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Mei C, Shi Y, Wang Y, Qiu Z, Yang H. Termitidicoccus mucosus gen. nov. sp. nov. a novel Verrucomicrobiota species isolated from Reticulitermes chinensis gives insights of high adaptability of symbiotic bacteria to termite gut ecosystem. Res Microbiol 2024; 175:104173. [PMID: 38157920 DOI: 10.1016/j.resmic.2023.104173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 10/27/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
Verrucomicrobiota is widely distributed in various habitats including insect guts. It was found to be prevalent in almost all investigated termite guts, whereas their physiological functions are not very clear. In this study we characterized the physiological and genomic properties of Verrucomicrobiota strain TSB47T isolated from Reticulitermes chinensis. The cells of strain TSB47T were Gram-stain-negative, non-motile, and non-spore-forming coccoid with one or more warts. 16S rRNA gene analysis showed that the closest relatives of strain TSB47T were Opitutaceae strain TAV1 and Ereboglobus luteus Ho45T (98.3% and 95.4% sequence similarity, respectively). Whole genome analysis revealed that there are a large number of glycoside hydrolase genes, amino acid metabolism genes, complete Mo-Fe nitrogenase and Fe-Fe nitrogenase gene clusters, as well as cbb3-type cytochrome oxidase gene in the genome of strain TSB47T. Strain TSB47T grows well under anaerobic and microaerophilic conditions with a strong tolerance to oxygen. Physiological and genomic characters of strain TSB47T indicated its high adaptability to termite gut ecosystem. Based on phenotypic and phylogenetic evidence, we suggest strain TSB47T as the type species of a novel genus in the family Opitutaceae, for which the name Termitidicoccus mucosus sp. nov. is proposed. The type strain is TSB47T (CCTCC AB2022447T; KCTC 102044T).
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Affiliation(s)
- Cheng Mei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yu Shi
- College of Food and Biotechnology, Wuhan Institute of Design and Sciences, Wuhan 430079, PR China
| | - Yu Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Zhengyong Qiu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Hong Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
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Moon S, Ham S, Jeong J, Ku H, Kim H, Lee C. Temperature Matters: Bacterial Response to Temperature Change. J Microbiol 2023; 61:343-357. [PMID: 37010795 DOI: 10.1007/s12275-023-00031-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 04/04/2023]
Abstract
Temperature is one of the most important factors in all living organisms for survival. Being a unicellular organism, bacterium requires sensitive sensing and defense mechanisms to tolerate changes in temperature. During a temperature shift, the structure and composition of various cellular molecules including nucleic acids, proteins, and membranes are affected. In addition, numerous genes are induced during heat or cold shocks to overcome the cellular stresses, which are known as heat- and cold-shock proteins. In this review, we describe the cellular phenomena that occur with temperature change and bacterial responses from a molecular perspective, mainly in Escherichia coli.
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Affiliation(s)
- Seongjoon Moon
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Soojeong Ham
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Juwon Jeong
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Heechan Ku
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
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Biswas S, Dhaked HPS, Keightley A, Biswas I. Involvement of ClpE ATPase in Physiology of Streptococcus mutans. Microbiol Spectr 2021; 9:e0163021. [PMID: 34851151 PMCID: PMC8635124 DOI: 10.1128/spectrum.01630-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/01/2021] [Indexed: 11/25/2022] Open
Abstract
Streptococcus mutans, a dental pathogen, harbors at least three Clp ATPases (ClpC, ClpE, and ClpX) that form complexes with ClpP protease and participate in regulated proteolysis. Among these, the function of ClpE ATPase is poorly understood. We have utilized an isogenic clpE-deficient strain derived from S. mutans UA159 and evaluated the role of ClpE in cellular physiology. We found that loss of ClpE leads to increased susceptibility against thiol stress but not to oxidative and thermal stress. Furthermore, we found that the mutant displays altered tolerance against some antibiotics and altered biofilm formation. We performed a label-free proteomic analysis by comparing the mutant with the wild-type UA159 strain under nonstressed conditions and found that ClpE modulates a relatively limited proteome in the cell compared to the proteomes modulated by ClpX and ClpP. Nevertheless, we found that ClpE deficiency leads to an overabundance of some cell wall synthesis enzymes, ribosomal proteins, and an unknown protease encoded by SMU.2153. Our proteomic data strongly support some of the stress-related phenotypes that we observed. Our study emphasizes the significance of ClpE in the physiology of S. mutans. IMPORTANCE When bacteria encounter environmental stresses, the expression of various proteins collectively known as heat shock proteins is induced. These heat shock proteins are necessary for cell survival specifically under conditions that induce protein denaturation. A subset of heat shock proteins known as the Clp proteolytic complex is required for the degradation of the misfolded proteins in the cell. The Clp proteolytic complex contains an ATPase and a protease. A specific Clp ATPase, ClpE, is uniquely present in Gram-positive bacteria, including streptococci. Here, we have studied the functional role of the ClpE protein in Streptococcus mutans, a dental pathogen. Our results suggest that ClpE is required for survival under certain antibiotic exposure and stress conditions but not others. Our results demonstrate that loss of ClpE leads to a significantly altered cellular proteome, and the analysis of those changes suggests that ClpE's functions in S. mutans are different from its functions in other Gram-positive bacteria.
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Affiliation(s)
- Saswati Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Hemendra Pal Singh Dhaked
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Andrew Keightley
- Department of Ophthalmology, University of Missouri School of Medicine, Kansas City, Missouri, USA
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
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Influence of Low-Shear Modeled Microgravity on Heat Resistance, Membrane Fatty Acid Composition, and Heat Stress-Related Gene Expression in Escherichia coli O157:H7 ATCC 35150, ATCC 43889, ATCC 43890, and ATCC 43895. Appl Environ Microbiol 2016; 82:2893-2901. [PMID: 26944847 DOI: 10.1128/aem.00050-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/01/2016] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED We previously showed that modeled microgravity conditions alter the physiological characteristics of Escherichia coli O157:H7. To examine how microgravity conditions affect bacterial heat stress responses, D values, membrane fatty acid composition, and heat stress-related gene expression (clpB, dnaK, grpE, groES, htpG, htpX, ibpB, and rpoH), E. coli O157:H7 ATCC 35150, ATCC 43889, ATCC 43890, and ATCC 43895 were cultured under two different conditions: low-shear modeled microgravity (LSMMG, an analog of spaceflight conditions) and normal gravity (NG, Earth-like conditions). When 24-h cultures were heated to 55°C, cells cultured under LSMMG conditions showed reduced survival compared with cells cultured under NG conditions at all time points (P < 0.05). D values of all tested strains were lower after LSMMG culture than after NG culture. Fourteen of 37 fatty acids examined were present in the bacterial membrane: nine saturated fatty acids (SFA) and five unsaturated fatty acids (USFA). The USFA/SFA ratio, a measure of membrane fluidity, was higher under LSMMG conditions than under NG conditions. Compared with control cells grown under NG conditions, cells cultured under LSMMG conditions showed downregulation of eight heat stress-related genes (average, -1.9- to -3.7-fold). The results of this study indicate that in a simulated space environment, heat resistance of E. coli O157:H7 decreased, and this might be due to the synergistic effects of the increases in membrane fluidity and downregulated relevant heat stress genes. IMPORTANCE Microgravity is a major factor that represents the environmental conditions in space. Since infectious diseases are difficult to deal with in a space environment, comprehensive studies on the behavior of pathogenic bacteria under microgravity conditions are warranted. This study reports the changes in heat stress resistance of E. coli O157:H7, the severe foodborne pathogen, under conditions that mimic microgravity. The results provide scientific clues for further understanding of the bacterial response under the simulated microgravity conditions. It will contribute not only to the improvement of scientific knowledge in the academic fields but also ultimately to the development of a prevention strategy for bacterial disease in the space environment.
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Singh LK, Dhasmana N, Sajid A, Kumar P, Bhaduri A, Bharadwaj M, Gandotra S, Kalia VC, Das TK, Goel AK, Pomerantsev AP, Misra R, Gerth U, Leppla SH, Singh Y. clpC operon regulates cell architecture and sporulation in Bacillus anthracis. Environ Microbiol 2014; 17:855-65. [PMID: 24947607 DOI: 10.1111/1462-2920.12548] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/12/2014] [Indexed: 12/29/2022]
Abstract
The clpC operon is known to regulate several processes such as genetic competence, protein degradation and stress survival in bacteria. Here, we describe the role of clpC operon in Bacillus anthracis. We generated knockout strains of the clpC operon genes to investigate the impact of CtsR, McsA, McsB and ClpC deletion on essential processes of B. anthracis. We observed that growth, cell division, sporulation and germination were severely affected in mcsB and clpC deleted strains, while none of deletions affected toxin secretion. Growth defect in these strains was pronounced at elevated temperature. The growth pattern gets restored on complementation of mcsB and clpC in respective mutants. Electron microscopic examination revealed that mcsB and clpC deletion also causes defect in septum formation leading to cell elongation. These vegetative cell deformities were accompanied by inability of mutant strains to generate morphologically intact spores. Higher levels of polyhydroxybutyrate granules accumulation were also observed in these deletion strains, indicating a defect in sporulation process. Our results demonstrate, for the first time, the vital role played by McsB and ClpC in physiology of B. anthracis and open up further interest on this operon, which might be of importance to success of B. anthracis as pathogen.
