151
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Regulatory response to carbon starvation in Caulobacter crescentus. PLoS One 2011; 6:e18179. [PMID: 21494595 PMCID: PMC3073932 DOI: 10.1371/journal.pone.0018179] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 02/22/2011] [Indexed: 11/19/2022] Open
Abstract
Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the regulatory response of C. crescentus to carbon starvation, based on combined high-throughput proteome and transcriptome analyses. Our results identify cell cycle changes in gene expression in response to carbon starvation that involve the prominent role of the FixK FNR/CAP family transcription factor and the CtrA cell cycle regulator. Notably, the SigT ECF sigma factor mediates the carbon starvation-induced degradation of CtrA, while activating a core set of general starvation-stress genes that respond to carbon starvation, osmotic stress, and exposure to heavy metals. Comparison of the response of swarmer cells and stalked cells to carbon starvation revealed four groups of genes that exhibit different expression profiles. Also, cell pole morphogenesis and initiation of chromosome replication normally occurring at the swarmer-to-stalked cell transition are uncoupled in carbon-starved cells.
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152
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YjbH-enhanced proteolysis of Spx by ClpXP in Bacillus subtilis is inhibited by the small protein YirB (YuzO). J Bacteriol 2011; 193:2133-40. [PMID: 21378193 DOI: 10.1128/jb.01350-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Spx protein of Bacillus subtilis is a global regulator of the oxidative stress response. Spx concentration is controlled at the level of proteolysis by the ATP-dependent protease ClpXP and a substrate-binding protein, YjbH, which interacts with Spx. A yeast two-hybrid screen was carried out using yjbH as bait to uncover additional substrates or regulators of YjbH activity. Of the several genes identified in the screen, one encoded a small protein, YirB (YuzO), which elevated Spx concentration and activity in vivo when overproduced from an isopropyl-β-D-thiogalactopyranoside (IPTG)-inducible yirB construct. Pulldown experiments using extracts of B. subtilis cells producing a His-tagged YirB showed that native YjbH interacts with YirB in B. subtilis. Pulldown experiments using affinity-tagged Spx showed that YirB inhibited YjbH interaction with Spx. In vitro, YjbH-mediated proteolysis of Spx by ClpXP was inhibited by YirB. The activity of YirB is similar to that of the antiadaptor proteins that were previously shown to reduce proteolysis of a specific ClpXP substrate by interacting with a substrate-binding protein.
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153
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Alternative split sites for fragment complementation, and glyphosate function as extra ligand and stabilizer for the AroA enzyme complexes. CHINESE SCIENCE BULLETIN-CHINESE 2011. [DOI: 10.1007/s11434-010-4323-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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154
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Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase. Proc Natl Acad Sci U S A 2011; 108:2234-9. [PMID: 21266546 DOI: 10.1073/pnas.1014278108] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clp ATPases are ring-shaped AAA+ motors in the degradation pathway that perform critical actions of unfolding and translocating substrate proteins (SPs) through narrow pores to deliver them to peptidase components. These actions are effected by conserved diaphragm-forming loops found in the central channel of the Clp ATPase hexamer. Conformational changes, that take place in the course of repetitive ATP-driven cycles, result in mechanical forces applied by the central channel loops onto the SP. We use coarse-grained simulations to elucidate allostery-driven mechanisms of unfolding and translocation of a tagged four-helix bundle protein by the ClpY ATPase. Unfolding is initiated at the tagged C-terminal region via an obligatory intermediate. The resulting nonnative conformation is competent for translocation, which proceeds on a different time scale than unfolding and involves sharp stepped transitions. Completion of the translocation process requires assistance from the ClpQ peptidase. These mechanisms contrast nonallosteric mechanical unfolding of the SP. In atomic force microscopy experiments, multiple unfolding pathways are available and large mechanical forces are required to unravel the SP relative to those exerted by the central channel loops of ClpY. SP threading through a nonallosteric ClpY nanopore involves simultaneous unfolding and translocation effected by strong pulling forces.
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155
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Wilson WA, Roach PJ, Montero M, Baroja-Fernández E, Muñoz FJ, Eydallin G, Viale AM, Pozueta-Romero J. Regulation of glycogen metabolism in yeast and bacteria. FEMS Microbiol Rev 2011; 34:952-85. [PMID: 20412306 DOI: 10.1111/j.1574-6976.2010.00220.x] [Citation(s) in RCA: 253] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Microorganisms have the capacity to utilize a variety of nutrients and adapt to continuously changing environmental conditions. Many microorganisms, including yeast and bacteria, accumulate carbon and energy reserves to cope with the starvation conditions temporarily present in the environment. Glycogen biosynthesis is a main strategy for such metabolic storage, and a variety of sensing and signaling mechanisms have evolved in evolutionarily distant species to ensure the production of this homopolysaccharide. At the most fundamental level, the processes of glycogen synthesis and degradation in yeast and bacteria share certain broad similarities. However, the regulation of these processes is sometimes quite distinct, indicating that they have evolved separately to respond optimally to the habitat conditions of each species. This review aims to highlight the mechanisms, both at the transcriptional and at the post-transcriptional level, that regulate glycogen metabolism in yeast and bacteria, focusing on selected areas where the greatest increase in knowledge has occurred during the last few years. In the yeast system, we focus particularly on the various signaling pathways that control the activity of the enzymes of glycogen storage. We also discuss our recent understanding of the important role played by the vacuole in glycogen metabolism. In the case of bacterial glycogen, special emphasis is placed on aspects related to the genetic regulation of glycogen metabolism and its connection with other biological processes.
