integration of genome sequence data with experimental studies is providing major new insights.
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Affiliation(s)
- Emily J Capra
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA
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Ng WL, Perez L, Cong J, Semmelhack MF, Bassler BL. Broad spectrum pro-quorum-sensing molecules as inhibitors of virulence in vibrios. PLoS Pathog 2012; 8:e1002767. [PMID: 22761573 PMCID: PMC3386246 DOI: 10.1371/journal.ppat.1002767] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 05/07/2012] [Indexed: 01/30/2023] Open
Abstract
Quorum sensing (QS) is a bacterial cell-cell communication process that relies on the production and detection of extracellular signal molecules called autoinducers. QS allows bacteria to perform collective activities. Vibrio cholerae, a pathogen that causes an acute disease, uses QS to repress virulence factor production and biofilm formation. Thus, molecules that activate QS in V. cholerae have the potential to control pathogenicity in this globally important bacterium. Using a whole-cell high-throughput screen, we identified eleven molecules that activate V. cholerae QS: eight molecules are receptor agonists and three molecules are antagonists of LuxO, the central NtrC-type response regulator that controls the global V. cholerae QS cascade. The LuxO inhibitors act by an uncompetitive mechanism by binding to the pre-formed LuxO-ATP complex to inhibit ATP hydrolysis. Genetic analyses suggest that the inhibitors bind in close proximity to the Walker B motif. The inhibitors display broad-spectrum capability in activation of QS in Vibrio species that employ LuxO. To the best of our knowledge, these are the first molecules identified that inhibit the ATPase activity of a NtrC-type response regulator. Our discovery supports the idea that exploiting pro-QS molecules is a promising strategy for the development of novel anti-infectives.
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Affiliation(s)
- Wai-Leung Ng
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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198
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Pyysalo S, Ohta T, Rak R, Sullivan D, Mao C, Wang C, Sobral B, Tsujii J, Ananiadou S. Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics 2012; 13 Suppl 11:S2. [PMID: 22759456 PMCID: PMC3384257 DOI: 10.1186/1471-2105-13-s11-s2] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI), and the supporting task on Entity Relations (REL). The two main tasks represent extensions of the event extraction model introduced in the BioNLP Shared Task 2009 (ST'09) to two new areas of biomedical scientific literature, each motivated by the needs of specific biocuration tasks. The ID task concerns the molecular mechanisms of infection, virulence and resistance, focusing in particular on the functions of a class of signaling systems that are ubiquitous in bacteria. The EPI task is dedicated to the extraction of statements regarding chemical modifications of DNA and proteins, with particular emphasis on changes relating to the epigenetic control of gene expression. By contrast to these two application-oriented main tasks, the REL task seeks to support extraction in general by separating challenges relating to part-of relations into a subproblem that can be addressed by independent systems. Seven groups participated in each of the two main tasks and four groups in the supporting task. The participating systems indicated advances in the capability of event extraction methods and demonstrated generalization in many aspects: from abstracts to full texts, from previously considered subdomains to new ones, and from the ST'09 extraction targets to other entities and events. The highest performance achieved in the supporting task REL, 58% F-score, is broadly comparable with levels reported for other relation extraction tasks. For the ID task, the highest-performing system achieved 56% F-score, comparable to the state-of-the-art performance at the established ST'09 task. In the EPI task, the best result was 53% F-score for the full set of extraction targets and 69% F-score for a reduced set of core extraction targets, approaching a level of performance sufficient for user-facing applications. In this study, we extend on previously reported results and perform further analyses of the outputs of the participating systems. We place specific emphasis on aspects of system performance relating to real-world applicability, considering alternate evaluation metrics and performing additional manual analysis of system outputs. We further demonstrate that the strengths of extraction systems can be combined to improve on the performance achieved by any system in isolation. The manually annotated corpora, supporting resources, and evaluation tools for all tasks are available from http://www.bionlp-st.org and the tasks continue as open challenges for all interested parties.
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Affiliation(s)
- Sampo Pyysalo
- School of Computer Science, University of Manchester, Manchester, UK
- National Centre for Text Mining, University of Manchester, Manchester, UK
| | - Tomoko Ohta
- Department of Computer Science, University of Tokyo, Tokyo, Japan
| | - Rafal Rak
- School of Computer Science, University of Manchester, Manchester, UK
- National Centre for Text Mining, University of Manchester, Manchester, UK
| | - Dan Sullivan
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Chunhong Mao
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Chunxia Wang
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Bruno Sobral
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Sophia Ananiadou
- School of Computer Science, University of Manchester, Manchester, UK
- National Centre for Text Mining, University of Manchester, Manchester, UK
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199
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Abstract
Infectious diseases can be difficult to cure, especially if the pathogen forms a biofilm. After decades of extensive research into the morphology, physiology and genomics of biofilm formation, attention has recently been directed toward the analysis of the cellular metabolome in order to understand the transformation of a planktonic cell to a biofilm. Metabolomics can play an invaluable role in enhancing our understanding of the underlying biological processes related to the structure, formation and antibiotic resistance of biofilms. A systematic view of metabolic pathways or processes responsible for regulating this 'social structure' of microorganisms may provide critical insights into biofilm-related drug resistance and lead to novel treatments. This review will discuss the development of NMR-based metabolomics as a technology to study medically relevant biofilms. Recent advancements from case studies reviewed in this manuscript have shown the potential of metabolomics to shed light on numerous biological problems related to biofilms.
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Affiliation(s)
- Bo Zhang
- Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304, USA
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200
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Wilke KE, Francis S, Carlson EE. Activity-based probe for histidine kinase signaling. J Am Chem Soc 2012; 134:9150-3. [PMID: 22606938 DOI: 10.1021/ja3041702] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacterial two-component systems (TCSs) are signaling pathways composed of two proteins: a histidine kinase (HK) and a response regulator (RR). Upon stimulation, the HK autophosphorylates at a conserved histidine. The phosphoryl group is subsequently transferred to an aspartate on an RR, eliciting an adaptive response, often up- or downregulation of gene expression. TCS signaling controls many functions in bacteria, including development, virulence, and antibiotic resistance, making the proteins involved in these systems potential therapeutic targets. Efficient methods for the profiling of HKs are currently lacking. For direct readout of HK activity, we sought to design a probe that enables detection of the phosphotransfer event; however, analysis of the phosphohistidine species is made difficult by the instability of the P-N bond. We anticipated that use of a γ-thiophosphorylated ATP analogue, which would yield a thiophosphorylated histidine intermediate, could overcome this challenge. We determined that the fluorophore-conjugated probe, BODIPY-FL-ATPγS, labels active HK proteins and is competitive for the ATP binding site. This activity-based probe provides a new strategy for analysis of TCSs and other HK-mediated processes and will facilitate both functional studies and inhibitor identification.
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Affiliation(s)
- Kaelyn E Wilke
- Department of Chemistry, Indiana University, Bloomington, 47405, United States
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