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Kamat A, Badrinarayanan A. SOS-independent bacterial DNA damage responses: diverse mechanisms, unifying function. Curr Opin Microbiol 2023; 73:102323. [PMID: 37148591 DOI: 10.1016/j.mib.2023.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/23/2023] [Accepted: 04/06/2023] [Indexed: 05/08/2023]
Abstract
Cells across domains of life have dedicated pathways to sense and respond to DNA damage. These responses are broadly termed as DNA damage responses (DDRs). In bacteria, the best studied DDR is the Save our Soul (SOS) response. More recently, several SOS-independent DDRs have also been discovered. Studies further report diversity in the types of repair proteins present across bacterial species as well as differences in their mechanisms of action. Although the primary function of DDRs is preservation of genome integrity, the diverse organization, conservation, and function of bacterial DDRs raises important questions about how genome error correction mechanisms could influence or be influenced by the genomes that encode them. In this review, we discuss recent insights on three SOS-independent bacterial DDRs. We consider open questions in our understanding of how diversity in response and repair mechanisms is generated, and how action of these pathways is regulated in cells to ensure maintenance of genome integrity.
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Affiliation(s)
- Aditya Kamat
- National Centre for Biological Sciences (TIFR), Bengaluru 560065, India
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2
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Modulation of Multiple Gene Clusters’ Expression by the PAS-LuxR Transcriptional Regulator PteF. Antibiotics (Basel) 2022; 11:antibiotics11080994. [PMID: 35892384 PMCID: PMC9394381 DOI: 10.3390/antibiotics11080994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
PAS-LuxR transcriptional regulators are conserved proteins governing polyene antifungal biosynthesis. PteF is the regulator of filipin biosynthesis from Streptomyces avermitilis. Its mutation drastically abates filipin, but also oligomycin production, a macrolide ATP-synthase inhibitor, and delays sporulation; thus, it has been considered a transcriptional activator. Transcriptomic analyses were performed in S. avermitilis DpteF and its parental strain. Both strains were grown in a YEME medium without sucrose, and the samples were taken at exponential and stationary growth phases. A total of 257 genes showed an altered expression in the mutant, most of them at the exponential growth phase. Surprisingly, despite PteF being considered an activator, most of the genes affected showed overexpression, thereby suggesting a negative modulation. The affected genes were related to various metabolic processes, including genetic information processing; DNA, energy, carbohydrate, and lipid metabolism; morphological differentiation; and transcriptional regulation, among others, but were particularly related to secondary metabolite biosynthesis. Notably, 10 secondary metabolite gene clusters out of the 38 encoded by the genome showed altered expression profiles in the mutant, suggesting a regulatory role for PteF that is wider than expected. The transcriptomic results were validated by quantitative reverse-transcription polymerase chain reaction. These findings provide important clues to understanding the intertwined regulatory machinery that modulates antibiotic biosynthesis in Streptomyces.
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Ogata S, Hirasawa T. Induction of glutamic acid production by copper in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2021; 105:6909-6920. [PMID: 34463802 DOI: 10.1007/s00253-021-11516-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/28/2022]
Abstract
From the previous transcriptome analysis (Hirasawa et al. Biotechnol J 13:e1700612, 2018), it was found that expression of genes whose expression is regulated by stress-responsive transcriptional regulators was altered during penicillin-induced glutamic acid production in Corynebacterium glutamicum. Therefore, we investigated whether stress treatments, such as copper and iron addition, could induce glutamic acid production in C. glutamicum and found that the addition of copper did induce glutamic acid production in this species. Moreover, we also determined that glutamic acid production levels upon copper addition in a gain-of-function mutant strain of the mechanosensitive channel, NCgl1221, involved in glutamic acid export, were comparable to glutamic acid levels produced upon penicillin addition and biotin limitation in the wild-type strain. Furthermore, disruption of the odhI gene, which encodes a protein responsible for the decreased activity of the 2-oxoglutarate dehydrogenase complex during glutamic acid production, significantly diminished glutamic acid production induced by copper. These results indicate that copper can induce glutamic acid production and this induction requires OdhI like biotin limitation and penicillin addition, but a gain-of-function mutation in the NCgl1221 mechanosensitive channel is necessary for its high-level glutamic acid production. However, a significant increase in odhI transcription was not observed with copper addition in both wild-type and NCgl1221 gain-of-function mutant strains. In addition, disruption of the csoR gene encoding a copper-responsive transcriptional repressor enhanced copper-induced glutamic acid production in the NCgl1221 gain-of-function mutant, indicating that unidentified CsoR-regulated genes may contribute to copper-induced glutamic acid production in C. glutamicum. KEY POINTS: • Copper can induce glutamic acid production by Corynebacterium glutamicum. • Copper-induced glutamic acid production requires OdhI protein. • Copper-induced glutamic acid production requires a gain-of-function mutation in the mechanosensitive channel NCgl1221, which is responsible for the production of glutamic acid.
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Affiliation(s)
- Shunsuke Ogata
- School of Life Science and Technology, Tokyo Institute of Technology, 4250 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Takashi Hirasawa
- School of Life Science and Technology, Tokyo Institute of Technology, 4250 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
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4
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Parise D, Teixeira Dornelles Parise M, Pinto Gomide AC, Figueira Aburjaile F, Bentes Kato R, Salgado-Albarrán M, Tauch A, Ariston de Carvalho Azevedo V, Baumbach J. The Transcriptional Regulatory Network of Corynebacterium pseudotuberculosis. Microorganisms 2021; 9:microorganisms9020415. [PMID: 33671149 PMCID: PMC7923171 DOI: 10.3390/microorganisms9020415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 12/26/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a Gram-positive, facultative intracellular, pathogenic bacterium that infects several different hosts, yielding serious economic losses in livestock farming. It causes several diseases including oedematous skin disease (OSD) in buffaloes, ulcerative lymphangitis (UL) in horses, and caseous lymphadenitis (CLA) in sheep, goats and humans. Despite its economic and medical-veterinary importance, our understanding concerning this organism’s transcriptional regulatory mechanisms is still limited. Here, we review the state of the art knowledge on transcriptional regulatory mechanisms of this pathogenic species, covering regulatory interactions mediated by two-component systems, transcription factors and sigma factors. Key transcriptional regulatory players involved in virulence and pathogenicity of C. pseudotuberculosis, such as the PhoPR system and DtxR, are in the focus of this review, as these regulators are promising targets for future vaccine design and drug development. We conclude that more experimental studies are needed to further understand the regulatory repertoire of this important zoonotic pathogen, and that regulators are promising targets for future vaccine design and drug development.