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Affiliation(s)
- Wayne A Wilson
- Biochemistry and Nutrition Department, Des Moines University, Des Moines, IA, USA
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156
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Kim JH, Wei JR, Wallach JB, Robbins RS, Rubin EJ, Schnappinger D. Protein inactivation in mycobacteria by controlled proteolysis and its application to deplete the beta subunit of RNA polymerase. Nucleic Acids Res 2010; 39:2210-20. [PMID: 21075796 PMCID: PMC3064785 DOI: 10.1093/nar/gkq1149] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Using a component of the Escherichia coli protein degradation machinery, we have established a system to regulate protein stability in mycobacteria. A protein tag derived from the E. coli SsrA degradation signal did not affect several reporter proteins in wild-type Mycobacterium smegmatis or Mycobacterium tuberculosis. Expression of the adaptor protein SspB, which recognizes this modified tag and helps deliver tagged proteins to the protease ClpXP, strongly decreased the activities and protein levels of different reporters. This inactivation did not occur when the function of ClpX was inhibited. Using this system, we constructed a conditional M. smegmatis knockdown mutant in which addition of anhydrotetracycline (atc) caused depletion of the beta subunit of RNA polymerase, RpoB. The impact of atc on this mutant was dose-dependent. Very low amounts of atc did not prevent growth but increased sensitivity to an antibiotic that inactivates RpoB. Intermediate amounts of RpoB knockdown resulted in bacteriostasis and a more substantial depletion led to a decrease in viability by up to 99%. These studies identify SspB-mediated proteolysis as an efficient approach to conditionally inactivate essential proteins in mycobacteria. They further demonstrate that depletion of RpoB by ∼93% is sufficient to cause death of M. smegmatis.
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Affiliation(s)
- Jee-Hyun Kim
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
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157
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Singh A, Grover A. Plant Hsp100/ClpB-like proteins: poorly-analyzed cousins of yeast ClpB machine. PLANT MOLECULAR BIOLOGY 2010; 74:395-404. [PMID: 20811767 DOI: 10.1007/s11103-010-9682-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 08/20/2010] [Indexed: 05/21/2023]
Abstract
ClpB/Hsp100 proteins act as chaperones, mediating disaggregation of denatured proteins. Recent work shows that apart from cytoplasm, these proteins are localized to nuclei, chloroplasts, mitochondria and plasma membrane. While ClpB/Hsp100 genes are essentially stress-induced (mainly heat stress) in vegetative organs of the plant body, expression of ClpB/Hsp100 proteins is noted to be constitutive in plant reproductive structures like pollen grains, developing embryos, seeds etc. With global warming looming large on the horizon, ways to genetically engineer plants against high temperature stress are urgently needed. Yeast mutants unable to synthesize active ClpB/Hsp100 protein show a clear thermosensitive phenotype. ClpB/Hsp100 proteins are implicated in high temperature stress tolerance in plants. We herein highlight the selected important facets of this protein family in plants.
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Affiliation(s)
- Amanjot Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
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158
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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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159
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Festa RA, Jones MB, Butler-Wu S, Sinsimer D, Gerads R, Bishai WR, Peterson SN, Darwin KH. A novel copper-responsive regulon in Mycobacterium tuberculosis. Mol Microbiol 2010; 79:133-48. [PMID: 21166899 DOI: 10.1111/j.1365-2958.2010.07431.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this work we describe the identification of a copper-inducible regulon in Mycobacterium tuberculosis (Mtb). Among the regulated genes was Rv0190/MT0200, a paralogue of the copper metalloregulatory repressor CsoR. The five-locus regulon, which includes a gene that encodes the copper-protective metallothionein MymT, was highly induced in wild-type Mtb treated with copper, and highly expressed in an Rv0190/MT0200 mutant. Importantly, the Rv0190/MT0200 mutant was hyper-resistant to copper. The promoters of all five loci share a palindromic motif that was recognized by the gene product of Rv0190/MT0200. For this reason we named Rv0190/MT0200 RicR for regulated in copper repressor. Intriguingly, several of the RicR-regulated genes, including MymT, are unique to pathogenic Mycobacteria. The identification of a copper-responsive regulon specific to virulent mycobacterial species suggests copper homeostasis must be maintained during an infection. Alternatively, copper may provide a cue for the expression of genes unrelated to metal homeostasis, but nonetheless necessary for survival in a host.
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Affiliation(s)
- Richard A Festa
- New York University School of Medicine, Department of Microbiology, 550 First Avenue MSB 236, New York, NY 10016, USA
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160
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Frost LS, Koraimann G. Regulation of bacterial conjugation: balancing opportunity with adversity. Future Microbiol 2010; 5:1057-71. [PMID: 20632805 DOI: 10.2217/fmb.10.70] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Conjugative plasmids are involved in the dissemination of important traits such as antibiotic resistance, virulence determinants and metabolic pathways involved in adapting to environmental niches, a process termed horizontal or lateral gene transfer. Conjugation is the process of transferring DNA from a donor to a recipient cell with the establishment of the incoming DNA and its cargo of genetic traits within the transconjugant. Conjugation is mediated by self-transmissible plasmids as well as phage-like sequences that have been integrated into the bacterial chromosome, such as integrative and conjugative elements (ICEs) that now include conjugative transposons. Both conjugative plasmids and ICEs can mediate the transfer of mobilizable elements by sharing their conjugative machinery. Conjugation can either be induced, usually by small molecules or peptides or by excision of the ICE from the host chromosome, or it can be tightly regulated by plasmid- and host-encoded factors. The transfer potential of these transfer regions depends on the integration of many signals in response to environmental and physiological cues. This review will focus on the mechanisms that influence transfer potential in these systems, particularly those of the IncF incompatibility group.
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Affiliation(s)
- Laura S Frost
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada.