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Affiliation(s)
- Lalit K Singh
- CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India
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Tripathy S, Sen R, Padhi SK, Mohanty S, Maiti NK. Upregulation of transcripts for metabolism in diverse environments is a shared response associated with survival and adaptation of Klebsiella pneumoniae in response to temperature extremes. Funct Integr Genomics 2014; 14:591-601. [PMID: 24890397 DOI: 10.1007/s10142-014-0382-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 05/17/2014] [Accepted: 05/26/2014] [Indexed: 11/28/2022]
Abstract
Klebsiella pneumoniae being ubiquitous in nature encounters wide differences in environmental condition. The organism's abundance in natural water reservoirs exposed to temperature variation forms the basis of its persistence and spread in the soil and other farm produce. In order to investigate the effect of temperature changes on the survival and adaptation of the bacteria, the transcriptional response of K. pneumoniae subjected to low (20 °C) and high (50 °C) temperature shock were executed using Applied Biosystems SOLiD platform. Approximately, 33 and 34% of protein coding genes expressed in response to 20 and 50 °C, respectively, displayed significant up- or downregulation (p < 0.01). Most of the significantly expressed transcripts mapped to metabolism, membrane transport, and cell motility were downregulated at 50 °C, except for protein folding, sorting, and degradation, suggesting that heat stress causes general downregulation of gene expression together with induction of heat shock proteins. While at 20 °C, the transcripts of carbohydrate, lipid, and amino acid metabolism were highly upregulated. Hypothetical proteins as well as canonical heat and cold shock proteins, viz. grpE, clpX, recA, and deaD were upregulated commonly in response to 20 and 50 °C. Significant upregulation of genes encoding ribosomal proteins at 20 and 50 °C possibly suggest their role in the survival of K. pneumoniae cells under low- and high-temperature stress.
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Affiliation(s)
- S Tripathy
- Microbiology unit, Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
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Arunasri K, Adil M, Khan PAA, Shivaji S. Global gene expression analysis of long-term stationary phase effects in E. coli K12 MG1655. PLoS One 2014; 9:e96701. [PMID: 24858919 PMCID: PMC4032248 DOI: 10.1371/journal.pone.0096701] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/11/2014] [Indexed: 12/27/2022] Open
Abstract
Global gene expression was monitored in long-term stationary phase (LSP) cells of E. coli K12 MG1655 and compared with stationary phase (SP) cells that were sub-cultured without prolonged delay to get an insight into the survival strategies of LSP cells. The experiments were carried out using both LB medium and LB supplemented with 10% of glycerol. In both the media the LSP cells showed decreased growth rate compared to SP cells. DNA microarray analysis of LSP cells in both the media resulted in the up- and down-regulation of several genes in LSP cells compared to their respective SP cells in the corresponding media. In LSP cells grown in LB 204 genes whereas cells grown in LB plus glycerol 321 genes were differentially regulated compared to the SP cells. Comparison of these differentially regulated genes indicated that irrespective of the medium used for growth in LSP cells expression of 95 genes (22 genes up-regulated and 73 down-regulated) were differentially regulated. These 95 genes could be associated with LSP status of the cells and are likely to influence survival and growth characteristics of LSP cells. This is indeed so since the up- and down-regulated genes include genes that protect E. coli LSP cells from stationary phase stress and genes that would help to recover from stress when transferred into fresh medium. The growth phenotype in LSP cells could be attributed to up-regulation of genes coding for insertion sequences that confer beneficial effects during starvation, genes coding for putative transposases and simultaneous down-regulation of genes coding for ribosomal protein synthesis, transport-related genes, non-coding RNA genes and metabolic genes. As yet we still do not know the role of several unknown genes and genes coding for hypothetical proteins which are either up- or down-regulated in LSP cells compared to SP cells.
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Affiliation(s)
| | - Mohammed Adil
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Sisinthy Shivaji
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- * E-mail:
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8
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Roberts LM, Davies JS, Sempowski GD, Frelinger JA. IFN-γ, but not IL-17A, is required for survival during secondary pulmonary Francisella tularensis Live Vaccine Stain infection. Vaccine 2014; 32:3595-603. [PMID: 24837506 DOI: 10.1016/j.vaccine.2014.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/02/2014] [Accepted: 05/01/2014] [Indexed: 01/01/2023]
Abstract
IL-17 and IFN-γ production by Th17 and Th1 cells, respectively, is critical for survival during primary respiratory infection with the pathogenic bacterium, Francisella tularensis Live Vaccine Strain (LVS). The importance, however, of these T cell subsets and their soluble mediators is not well understood during a secondary or memory response. We measured the number of CD4(+) T cells producing IFN-γ or IL-17 in the spleen and lungs of vaccinated mice on day four of the secondary response using intracellular cytokine staining in order to identify protective T cell subsets participating in the memory response. Few bacteria were present in spleens of vaccinated mice on day four and a T cell response was not observed. In the lung, where more bacteria were present, there was a robust Th1 response in vaccinated mice but Th17 cells were not present at higher numbers in vaccinated mice compared to unvaccinated mice. These data show that the lung is the dominant site of the secondary immune response and suggest that Th17 cells are not required for survival during secondary challenge. To further investigate the importance of IFN-γ and IL-17 during the secondary response to F. tularensis, we neutralized either IFN-γ or IL-17 in vivo using monoclonal antibody treatment. Vaccinated mice treated with anti-IFN-γ lost more weight and had higher bacterial burdens compared to vaccinated mice treated with isotype control antibody. In contrast, treatment with anti-IL-17A antibody did not alter weight loss profiles or bacterial burdens compared to mice treated with isotype control antibody. Together, these results suggested that IFN-γ is required during both primary and secondary respiratory F. tularensis infection. IL-17, on the other hand, is only critical during the primary response to respiratory F. tularensis but dispensable during the secondary response.
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Affiliation(s)
- Lydia M Roberts
- Department of Immunobiology, University of Arizona, 1656 E. Mabel Street, MRB 218,Tucson, AZ 85718, United States
| | - John S Davies
- Department of Immunobiology, University of Arizona, 1656 E. Mabel Street, MRB 218,Tucson, AZ 85718, United States
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, 909 S. LaSalle Street, Durham, NC 27710, United States
| | - Jeffrey A Frelinger
- Department of Immunobiology, University of Arizona, 1656 E. Mabel Street, MRB 218,Tucson, AZ 85718, United States.
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Desimone M, Weiß-Wichert C, Wagner E, Altenfeld U, Johanningmeier U. Immunochemical Studies on the Clp-protease in Chloroplasts: Evidence for the Formation of a CIpC/P Complex*. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1997.tb00634.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJH, Hranueli D, Cullum J, Long PF. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 2013; 14:509. [PMID: 23889801 PMCID: PMC3750612 DOI: 10.1186/1471-2164-14-509] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. DESCRIPTION Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. CONCLUSIONS We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
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Affiliation(s)
- Walter C Dunlap
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Damir Baranasic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Janko Diminic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ranko Gacesa
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Madeleine JH van Oppen
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
| | - Daslav Hranueli
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - John Cullum
- Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Paul F Long
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
- Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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A Clp/Hsp100 chaperone functions in Myxococcus xanthus sporulation and self-organization. J Bacteriol 2012; 194:1689-96. [PMID: 22287524 DOI: 10.1128/jb.06492-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Clp/Hsp100 proteins are chaperones that play a role in protein degradation and reactivation. In bacteria, they exhibit a high degree of pleiotropy, affecting both individual and multicellular phenotypes. In this article, we present the first characterization of a Clp/Hsp100 homolog in Myxococcus xanthus (MXAN_4832 gene locus). Deletion of MXAN_4832 causes defects in both swarming and aggregation related to cell motility and the production of fibrils, which are an important component of the extracellular matrix of a swarm. The deletion also affects the formation of myxospores during development, causing them to become sensitive to heat. The protein product of MXAN_4832 can act as a chaperone in vitro, providing biochemical evidence in support of our hypothesis that MXAN_4832 is a functional Clp/Hsp100 homolog. There are a total of 12 Clp/Hsp100 homologs in M. xanthus, including MXAN_4832, and, based on its mutational and biochemical characterization, they may well represent an important group.
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12
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Zhang Q, Huang Y, Wang H, Xu W, Liu L, Yin Y, Zhang X. The role of ClpP in protein expression of Streptococcus pneumoniae. Curr Microbiol 2011; 64:294-9. [PMID: 22198546 DOI: 10.1007/s00284-011-0060-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/25/2011] [Indexed: 01/07/2023]
Abstract
Previous reports suggest that ClpP proteolytic activity is important not only for cell physiology but also for regulation of virulence properties of Streptococcus pneumoniae (S. pneumoniae). In order to get a more comprehensive picture of the role of ClpP protease on protein expression in S. pneumoniae D39 and how it relates to physiology and virulence, a clpP mutant strain was constructed in S. pneumoniae D39, and global proteome expression was studied by 2-dimensional electrophoresis and matrix-assisted laser desorption-ionization-time of flight mass spectrometry. We report here that clpP deletion affects the expression of proteins which are involved in the general stress response, nucleotide metabolism, energy metabolism, and proteins metabolism. These provide clues for understanding the role of ClpP in the physiology and pathogenesis of pneumococcus.