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Affiliation(s)
- Doglas Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
- Correspondence: or
| | - Mariana Teixeira Dornelles Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | - Anne Cybelle Pinto Gomide
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | | | - Rodrigo Bentes Kato
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | - Marisol Salgado-Albarrán
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana Cuajimalpa, Mexico City 05348, Mexico
| | - Andreas Tauch
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany;
| | - Vasco Ariston de Carvalho Azevedo
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Computational BioMedicine lab, Institute of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
- Chair of Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany
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5
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Zhang X, Zhang F, Mi Y, Liu Y, Zheng K, Zhou Y, Jiang T, Wang M, Jiang Y, Guo C, Shao H, He H, He J, Liang Y, Wang M, McMinn A. Characterization and genome analysis of phage AL infecting Pseudoalteromonas marina. Virus Res 2021; 295:198265. [PMID: 33550041 DOI: 10.1016/j.virusres.2020.198265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 11/29/2022]
Abstract
Although Pseudoalteromonas is an abundant, ubiquitous, marine algae-associated bacterial genus, there is still little information on their phages. In the present study, a marine phage AL, infecting Pseudoalteromonas marina, was isolated from the coastal waters off Qingdao. The AL phage is a siphovirus with an icosahedral head of 53 ± 1 nm and a non-contractile tail, length of 99 ± 1 nm. A one-step growth curve showed that the latent period was approximately 70 min, the rise period was 50 min, and the burst size was 227 pfu/cell. The genome sequence of this phage is a 33,582 bp double-stranded DNA molecule with a GC content of 40.1 %, encoding 52 open reading frames (ORFs). The order of the functional genes, especially those related to the structure module, is highly conserved and basically follows the common pattern used by siphovirus. The stable order has been formed during the long-term evolution of phages in the siphovirus group, which has helped the phages to maintain their normal morphology and function. Phylogenetic trees based on the major capsid protein (mcp) and genome-wide sequence have shown that the AL phage is closely related to four Pseudoalteromonas phages, including PHS21, PHS3, SL25 and Pq0. Further analysis using all-to-all BLASTP also confirmed that this phage shared high sequence homology with the same four Pseudoalteromonas phages, with amino acid sequence identities ranging from 44 % to 71 %. In particular, their similarity in virion structure module may imply that these phages share common assembly mechanism characteristics and infection pathways. Pseudoalteromonas phage AL not only provides basic information for the further study of the evolution of Pseudoalteromonas phages and interactions between marine phage and host but also helps to explain the unknown viral sequences in the metagenomic databases.
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Affiliation(s)
- Xinran Zhang
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fang Zhang
- The Key Laboratory for Polar Science MNR, Polar Research Institute of China, Shanghai, 200136, China
| | - Ye Mi
- Qingdao City Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong, 266033, China
| | - Yundan Liu
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yao Zhou
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Tong Jiang
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Meiwen Wang
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hui He
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jianfeng He
- The Key Laboratory for Polar Science MNR, Polar Research Institute of China, Shanghai, 200136, China
| | - Yantao Liang
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Min Wang
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Andrew McMinn
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
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6
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Müller AU, Imkamp F, Weber-Ban E. The Mycobacterial LexA/RecA-Independent DNA Damage Response Is Controlled by PafBC and the Pup-Proteasome System. Cell Rep 2019; 23:3551-3564. [PMID: 29924998 DOI: 10.1016/j.celrep.2018.05.073] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/16/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
Mycobacteria exhibit two DNA damage response pathways: the LexA/RecA-dependent SOS response and a LexA/RecA-independent pathway. Using a combination of transcriptomics and genome-wide binding site analysis, we demonstrate that PafBC (proteasome accessory factor B and C), encoded in the Pup-proteasome system (PPS) gene locus, is the transcriptional regulator of the predominant LexA/RecA-independent pathway. Comparison of the resulting PafBC regulon with the DNA damage response of Mycobacterium smegmatis reveals that the majority of induced DNA repair genes are upregulated by PafBC. We further demonstrate that RecA, a member of the PafBC regulon and principal regulator of the SOS response, is degraded by the PPS when DNA damage stress has been overcome. Our results suggest a model for the regulation of the mycobacterial DNA damage response that employs the concerted action of PafBC as master transcriptional activator and the PPS for removal of DNA repair proteins to maintain a temporally controlled stress response.
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Affiliation(s)
- Andreas U Müller
- ETH Zurich, Institute of Molecular Biology and Biophysics, 8093 Zurich, Switzerland
| | - Frank Imkamp
- University of Zurich, Institute of Medical Microbiology, 8006 Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology and Biophysics, 8093 Zurich, Switzerland.
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7
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Chen C, Pan J, Yang X, Xiao H, Zhang Y, Si M, Shen X, Wang Y. Global transcriptomic analysis of the response of Corynebacterium glutamicum to ferulic acid. Arch Microbiol 2016; 199:325-334. [DOI: 10.1007/s00203-016-1306-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/24/2016] [Accepted: 10/08/2016] [Indexed: 10/20/2022]
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8
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Toyoda K, Inui M. Regulons of global transcription factors in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2015; 100:45-60. [DOI: 10.1007/s00253-015-7074-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/03/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
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9
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Zhang Y, Mandava CS, Cao W, Li X, Zhang D, Li N, Zhang Y, Zhang X, Qin Y, Mi K, Lei J, Sanyal S, Gao N. HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions. Nat Struct Mol Biol 2015; 22:906-13. [PMID: 26458047 DOI: 10.1038/nsmb.3103] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/04/2015] [Indexed: 12/16/2022]
Abstract
Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock. These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.
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Affiliation(s)
- Yanqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | | | - Wei Cao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaojing Li
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dejiu Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ningning Li
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yixiao Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoxiao Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Qin
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kaixia Mi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianlin Lei
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
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Expanding the regulatory network governed by the extracytoplasmic function sigma factor σH in Corynebacterium glutamicum. J Bacteriol 2014; 197:483-96. [PMID: 25404703 DOI: 10.1128/jb.02248-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extracytoplasmic function sigma factor σ(H) is responsible for the heat and oxidative stress response in Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, previous transcriptome analyses have not been able to discriminate between direct and indirect targets of σ(H). Here, we determined the direct genome-wide targets of σ(H) using chromatin immunoprecipitation with microarray technology (ChIP-chip) for analysis of a deletion mutant of rshA, encoding an anti-σ factor of σ(H). Seventy-five σ(H)-dependent promoters, including 39 new ones, were identified. σ(H)-dependent, heat-inducible transcripts for several of the new targets, including ilvD encoding a labile Fe-S cluster enzyme, dihydroxy-acid dehydratase, were detected, and their 5' ends were mapped to the σ(H)-dependent promoters identified. Interestingly, functional internal σ(H)-dependent promoters were found in operon-like gene clusters involved in the pentose phosphate pathway, riboflavin biosynthesis, and Zn uptake. Accordingly, deletion of rshA resulted in hyperproduction of riboflavin and affected expression of Zn-responsive genes, possibly through intracellular Zn overload, indicating new physiological roles of σ(H). Furthermore, sigA encoding the primary σ factor was identified as a new target of σ(H). Reporter assays demonstrated that the σ(H)-dependent promoter upstream of sigA was highly heat inducible but much weaker than the known σ(A)-dependent one. Our ChIP-chip analysis also detected the σ(H)-dependent promoters upstream of rshA within the sigH-rshA operon and of sigB encoding a group 2 σ factor, supporting the previous findings of their σ(H)-dependent expression. Taken together, these results reveal an additional layer of the sigma factor regulatory network in C. glutamicum.
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Personne Y, Brown AC, Schuessler DL, Parish T. Mycobacterium tuberculosis ClpP proteases are co-transcribed but exhibit different substrate specificities. PLoS One 2013; 8:e60228. [PMID: 23560081 PMCID: PMC3613350 DOI: 10.1371/journal.pone.0060228] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 02/23/2013] [Indexed: 11/19/2022] Open
Abstract
Caseinolytic (Clp) proteases are widespread energy-dependent proteases; the functional ATP-dependent protease is comprised of multimers of proteolytic and regulatory subunits. Mycobacterium tuberculosis has two ClpP proteolytic subunits (ClpP1 and ClpP2), with both being essential for growth in vitro. ClpP1 and clpP2 are arranged in an apparent operon; we demonstrated that the two genes are co-expressed under normal growth conditions. We identified a single promoter region for the clpP1P2 operon; no promoter was detected upstream of clpP2 demonstrating that independent expression of clpP1 and clpP2 was highly unlikely. Promoter activity was not induced by heat shock or oxidative stress. We identified a regulatory region upstream of the promoter with a consensus sequence matching the ClgR regulator motif; we determined the limits of the region by mutagenesis and confirmed that positive regulation of the promoter occurs in M. tuberculosis. We developed a reporter system to monitor ClpP1 and ClpP2 enzymatic activities based on LacZ incorporating ssrAtag sequences. We showed that whilst both ClpP1 and ClpP2 degrade SsrA-tagged LacZ, ClpP2 (but not ClpP1) degrades untagged proteins. Our data suggest that the two proteolytic subunits display different substrate specificities and therefore have different, but overlapping roles in M. tuberculosis.