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161
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Kuhn D, Blank LM, Schmid A, Bühler B. Systems biotechnology - Rational whole-cell biocatalyst and bioprocess design. Eng Life Sci 2010. [DOI: 10.1002/elsc.201000009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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162
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Ezquer I, Li J, Ovecka M, Baroja-Fernández E, Muñoz FJ, Montero M, Díaz de Cerio J, Hidalgo M, Sesma MT, Bahaji A, Etxeberria E, Pozueta-Romero J. Microbial volatile emissions promote accumulation of exceptionally high levels of starch in leaves in mono- and dicotyledonous plants. PLANT & CELL PHYSIOLOGY 2010; 51:1674-93. [PMID: 20739303 DOI: 10.1093/pcp/pcq126] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Microbes emit volatile compounds that affect plant growth and development. However, little or nothing is known about how microbial emissions may affect primary carbohydrate metabolism in plants. In this work we explored the effect on leaf starch metabolism of volatiles released from different microbial species ranging from Gram-negative and Gram-positive bacteria to fungi. Surprisingly, we found that all microbial species tested (including plant pathogens and species not normally interacting with plants) emitted volatiles that strongly promoted starch accumulation in leaves of both mono- and dicotyledonous plants. Starch content in leaves of plants treated for 2 d with microbial volatiles was comparable with or even higher than that of reserve organs such as potato tubers. Transcriptome and enzyme activity analyses of potato leaves exposed to volatiles emitted by Alternaria alternata revealed that starch overaccumulation was accompanied by up-regulation of sucrose synthase, invertase inhibitors, starch synthase class III and IV, starch branching enzyme and glucose-6-phosphate transporter. This phenomenon, designated as MIVOISAP (microbial volatiles-induced starch accumulation process), was also accompanied by down-regulation of acid invertase, plastidial thioredoxins, starch breakdown enzymes, proteins involved in internal amino acid provision and less well defined mechanisms involving a bacterial- type stringent response. Treatment of potato leaves with fungal volatiles also resulted in enhanced levels of sucrose, ADPglucose, UDPglucose and 3-phosphoglycerate. MIVOISAP is independent of the presence of sucrose in the culture medium and is strongly repressed by cysteine supplementation. The discovery that microbial volatiles trigger starch accumulation enhancement in leaves constitutes an unreported mechanism for the elicidation of plant carbohydrate metabolism by microbes.
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Affiliation(s)
- Ignacio Ezquer
- Instituto de Agrobiotecnología (CSIC/UPNA/Gobierno de Navarra), Mutiloako etorbidea z/g, 31192 Mutiloabeti, Nafarroa, Spain
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163
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Sundar S, McGinness KE, Baker TA, Sauer RT. Multiple sequence signals direct recognition and degradation of protein substrates by the AAA+ protease HslUV. J Mol Biol 2010; 403:420-9. [PMID: 20837023 DOI: 10.1016/j.jmb.2010.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/02/2010] [Accepted: 09/03/2010] [Indexed: 11/25/2022]
Abstract
Proteolysis is important for protein quality control and for the proper regulation of many intracellular processes in prokaryotes and eukaryotes. Discerning substrates from other cellular proteins is a key aspect of proteolytic function. The Escherichia coli HslUV protease is a member of a major family of ATP-dependent AAA+ degradation machines. HslU hexamers recognize and unfold native protein substrates and then translocate the polypeptide into the degradation chamber of the HslV peptidase. Although a wealth of structural information is available for this system, relatively little is known about mechanisms of substrate recognition. Here, we demonstrate that mutations in the unstructured N-terminal and C-terminal sequences of two model substrates alter HslUV recognition and degradation kinetics, including changes in V(max). By introducing N- or C-terminal sequences that serve as recognition sites for specific peptide-binding proteins, we show that blocking either terminus of the substrate interferes with HslUV degradation, with synergistic effects when both termini are obstructed. These results support a model in which one terminus of the substrate is tethered to the protease and the other terminus is engaged by the translocation/unfolding machinery in the HslU pore. Thus, degradation appears to consist of discrete steps, which involve the interaction of different terminal sequence signals in the substrate with different receptor sites in the HslUV protease.
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Affiliation(s)
- Shankar Sundar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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164
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Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber. EMBO J 2010; 29:3520-30. [PMID: 20834233 DOI: 10.1038/emboj.2010.226] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 08/19/2010] [Indexed: 11/08/2022] Open
Abstract
Lon proteases are distributed in all kingdoms of life and are required for survival of cells under stress. Lon is a tandem fusion of an AAA+ molecular chaperone and a protease with a serine-lysine catalytic dyad. We report the 2.0-Å resolution crystal structure of Thermococcus onnurineus NA1 Lon (TonLon). The structure is a three-tiered hexagonal cylinder with a large sequestered chamber accessible through an axial channel. Conserved loops extending from the AAA+ domain combine with an insertion domain containing the membrane anchor to form an apical domain that serves as a gate governing substrate access to an internal unfolding and degradation chamber. Alternating AAA+ domains are in tight- and weak-binding nucleotide states with different domain orientations and intersubunit contacts, reflecting intramolecular dynamics during ATP-driven protein unfolding and translocation. The bowl-shaped proteolytic chamber is contiguous with the chaperone chamber allowing internalized proteins direct access to the proteolytic sites without further gating restrictions.
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165
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Effantin G, Ishikawa T, De Donatis GM, Maurizi MR, Steven AC. Local and global mobility in the ClpA AAA+ chaperone detected by cryo-electron microscopy: functional connotations. Structure 2010; 18:553-62. [PMID: 20462489 DOI: 10.1016/j.str.2010.02.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 02/16/2010] [Accepted: 02/17/2010] [Indexed: 10/19/2022]
Abstract
The ClpA chaperone combines with the ClpP peptidase to perform targeted proteolysis in the bacterial cytoplasm. ClpA monomer has an N-terminal substrate-binding domain and two AAA+ ATPase domains (D1 and D2). ClpA hexamers stack axially on ClpP heptamers to form the symmetry-mismatched protease. We used cryo-electron microscopy to visualize the ClpA-ATPgammaS hexamer, in the context of ClpAP complexes. Two segments lining the axial channel show anomalously low density, indicating that these motifs, which have been implicated in substrate translocation, are mobile. We infer that ATP hydrolysis is accompanied by substantial structural changes in the D2 but not the D1 tier. The entire N domain is rendered invisible by large-scale fluctuations. When deletions of 10 and 15 residues were introduced into the linker, N domain mobility was reduced but not eliminated and changes were observed in enzymatic activities. Based on these observations, we present a pseudo-atomic model of ClpAP holoenzyme, a dynamic proteolytic nanomachine.