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Affiliation(s)
- Qun Zhang
- Clinical Laboratories Center, Affiliated Children's Hospital, Chongqing Medical University, Chongqing, People's Republic of China
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Sianglum W, Srimanote P, Wonglumsom W, Kittiniyom K, Voravuthikunchai SP. Proteome analyses of cellular proteins in methicillin-resistant Staphylococcus aureus treated with rhodomyrtone, a novel antibiotic candidate. PLoS One 2011; 6:e16628. [PMID: 21326597 PMCID: PMC3033880 DOI: 10.1371/journal.pone.0016628] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 01/05/2011] [Indexed: 11/19/2022] Open
Abstract
The ethanolic extract from Rhodomyrtus tomentosa leaf exhibited good antibacterial activities against both methicillin-resistant Staphylococcus aureus (MRSA) and S. aureus ATCC 29213. Its minimal inhibitory concentration (MIC) values ranged from 31.25–62.5 µg/ml, and the minimal bactericidal concentration (MBC) was 250 µg/ml. Rhodomyrtone, an acylphloroglucinol derivative, was 62.5–125 times more potent at inhibiting the bacteria than the ethanolic extract, the MIC and MBC values were 0.5 µg/ml and 2 µg/ml, respectively. To provide insights into antibacterial mechanisms involved, the effects of rhodomyrtone on cellular protein expression of MRSA have been investigated using proteomic approaches. Proteome analyses revealed that rhodomyrtone at subinhibitory concentration (0.174 µg/ml) affected the expression of several major functional classes of whole cell proteins in MRSA. The identified proteins involve in cell wall biosynthesis and cell division, protein degradation, stress response and oxidative stress, cell surface antigen and virulence factor, and various metabolic pathways such as amino acid, carbohydrate, energy, lipid, and nucleotide metabolism. Transmission electron micrographs confirmed the effects of rhodomyrtone on morphological and ultrastructural alterations in the treated bacterial cells. Biological processes in cell wall biosynthesis and cell division were interrupted. Prominent changes including alterations in cell wall, abnormal septum formation, cellular disintegration, and cell lysis were observed. Unusual size and shape of staphylococcal cells were obviously noted in the treated MRSA. These pioneer findings on proteomic profiling and phenotypic features of rhodomyrtone-treated MRSA may resolve its antimicrobial mechanisms which could lead to the development of a new effective regimen for the treatment of MRSA infections.
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Affiliation(s)
- Wipawadee Sianglum
- Department of Microbiology and Natural Products Research Center, Faculty of Science, Prince of Songkla University, Songkla, Thailand
| | - Potjanee Srimanote
- Graduate Study, Faculty of Allied Health Sciences, Thammasat University, Pathumtanee, Thailand
| | - Wijit Wonglumsom
- Department of Clinical Microbiology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Kanokwan Kittiniyom
- Department of Clinical Microbiology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Supayang P. Voravuthikunchai
- Department of Microbiology and Natural Products Research Center, Faculty of Science, Prince of Songkla University, Songkla, Thailand
- * E-mail:
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14
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Bojer MS, Struve C, Ingmer H, Hansen DS, Krogfelt KA. Heat resistance mediated by a new plasmid encoded Clp ATPase, ClpK, as a possible novel mechanism for nosocomial persistence of Klebsiella pneumoniae. PLoS One 2010; 5:e15467. [PMID: 21085699 PMCID: PMC2976762 DOI: 10.1371/journal.pone.0015467] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 09/29/2010] [Indexed: 12/03/2022] Open
Abstract
Klebsiella pneumoniae is an important opportunistic pathogen and a frequent cause of nosocomial infections. We have characterized a K. pneumoniae strain responsible for a series of critical infections in an intensive care unit over a two-year period. The strain was found to be remarkably thermotolerant providing a conceivable explanation of its persistence in the hospital environment. This marked phenotype is mediated by a novel type of Clp ATPase, designated ClpK. The clpK gene is encoded by a conjugative plasmid and we find that the clpK gene alone renders an otherwise sensitive E. coli strain resistant to lethal heat shock. Furthermore, one third of a collection of nosocomial K. pneumoniae isolates carry clpK and exhibit a heat resistant phenotype. The discovery of ClpK as a plasmid encoded factor and its profound impact on thermal stress survival sheds new light on the biological relevance of Clp ATPases in acquired environmental fitness and highlights the challenges of mobile genetic elements in fighting nosocomial infections.
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Affiliation(s)
- Martin Saxtorph Bojer
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Carsten Struve
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
| | - Hanne Ingmer
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Dennis Schrøder Hansen
- Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark
- Department of Clinical Microbiology, Hillerød Hospital, Hillerød, Denmark
| | - Karen Angeliki Krogfelt
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
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15
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Wendler P, Saibil HR. Cryo electron microscopy structures of Hsp100 proteins: crowbars in or out? Biochem Cell Biol 2010; 88:89-96. [PMID: 20130682 DOI: 10.1139/o09-164] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Independent cryo electron microscopy (cryo-EM) studies of the closely related protein disaggregases ClpB and Hsp104 have resulted in two different models of subunit arrangement in the active hexamer. We compare the EM maps and resulting atomic structure fits, discuss their differences, and relate them to published experimental information in an attempt to discriminate between models. In addition, we present some general assessment criteria for low-resolution cryo-EM maps to offer non-structural biologists tools to evaluate these structures.
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Affiliation(s)
- Petra Wendler
- Department of Crystallography, Birkbeck College, Malet St., London WC1E 7HX, UK
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16
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Nian R, Kim DS, Tan L, Kim CW, Choe WS. Synergistic coordination of polyethylene glycol with ClpB/DnaKJE bichaperone for refolding of heat-denatured malate dehydrogenase. Biotechnol Prog 2009; 25:1078-85. [PMID: 19551876 DOI: 10.1002/btpr.175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The use of polyethylene glycol (PEG) as a refolding additive to a refolding cocktail comprising the molecular bichaperone ClpB and DnaKJE significantly enhances chaperone-mediated refolding of heat-denatured malate dehydrogenase (MDH). The critical factor to affect the refolding yield is the time point of introducing PEG to the refolding cocktail. The refolding efficiency reached approximately 90% only when PEG was added at the beginning of refolding reaction. The synergistic coordination of an inexpensive refolding additive PEG with the ClpB/DnaKJE bichaperone system may provide an economical route to further enhance the efficacy of ClpB/DnaKJE refolding cocktail approach, facilitating its implementation in large-scale refolding processes.
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Affiliation(s)
- Rui Nian
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
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17
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Nikodinovic-Runic J, Flanagan M, Hume AR, Cagney G, O'Connor KE. Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions. Microbiology (Reading) 2009; 155:3348-3361. [DOI: 10.1099/mic.0.031153-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas putida CA-3 is a styrene-degrading bacterium capable of accumulating medium-chain-length polyhydroxyalkanoate (mclPHA) when exposed to limiting concentrations of a nitrogen source in the growth medium. Using shotgun proteomics we analysed global proteome expression in P. putida CA-3 supplied with styrene as the sole carbon and energy source under N-limiting (condition permissive for mclPHA synthesis) and non-limiting (condition non-permissive for mclPHA accumulation) growth conditions in order to provide insight into the molecular response of P. putida CA-3 to limitation of nitrogen when grown on styrene. A total of 1761 proteins were identified with high confidence and the detected proteins could be assigned to functional groups including styrene degradation, energy, nucleotide metabolism, protein synthesis, transport, stress response and motility. Proteins involved in the upper and lower styrene degradation pathway were expressed throughout the 48 h growth period under both nitrogen limitation and excess. Proteins involved in polyhydroxyalkanoate (PHA) biosynthesis, nitrogen assimilation and amino acid transport, and outer membrane proteins were upregulated under nitrogen limitation. PHA accumulation and biosynthesis were only expressed under nitrogen limitation. Nitrogen assimilation proteins were detected on average at twofold higher amounts under nitrogen limitation. Expression of the branched-chain amino acid ABC transporter was up to 16-fold higher under nitrogen-limiting conditions. Branched chain amino acid uptake by nitrogen-limited cultures was also higher than that by non-limited cultures. Outer membrane lipoproteins were expressed at twofold higher levels under nitrogen limitation. This was confirmed by Western blotting (immunochemical detection) of cells grown under nitrogen limitation. Our study provides the first global description of protein expression changes during growth of any organism on styrene and accumulating mclPHA (nitrogen-limited growth).
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Affiliation(s)
- Jasmina Nikodinovic-Runic
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michelle Flanagan
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling R. Hume
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gerard Cagney
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin E. O'Connor
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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18
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Pinsach J, de Mas C, López-Santín J, Striedner G, Bayer K. Influence of process temperature on recombinant enzyme activity in Escherichia coli fed-batch cultures. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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20
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Meibom KL, Dubail I, Dupuis M, Barel M, Lenco J, Stulik J, Golovliov I, Sjöstedt A, Charbit A. The heat-shock protein ClpB of Francisella tularensis is involved in stress tolerance and is required for multiplication in target organs of infected mice. Mol Microbiol 2008; 67:1384-401. [PMID: 18284578 DOI: 10.1111/j.1365-2958.2008.06139.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Intracellular bacterial pathogens generally express chaperones such as Hsp100s during multiplication in host cells, allowing them to survive potentially hostile conditions. Francisella tularensis is a highly infectious bacterium causing the zoonotic disease tularaemia. The ability of F. tularensis to multiply and survive in macrophages is considered essential for its virulence. Although previous mutant screens in Francisella have identified the Hsp100 chaperone ClpB as important for intracellular survival, no detailed study has been performed. We demonstrate here that ClpB of F. tularensis live vaccine strain (LVS) is important for resistance to cellular stress. Promoter analysis shows that the transcriptional start is preceded by a sigma32-like promoter sequence and we demonstrate that expression of clpB is induced by heat shock. This indicates that expression of clpB is dependent on the heat-shock response mediated by sigma32, the only alternative sigma-factor present in Francisella. Our studies demonstrate that ClpB contributes to intracellular multiplication in vitro, but is not essential. However, ClpB is absolutely required for Francisella to replicate in target organs and induce disease in mice. Proteomic analysis of membrane-enriched fractions shows that five proteins are recovered at lower levels in the mutant strain. The crucial role of ClpB for in vivo persistence of Francisella may be linked to its assumed function in reactivation of aggregated proteins under in vivo stress conditions.