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Affiliation(s)
- Yoann Personne
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, United Kingdom
| | - Amanda C. Brown
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, United Kingdom
| | - Dorothée L. Schuessler
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, United Kingdom
| | - Tanya Parish
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, United Kingdom
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12
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Vertès AA. Protein Secretion Systems of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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EbfC (YbaB) is a new type of bacterial nucleoid-associated protein and a global regulator of gene expression in the Lyme disease spirochete. J Bacteriol 2012; 194:3395-406. [PMID: 22544270 DOI: 10.1128/jb.00252-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nearly every known species of Eubacteria encodes a homolog of the Borrelia burgdorferi EbfC DNA-binding protein. We now demonstrate that fluorescently tagged EbfC associates with B. burgdorferi nucleoids in vivo and that chromatin immunoprecipitation (ChIP) of wild-type EbfC showed it to bind in vivo to sites throughout the genome, two hallmarks of nucleoid-associated proteins. Comparative RNA sequencing (RNA-Seq) of a mutant B. burgdorferi strain that overexpresses EbfC indicated that approximately 4.5% of borrelial genes are significantly impacted by EbfC. The ebfC gene was highly expressed in rapidly growing bacteria, but ebfC mRNA was undetectable in stationary phase. Combined with previous data showing that EbfC induces bends in DNA, these results demonstrate that EbfC is a nucleoid-associated protein and lead to the hypothesis that B. burgdorferi utilizes cellular fluctuations in EbfC levels to globally control transcription of numerous genes. The ubiquity of EbfC proteins in Eubacteria suggests that these results apply to a wide range of pathogens and other bacteria.
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14
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The universally conserved prokaryotic GTPases. Microbiol Mol Biol Rev 2012; 75:507-42, second and third pages of table of contents. [PMID: 21885683 DOI: 10.1128/mmbr.00009-11] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Members of the large superclass of P-loop GTPases share a core domain with a conserved three-dimensional structure. In eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. As targets of mutation and toxins, GTPases are involved in the pathogenesis of cancer and infectious diseases. In prokaryotes also, it is hard to overestimate the importance of GTPases in cell physiology. Numerous papers have shed new light on the role of bacterial GTPases in cell cycle regulation, ribosome assembly, the stress response, and other cellular processes. Moreover, bacterial GTPases have been identified as high-potential drug targets. A key paper published over 2 decades ago stated that, "It may never again be possible to capture [GTPases] in a family portrait" (H. R. Bourne, D. A. Sanders, and F. McCormick, Nature 348:125-132, 1990) and indeed, the last 20 years have seen a tremendous increase in publications on the subject. Sequence analysis identified 13 bacterial GTPases that are conserved in at least 75% of all bacterial species. We here provide an overview of these 13 protein subfamilies, covering their cellular functions as well as cellular localization and expression levels, three-dimensional structures, biochemical properties, and gene organization. Conserved roles in eukaryotic homologs will be discussed as well. A comprehensive overview summarizing current knowledge on prokaryotic GTPases will aid in further elucidating the function of these important proteins.
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15
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Schelder S, Zaade D, Litsanov B, Bott M, Brocker M. The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress. PLoS One 2011; 6:e22143. [PMID: 21799779 PMCID: PMC3140484 DOI: 10.1371/journal.pone.0022143] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/16/2011] [Indexed: 12/11/2022] Open
Abstract
Copper is an essential cofactor for many enzymes but at high concentrations it is toxic for the cell. Copper ion concentrations ≥50 µM inhibited growth of Corynebacterium glutamicum. The transcriptional response to 20 µM Cu2+ was studied using DNA microarrays and revealed 20 genes that showed a ≥ 3-fold increased mRNA level, including cg3281-cg3289. Several genes in this genomic region code for proteins presumably involved in the adaption to copper-induced stress, e. g. a multicopper oxidase (CopO) and a copper-transport ATPase (CopB). In addition, this region includes the copRS genes (previously named cgtRS9) which encode a two-component signal transduction system composed of the histidine kinase CopS and the response regulator CopR. Deletion of the copRS genes increased the sensitivity of C. glutamicum towards copper ions, but not to other heavy metal ions. Using comparative transcriptome analysis of the ΔcopRS mutant and the wild type in combination with electrophoretic mobility shift assays and reporter gene studies the CopR regulon and the DNA-binding motif of CopR were identified. Evidence was obtained that CopR binds only to the intergenic region between cg3285 (copR) and cg3286 in the genome of C. glutamicum and activates expression of the divergently oriented gene clusters cg3285-cg3281 and cg3286-cg3289. Altogether, our data suggest that CopRS is the key regulatory system in C. glutamicum for the extracytoplasmic sensing of elevated copper ion concentrations and for induction of a set of genes capable of diminishing copper stress.
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Affiliation(s)
- Stephanie Schelder
- Institut für Bio-und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Daniela Zaade
- Institut für Bio-und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Boris Litsanov
- Institut für Bio-und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institut für Bio-und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Melanie Brocker
- Institut für Bio-und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
- * E-mail:
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16
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Wang Y, Huang Y, Xue C, He Y, He ZG. ClpR protein-like regulator specifically recognizes RecA protein-independent promoter motif and broadly regulates expression of DNA damage-inducible genes in mycobacteria. J Biol Chem 2011; 286:31159-67. [PMID: 21771781 DOI: 10.1074/jbc.m111.241802] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The RecA-dependent DNA damage response pathway (SOS response) appears to be the major DNA repair mechanism in most bacteria, but it has been suggested that a RecA-independent mechanism is responsible for controlling expression of most damage-inducible DNA repair genes in Mycobacterium tuberculosis. The specific reparative responses and molecular mediators involved in the DNA repair mechanism remain largely unclear in this pathogen and its related species. In this study, a mycobacterial ClpR-like regulator, corresponding to Rv2745c in M. tuberculosis and to Ms2694 in M. smegmatis mc(2)155, was found to interact with the promoter regions of multiple damage-inducible DNA repair genes. Specific binding of the ClpR-like factor to the conserved RecA-independent promoter RecA-NDp motif was then confirmed using in vitro electrophoretic mobility shift assays as well as in vivo chromatin immunoprecipitation experiments. The ClpR knock-out experiments, in combination with quantitative real time PCR assays, demonstrated that the expression of these RecA-independent genes were significantly down-regulated in the mutant strain of M. smegmatis in response to a DNA-damaging agent compared with the wild type strain. Furthermore, the ClpR-like factor was shown to contribute to mycobacterial genomic stability. These results enhance our understanding of the function of the ClpR regulator and the regulatory mechanism of RecA-independent DNA repair in mycobacteria.
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Affiliation(s)
- Yi Wang
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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An HflX-type GTPase from Sulfolobus solfataricus binds to the 50S ribosomal subunit in all nucleotide-bound states. J Bacteriol 2011; 193:2861-7. [PMID: 21478358 DOI: 10.1128/jb.01552-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
HflX GTPases are found in all three domains of life, the Bacteria, Archaea, and Eukarya. HflX from Escherichia coli has been shown to bind to the 50S ribosomal subunit in a nucleotide-dependent manner, and this interaction strongly stimulates its GTPase activity. We recently determined the structure of an HflX ortholog from the archaeon Sulfolobus solfataricus (SsoHflX). It revealed the presence of a novel HflX domain that might function in RNA binding and is linked to a canonical G domain. This domain arrangement is common to all archaeal, bacterial, and eukaryotic HflX GTPases. This paper shows that the archaeal SsoHflX, like its bacterial orthologs, binds to the 50S ribosomal subunit. This interaction does not depend on the presence of guanine nucleotides. The HflX domain is sufficient for ribosome interaction. Binding appears to be restricted to free 50S ribosomal subunits and does not occur with 70S ribosomes engaged in translation. The fingerprint (1)H-(15)N heteronuclear correlation nuclear magnetic resonance (NMR) spectrum of SsoHflX reveals a large number of well-resolved resonances that are broadened upon binding to the 50S ribosomal subunit. The GTPase activity of SsoHflX is stimulated by crude fractions of 50S ribosomal subunits, but this effect is lost with further high-salt purification of the 50S ribosomal subunits, suggesting that the stimulation depends on an extrinsic factor bound to the 50S ribosomal subunit. Our results reveal common properties but also marked differences between archaeal and bacterial HflX proteins.