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Affiliation(s)
- Grégory Effantin
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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166
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Timmermans J, Van Melderen L. Post-transcriptional global regulation by CsrA in bacteria. Cell Mol Life Sci 2010; 67:2897-908. [PMID: 20446015 PMCID: PMC11115721 DOI: 10.1007/s00018-010-0381-z] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 04/14/2010] [Accepted: 04/20/2010] [Indexed: 12/16/2022]
Abstract
Global regulation allows bacteria to rapidly modulate the expression of a large variety of unrelated genes in response to environmental changes. Global regulators act at different levels of gene expression. This review focuses on CsrA, a post-transcriptional regulator that affects translation of its gene targets by binding mRNAs. CsrA controls a large variety of physiological processes such as central carbon metabolism, motility and biofilm formation. The activity of CsrA is itself tightly regulated by the CsrB and CsrC small RNAs and the BarA-UvrY two-component system.
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Affiliation(s)
- Johan Timmermans
- Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires, Faculté des Sciences, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Laurence Van Melderen
- Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires, Faculté des Sciences, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
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167
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Biogenesis of Salmonella enterica serovar typhimurium membrane vesicles provoked by induction of PagC. J Bacteriol 2010; 192:5645-56. [PMID: 20802043 DOI: 10.1128/jb.00590-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gram-negative bacteria ubiquitously release membrane vesicles (MVs) into the extracellular milieu. Although MVs are the product of growing bacteria, not of cell lysis or death, the regulatory mechanisms underlying MV formation remained unknown. We have found that MV biogenesis is provoked by the induction of PagC, a Salmonella-specific protein whose expression is activated by conditions that mimic acidified macrophage phagosomes. PagC is a major constituent of Salmonella MVs, and increased expression accelerates vesiculation. Expression of PagC is regulated at the posttranscriptional and/or posttranslational level in a sigmaS (RpoS)-dependent manner. Serial quantitative analysis has demonstrated that MV formation can accelerate when the quantity of the MV constituents, OmpX and PagC, rises. Overproduction of PagC dramatically impacts the difference in the relative amount of vesiculation, but the corresponding overproduction of OmpX was less pronounced. Quantitative examination of the ratios of PagC and OmpX in the periplasm, outer membrane, and MVs demonstrates that PagC is preferentially enriched in MVs released from Salmonella cells. This suggests that specific protein sorting mechanisms operate when MVs are formed. The possible role(s) of PagC-MV in host cells is discussed.
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168
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Gandotra S, Lebron MB, Ehrt S. The Mycobacterium tuberculosis proteasome active site threonine is essential for persistence yet dispensable for replication and resistance to nitric oxide. PLoS Pathog 2010; 6:e1001040. [PMID: 20711362 PMCID: PMC2920845 DOI: 10.1371/journal.ppat.1001040] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 07/13/2010] [Indexed: 11/17/2022] Open
Abstract
Previous work revealed that conditional depletion of the core proteasome subunits PrcB and PrcA impaired growth of Mycobacterium tuberculosis in vitro and in mouse lungs, caused hypersusceptibility to nitric oxide (NO) and impaired persistence of the bacilli during chronic mouse infections. Here, we show that genetic deletion of prcBA led to similar phenotypes. Surprisingly, however, an active site mutant proteasome complemented the in vitro and in vivo growth defects of the prcBA knockout (Delta prcBA) as well as its NO hypersensitivity. In contrast, long-term survival of M. tuberculosis in stationary phase and during starvation in vitro and in the chronic phase of mouse infection required a proteolytically active proteasome. Inhibition of inducible nitric oxide synthase did not rescue survival of Delta prcBA, revealing a function beyond NO defense, by which the proteasome contributes to M. tuberculosis fitness during chronic mouse infections. These findings suggest that proteasomal proteolysis facilitates mycobacterial persistence, that M. tuberculosis faces starvation during chronic mouse infections and that the proteasome serves a proteolysis-independent function.
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Affiliation(s)
- Sheetal Gandotra
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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169
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Liang W, Deutscher MP. A novel mechanism for ribonuclease regulation: transfer-messenger RNA (tmRNA) and its associated protein SmpB regulate the stability of RNase R. J Biol Chem 2010; 285:29054-8. [PMID: 20688916 DOI: 10.1074/jbc.c110.168641] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The amount of RNase R, an important degradative exoribonuclease, increases 3-10-fold under a variety of stress conditions. This elevation is due to posttranslational regulation in which the highly unstable RNase R protein becomes stabilized during stress. Here we identify two components of the trans-translation machinery, transfer-messenger RNA (tmRNA) and SmpB, that are responsible for the short half-life of RNase R in exponential phase cells. The absence of either lengthens the half-life of RNase R in vivo >6-fold. SmpB directly interacts with RNase R in vitro and is stimulated by tmRNA. The C-terminal region of RNase R, encompassing its basic region and adjacent S1 domain are required for the interaction; their removal eliminates binding and stabilizes RNase R in vivo. However, the binding of SmpB and tmRNA does not alter RNase R activity. These data define a previously unknown regulatory process in which the stability of an RNase is determined by its interaction with an RNA and an RNA-associated protein.