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Affiliation(s)
- Karin L Meibom
- Université Paris Descartes, Faculté de Médecine René Descartes, Paris F-75015, France.
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21
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Shih CJ, Lai MC. Analysis of the AAA+ chaperone clpB gene and stress-response expression in the halophilic methanogenic archaeon Methanohalophilus portucalensis. MICROBIOLOGY-SGM 2007; 153:2572-2583. [PMID: 17660421 DOI: 10.1099/mic.0.2007/007633-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ClpB is a member of the protein-disaggregating chaperone machinery belonging to the AAA+ superfamily. This paper describes a new clpB gene from the halophilic methanoarchaeon Methanohalophilus portucalensis, which has not been reported previously in Archaea. The partial sequence of clpB was identified from the investigation of the salt-stress response of Meh. portucalensis by differential-display RT-PCR (DDRT-PCR). Furthermore, the complete clpB sequence (2610 nt) and its upstream genes encoding the type I chaperonin GroEL/ES were obtained through inverse PCR, Southern hybridization and sequencing. The G+C ratio of clpB is 49.6 mol%. The predicted ClpB polypeptide contains 869 aa and possesses a long central domain and a predicted distinctly discontinuous coiled-coil motif separating two nucleotide-binding domains (NBD1 and NBD2). NBD1 has a single Walker A and two Walker B motifs and NBD2 has only one of each Walker motif, a characteristic of HSP100 proteins. Two repeated Clp amino-terminal domain motifs (ClpN) were identified in ClpB. The putative amino acid sequence shared 75.6 % identity with the predicted clpB homologue annotated as ATPase AAA-2 of Methanococcoides burtonii DSM 6242. Preliminary phylogenetic analysis clustered Meh. portucalensis ClpB (MpClpB) with the low G+C Gram-positive bacteria. Stress response analysis of clpB by Northern blotting showed up to 1.5-fold increased transcription levels in response to both salt up-shock (from 2.1 to 3.1 M NaCl) and down-shock (from 2.1 to 0.9 M NaCl). Both clpB and groEL/ES transcript levels increased when the temperature was shifted from 37 degrees C to 55 degrees C. Under heat stress clpB transcription was repressed by the addition of the osmolyte betaine (1 mM). In conclusion, a novel AAA+ chaperone clpB gene from a halophilic methanogen that responded to the fluctuations in temperature, salt concentration and betaine has been identified and analysed for the first time.
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MESH Headings
- Adaptation, Physiological/genetics
- Adenosine Triphosphatases/genetics
- Amino Acid Motifs
- Archaeal Proteins/biosynthesis
- Archaeal Proteins/genetics
- Base Composition
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Chaperonin 10/genetics
- Chaperonin 60/genetics
- Chaperonins/biosynthesis
- Chaperonins/genetics
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Archaeal
- Heat-Shock Proteins/biosynthesis
- Heat-Shock Proteins/genetics
- Hot Temperature
- Methanosarcinaceae/genetics
- Methanosarcinaceae/metabolism
- Molecular Sequence Data
- Phylogeny
- Protein Structure, Tertiary
- RNA, Messenger/biosynthesis
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sodium Chloride/metabolism
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Affiliation(s)
- Chao-Jen Shih
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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22
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Santos PM, Roma V, Benndorf D, von Bergen M, Harms H, Sá-Correia I. Mechanistic Insights Into the Global Response to Phenol in the Phenol-biodegrading StrainPseudomonassp. M1 Revealed by Quantitative Proteomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 11:233-51. [PMID: 17883337 DOI: 10.1089/omi.2007.0009] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Quantitative proteomics was used to gain insights into the global adaptive response to phenol in the phenol-biodegrading strain Pseudomonas sp. M1 when an alternative carbon source (pyruvate or succinate) is present. A phylogenetic analysis indicated Pseudomonas citronellolis as the closest species to the environmental strain M1, while P. aeruginosa is the closest species with the genome sequence available. After two-dimensional gel electrophoresis (2-DE) separation, protein identification by MS/MS ion search allowed the assignment of 87 out of 136 selected protein spots, 56 of which matched P. aeruginosa proteins present in databases. Coordinate induction of six enzymes of the phenol catabolic pathway in cells grown in pyruvate and phenol was revealed by expression proteomics. When succinate was the alternative carbon source (C-source), these catabolic proteins were not expressed. The global response of Pseudomonas sp. M1 to phenol-induced stress involved, among others, proteins of the energy metabolism, stress response proteins, and transport proteins. Quantitative and/or qualitative differences were registered in M1 response to different phenol concentrations or to identical phenol concentrations when cells were grown in pyruvate or succinate medium. They were attributed to differences observed in the specific growth rate, in the expression of phenol catabolism, and in resistance to phenol of Pseudomonas sp. M1 grown under different conditions.
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Affiliation(s)
- Pedro M Santos
- Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Lisboa, Portugal
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23
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De Dea Lindner J, Canchaya C, Zhang Z, Neviani E, Fitzgerald GF, van Sinderen D, Ventura M. Exploiting Bifidobacterium genomes: the molecular basis of stress response. Int J Food Microbiol 2007; 120:13-24. [PMID: 17629583 DOI: 10.1016/j.ijfoodmicro.2007.06.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 01/17/2007] [Indexed: 11/18/2022]
Abstract
Bifidobacteria represent important human commensals because of their perceived contribution to the maintenance of a balanced gastro intestinal tract (GIT). In recent years bifidobacteria have drawn much scientific attention because of their use as live bacteria in numerous food preparations with various health-related claims. For such reasons these bacteria constitute a growing area of interest with respect to genomics, molecular biology and genetics. This review will discuss the current knowledge on the molecular players that allow bifidobacteria to contend with heat-, osmotic-, bile-and acidic stress. Here, we describe the principal molecular chaperones involved in such stresses, as well as their use as phylogenetic markers for gaining insight into the evolutionary history of high G+C Gram positive bacteria.
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Affiliation(s)
- Juliano De Dea Lindner
- Department of Genetics, Anthropology and Evolution, University of Parma, parco Area delle Scienze 11a, 43100 Parma, Italy
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24
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KELLY ROBERTM, PEEPLES TONYAL, HALIO SHERYLB, RINKER KRISTINAD, DUFFAUD GUYD. Extremely Thermophilic Microorganisms. Ann N Y Acad Sci 2006. [DOI: 10.1111/j.1749-6632.1994.tb44393.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Lee JO, Jeong MJ, Kwon TR, Lee SK, Byun MO, Chung IM, Park SC. Pleurotus sajor-caju HSP100 complements a thermotolerance defect inhsp104 mutantSaccharomyces cerevisiae. J Biosci 2006; 31:223-33. [PMID: 16809855 DOI: 10.1007/bf02703915] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A putative Hsp100 gene was cloned from the fungus Pleurotus sajor-caju. mRNA expression studies demonstrated that this gene (designated PsHsp100) is highly induced by high temperature,induced less strongly by exposure to ethanol, and not induced by drought or salinity. Heat shock induction is detectable at 37 degrees C and reaches a maximum level at 42 degrees C. PsHsp100 mRNA levels sharply increased within 15 min of exposure to high temperature, and reached a maximum expression level at 2 h that was maintained for several hours. These results indicate that PsHsp100 could work at an early step in thermotolerance. To examine its function, PsHsp100 was transformed into a temperature-sensitive hsp104 deletion mutant Saccharomycetes cerivisiae strain to test the hypothesis that PsHSP100 is an protein that functions in thermotolerance. Overexpression of PsHSP100 complemented the thermotolerance defect of the hsp104 mutant yeast, allowing them being survive even at 50 degree C for 4 h. These results indicate that PsHSP100 protein is functional as an HSP100 in yeast and could play and important role in thermotolerance in P. sajor-caju.