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18
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Mogk A, Huber D, Bukau B. Integrating protein homeostasis strategies in prokaryotes. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a004366. [PMID: 21441580 DOI: 10.1101/cshperspect.a004366] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacterial cells are frequently exposed to dramatic fluctuations in their environment, which cause perturbation in protein homeostasis and lead to protein misfolding. Bacteria have therefore evolved powerful quality control networks consisting of chaperones and proteases that cooperate to monitor the folding states of proteins and to remove misfolded conformers through either refolding or degradation. The levels of the quality control components are adjusted to the folding state of the cellular proteome through the induction of compartment specific stress responses. In addition, the activities of several quality control components are directly controlled by these stresses, allowing for fast activation. Severe stress can, however, overcome the protective function of the proteostasis network leading to the formation of protein aggregates, which are sequestered at the cell poles. Protein aggregates are either solubilized by AAA+ chaperones or eliminated through cell division, allowing for the generation of damage-free daughter cells.
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Affiliation(s)
- Axel Mogk
- Zentrum für Molekulare Biologie Heidelberg, DKFZ-ZMBH Alliance, Universität Heidelberg, Heidelberg, Germany
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19
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Target genes, consensus binding site, and role of phosphorylation for the response regulator MtrA of Corynebacterium glutamicum. J Bacteriol 2010; 193:1237-49. [PMID: 21183673 DOI: 10.1128/jb.01032-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The two-component signal transduction system consisting of the sensor kinase MtrB and the response regulator MtrA is highly conserved in corynebacteria and mycobacteria. Whereas mtrA of Mycobacterium tuberculosis was reported to be essential, we recently succeeded in creating ΔmtrAB and ΔmtrA deletion mutants of Corynebacterium glutamicum and provided evidence that mepA and nlpC, both encoding putative cell wall peptidases, are directly repressed by MtrA, whereas proP and betP, both encoding carriers for compatible solutes, are directly activated by MtrA. In the present study, novel MtrA target genes were identified, including mepB, encoding another putative cell wall peptidase. The repressor or activator functions of MtrA correlate with the distance between the MtrA binding site and the transcriptional start site. From the identified binding sites within 20 target promoters, a 19-bp MtrA consensus motif was derived which represents a direct repeat of 8 base pairs separated by 3 base pairs. Gene expression of a strain containing MtrA with a D53N mutation instead of wild-type MtrA resembled that of a ΔmtrA mutant, indicating that MtrA is active in its phosphorylated form. This result was confirmed by electrophoretic mobility shift assays with phosphorylated MtrA which showed an increased binding affinity.
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20
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Estorninho M, Smith H, Thole J, Harders-Westerveen J, Kierzek A, Butler RE, Neyrolles O, Stewart GR. ClgR regulation of chaperone and protease systems is essential for Mycobacterium tuberculosis parasitism of the macrophage. Microbiology (Reading) 2010; 156:3445-3455. [DOI: 10.1099/mic.0.042275-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chaperone and protease systems play essential roles in cellular homeostasis and have vital functions in controlling the abundance of specific cellular proteins involved in processes such as transcription, replication, metabolism and virulence. Bacteria have evolved accurate regulatory systems to control the expression and function of chaperones and potentially destructive proteases. Here, we have used a combination of transcriptomics, proteomics and targeted mutagenesis to reveal that the clp gene regulator (ClgR) of Mycobacterium tuberculosis activates the transcription of at least ten genes, including four that encode protease systems (ClpP1/C, ClpP2/C, PtrB and HtrA-like protease Rv1043c) and three that encode chaperones (Acr2, ClpB and the chaperonin Rv3269). Thus, M. tuberculosis ClgR controls a larger network of protein homeostatic and regulatory systems than ClgR in any other bacterium studied to date. We demonstrate that ClgR-regulated transcriptional activation of these systems is essential for M. tuberculosis to replicate in macrophages. Furthermore, we observe that this defect is manifest early in infection, as M. tuberculosis lacking ClgR is deficient in the ability to control phagosome pH 1 h post-phagocytosis.
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Affiliation(s)
- Megan Estorninho
- Division of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Hilde Smith
- Central Veterinary Institute of Wageningen UR, Division of Infectious Diseases, Animal Sciences Group, Edelhertweg 15, 8219 PH Lelystad, The Netherlands
| | - Jelle Thole
- Central Veterinary Institute of Wageningen UR, Division of Infectious Diseases, Animal Sciences Group, Edelhertweg 15, 8219 PH Lelystad, The Netherlands
| | - Jose Harders-Westerveen
- Central Veterinary Institute of Wageningen UR, Division of Infectious Diseases, Animal Sciences Group, Edelhertweg 15, 8219 PH Lelystad, The Netherlands
| | - Andrzej Kierzek
- Division of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Rachel E. Butler
- Division of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique and Université Paul Sabatier (UMR 5089), 205 Route de Narbonne, 31000 Toulouse, France
| | - Graham R. Stewart
- Division of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
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21
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Bussmann M, Baumgart M, Bott M. RosR (Cg1324), a hydrogen peroxide-sensitive MarR-type transcriptional regulator of Corynebacterium glutamicum. J Biol Chem 2010; 285:29305-18. [PMID: 20643656 PMCID: PMC2937963 DOI: 10.1074/jbc.m110.156372] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Revised: 07/14/2010] [Indexed: 11/06/2022] Open
Abstract
The cg1324 gene (rosR) of Corynebacterium glutamicum encodes a MarR-type transcriptional regulator. By a comparative transcriptome analysis with DNA microarrays of a ΔrosR mutant and the wild type and subsequent EMSAs with purified RosR protein, direct target genes of RosR were identified. The narKGHJI operon, which encodes a nitrate/nitrite transporter and the dissimilatory nitrate reductase complex, was activated by RosR. All other target genes were repressed by RosR. They encode four putative monooxygenases, two putative FMN reductases, a protein of the glutathione S-transferase family, a putative polyisoprenoid-binding protein, and RosR itself. The DNA binding site of RosR was characterized as an 18-bp inverted repeat with the consensus sequence TTGTTGAYRYRTCAACWA. The in vitro DNA binding activity of RosR was reversibly inhibited by the oxidant H(2)O(2). Mutational analysis of the three cysteine residues present in RosR (Cys-64, Cys-92, and Cys-151) showed that these are responsible for the inhibition of DNA binding by H(2)O(2). A deletion mutant (Δcg1322) lacking the putative polyisoprenoid-binding protein showed an increased sensitivity to H(2)O(2), supporting the role of RosR in the oxidative stress response of C. glutamicum.