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Affiliation(s)
- Wenxing Liang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101, USA
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170
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Ayuso-Tejedor S, Nishikori S, Okuno T, Ogura T, Sancho J. FtsH cleavage of non-native conformations of proteins. J Struct Biol 2010; 171:117-24. [DOI: 10.1016/j.jsb.2010.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 05/01/2010] [Accepted: 05/03/2010] [Indexed: 11/17/2022]
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171
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Lorenzon RZ, Cunha CE, Marcondes MF, Machado MF, Juliano MA, Oliveira V, Travassos LR, Paschoalin T, Carmona AK. Kinetic characterization of the Escherichia coli oligopeptidase A (OpdA) and the role of the Tyr607 residue. Arch Biochem Biophys 2010; 500:131-6. [PMID: 20513640 DOI: 10.1016/j.abb.2010.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 05/19/2010] [Accepted: 05/24/2010] [Indexed: 10/19/2022]
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172
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Mycobacterium tuberculosis ClpX interacts with FtsZ and interferes with FtsZ assembly. PLoS One 2010; 5:e11058. [PMID: 20625433 PMCID: PMC2897852 DOI: 10.1371/journal.pone.0011058] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 05/14/2010] [Indexed: 11/19/2022] Open
Abstract
FtsZ assembly at the midcell division site in the form of a Z-ring is crucial for initiation of the cell division process in eubacteria. It is largely unknown how this process is regulated in the human pathogen Mycobacterium tuberculosis. Here we show that the expression of clpX was upregulated upon macrophage infection and exposure to cephalexin antibiotic, the conditions where FtsZ-ring assembly is delayed. Independently, we show using pull-down, solid-phase binding, bacterial two-hybrid and mycobacterial protein fragment complementation assays, that M. tuberculosis FtsZ interacts with ClpX, the substrate recognition domain of the ClpXP protease. Incubation of FtsZ with ClpX increased the critical concentration of GTP-dependent polymerization of FtsZ. Immunoblotting revealed that the intracellular ratio of ClpX to FtsZ in wild type M. tuberculosis is approximately 1:2. Overproduction of ClpX increased cell length and modulated the localization of FtsZ at midcell sites; however, intracellular FtsZ levels were unaffected. A ClpX-CFP fusion protein localized to the cell poles and midcell sites and colocalized with the FtsZ-YFP protein. ClpX also interacted with FtsZ mutant proteins defective for binding to and hydrolyzing GTP and possibly for interactions with other proteins. Taken together, our results suggest that M. tuberculosis ClpX interacts stoichiometrically with FtsZ protomers, independent of its nucleotide-bound state and negatively regulates FtsZ activities, hence cell division.
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173
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Li Y, Yamazaki A, Zou L, Biddle E, Zeng Q, Wang Y, Lin H, Wang Q, Yang CH. ClpXP protease regulates the type III secretion system of Dickeya dadantii 3937 and is essential for the bacterial virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:871-878. [PMID: 20521950 DOI: 10.1094/mpmi-23-7-0871] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The type III secretion system (T3SS) is considered one of the major virulence factors in many bacterial pathogens. This report demonstrates that RssB, ClpXP, and RpoS play a role in T3SS regulation of Dickeya dadantii 3937. ClpP is a serine-type protease which associates with the ClpX chaperone to form a functional Clp proteolytic complex for degradation of proteins. With the assistance of recognition factor RssB, ClpXP degrades the RpoS sigma factor. RpoS positively regulates the expression of the rsmA gene encoding an RNA-binding regulatory protein. By interacting with the hrpL mRNA, RsmA reduces HrpL production and downregulates the T3SS genes in the HrpL regulon. In addition, ClpXP, RssB, and RpoS affect pectinolytic enzyme production in D. dadantii 3937, probably through RsmA. The ClpXP and RssB proteins are essential for bacterial virulence.
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Affiliation(s)
- Yan Li
- Department of Plant Pathology, College of Agronomy & Biotechnology, China Agricultural University, Bejing, China
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174
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Andrews-Polymenis HL, Bäumler AJ, McCormick BA, Fang FC. Taming the elephant: Salmonella biology, pathogenesis, and prevention. Infect Immun 2010; 78:2356-69. [PMID: 20385760 PMCID: PMC2876576 DOI: 10.1128/iai.00096-10] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella infections continue to cause substantial morbidity and mortality throughout the world. However, recent discoveries and new paradigms promise to lead to novel strategies to diagnose, treat, and prevent Salmonella infections. This review provides an update of the Salmonella field based on oral presentations given at the recent 3rd ASM Conference on Salmonella: Biology, Pathogenesis and Prevention.
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Affiliation(s)
- Helene L. Andrews-Polymenis
- Department of Microbiology and Molecular Pathogenesis, Texas A&M University System Health Science Center, College Station, Texas, Department of Medical Microbiology and Immunology, University of California at Davis, Davis, California, Department of Molecular Genetics and Microbiology, University of Massachusetts Medical Center, Worcester, Massachusetts, Departments of Microbiology and Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Andreas J. Bäumler
- Department of Microbiology and Molecular Pathogenesis, Texas A&M University System Health Science Center, College Station, Texas, Department of Medical Microbiology and Immunology, University of California at Davis, Davis, California, Department of Molecular Genetics and Microbiology, University of Massachusetts Medical Center, Worcester, Massachusetts, Departments of Microbiology and Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Beth A. McCormick
- Department of Microbiology and Molecular Pathogenesis, Texas A&M University System Health Science Center, College Station, Texas, Department of Medical Microbiology and Immunology, University of California at Davis, Davis, California, Department of Molecular Genetics and Microbiology, University of Massachusetts Medical Center, Worcester, Massachusetts, Departments of Microbiology and Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Ferric C. Fang
- Department of Microbiology and Molecular Pathogenesis, Texas A&M University System Health Science Center, College Station, Texas, Department of Medical Microbiology and Immunology, University of California at Davis, Davis, California, Department of Molecular Genetics and Microbiology, University of Massachusetts Medical Center, Worcester, Massachusetts, Departments of Microbiology and Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington
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175
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Sakr S, Cirinesi AM, Ullers RS, Schwager F, Georgopoulos C, Genevaux P. Lon protease quality control of presecretory proteins in Escherichia coli and its dependence on the SecB and DnaJ (Hsp40) chaperones. J Biol Chem 2010; 285:23506-14. [PMID: 20504766 DOI: 10.1074/jbc.m110.133058] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Various environmental insults result in irreversible damage to proteins and protein complexes. To cope, cells have evolved dedicated protein quality control mechanisms involving molecular chaperones and proteases. Here, we provide both genetic and biochemical evidence that the Lon protease and the SecB and DnaJ/Hsp40 chaperones are involved in the quality control of presecretory proteins in Escherichia coli. We showed that mutations in the lon gene alleviate the cold-sensitive phenotype of a secB mutant. Such suppression was not observed with either clpP or clpQ protease mutants. In comparison to the respective single mutants, the double secB lon mutant strongly accumulates aggregates of SecB substrates at physiological temperatures, suggesting that the chaperone and the protease share substrates. These observations were extended in vitro by showing that the main substrates identified in secB lon aggregates, namely proOmpF and proOmpC, are highly sensitive to specific degradation by Lon. In contrast, both substrates are significantly protected from Lon degradation by SecB. Interestingly, the chaperone DnaJ by itself protects substrates better from Lon degradation than SecB or the complete DnaK/DnaJ/GrpE chaperone machinery. In agreement with this finding, a DnaJ mutant protein that does not functionally interact in vivo with DnaK efficiently suppresses the SecB cold-sensitive phenotype, highlighting the role of DnaJ in assisting presecretory proteins. Taken together, our data suggest that when the Sec secretion pathway is compromised, a pool of presecretory proteins is transiently maintained in a translocation-competent state and, thus, protected from Lon degradation by either the SecB or DnaJ chaperones.