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Affiliation(s)
- Jin-Ohk Lee
- National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea
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26
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Ventura M, Zhang Z, Cronin M, Canchaya C, Kenny JG, Fitzgerald GF, van Sinderen D. The ClgR protein regulates transcription of the clpP operon in Bifidobacterium breve UCC 2003. J Bacteriol 2006; 187:8411-26. [PMID: 16321946 PMCID: PMC1317013 DOI: 10.1128/jb.187.24.8411-8426.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five clp genes (clpC, clpB, clpP1, clpP2, and clpX), representing chaperone- and protease-encoding genes, were previously identified in Bifidobacterium breve UCC 2003. In the present study, we characterize the B. breve UCC 2003 clpP locus, which consists of two paralogous genes, designated clpP1 and clpP2, whose deduced protein products display significant similarity to characterized ClpP peptidases. Transcriptional analyses showed that the clpP1 and clpP2 genes are transcribed in response to moderate heat shock as a bicistronic unit with a single promoter. The role of a clgR homologue, known to control the regulation of clpP gene expression in Streptomyces lividans and Corynebacterium glutamicum, was investigated by gel mobility shift assays and DNase I footprint experiments. We show that ClgR, which in its purified form appears to exist as a dimer, requires a proteinaceous cofactor to assist in specific binding to a 30-bp region of the clpP promoter region. In pull-down experiments, a 56-kDa protein copurified with ClgR, providing evidence that the two proteins also interact in vivo and that the copurified protein represents the cofactor required for ClgR activity. The prediction of the ClgR three-dimensional structure provides further insights into the binding mode of this protein to the clpP1 promoter region and highlights the key amino acid residues believed to be involved in the protein-DNA interaction.
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MESH Headings
- Adaptation, Physiological
- Amino Acid Sequence
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- Base Sequence
- Bifidobacterium/genetics
- Bifidobacterium/metabolism
- Corynebacterium glutamicum/genetics
- DNA Footprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA-Binding Proteins/metabolism
- Dimerization
- Electrophoretic Mobility Shift Assay
- Gene Expression Regulation, Bacterial
- Genes, Regulator
- Hot Temperature
- Models, Molecular
- Molecular Sequence Data
- Operon
- Peptide Hydrolases/genetics
- Promoter Regions, Genetic
- Protein Binding
- RNA, Bacterial
- RNA, Messenger/analysis
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Streptomyces lividans/genetics
- Transcription, Genetic
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Affiliation(s)
- Marco Ventura
- Department of Genetics, Evolution and Anthropology, University of Parma, Parma, Italy.
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27
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Simão RCG, Susin MF, Alvarez-Martinez CE, Gomes SL. Cells lacking ClpB display a prolonged shutoff phase of the heat shock response in Caulobacter crescentus. Mol Microbiol 2005; 57:592-603. [PMID: 15978087 DOI: 10.1111/j.1365-2958.2005.04713.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The heat shock response in Caulobacter crescentus was previously shown to be positively regulated by the alternative sigma factor of RNA polymerase (RNAP) sigma(32), and negatively modulated by DnaK during the induction phase of the heat shock response but not during the recovery phase. In the present work we have investigated the involvement of the chaperone ClpB in the control of the heat shock response in C. crescentus. Data obtained indicated a role of ClpB in downregulation of heat shock protein (HSP) synthesis, as cells lacking this chaperone showed a prolonged shutoff phase of the heat shock response. In Escherichia coli, it has been proposed that the DnaK chaperone system switches transcription back to constitutively expressed genes through simultaneous reactivation of heat-aggregated sigma(70), as well as sequestration of sigma(32) away from RNAP. In C. crescentus, results obtained with a clpB null mutant indicate that ClpB could be involved in the reactivation of the major sigma factor sigma(73). In support of this hypothesis, we showed that transcription directed from sigma(73)-dependent promoters is not switched back in the clpB null mutant during the recovery phase. Furthermore, we observed that resolubilization of heat-aggregated sigma(73) is dependent on the presence of ClpB. Our findings also indicated that the absence of ClpB made cells more sensitive to heat shock and ethanol but not to other stresses, and unable to acquire thermotolerance.
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Affiliation(s)
- Rita C G Simão
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, C. P. 26077, São Paulo, SP, 05513-970, Brazil
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28
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Ventura M, Fitzgerald GF, van Sinderen D. Genetic and transcriptional organization of the clpC locus in Bifidobacterium breve UCC 2003. Appl Environ Microbiol 2005; 71:6282-91. [PMID: 16204550 PMCID: PMC1266005 DOI: 10.1128/aem.71.10.6282-6291.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A homolog of the clpC ATPase gene was identified in the genome of Bifidobacterium breve UCC 2003. Since this gene is very well conserved among eubacteria, we employed a PCR-based approach using primers based on highly conserved regions of ClpC proteins in order to identify homologous genes in other bifidobacterial species. Analysis by slot blot, Northern blot, and primer extension experiments showed that transcription of clpC is induced in response to moderate heat shock regimes. Moreover, we identified in the genome sequence of B. breve UCC 2003 a gene, designated clgR, which is predicted to encode a transcriptional regulator involved in regulation of the bifidobacterial clpC gene. The role of this protein in the regulation of B. breve UCC 2003 clpC gene expression was investigated by performing gel retardation experiments. We show that a biologically active ClgR molecule requires one or more proteinaceous coactivators to assist in the specific binding of ClgR to the clpC promoter region.
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Affiliation(s)
- Marco Ventura
- Department of Microbiology, National University of Ireland, Western Road, Cork, Ireland.
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29
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Camargos Oliveira J, Da Silva Castro N, Soares Felipe MS, Pereira M, De Almeida Soares CM. Comparative analysis of the cDNA encoding a ClpA homologue of Paracoccidioides brasiliensis. ACTA ACUST UNITED AC 2005; 109:707-16. [PMID: 16080393 DOI: 10.1017/s0953756205002789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A cDNA encoding a chaperone ClpA homologue of Paracoccidioides brasiliensis was isolated and characterized. The ClpA belongs to a group of ClpATPAses proteins, which are highly conserved, and include several heat inducible molecular chaperones. In this study, a 2879 bp cDNA designated as Pbclpa was obtained which encodes a predicted protein of 927 amino acids. Characteristic consensus motifs of the ClpATPases family are present. The PbClpA middle region was compared to other related ClpA and ClpB proteins from fungi and bacteria. Comparative analysis demonstrated in the middle region the presence of a heptad repeat sequence, characteristic of ClpBs from prokaryotes and fungi, which are absent in ClpAs from prokaryotes but were present in all described fungal ClpAs. Our comparative analysis reveals that one of the criteria typically used to distinguish the prokaryotic subfamilies ClpA and ClpB, the size of the middle sequence, may not be useful in fungi. Phylogenetic analyses were performed with the complete sequences of ClpAs from fungi and bacteria and with the middle regions of those ClpAs present at NCBI and Pfam databases. Our results indicated that both types of analysis can be useful as a tool in the determination of phylogenetic relationships.
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Affiliation(s)
- Juliana Camargos Oliveira
- Laboratório de Biologia Molecular, ICB, Universidade Federal de Goiás, 74.001-970, Goiânia, Goiás, Brazil
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30
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Ventura M, Kenny JG, Zhang Z, Fitzgerald GF, van Sinderen D. The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction. Microbiology (Reading) 2005; 151:2861-2872. [PMID: 16151199 DOI: 10.1099/mic.0.28176-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The so-called clp genes, which encode components of the Clp proteolytic complex, are widespread among bacteria. The Bifidobacterium breve UCC 2003 genome contains a clpB gene with significant homology to predicted clpB genes from other members of the Actinobacteridae group. The heat- and osmotic-inducibility of the B. breve UCC 2003 clpB homologue was verified by slot-blot analysis, while Northern blot and primer extension analyses showed that the clpB gene is transcribed as a monocistronic unit with a single promoter. The role of a hspR homologue, known to control the regulation of clpB and dnaK gene expression in other high G+C content bacteria was investigated by gel mobility shift assays. Moreover the predicted 3D structure of HspR provides further insight into the binding mode of this protein to the clpB promoter region, and highlights the key amino acid residues believed to be involved in the protein–DNA interaction.
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Affiliation(s)
- Marco Ventura
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - John G Kenny
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Ziding Zhang
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Gerald F Fitzgerald
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
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31
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Nag S, Das S, Chaudhuri K. In vivo induced clpB1 gene of Vibrio cholerae is involved in different stress responses and affects in vivo cholera toxin production. Biochem Biophys Res Commun 2005; 331:1365-73. [PMID: 15883026 DOI: 10.1016/j.bbrc.2005.04.052] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Indexed: 11/17/2022]
Abstract
Previously in global transcription profile approach one of the cosmid clones of Vibrio cholerae containing the genes pnuC, icmF, and a fragment of clpB2 showed higher expression in V. cholerae grown inside rabbit intestine. In the present report, both the stress responsive clpB genes of V. cholerae O395 were cloned, clpB1 from chromosome I and clpB2 present in chromosome II. From the Northern blot hybridization it was observed that the level of transcription of clpB2 was very low which could be due to the weak promoter strength of clpB2 as predicted in silico. The deduced amino acid sequence showed that clpB1 possesses features typical of the ClpB ATPase family of stress response proteins. The clpB1 gene showed about three times higher expression under in vivo condition than in vitro. Increased expression of clpB1 gene was also observed at high temperature, high salt, and in the condition mimicking human intestine viz., 37 degrees C, pH 8.5, 300 mM NaCl, which is known to be the repressive condition for ToxR, the global transcriptional regulator of virulence in V. cholerae. The clpB1 insertion mutant showed increased sensitivity towards high temperature, oxidative stress, and acid pH. ClpB1 also conferred thermotolerance to V. cholerae. These effects could be reversed by complementation. Although clpB1 appeared not to be under the control of virulence regulatory cascade of V. cholerae, the CT production was reduced in clpB1 mutant when tested in vivo in an infant mice model.