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Affiliation(s)
- Michael Bussmann
- From the Institut für Biotechnologie 1, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Meike Baumgart
- From the Institut für Biotechnologie 1, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Michael Bott
- From the Institut für Biotechnologie 1, Forschungszentrum Jülich, D-52425 Jülich, Germany
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22
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Schröder J, Tauch A. Transcriptional regulation of gene expression inCorynebacterium glutamicum: the role of global, master and local regulators in the modular and hierarchical gene regulatory network. FEMS Microbiol Rev 2010; 34:685-737. [DOI: 10.1111/j.1574-6976.2010.00228.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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23
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Sherrid AM, Rustad TR, Cangelosi GA, Sherman DR. Characterization of a Clp protease gene regulator and the reaeration response in Mycobacterium tuberculosis. PLoS One 2010; 5:e11622. [PMID: 20661284 PMCID: PMC2905415 DOI: 10.1371/journal.pone.0011622] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 06/19/2010] [Indexed: 12/27/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) enters a non-replicating state when exposed to low oxygen tension, a condition the bacillus encounters in granulomas during infection. Determining how mycobacteria enter and maintain this state is a major focus of research. However, from a public health standpoint the importance of latent TB is its ability to reactivate. The mechanism by which mycobacteria return to a replicating state upon re-exposure to favorable conditions is not understood. In this study, we utilized reaeration from a defined hypoxia model to characterize the adaptive response of MTB following a return to favorable growth conditions. Global transcriptional analysis identified the approximately 100 gene Reaeration Response, induced relative to both log-phase and hypoxic MTB. This response includes chaperones and proteases, as well as the transcription factor Rv2745c, which we characterize as a Clp protease gene regulator (ClgR) orthologue. During reaeration, genes repressed during hypoxia are also upregulated in a wave of transcription that includes genes crucial to transcription, translation and oxidative phosphorylation and culminates in bacterial replication. In sum, this study defines a new transcriptional response of MTB with potential relevance to disease, and implicates ClgR as a regulator involved in resumption of replication following hypoxia.
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Affiliation(s)
- Ashley M. Sherrid
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Molecular and Cellular Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Tige R. Rustad
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Gerard A. Cangelosi
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Pathobiology Program and Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - David R. Sherman
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Pathobiology Program and Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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24
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Wu H, Sun L, Blombach F, Brouns SJJ, Snijders APL, Lorenzen K, van den Heuvel RHH, Heck AJR, Fu S, Li X, Zhang XC, Rao Z, van der Oost J. Structure of the ribosome associating GTPase HflX. Proteins 2010; 78:705-13. [PMID: 19787775 DOI: 10.1002/prot.22599] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The HflX-family is a widely distributed but poorly characterized family of translation factor-related guanosine triphosphatases (GTPases) that interact with the large ribosomal subunit. This study describes the crystal structure of HflX from Sulfolobus solfataricus solved to 2.0-A resolution in apo- and GDP-bound forms. The enzyme displays a two-domain architecture with a novel "HflX domain" at the N-terminus, and a classical G-domain at the C-terminus. The HflX domain is composed of a four-stranded parallel beta-sheet flanked by two alpha-helices on either side, and an anti-parallel coiled coil of two long alpha-helices that lead to the G-domain. The cleft between the two domains accommodates the nucleotide binding site as well as the switch II region, which mediates interactions between the two domains. Conformational changes of the switch regions are therefore anticipated to reposition the HflX-domain upon GTP-binding. Slow GTPase activity has been confirmed, with an HflX domain deletion mutant exhibiting a 24-fold enhanced turnover rate, suggesting a regulatory role for the HflX domain. The conserved positively charged surface patches of the HflX-domain may mediate interaction with the large ribosomal subunit. The present study provides a structural basis to uncover the functional role of this GTPases family whose function is largely unknown.
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Affiliation(s)
- Hao Wu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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25
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Kallifidas D, Thomas D, Doughty P, Paget MSB. The sigmaR regulon of Streptomyces coelicolor A32 reveals a key role in protein quality control during disulphide stress. MICROBIOLOGY-SGM 2010; 156:1661-1672. [PMID: 20185507 DOI: 10.1099/mic.0.037804-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Diamide is an artificial disulphide-generating electrophile that mimics an oxidative shift in the cellular thiol-disulphide redox state (disulphide stress). The Gram-positive bacterium Streptomyces coelicolor senses and responds to disulphide stress through the sigma(R)-RsrA system, which comprises an extracytoplasmic function (ECF) sigma factor and a redox-active anti-sigma factor. Known targets that aid in the protection and recovery from disulphide stress include the thioredoxin system and genes involved in producing the major thiol buffer mycothiol. Here we determine the global response to diamide in wild-type and sigR mutant backgrounds to understand the role of sigma(R) in this response and to reveal additional regulatory pathways that allow cells to cope with disulphide stress. In addition to thiol oxidation, diamide was found to cause protein misfolding and aggregation, which elicited the induction of the HspR heat-shock regulon. Although this response is sigma(R)-independent, sigma(R) does directly control Clp and Lon ATP-dependent AAA(+) proteases, which may partly explain the reduced ability of a sigR mutant to resolubilize protein aggregates. sigma(R) also controls msrA and msrB methionine sulphoxide reductase genes, implying that sigma(R)-RsrA is responsible for the maintenance of both cysteine and methionine residues during oxidative stress. This work shows that the sigma(R)-RsrA system plays a more significant role in protein quality control than previously realized, and emphasizes the importance of controlling the cellular thiol-disulphide redox balance.
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Affiliation(s)
- Dimitris Kallifidas
- Department of Chemistry and Biochemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Derek Thomas
- Department of Chemistry and Biochemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Phillip Doughty
- Department of Chemistry and Biochemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Mark S B Paget
- Department of Chemistry and Biochemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
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26
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Schultz C, Niebisch A, Schwaiger A, Viets U, Metzger S, Bramkamp M, Bott M. Genetic and biochemical analysis of the serine/threonine protein kinases PknA, PknB, PknG and PknL of Corynebacterium glutamicum: evidence for non-essentiality and for phosphorylation of OdhI and FtsZ by multiple kinases. Mol Microbiol 2009; 74:724-41. [PMID: 19788543 PMCID: PMC2784874 DOI: 10.1111/j.1365-2958.2009.06897.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2009] [Indexed: 12/04/2022]
Abstract
We previously showed that the 2-oxoglutarate dehydrogenase inhibitor protein OdhI of Corynebacterium glutamicum is phosphorylated by PknG at Thr14, but that also additional serine/threonine protein kinases (STPKs) can phosphorylate OdhI. To identify these, a set of three single (DeltapknA, DeltapknB, DeltapknL), five double (DeltapknAG, DeltapknAL, DeltapknBG, DeltapknBL, DeltapknLG) and two triple deletion mutants (DeltapknALG, DeltapknBLG) were constructed. The existence of these mutants shows that PknA, PknB, PknG and PknL are not essential in C. glutamicum. Analysis of the OdhI phosphorylation status in the mutant strains revealed that all four STPKs can contribute to OdhI phosphorylation, with PknG being the most important one. Only mutants in which pknG was deleted showed a strong growth inhibition on agar plates containing glutamine as carbon and nitrogen source. Thr14 and Thr15 of OdhI were shown to be phosphorylated in vivo, either individually or simultaneously, and evidence for up to two additional phosphorylation sites was obtained. Dephosphorylation of OdhI was shown to be catalysed by the phospho-Ser/Thr protein phosphatase Ppp. Besides OdhI, the cell division protein FtsZ was identified as substrate of PknA, PknB and PknL and of the phosphatase Ppp, suggesting a role of these proteins in cell division.