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Affiliation(s)
- Samer Sakr
- Laboratoire de Microbiologie et Génétique Moléculaire, CNRS and the Université Paul Sabatier, 31062 Toulouse Cedex 9, France
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176
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Effantin G, Maurizi MR, Steven AC. Binding of the ClpA unfoldase opens the axial gate of ClpP peptidase. J Biol Chem 2010; 285:14834-40. [PMID: 20236930 PMCID: PMC2863180 DOI: 10.1074/jbc.m109.090498] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/06/2010] [Indexed: 11/06/2022] Open
Abstract
ClpP is a serine protease whose active sites are sequestered in a cavity enclosed between two heptameric rings of subunits. The ability of ClpP to process folded protein substrates depends on its being partnered by an AAA+ ATPase/unfoldase, ClpA or ClpX. In active complexes, substrates are unfolded and fed along an axial channel to the degradation chamber inside ClpP. We have used cryoelectron microscopy at approximately 11-A resolution to investigate the three-dimensional structure of ClpP complexed with either one or two end-mounted ClpA hexamers. In the absence of ClpA, the apical region of ClpP is sealed; however, it opens on ClpA binding, creating an access channel. This region is occupied by the N-terminal loops (residues 1-17) of ClpP, which tend to be poorly visible in crystal structures, indicative of conformational variability. Nevertheless, we were able to model the closed-to-open transition that accompanies ClpA binding in terms of movements of these loops; in particular, "up" conformations of the loops correlate with the open state. The main part of ClpP, the barrel formed by 14 copies of residues 18-193, is essentially unchanged by the interaction with ClpA. Using difference mapping, we localized the binding site for ClpA to a peripheral pocket between adjacent ClpP subunits. Based on these observations, we propose that access to the ClpP degradation chamber is controlled allosterically by hinged movements of its N-terminal loops, which the symmetry-mismatched binding of ClpA suffices to induce.
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Affiliation(s)
| | - Michael R. Maurizi
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
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177
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YneA, an SOS-induced inhibitor of cell division in Bacillus subtilis, is regulated posttranslationally and requires the transmembrane region for activity. J Bacteriol 2010; 192:3159-73. [PMID: 20400548 DOI: 10.1128/jb.00027-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cell viability depends on the stable transmission of genetic information to each successive generation. Therefore, in the event of intrinsic or extrinsic DNA damage, it is important that cell division be delayed until DNA repair has been completed. In Bacillus subtilis, this is accomplished in part by YneA, an inhibitor of division that is induced as part of the SOS response. We sought to gain insight into the mechanism by which YneA blocks cell division and the processes involved in shutting off YneA activity. Our data suggest that YneA is able to inhibit daughter cell separation as well as septum formation. YneA contains a LysM peptidoglycan binding domain and is predicted to be exported. We established that the YneA signal peptide is rapidly cleaved, resulting in secretion of YneA into the medium. Mutations within YneA affect both the rate of signal sequence cleavage and the activity of YneA. YneA does not stably associate with the cell wall and is rapidly degraded by extracellular proteases. Based on these results, we hypothesize that exported YneA is active prior to signal peptide cleavage and that proteolysis contributes to the inactivation of YneA. Finally, we identified mutations in the transmembrane segment of YneA that abolish the ability of YneA to inhibit cell division, while having little or no effect on YneA export or stability. These data suggest that protein-protein interactions mediated by the transmembrane region may be required for YneA activity.
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178
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Jiao XD, Zhang M, Cheng S, Sun L. Analysis of Edwardsiella tarda DegP, a serine protease and a protective immunogen. FISH & SHELLFISH IMMUNOLOGY 2010; 28:672-677. [PMID: 20060910 DOI: 10.1016/j.fsi.2010.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 12/23/2009] [Accepted: 01/03/2010] [Indexed: 05/28/2023]
Abstract
Edwardsiella tarda is a severe aquaculture pathogen with a broad host range that includes humans, animal, and fish. A gene (degP(Et)) encoding a DegP homologue was cloned from TX01, a pathogenic E. tarda strain isolated from diseased fish. DegP(Et) shares high sequence identities with the DegP proteins of several bacterial species. Functional analyses showed that degP(Et) could complement the temperature-sensitive phenotype of an Escherichia coli degP null mutant. Expression of degP(Et) in TX01 was modulated by growth phase and temperature, the latter possibly through the action of the sigma(E)-like factor. Overexpression of degP(Et) (i) enhanced the ability of TX01 to disseminate in fish blood at the advanced stage of infection, (ii) heightened the activity of type 2 autoinducer, and (iii) increased the expression of luxS and the genes encoding components of the virulence-associated type III secretion system. Recombinant DegP(Et) purified from E. coli was a serine protease that exhibited maximum activity at 40 degrees C and pH8.0. The proteolytic activity of recombinant DegP(Et) depended on the catalytic triad and the PDZ domains. Immunoprotective analyses showed that purified recombinant DegP(Et) was a protective immunogen that could induce the production of specific serum antibodies and elicit strong protective immunity in fish vaccinated with DegP(Et).