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Affiliation(s)
- Sanjay Nag
- Human Genetics and Genomics Group, Indian Institute of Chemical Biology, Jadavpur, Calcutta 700 032, India
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32
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Ibrahim YM, Kerr AR, Silva NA, Mitchell TJ. Contribution of the ATP-dependent protease ClpCP to the autolysis and virulence of Streptococcus pneumoniae. Infect Immun 2005; 73:730-40. [PMID: 15664911 PMCID: PMC546992 DOI: 10.1128/iai.73.2.730-740.2005] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ATP-dependent caseinolytic proteases (Clp) are fundamental for stress tolerance and virulence in many pathogenic bacteria. The role of ClpC in the autolysis and virulence of Streptococcus pneumoniae is controversial. In this study, we tested the role of ClpC in a number of S. pneumoniae strains and found that the contribution of ClpC to autolysis is strain dependent. ClpC is required for the release of autolysin A and pneumolysin in serotype 2 S. pneumoniae strain D39. In vivo, ClpC is required for the growth of the pneumococcus in the lungs and blood in a murine model of disease, but it does not affect the overall outcome of pneumococcal disease. We also report the requirement of ClpP for the growth at elevated temperature and virulence of serotype 4 strain TIGR4 and confirm its contribution to the thermotolerance, oxidative stress resistance, and virulence of D39.
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Affiliation(s)
- Yasser Musa Ibrahim
- Division of Infection and Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12-8QQ, Scotland, United Kingdom
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33
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Nascimento ALTO, Verjovski-Almeida S, Van Sluys MA, Monteiro-Vitorello CB, Camargo LEA, Digiampietri LA, Harstkeerl RA, Ho PL, Marques MV, Oliveira MC, Setubal JC, Haake DA, Martins EAL. Genome features of Leptospira interrogans serovar Copenhageni. Braz J Med Biol Res 2004; 37:459-77. [PMID: 15064809 PMCID: PMC2666282 DOI: 10.1590/s0100-879x2004000400003] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report novel features of the genome sequence of Leptospira interrogans serovar Copenhageni, a highly invasive spirochete. Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in mammals. Genomic sequence analysis reveals the presence of a competent transport system with 13 families of genes encoding for major transporters including a three-member component efflux system compatible with the long-term survival of this organism. The leptospiral genome contains a broad array of genes encoding regulatory system, signal transduction and methyl-accepting chemotaxis proteins, reflecting the organism's ability to respond to diverse environmental stimuli. The identification of a complete set of genes encoding the enzymes for the cobalamin biosynthetic pathway and the novel coding genes related to lipopolysaccharide biosynthesis should bring new light to the study of Leptospira physiology. Genes related to toxins, lipoproteins and several surface-exposed proteins may facilitate a better understanding of the Leptospira pathogenesis and may serve as potential candidates for vaccine.
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34
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Chastanet A, Derre I, Nair S, Msadek T. clpB, a novel member of the Listeria monocytogenes CtsR regulon, is involved in virulence but not in general stress tolerance. J Bacteriol 2004; 186:1165-74. [PMID: 14762012 PMCID: PMC344206 DOI: 10.1128/jb.186.4.1165-1174.2004] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clp-HSP100 ATPases are a widespread family of ubiquitous proteins that occur in both prokaryotes and eukaryotes and play important roles in the folding of newly synthesized proteins and refolding of aggregated proteins. They have also been shown to participate in the virulence of several pathogens, including Listeria monocytogenes. Here, we describe a member of the Clp-HSP100 family of L. monocytogenes that harbors all the characteristics of the ClpB subclass, which is absent in the closely related gram-positive model organism, Bacillus subtilis. Transcriptional analysis of clpB revealed a heat shock-inducible sigma(A)-type promoter. Potential binding sites for the CtsR regulator of stress response were identified in the promoter region. In vivo and in vitro approaches were used to show that expression of clpB is repressed by CtsR, a finding indicating that clpB is a novel member of the L. monocytogenes CtsR regulon. We showed that ClpB is involved in the pathogenicity of L. monocytogenes since the DeltaclpB mutant is significantly affected by virulence in a murine model of infection; we also demonstrate that this effect is apparently not due to a defect in general stress resistance. Indeed, ClpB is not involved in tolerance to heat, salt, detergent, puromycin, or cold stress, even though its synthesis is inducible by heat shock. However, ClpB was shown to play a role in induced thermotolerance, allowing increased resistance of L. monocytogenes to lethal temperatures. This work gives the first example of a clpB gene directly controlled by CtsR and describes the first role for a ClpB protein in induced thermotolerance and virulence in a gram-positive organism.
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Affiliation(s)
- Arnaud Chastanet
- Unité de Biochimie Microbienne, Institut Pasteur, CNRS URA 2172, 75724 Paris Cedex 15, France
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35
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Nair S, Poyart C, Beretti JL, Veiga-Fernandes H, Berche P, Trieu-Cuot P. Role of the Streptococcus agalactiae ClpP serine protease in heat-induced stress defence and growth arrest. MICROBIOLOGY (READING, ENGLAND) 2003; 149:407-417. [PMID: 12624203 DOI: 10.1099/mic.0.25783-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The main causes of microbial death after heat exposure are not well understood. Here, it is shown that the heat-shock protein ClpP plays a major role in heat-induced growth arrest in Streptococcus agalactiae. A mutant lacking the ClpP protease was more sensitive to the inhibitory effects of heat, salt and oxidative stress than the isogenic wild-type strain. During growth arrest, this mutant displayed important modifications of its total protein content, including a decreased level of essential metabolic enzymes such as the alcohol dehydrogenase. Analysis of protein carbonylation demonstrated that the ClpP protease plays a role in preventing accelerated protein oxidation. Higher levels of oxidized DnaK, a key modulator of the heat-shock regulon, were observed in the ClpP mutant and these were increased following heat shock. Accumulation of oxidized/inactivated DnaK might explain why the ClpP mutant was unable to properly synthesize DNA and proteins, and why it exhibited an aberrant cell morphology. Even though ClpP plays a minor role in the virulence of S. agalactiae in a murine infection model, the data presented here point to the importance of ClpP in oxidative stress defence in preventing heat-induced cell alterations.
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Affiliation(s)
- Shamila Nair
- INSERM U411, Faculté de Médecine Necker, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
| | - Claire Poyart
- Laboratoire Mixte Pasteur-Necker de Recherche sur les Streptocoques et Streptococcies, Faculté de Médecine Necker, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
- INSERM U411, Faculté de Médecine Necker, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
| | - Jean-Luc Beretti
- INSERM U411, Faculté de Médecine Necker, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
| | | | - Patrick Berche
- INSERM U411, Faculté de Médecine Necker, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
| | - Patrick Trieu-Cuot
- Laboratoire Mixte Pasteur-Necker de Recherche sur les Streptocoques et Streptococcies, Faculté de Médecine Necker, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
- INSERM U411, Faculté de Médecine Necker, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
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36
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Lemos JAC, Burne RA. Regulation and Physiological Significance of ClpC and ClpP in Streptococcus mutans. J Bacteriol 2002; 184:6357-66. [PMID: 12399506 PMCID: PMC151938 DOI: 10.1128/jb.184.22.6357-6366.2002] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tolerance of environmental stress, especially low pH, by Streptococcus mutans is central to the virulence of this organism. The Clp ATPases are implicated in the tolerance of, and regulation of the response to, stresses by virtue of their protein reactivation and remodeling activities and their capacity to target misfolded proteins for degradation by the ClpP peptidase. The purpose of this study was to dissect the role of selected clp genes in the stress responses of S. mutans, with a particular focus on acid tolerance and adaptation. Homologues of the clpB, clpC, clpE, clpL, clpX, and clpP genes were identified in the S. mutans genome. The expression of clpC and clpP, which were chosen as the focus of this study, was induced at low pH and at growth above 40 degrees C. Inactivation of ctsR, the first of two genes in the clpC operon, demonstrated that CtsR acts as a repressor of clp and groES-EL gene expression. Strains lacking ClpP, but not strains lacking ClpC, were impaired in their ability to grow under stress-inducing conditions, formed long chains, aggregated in culture, had reduced genetic transformation efficiencies, and had a reduced capacity to form biofilms. Comparison of two-dimensional protein gels from wild-type cells and the ctsR and clpP mutants revealed many changes in the protein expression patterns. In particular, in the clpP mutant, there was an increased production of GroESL and DnaK, suggesting that cells were stressed, probably due to the accumulation of denatured proteins.
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Affiliation(s)
- José A C Lemos
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville 32610, USA
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37
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Glaser P, Rusniok C, Buchrieser C, Chevalier F, Frangeul L, Msadek T, Zouine M, Couvé E, Lalioui L, Poyart C, Trieu-Cuot P, Kunst F. Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease. Mol Microbiol 2002; 45:1499-513. [PMID: 12354221 DOI: 10.1046/j.1365-2958.2002.03126.x] [Citation(s) in RCA: 350] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Streptococcus agalactiae is a commensal bacterium colonizing the intestinal tract of a significant proportion of the human population. However, it is also a pathogen which is the leading cause of invasive infections in neonates and causes septicaemia, meningitis and pneumonia. We sequenced the genome of the serogroup III strain NEM316, responsible for a fatal case of septicaemia. The genome is 2 211 485 base pairs long and contains 2118 protein coding genes. Fifty-five per cent of the predicted genes have an ortholog in the Streptococcus pyogenes genome, representing a conserved backbone between these two streptococci. Among the genes in S. agalactiae that lack an ortholog in S. pyogenes, 50% are clustered within 14 islands. These islands contain known and putative virulence genes, mostly encoding surface proteins as well as a number of genes related to mobile elements. Some of these islands could therefore be considered as pathogenicity islands. Compared with other pathogenic streptococci, S. agalactiae shows the unique feature that pathogenicity islands may have an important role in virulence acquisition and in genetic diversity.