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Affiliation(s)
- Christian Schultz
- Institut für Biotechnologie 1, Forschungszentrum JülichD-52425 Jülich, Germany
| | - Axel Niebisch
- Institut für Biotechnologie 1, Forschungszentrum JülichD-52425 Jülich, Germany
| | - Astrid Schwaiger
- Institut für Biochemie, Universität zu KölnD-50674 Köln, Germany
| | - Ulrike Viets
- Institut für Biotechnologie 1, Forschungszentrum JülichD-52425 Jülich, Germany
| | - Sabine Metzger
- Biologisch-Medizinisches Forschungszentrum, Heinrich-Heine-Universität DüsseldorfD-40225 Düsseldorf, Germany
| | - Marc Bramkamp
- Institut für Biochemie, Universität zu KölnD-50674 Köln, Germany
| | - Michael Bott
- Institut für Biotechnologie 1, Forschungszentrum JülichD-52425 Jülich, Germany
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27
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An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003. J Bacteriol 2009; 191:7039-49. [PMID: 19734308 DOI: 10.1128/jb.00897-09] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the genus Bifidobacterium are gram-positive bacteria that commonly are found in the gastrointestinal tract (GIT) of mammals, including humans. Because of their perceived probiotic properties, they frequently are incorporated as functional ingredients in food products. From probiotic production to storage and GIT delivery, bifidobacteria encounter a plethora of stresses. To cope with these environmental challenges, they need to protect themselves through stress-induced adaptive responses. We have determined the response of B. breve UCC2003 to various stresses (heat, osmotic, and solvent) using transcriptome analysis, DNA-protein interactions, and GusA reporter fusions, and we combined these with results from an in silico analysis. The integration of these results allowed the formulation of a model for an interacting regulatory network for stress response in B. breve UCC2003 where HspR controls the SOS response and the ClgR regulon, which in turn regulates and is regulated by HrcA. This model of an interacting regulatory network is believed to represent the paradigm for stress adaptation in bifidobacteria.
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28
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Cooley AE, Riley SP, Kral K, Miller MC, DeMoll E, Fried MG, Stevenson B. DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family. BMC Microbiol 2009; 9:137. [PMID: 19594923 PMCID: PMC2720974 DOI: 10.1186/1471-2180-9-137] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 07/13/2009] [Indexed: 01/09/2023] Open
Abstract
Background Genes orthologous to the ybaB loci of Escherichia coli and Haemophilus influenzae are widely distributed among eubacteria. Several years ago, the three-dimensional structures of the YbaB orthologs of both E. coli and H. influenzae were determined, revealing a novel "tweezer"-like structure. However, a function for YbaB had remained elusive, with an early study of the H. influenzae ortholog failing to detect DNA-binding activity. Our group recently determined that the Borrelia burgdorferi YbaB ortholog, EbfC, is a DNA-binding protein. To reconcile those results, we assessed the abilities of both the H. influenzae and E. coli YbaB proteins to bind DNA to which B. burgdorferi EbfC can bind. Results Both the H. influenzae and the E. coli YbaB proteins bound to tested DNAs. DNA-binding was not well competed with poly-dI-dC, indicating some sequence preferences for those two proteins. Analyses of binding characteristics determined that both YbaB orthologs bind as homodimers. Different DNA sequence preferences were observed between H. influenzae YbaB, E. coli YbaB and B. burgdorferi EbfC, consistent with amino acid differences in the putative DNA-binding domains of these proteins. Conclusion Three distinct members of the YbaB/EbfC bacterial protein family have now been demonstrated to bind DNA. Members of this protein family are encoded by a broad range of bacteria, including many pathogenic species, and results of our studies suggest that all such proteins have DNA-binding activities. The functions of YbaB/EbfC family members in each bacterial species are as-yet unknown, but given the ubiquity of these DNA-binding proteins among Eubacteria, further investigations are warranted.
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Affiliation(s)
- Anne E Cooley
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA.
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29
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Transcriptional control of the succinate dehydrogenase operon sdhCAB of Corynebacterium glutamicum by the cAMP-dependent regulator GlxR and the LuxR-type regulator RamA. J Biotechnol 2009; 143:173-82. [PMID: 19583988 DOI: 10.1016/j.jbiotec.2009.06.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 06/22/2009] [Accepted: 06/26/2009] [Indexed: 01/31/2023]
Abstract
In experiments performed to identify transcriptional regulators of the tricarboxylic acid cycle of Corynebacterium glutamicum, the cAMP-dependent regulator GlxR and the regulators of acetate metabolism RamA and RamB were enriched by DNA affinity chromatography with the promoter region of the sdhCAB operon encoding succinate dehydrogenase. The binding of purified GlxR, RamA and RamB was verified by electrophoretic mobility shift assays and the regulatory effects of these proteins on sdhCAB gene expression were tested by promoter activity assays and SDH activity measurements. Evidence was obtained that GlxR functions as a repressor and RamA as an activator of sdhCAB expression, whereas RamB had no obvious influence under the conditions tested.
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Russo S, Schweitzer JE, Polen T, Bott M, Pohl E. Crystal Structure of the Caseinolytic Protease Gene Regulator, a Transcriptional Activator in Actinomycetes. J Biol Chem 2009; 284:5208-16. [DOI: 10.1074/jbc.m806591200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Abstract
The Escherichia coli gene hflX was first identified as part of the hflA operon, mutations in which led to an increased frequency of lysogenization upon infection of the bacterium by the temperate coliphage lambda. Independent mutational studies have also indicated that the HflX protein has a role in transposition. Based on the sequence of its gene, HflX is predicted to be a GTP-binding protein, very likely a GTPase. We report here purification and characterization of the HflX protein. We also specifically examined its suggested functional roles mentioned above. Our results show that HflX is a monomeric protein with a high (30% to 40%) content of helices. It exhibits GTPase as well as ATPase activities, but it has no role in lambda lysogeny or in transposition.
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Polkinghorne A, Ziegler U, González-Hernández Y, Pospischil A, Timms P, Vaughan L. Chlamydophila pneumoniae HflX belongs to an uncharacterized family of conserved GTPases and associates with the Escherichia coli 50S large ribosomal subunit. MICROBIOLOGY-SGM 2008; 154:3537-3546. [PMID: 18957606 DOI: 10.1099/mic.0.2008/022137-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Predicted members of the HflX subfamily of phosphate-binding-loop guanosine triphosphatases (GTPases) are widely distributed in the bacterial kingdom but remain virtually uncharacterized. In an attempt to understand mechanisms used for regulation of growth and development in the chlamydiae, obligate intracellular and developmentally complex bacteria, we have begun investigations into chlamydial GTPases; we report here what appears to be the first analysis of a HflX family GTPase using a predicted homologue from Chlamydophila pneumoniae. In agreement with phylogenetic predictions for members of this GTPase family, purified recombinant Cp. pneumoniae HflX was specific for guanine nucleotides and exhibited a slow intrinsic GTPase activity when incubated with [gamma-(32)P]GTP. Using HflX-specific monoclonal antibodies, HflX could be detected by Western blotting and high-resolution confocal microscopy throughout the vegetative growth cycle of Cp. pneumoniae and, at early time points, appeared to partly localize to the membrane. Ectopic expression of Cp. pneumoniae HflX in Escherichia coli revealed co-sedimentation of HflX with the E. coli 50S large ribosomal subunit. The results of this work open up some intriguing possibilities for the role of GTPases belonging to this previously uncharacterized family of bacterial GTPases. Ribosome association is a feature shared by other important conserved GTPase families and more detailed investigations will be required to delineate the role of HflX in bacterial ribosome function.