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Affiliation(s)
- Xu-dong Jiao
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China; Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China
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179
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Chen C, Deutscher MP. RNase R is a highly unstable protein regulated by growth phase and stress. RNA (NEW YORK, N.Y.) 2010; 16:667-672. [PMID: 20185542 PMCID: PMC2844616 DOI: 10.1261/rna.1981010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 01/12/2010] [Indexed: 05/28/2023]
Abstract
RNase R is an important exoribonuclease that participates in the degradation of structured RNAs in Escherichia coli. In earlier work, it was shown that RNase R levels increase dramatically under certain stress conditions, particularly during cold shock and stationary phase. However, the regulatory processes that lead to this elevation are not well understood. We show here that the increase in RNase R in stationary phase is unaffected by the global regulators, RpoS and (p)ppGpp, and that it occurs despite a major reduction in rnr message. Rather, we find that RNase R is a highly unstable protein in exponential phase, with a half-life of approximately 10 min, and that the protein is stabilized in stationary phase, leading to its relative increase. RNase R is also stabilized during cold shock and by growth in minimal medium, two other conditions that lead to its elevation. These data demonstrate that RNase R is subject to regulation by a novel, posttranslational mechanism that may have important implications for our complete understanding of RNA metabolism.
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Affiliation(s)
- Chenglu Chen
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33101, USA
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180
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Lee BG, Park EY, Lee KE, Jeon H, Sung KH, Paulsen H, Rübsamen-Schaeff H, Brötz-Oesterhelt H, Song HK. Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism. Nat Struct Mol Biol 2010; 17:471-8. [DOI: 10.1038/nsmb.1787] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 02/08/2010] [Indexed: 11/09/2022]
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181
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Two Spx proteins modulate stress tolerance, survival, and virulence in Streptococcus mutans. J Bacteriol 2010; 192:2546-56. [PMID: 20233935 DOI: 10.1128/jb.00028-10] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Previous work suggested that the underlying mechanisms by which the Streptococcus mutans ClpXP protease affects virulence traits are associated with accumulation of two orthologues of the Spx regulator, named SpxA and SpxB. Here, a thorough characterization of strains lacking the spx genes (Delta spxA, Delta spxB, and Delta spxA Delta spxB) revealed that Spx, indeed, participates in the regulation of processes associated with S. mutans pathogenesis. The Delta spxA strain displayed impaired ability to grow under acidic and oxidative stress conditions and had diminished long-term viability at low pH. Although the Delta spxB strain did not show any inherent stress-sensitive phenotype, the phenotypes observed in Delta spxA were more pronounced in the Delta spxA Delta spxB double mutant. By using two in vivo models, we demonstrate for the first time that Spx is required for virulence in a gram-positive pathogen. Microarrays confirmed the global regulatory role of SpxA and SpxB. In particular, SpxA was shown to positively regulate genes associated with oxidative stress, a finding supported by enzymatic assays. SpxB had a secondary role in regulation of oxidative stress genes but appeared to play a larger role in controlling processes associated with cell wall homeostasis. Given the high degree of conservation between Spx proteins of low-GC gram-positive bacteria, these results are likely to have broad implications.
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182
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Chowdhury T, Chien P, Ebrahim S, Sauer RT, Baker TA. Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species. Protein Sci 2010; 19:242-54. [PMID: 20014030 DOI: 10.1002/pro.306] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
ClpXP, an AAA+ protease, plays key roles in protein-quality control and many regulatory processes in bacteria. The N-terminal domain of the ClpX component of ClpXP is involved in recognition of many protein substrates, either directly or by binding the SspB adaptor protein, which delivers specific classes of substrates for degradation. Despite very limited sequence homology between the E. coli and C. crescentus SspB orthologs, each of these adaptors can deliver substrates to the ClpXP enzyme from the other bacterial species. We show that the ClpX N domain recognizes different sequence determinants in the ClpX-binding (XB) peptides of C. crescentus SspBalpha and E. coli SspB. The C. crescentus XB determinants span 10 residues and involve interactions with multiple side chains, whereas the E. coli XB determinants span half as many residues with only a few important side chain contacts. These results demonstrate that the N domain of ClpX functions as a highly versatile platform for peptide recognition, allowing the emergence during evolution of alternative adaptor-binding specificities. Our results also reveal highly conserved residues in the XB peptides of both E. coli SspB and C. crescentus SspBalpha that play no detectable role in ClpX-binding or substrate delivery.
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Affiliation(s)
- Tahmeena Chowdhury
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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183
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Kirstein J, Hoffmann A, Lilie H, Schmidt R, Rübsamen-Waigmann H, Brötz-Oesterhelt H, Mogk A, Turgay K. The antibiotic ADEP reprogrammes ClpP, switching it from a regulated to an uncontrolled protease. EMBO Mol Med 2010; 1:37-49. [PMID: 20049702 PMCID: PMC3378108 DOI: 10.1002/emmm.200900002] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel class of antibiotic acyldepsipeptides (designated ADEPs) exerts its unique antibacterial activity by targeting the peptidase caseinolytic protease P (ClpP). ClpP forms proteolytic complexes with heat shock proteins (Hsp100) that select and process substrate proteins for ClpP-mediated degradation. Here, we analyse the molecular mechanism of ADEP action and demonstrate that ADEPs abrogate ClpP interaction with cooperating Hsp100 adenosine triphosphatases (ATPases). Consequently, ADEP treated bacteria are affected in ClpP-dependent general and regulatory proteolysis. At the same time, ADEPs also activate ClpP by converting it from a tightly regulated peptidase, which can only degrade short peptides, into a proteolytic machinery that recognizes and degrades unfolded polypeptides. In vivo nascent polypeptide chains represent the putative primary target of ADEP-activated ClpP, providing a rationale for the antibacterial activity of the ADEPs. Thus, ADEPs cause a complete functional reprogramming of the Clp–protease complex.