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Affiliation(s)
- Philippe Glaser
- Laboratoire de Génomique des Microorganismes Pathogènes, Institute Pasteur, Paris, France
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38
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Hoskins JR, Sharma S, Sathyanarayana BK, Wickner S. Clp ATPases and their role in protein unfolding and degradation. ADVANCES IN PROTEIN CHEMISTRY 2002; 59:413-29. [PMID: 11868279 DOI: 10.1016/s0065-3233(01)59013-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Although much has been learned about the structure and function of Clp chaperones and their role in proteolysis, the mechanism of protein unfolding catalyzed by Clp ATPases and the mechanism of translocation of the unfolded proteins from Clp ATPases to partner proteases remain unsolved puzzles. However, models in which mechanical force is used to destabilize the structure of the substrate in a processive and directional manner are probable. It also seems likely that when ClpA ATPases are associated with proteases, unfolding is coupled to extrusion of the unfolded protein into the proteolytic cavity. In summary, it is anticipated that the large family of Clp ATPases will accomplish their many important cellular functions by similar mechanisms and what has been learned by studying the prokaryotic members reviewed here will shed a great deal of light on all members of the family.
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Affiliation(s)
- J R Hoskins
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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39
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Jesuino RSA, Azevedo MO, Felipe MSS, Pereira M, De Almeida Soares CM. Characterization of a chaperone ClpB homologue of Paracoccidioides brasiliensis. Yeast 2002; 19:963-72. [PMID: 12125053 DOI: 10.1002/yea.888] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the cloning and sequence analysis of a genomic clone encoding a Paracoccidioides brasiliensis ClpB chaperone homologue (PbClpB). The clpb gene was identified in a lambda Dash II library. Sequencing of Pbclpb revealed a long open reading frame capable of encoding a 792 amino acid, 87.9 kDa protein, pI of 5.34. The predicted polypeptide contains several consensus motifs of the ClpB proteins. Canonical sequences such as two putative nucleotide-binding sites, chaperonins ClpA/B signatures and highly conserved casein kinase phosphorylation domains are present. ClpB is 69% to 49% identical to members of the ClpB family from several organisms from prokaryotes to eukaryotes. The transcript of PbclpB was detected as a mRNA species of 3.0 kb, preferentially expressed in the yeast parasitic phase of the fungus. A 89 kDa protein was also detected in yeast cells of P. brasiliensis.
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Affiliation(s)
- Rosália S A Jesuino
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, ICB II, Campus II, 74001-970, Goiânia, Goiás, Brazil
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40
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Rajagopal S, Sudarsan N, Nickerson KW. Sodium dodecyl sulfate hypersensitivity of clpP and clpB mutants of Escherichia coli. Appl Environ Microbiol 2002; 68:4117-21. [PMID: 12147516 PMCID: PMC124035 DOI: 10.1128/aem.68.8.4117-4121.2002] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the hypersensitivity of clpP and clpB mutants of Escherichia coli to sodium dodecyl sulfate (SDS). Both wild-type E. coli MC4100 and lon mutants grew in the presence of 10% SDS, whereas isogenic clpP and clpB single mutants could not grow above 0.5% SDS and clpA and clpX single mutants could not grow above 5.0% SDS. For wild-type E. coli, cellular ClpP levels as determined by Western immunoblot analysis increased ca. sixfold as the levels of added SDS increased from 0 to 2%. Capsular colanic acid, measured as uronic acid, increased ca. sixfold as the levels of added SDS increased from 2 to 10%. Based on these findings, 3 of the 19 previously identified SDS shock proteins (M. Adamowicz, P. M. Kelley, and K. W. Nickerson, J. Bacteriol. 173:229-233, 1991) are tentatively identified as ClpP, ClpX, and ClpB.
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Affiliation(s)
- Soumitra Rajagopal
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
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41
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Narberhaus F. Alpha-crystallin-type heat shock proteins: socializing minichaperones in the context of a multichaperone network. Microbiol Mol Biol Rev 2002; 66:64-93; table of contents. [PMID: 11875128 PMCID: PMC120782 DOI: 10.1128/mmbr.66.1.64-93.2002] [Citation(s) in RCA: 399] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alpha-crystallins were originally recognized as proteins contributing to the transparency of the mammalian eye lens. Subsequently, they have been found in many, but not all, members of the Archaea, Bacteria, and Eucarya. Most members of the diverse alpha-crystallin family have four common structural and functional features: (i) a small monomeric molecular mass between 12 and 43 kDa; (ii) the formation of large oligomeric complexes; (iii) the presence of a moderately conserved central region, the so-called alpha-crystallin domain; and (iv) molecular chaperone activity. Since alpha-crystallins are induced by a temperature upshift in many organisms, they are often referred to as small heat shock proteins (sHsps) or, more accurately, alpha-Hsps. Alpha-crystallins are integrated into a highly flexible and synergistic multichaperone network evolved to secure protein quality control in the cell. Their chaperone activity is limited to the binding of unfolding intermediates in order to protect them from irreversible aggregation. Productive release and refolding of captured proteins into the native state requires close cooperation with other cellular chaperones. In addition, alpha-Hsps seem to play an important role in membrane stabilization. The review compiles information on the abundance, sequence conservation, regulation, structure, and function of alpha-Hsps with an emphasis on the microbial members of this chaperone family.
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Affiliation(s)
- Franz Narberhaus
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule, CH-8092 Zürich, Switzerland.
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42
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Abstract
Recently, the Escherichia coli umuD and umuC genes have been shown to encode E. coli's fifth DNA polymerase, pol V (consisting of a heterotrimer of UmuD'(2)C). The main function of pol V appears to be the bypass of DNA lesions that would otherwise block replication by pols I-IV. This process is error-prone and leads to a striking increase in mutations at sites of DNA damage. While the enzymatic properties of pol V are now only beginning to be fully appreciated, a great deal is known about how E. coli regulates the intracellular levels of the Umu proteins so that the lesion-bypassing activity of pol V is available to help cells survive the deleterious consequences of DNA damage, yet keeps any unwarranted activity on undamaged templates to a minimum. Our review summarizes the multiple restrictions imposed upon pol V, so as to limit its activity in vivo and, in particular, highlights the pivotal role that the N-terminal tail of UmuD plays in regulating SOS mutagenesis.
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Affiliation(s)
- Martín Gonzalez
- Department of Biology, University of Colorado-Denver, Denver, CO, USA
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43
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Abstract
Cytoplasmic proteolysis is an indispensable process for proper function of a cell. Degradation of many intracellular proteins is initiated by ATP-dependent proteinases, which are involved in the regulation of the level of proteins with short half-lives. In addition, they remove many damaged and abnormal proteins and thus play also an important role during stress. ATP-dependent proteinases are large multi-subunit assemblies composed of proteolytic core domains and ATPase-containing regulatory domains on a single polypeptide chain or on distinct subunits, which can act as molecular chaperones. This review briefly summarizes the data about four main groups of these proteinases in bacteria (i.e. Lon, Clp family, HslUV and FtsH) and characterizes their structure, mechanism of action and properties.
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Affiliation(s)
- O Hlavácek
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia
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44
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Hill C, Cotter PD, Sleator RD, Gahan CG. Bacterial stress response in Listeria monocytogenes: jumping the hurdles imposed by minimal processing. Int Dairy J 2002. [DOI: 10.1016/s0958-6946(01)00125-x] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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45
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Borezée E, Pellegrini E, Beretti JL, Berche P. SvpA, a novel surface virulence-associated protein required for intracellular survival of Listeria monocytogenes. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2913-23. [PMID: 11700342 DOI: 10.1099/00221287-147-11-2913] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A previously unknown protein, designated SvpA (surface virulence-associated protein) and implicated in the virulence of the intracellular pathogen Listeria monocytogenes, was identified. This 64 kDa protein, encoded by svpA, is both secreted in culture supernatants and surface-exposed, as shown by immunogold labelling of whole bacteria with an anti-SvpA antibody. Analysis of the peptide sequence revealed that SvpA contains a leader peptide, a predicted C-terminal transmembrane region and a positively charged tail resembling that of the surface protein ActA, suggesting that SvpA might partially reassociate with the bacterial surface by its C-terminal membrane anchor. An allelic mutant was constructed by disrupting svpA in the wild-type strain LO28. The virulence of this mutant was strongly attenuated in the mouse, with a 2 log decrease in the LD50 and restricted bacterial growth in organs as compared to the wild-type strain. This reduced virulence was not related either to a loss of adherence or to a lower expression of known virulence factors, which remained unaffected in the svpA mutant. It was caused by a restriction of intracellular growth of mutant bacteria. By following the intracellular behaviour of bacteria within bone-marrow-derived macrophages by confocal and electron microscopy studies, it was found that most svpA mutant bacteria remained confined within phagosomes, in contrast to wild-type bacteria which rapidly escaped to the cytoplasm. The regulation of svpA was independent of PrfA, the transcriptional activator of virulence genes in L. monocytogenes. In fact, SvpA was down-regulated by MecA, ClpC and ClpP, which are highly homologous to proteins of Bacillus subtilis forming a regulatory complex controlling the competence state of this saprophyte. The results indicate that: (i) SvpA is a novel factor involved in the virulence of L. monocytogenes, promoting bacterial escape from phagosomes of macrophages; (ii) SvpA is, at least partially, associated with the surface of bacteria; and (iii) SvpA is PrfA-independent and controlled by a MecA-dependent regulatory network.