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Affiliation(s)
- Adam Polkinghorne
- Institute of Veterinary Pathology, University of Zurich, Winterthurerstrasse 268, Zurich 8057, Switzerland
| | - Urs Ziegler
- Institute of Anatomy and Center for Microscopy and Image Analysis, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | | | - Andreas Pospischil
- Institute of Veterinary Pathology, University of Zurich, Winterthurerstrasse 268, Zurich 8057, Switzerland
| | - Peter Timms
- Institute of Health and Biomedical Innovation and School of Life Sciences, Faculty of Science, Queensland University of Technology, Brisbane, Australia
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, Winterthurerstrasse 268, Zurich 8057, Switzerland
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Transcription of clpP is enhanced by a unique tandem repeat sequence in Streptococcus mutans. J Bacteriol 2008; 191:1056-65. [PMID: 19047352 DOI: 10.1128/jb.01436-08] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus mutans, the primary causative agent of human dental caries, contains a single copy of the gene encoding ClpP, the chief intracellular protease responsible for tolerance to various environmental stresses. To better understand the role of ClpP in stress response, we investigated the regulation of clpP expression in S. mutans. Using semiquantitative reverse transcription-PCR analysis, we observed that, under nonstressed conditions, clpP expression is somewhat constant throughout the growth phases, although it gradually decreases as cells enter the late stationary phase. The half-life of the clpP transcript was found to be less than 1 minute. Sequence analysis of the clpP locus reveals the presence of a 50-bp tandem repeat sequence located immediately upstream of the clpP promoter (PclpP). PCR and DNA sequence analyses suggest that the number of tandem repeat units can vary from as few as two to as many as nine, depending on the particular S. mutans isolate. Further analysis, using a transcriptional reporter fusion consisting of PclpP fused to a promoterless gusA gene, indicates that the presence of the repeat sequence region within PclpP results in an approximately fivefold increase in expression from PclpP compared to the repeat-free transcriptional reporter fusion. CtsR, a transcriptional repressor that negatively regulates clpP expression, has no effect on this repeat-mediated induction of clpP transcription. Furthermore, the repeat sequence is not necessary for the induction of clpP under stress conditions. Database searches indicate that the region containing the tandem repeats is absent in the clpP loci in other bacteria, including other closely related Streptococcus spp., suggesting that the repeat sequences are specific for the induction of clpP expression in S. mutans. We speculate that a host-specific transcriptional activator might be involved in the upregulation of clpP expression in S. mutans.
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Ventura M, O'Connell-Motherway M, Leahy S, Moreno-Munoz JA, Fitzgerald GF, van Sinderen D. From bacterial genome to functionality; case bifidobacteria. Int J Food Microbiol 2007; 120:2-12. [PMID: 17629975 DOI: 10.1016/j.ijfoodmicro.2007.06.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Revised: 01/18/2007] [Indexed: 11/24/2022]
Abstract
The availability of complete bacterial genome sequences has significantly furthered our understanding of the genetics, physiology and biochemistry of the microorganisms in question, particularly those that have commercially important applications. Bifidobacteria are among such microorganisms, as they constitute mammalian commensals of biotechnological significance due to their perceived role in maintaining a balanced gastrointestinal (GIT) microflora. Bifidobacteria are therefore frequently used as health-promoting or probiotic components in functional food products. A fundamental understanding of the metabolic activities employed by these commensal bacteria, in particular their capability to utilize a wide range of complex oligosaccharides, can reveal ways to provide in vivo growth advantages relative to other competing gut bacteria or pathogens. Furthermore, an in depth analysis of adaptive responses to nutritional or environmental stresses may provide methodologies to retain viability and improve functionality during commercial preparation, storage and delivery of the probiotic organism.
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Affiliation(s)
- Marco Ventura
- Department of Genetics, Anthropology and Evolution, University of Parma, Italy
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Bott M. Offering surprises: TCA cycle regulation in Corynebacterium glutamicum. Trends Microbiol 2007; 15:417-25. [PMID: 17764950 DOI: 10.1016/j.tim.2007.08.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 06/19/2007] [Accepted: 08/09/2007] [Indexed: 11/23/2022]
Abstract
Corynebacterium glutamicum, a Gram-positive soil bacterium, is used for the production of l-glutamate and l-lysine, both of which are derived from intermediates of the tricarboxylic acid (TCA) cycle. Recent studies have revealed that this amphibolic pathway is subject to complex regulation not only at the transcriptional level, but also at the post-transcriptional level. The latter involves serine/threonine protein kinase G and its target protein OdhI. Depending on its phosphorylation state, OdhI inhibits the 2-oxoglutarate dehydrogenase complex. This new type of TCA cycle control will be reviewed here together with regulation at the level of gene expression.
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Affiliation(s)
- Michael Bott
- Institut für Biotechnologie 1, Forschungszentrum Jülich, D-52425 Jülich, Germany.
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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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Brinkrolf K, Brune I, Tauch A. The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum. J Biotechnol 2007; 129:191-211. [PMID: 17227685 DOI: 10.1016/j.jbiotec.2006.12.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 11/14/2006] [Accepted: 12/04/2006] [Indexed: 11/18/2022]
Abstract
The complete nucleotide sequence of the Corynebacterium glutamicum ATCC 13032 genome was previously determined and allowed the reliable prediction of 3002 protein-coding genes within this genome. Using computational methods, we have defined 158 genes, which form the minimal repertoire for proteins that presumably act as transcriptional regulators of gene expression. Most of these regulatory proteins have a direct role as DNA-binding transcriptional regulator, while others either have less well-defined functions in transcriptional regulation or even more general functions, such as the sigma factors. Recent advances in genome-wide transcriptional profiling of C. glutamicum generated a huge amount of data on regulation of gene expression. To understand transcriptional regulation of gene expression from the perspective of systems biology, rather than from the analysis of an individual regulatory protein, we compiled the current knowledge on the defined DNA-binding transcriptional regulators and their physiological role in modulating transcription in response to environmental signals. This comprehensive data collection provides a solid basis for database-guided reconstructions of the gene regulatory network of C. glutamicum, currently comprising 56 transcriptional regulators that exert 411 regulatory interactions to control gene expression. A graphical reconstruction revealed first insights into the functional modularity, the hierarchical architecture and the topological design principles of the transcriptional regulatory network of C. glutamicum.
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Affiliation(s)
- Karina Brinkrolf
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
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Tsilibaris V, Maenhaut-Michel G, Van Melderen L. Biological roles of the Lon ATP-dependent protease. Res Microbiol 2006; 157:701-13. [PMID: 16854568 DOI: 10.1016/j.resmic.2006.05.004] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 05/22/2006] [Accepted: 05/23/2006] [Indexed: 12/24/2022]
Abstract
The Lon ATP-dependent protease plays a major role in protein quality control. An increasing number of regulatory proteins, however, are being identified as Lon substrates, thus indicating that in addition to its housekeeping function, Lon plays an important role in regulating many biological processes in bacteria. This review presents and discusses the involvement of Lon in different aspects of bacterial physiology, including cell differentiation, sporulation, pathogenicity and survival under starvation conditions.
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Affiliation(s)
- Virginie Tsilibaris
- Laboratoire de Génétique des Procaryotes, IBMM, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
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Ventura M, Canchaya C, Zhang Z, Bernini V, Fitzgerald GF, van Sinderen D. How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators. FEMS Microbiol Rev 2006; 30:734-59. [PMID: 16911042 DOI: 10.1111/j.1574-6976.2006.00031.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The Actinobacteridae group of bacteria includes pathogens, plant commensals, endosymbionts as well as inhabitants of the gastrointestinal tract. For various reasons, these microorganisms represent 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 actinobacteria to contend with heat stress, with an emphasis on bifidobacteria. We describe the principal molecular chaperones involved in heat stress. Temporal expression of heat-shock genes based on functional genomics in members of the Actinobacteridae group is also discussed, as well as the emerging molecular mechanisms controlling the heat-stress response.
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Affiliation(s)
- Marco Ventura
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.