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Affiliation(s)
- E Borezée
- Laboratoire de Microbiologie, Institut National de la Santé et de la Recherche Médicale U411, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
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46
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Forng RY, Champagne C, Simpson W, Genco CA. Environmental cues and gene expression in Porphyromonas gingivalis and Actinobacillus actinomycetemcomitans. Oral Dis 2001; 6:351-65. [PMID: 11355267 DOI: 10.1111/j.1601-0825.2000.tb00127.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Microorganisms typically adapt to environmental cues by turning on and off the expression of virulence genes which, in turn, allows for optimal growth and survival within different environmental niches. This adaptation strategy includes sensing and responding to changes in nutrients, pH, temperature, oxygen tension, redox potential, microbial flora, and osmolarity. For a bacterium to adhere to, penetrate, replicate in, and colonize host cells, it is critical that virulence genes are expressed during certain periods of the infection process. Thus, throughout the different stages of an infection, different sets of virulence factors are turned on and off in response to different environmental signals, allowing the bacterium to effectively adapt to its varying niche. In this review, we focus on the regulation of virulence gene expression in two pathogens which have been implicated as major etiological agents in adult and juvenile periodontal diseases: Porphyromonas gingivalis and Actinobacillus actinomycetemcomitans. Understanding the mechanisms of virulence gene expression in response to the local environment of the host will provide crucial information in the development of effective treatments targeted at eradication of these periodontal disease pathogens.
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Affiliation(s)
- R Y Forng
- Department of Plasma Derivatives, Jerome H. Holland Laboratory, American Red Cross, Rockville, MD 20855, USA
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47
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Vázquez-Boland JA, Kuhn M, Berche P, Chakraborty T, Domínguez-Bernal G, Goebel W, González-Zorn B, Wehland J, Kreft J. Listeria pathogenesis and molecular virulence determinants. Clin Microbiol Rev 2001; 14:584-640. [PMID: 11432815 PMCID: PMC88991 DOI: 10.1128/cmr.14.3.584-640.2001] [Citation(s) in RCA: 1484] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gram-positive bacterium Listeria monocytogenes is the causative agent of listeriosis, a highly fatal opportunistic foodborne infection. Pregnant women, neonates, the elderly, and debilitated or immunocompromised patients in general are predominantly affected, although the disease can also develop in normal individuals. Clinical manifestations of invasive listeriosis are usually severe and include abortion, sepsis, and meningoencephalitis. Listeriosis can also manifest as a febrile gastroenteritis syndrome. In addition to humans, L. monocytogenes affects many vertebrate species, including birds. Listeria ivanovii, a second pathogenic species of the genus, is specific for ruminants. Our current view of the pathophysiology of listeriosis derives largely from studies with the mouse infection model. Pathogenic listeriae enter the host primarily through the intestine. The liver is thought to be their first target organ after intestinal translocation. In the liver, listeriae actively multiply until the infection is controlled by a cell-mediated immune response. This initial, subclinical step of listeriosis is thought to be common due to the frequent presence of pathogenic L. monocytogenes in food. In normal individuals, the continual exposure to listerial antigens probably contributes to the maintenance of anti-Listeria memory T cells. However, in debilitated and immunocompromised patients, the unrestricted proliferation of listeriae in the liver may result in prolonged low-level bacteremia, leading to invasion of the preferred secondary target organs (the brain and the gravid uterus) and to overt clinical disease. L. monocytogenes and L. ivanovii are facultative intracellular parasites able to survive in macrophages and to invade a variety of normally nonphagocytic cells, such as epithelial cells, hepatocytes, and endothelial cells. In all these cell types, pathogenic listeriae go through an intracellular life cycle involving early escape from the phagocytic vacuole, rapid intracytoplasmic multiplication, bacterially induced actin-based motility, and direct spread to neighboring cells, in which they reinitiate the cycle. In this way, listeriae disseminate in host tissues sheltered from the humoral arm of the immune system. Over the last 15 years, a number of virulence factors involved in key steps of this intracellular life cycle have been identified. This review describes in detail the molecular determinants of Listeria virulence and their mechanism of action and summarizes the current knowledge on the pathophysiology of listeriosis and the cell biology and host cell responses to Listeria infection. This article provides an updated perspective of the development of our understanding of Listeria pathogenesis from the first molecular genetic analyses of virulence mechanisms reported in 1985 until the start of the genomic era of Listeria research.
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Affiliation(s)
- J A Vázquez-Boland
- Grupo de Patogénesis Molecular Bacteriana, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.
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Banecki B, Wawrzynow A, Puzewicz J, Georgopoulos C, Zylicz M. Structure-function analysis of the zinc-binding region of the Clpx molecular chaperone. J Biol Chem 2001; 276:18843-8. [PMID: 11278349 DOI: 10.1074/jbc.m007507200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C(4) type. The ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. Using an improved purification procedure we show that the ClpX protein is a metalloprotein complexed with Zn(II) cations. Contrary to other Hsp100 family members, ClpXZn(II) exists in an oligomeric form even in the absence of ATP. We show that the single ATP-binding site of ClpX is required for a variety of tasks, namely, the stabilization of the ClpXZn(II) oligomeric structure, binding to ClpP, and the ClpXP-dependent proteolysis of the lambdaO replication protein. Release of Zn(II) from ClpX protein affects the ability of ClpX to bind ATP. ClpX, free of Zn(II), cannot oligomerize, bind to ClpP, or participate in ClpXP-dependent proteolysis. We also show that ClpXDeltaCys, a mutant protein whose four cysteine residues at the putative zinc finger motif have been replaced by serine, behaves in similar fashion as wild type ClpX protein whose Zn(II) has been released either by denaturation and renaturation, or chemically by p-hydroxymercuriphenylsulfonic acid.
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Affiliation(s)
- B Banecki
- Department of Molecular and Cellular Biology, Faculty of Biotechnology, University of Gdansk, 80-822 Gdansk, Kladki 24, Poland
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Guzman-Verri C, Chaves-Olarte E, García F, Arvidson S, Moreno E. In vivo proteolytic degradation of the Escherichia coli acyltransferase HlyC. J Biol Chem 2001; 276:16660-6. [PMID: 11278516 DOI: 10.1074/jbc.m009514200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli hemolysin (HlyA) is the prototype toxin of a major family of exoproteins produced by Gram-negative bacteria known as "repeats in toxins." Only fatty acid-acylated HlyA molecules at residues Lys564 and Lys690 are able to damage the target cell membrane. Fatty acylation of pro-HlyA is dependent on the co-synthesized acyltransferase HlyC and the acylated form of acyl-carrier protein. By using a collection of hlyA and hlyC mutant strains, the processing of HlyC was investigated. HlyC was not detected by Western blot in an E. coli strain encoding hlyC and hlyA, but it was present in a strain encoding only hlyC. The hlyC mRNA pattern, however, was similar in both strains indicating that the turnover of HlyC does not occur at the transcriptional level. HlyC was detected in Western blots of cell lysates from an E. coli strain encoding HlyC and a HlyA derivative where both acylation sites were substituted. Similar results were obtained when HlyC was expressed in a hlyA mutant strain lacking part of a putative HlyC binding domain, indicating that this particular HlyA region affects HlyC stability. We did not detect HlyC in cell lysates from hlyC mutants with different abilities to acylate pro-HlyA, suggesting that the degradation of HlyC is not related to the HlyA acylation process. The protease systems ClpAP, ClpXP, and FtsH were found to be responsible for the HlyA-dependent processing of HlyC.
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Affiliation(s)
- C Guzman-Verri
- Microbiology & Tumorbiology Center, Box 280, Karolinska Institute, S-171-77 Stockholm, Sweden.
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Ekaza E, Teyssier J, Ouahrani-Bettache S, Liautard JP, Köhler S. Characterization of Brucella suis clpB and clpAB mutants and participation of the genes in stress responses. J Bacteriol 2001; 183:2677-81. [PMID: 11274130 PMCID: PMC95187 DOI: 10.1128/jb.183.8.2677-2681.2001] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogens often encounter stressful conditions inside their hosts. In the attempt to characterize the stress response in Brucella suis, a gene highly homologous to Escherichia coli clpB was isolated from Brucella suis, and the deduced amino acid sequence showed features typical of the ClpB ATPase family of stress response proteins. Under high-temperature stress conditions, ClpB of B. suis was induced, and an isogenic B. suis clpB mutant showed increased sensitivity to high temperature, but also to ethanol stress and acid pH. The effects were reversible by complementation. Simultaneous inactivation of clpA and clpB resulted in a mutant that was sensitive to oxidative stress. In B. suis expressing gfp, ClpA but not ClpB participated in degradation of the green fluorescent protein at 42 degrees C. We concluded that ClpB was responsible for tolerance to several stresses and that the lethality caused by harsh environmental conditions may have similar molecular origins.
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Affiliation(s)
- E Ekaza
- Institut National de la Santé et de la Recherche Médicale U-431, Université Montpellier II, F-34095 Montpellier, France
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