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Bellier A, Gominet M, Mazodier P. Post-translational control of the Streptomyces lividans ClgR regulon by ClpP. MICROBIOLOGY-SGM 2006; 152:1021-1027. [PMID: 16549666 DOI: 10.1099/mic.0.28564-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
It has been shown previously that expression of the Streptomyces lividans clpP1P2 operon, encoding proteolytic subunits of the Clp complex, the clpC1 gene, encoding the ATPase subunit, and the lon gene, encoding another ATP-dependent protease, are all activated by ClgR. The ClgR regulon also includes the clgR gene itself. It is shown here that the degradation of ClgR and Lon is ClpP1/P2-dependent and that the two C-terminal alanines of these new substrates are involved in their stability. The ClpC1 protein, which does not end with two alanines, is also accumulated in a clpP1P2 mutant. The results presented here support the idea that ClpP1/P2 ensure post-translational control of ClgR regulon members, including ClgR itself.
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Affiliation(s)
- Audrey Bellier
- Unité Postulante de Génétique Bactérienne et Différenciation, CNRS URA 2172, Institut Pasteur, 25 rue Dr Roux, 75724 Paris Cedex 15, France
| | - Myriam Gominet
- Unité Postulante de Génétique Bactérienne et Différenciation, CNRS URA 2172, Institut Pasteur, 25 rue Dr Roux, 75724 Paris Cedex 15, France
| | - Philippe Mazodier
- Unité Postulante de Génétique Bactérienne et Différenciation, CNRS URA 2172, Institut Pasteur, 25 rue Dr Roux, 75724 Paris Cedex 15, France
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Wendisch VF, Bott M, Kalinowski J, Oldiges M, Wiechert W. Emerging Corynebacterium glutamicum systems biology. J Biotechnol 2006; 124:74-92. [PMID: 16406159 DOI: 10.1016/j.jbiotec.2005.12.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Revised: 10/12/2005] [Accepted: 12/01/2005] [Indexed: 10/25/2022]
Abstract
Corynebacterium glutamicum is widely used for the biotechnological production of amino acids. Amino acid producing strains have been improved classically by mutagenesis and screening as well as in a rational manner using recombinant DNA technology. Metabolic flux analysis may be viewed as the first systems approach to C. glutamicum physiology since it combines isotope labeling data with metabolic network models of the biosynthetic and central metabolic pathways. However, only the complete genome sequence of C. glutamicum and post-genomics methods such as transcriptomics and proteomics have allowed characterizing metabolic and regulatory properties of this bacterium on a truly global level. Besides transcriptomics and proteomics, metabolomics and modeling approaches have now been established. Systems biology, which uses systematic genomic, proteomic and metabolomic technologies with the final aim of constructing comprehensive and predictive models of complex biological systems, is emerging for C. glutamicum. We will present current developments that advanced our insight into fundamental biology of C. glutamicum and that in the future will enable novel biotechnological applications for the improvement of amino acid production.
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Babb K, Bykowski T, Riley SP, Miller MC, Demoll E, Stevenson B. Borrelia burgdorferi EbfC, a novel, chromosomally encoded protein, binds specific DNA sequences adjacent to erp loci on the spirochete's resident cp32 prophages. J Bacteriol 2006; 188:4331-9. [PMID: 16740939 PMCID: PMC1482946 DOI: 10.1128/jb.00005-06] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Accepted: 04/03/2006] [Indexed: 11/20/2022] Open
Abstract
All examined isolates of the Lyme disease spirochete, Borrelia burgdorferi, naturally maintain numerous variants of a prophage family as circular cp32 episomes. Each cp32 carries a locus encoding one or two different Erp outer membrane, surface-exposed lipoproteins. Many of the Erp proteins bind a host complement regulator, factor H, which is hypothesized to protect the spirochete from complement-mediated killing. We now describe the isolation and characterization of a novel, chromosomally encoded protein, EbfC, that binds specific DNA sequences located immediately 5' of all erp loci. This is one of the first site-specific DNA-binding proteins to be identified in any spirochete. The location of the ebfC gene on the B. burgdorferi chromosome suggests that the cp32 prophages have evolved to use this bacterial host protein for their own benefit and that EbfC probably plays additional roles in the bacterium. A wide range of other bacteria encode homologs of EbfC, none of which have been well characterized, so demonstration that B. burgdorferi EbfC is a site-specific DNA-binding protein has broad implications across the eubacterial kingdom.
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Affiliation(s)
- Kelly Babb
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, MS421 W. R. Willard Medical Education Building, Lexington, KY 40536-0298, USA
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Letek M, Valbuena N, Ramos A, Ordóñez E, Gil JA, Mateos LM. Characterization and use of catabolite-repressed promoters from gluconate genes in Corynebacterium glutamicum. J Bacteriol 2006; 188:409-23. [PMID: 16385030 PMCID: PMC1347311 DOI: 10.1128/jb.188.2.409-423.2006] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genes involved in gluconate catabolism (gntP and gntK) in Corynebacterium glutamicum are scattered in the chromosome, and no regulatory genes are apparently associated with them, in contrast with the organization of the gnt operon in Escherichia coli and Bacillus subtilis. In C. glutamicum, gntP and gntK are essential genes when gluconate is the only carbon and energy source. Both genes contain upstream regulatory regions consisting of a typical promoter and a hypothetical cyclic AMP (cAMP) receptor protein (CRP) binding region but lack the expected consensus operator region for binding of the GntR repressor protein. Expression analysis by Northern blotting showed monocistronic transcripts for both genes. The expression of gntP and gntK is not induced by gluconate, and the gnt genes are subject to catabolite repression by sugars, such as glucose, fructose, and sucrose, as was detected by quantitative reverse transcription-PCR (qRT-PCR). Specific analysis of the DNA promoter sequences (PgntK and PgntP) was performed using bifunctional promoter probe vectors containing mel (involved in melanin production) or egfp2 (encoding a green fluorescent protein derivative) as the reporter gene. Using this approach, we obtained results parallel to those from qRT-PCR. An applied example of in vivo gene expression modulation of the divIVA gene in C. glutamicum is shown, corroborating the possible use of the gnt promoters to control gene expression. glxR (which encodes GlxR, the hypothetical CRP protein) was subcloned from the C. glutamicum chromosomal DNA and overexpressed in corynebacteria; we found that the level of gnt expression was slightly decreased compared to that of the control strains. The purified GlxR protein was used in gel shift mobility assays, and a specific interaction of GlxR with sequences present on PgntP and PgntK fragments was detected only in the presence of cAMP.
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Affiliation(s)
- Michal Letek
- Area de Microbiología, Dpto. Ecología, Genética y Microbiología, Universidad de León, 24071 León, Spain
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Kocan M, Schaffer S, Ishige T, Sorger-Herrmann U, Wendisch VF, Bott M. Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response. J Bacteriol 2006; 188:724-32. [PMID: 16385062 PMCID: PMC1347282 DOI: 10.1128/jb.188.2.724-732.2006] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium glutamicum contains genes for 13 two-component signal transduction systems. In order to test for their essentiality and involvement in the adaptive response to phosphate (Pi) starvation, a set of 12 deletion mutants was constructed. One of the mutants was specifically impaired in its ability to grow under Pi limitation, and therefore the genes lacking in this strain were named phoS (encoding the sensor kinase) and phoR (encoding the response regulator). DNA microarray analyses with the C. glutamicum wild type and the DeltaphoRS mutant supported a role for the PhoRS system in the adaptation to Pi starvation. In contrast to the wild type, the DeltaphoRS mutant did not induce the known Pi starvation-inducible (psi) genes within 1 hour after a shift from Pi excess to Pi limitation, except for the pstSCAB operon, which was still partially induced. This indicates an activator function for PhoR and the existence of at least one additional regulator of the pst operon. Primer extension analysis of selected psi genes (pstS, ugpA, phoR, ushA, and nucH) confirmed the microarray data and provided evidence for positive autoregulation of the phoRS genes.
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Affiliation(s)
- Martina Kocan
- Institut für Biotechnologie 1, Forschungszentrum Jülich, D-52425 Jülich, Germany.
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