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Affiliation(s)
- Janine Kirstein
- Institut für Biologie-Mikrobiologie, FU Berlin, Berlin, Germany
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184
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Kang KH, Lee JS, Yoo M, Jin I. The influence of HtrA expression on the growth of Streptococcus mutans during acid stress. Mol Cells 2010; 29:297-304. [PMID: 20387036 DOI: 10.1007/s10059-010-0036-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 11/25/2009] [Accepted: 11/25/2009] [Indexed: 11/26/2022] Open
Abstract
When proteins are damaged under stresses conditions, these proteins are either refolded or degraded by quality control system of molecular chaperones and protease. High-temperature requirement A (htrA) is of particular interest because it can perform the roles of both protease and a chaperone. HtrA plays an important role in maintaining the physiological homeostasis of bacteria against environmental stress such as elevated temperature, oxidative and osmotic stress. Inactivation of htrA genes can thus restrict the survival ability of bacteria. These observations suggested that htrA might be responsible for acid tolerance of Streptococcus mutans. In this study, we have generated an htrA mutant and an htrA-complemented strain of S. mutans K7 isolated from a Korean in order to investigate the role of htrA in growth under acidic conditions. In terms of growth under cidic conditions, the htrA mutant exhibited 20% to 23% lower growth than the control group. In addition, glucosyltransferase B and glucosyltransferase C expression levels significantly decreased. When the htrA expression level was restored by adding the htrA gene to the htrA mutant strain, the normal growth phenotype was restored under acid stress. Further, similar results were obtained for S. mutans UA159. Thus, htrA in S. mutans K7, as well as S. mutans UA159, can be concluded to play an important role during acid stress.
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Affiliation(s)
- Kyung-hee Kang
- Department of Dental Hygiene, Konyang University, Daejeon, 302-718, Korea
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185
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Haynes CM, Yang Y, Blais SP, Neubert TA, Ron D. The matrix peptide exporter HAF-1 signals a mitochondrial UPR by activating the transcription factor ZC376.7 in C. elegans. Mol Cell 2010; 37:529-40. [PMID: 20188671 PMCID: PMC2846537 DOI: 10.1016/j.molcel.2010.01.015] [Citation(s) in RCA: 386] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 06/15/2009] [Accepted: 11/17/2009] [Indexed: 01/02/2023]
Abstract
Genetic analyses previously implicated the matrix-localized protease ClpP in signaling the stress of protein misfolding in the mitochondrial matrix to activate nuclear-encoded mitochondrial chaperone genes in C. elegans (UPR(mt)). Here, we report that haf-1, a gene encoding a mitochondria-localized ATP-binding cassette protein, is required for signaling within the UPR(mt) and for coping with misfolded protein stress. Peptide efflux from isolated mitochondria was ATP dependent and required HAF-1 and the protease ClpP. Defective UPR(mt) signaling in the haf-1-deleted worms was associated with failure of the bZIP protein, ZC376.7, to localize to nuclei in worms with perturbed mitochondrial protein folding, whereas zc376.7(RNAi) strongly inhibited the UPR(mt). These observations suggest a simple model whereby perturbation of the protein-folding environment in the mitochondrial matrix promotes ClpP-mediated generation of peptides whose haf-1-dependent export from the matrix contributes to UPR(mt) signaling across the mitochondrial inner membrane.
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Affiliation(s)
- Cole M. Haynes
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Yun Yang
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Steven P. Blais
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Thomas A. Neubert
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016
| | - David Ron
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
- Department of Cell Biology, New York University School of Medicine, New York, New York 10016
- Department of Medicine, New York University School of Medicine, New York, New York 10016
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186
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The ClpP protease homologue is required for the transmission traits and cell division of the pathogen Legionella pneumophila. BMC Microbiol 2010; 10:54. [PMID: 20167127 PMCID: PMC2838875 DOI: 10.1186/1471-2180-10-54] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 02/19/2010] [Indexed: 01/04/2023] Open
Abstract
Background Legionella pneumophila, the intracellular bacterial pathogen that causes Legionnaires' disease, exhibit characteristic transmission traits such as elevated stress tolerance, shortened length and virulence during the transition from the replication phase to the transmission phase. ClpP, the catalytic core of the Clp proteolytic complex, is widely involved in many cellular processes via the regulation of intracellular protein quality. Results In this study, we showed that ClpP was required for optimal growth of L. pneumophila at high temperatures and under several other stress conditions. We also observed that cells devoid of clpP exhibited cell elongation, incomplete cell division and compromised colony formation. Furthermore, we found that the clpP-deleted mutant was more resistant to sodium stress and failed to proliferate in the amoebae host Acanthamoeba castellanii. Conclusions The data present in this study illustrate that the ClpP protease homologue plays an important role in the expression of transmission traits and cell division of L. pneumophila, and further suggest a putative role of ClpP in virulence regulation.
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187
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Luce K, Weil AC, Osiewacz HD. Mitochondrial protein quality control systems in aging and disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 694:108-25. [PMID: 20886760 DOI: 10.1007/978-1-4419-7002-2_9] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Preserving the integrity of proteins, biomolecules prone to molecular damage, is a fundamental function of all biological systems. Impairments in protein quality control (PQC) may lead to degenerative processes, such as aging and various disorders and diseases. Fortunately, cells contain a hierarchical system of pathways coping protein damage. Specific molecular pathways detect misfolded proteins and act either to unfold or degrade them. Degradation of proteins generates peptides and amino acids that can be used for remodelling of impaired pathways and cellular functions. At increased levels of cellular damage whole organelles can be removed via autophagy, a process that depends on the activity oflysosomes. In addition, cells may undergo apoptosis, a form of programmed cell death, which in single-cellular and lower multicellular organisms can lead to death of the individual. Molecular damage of cellular compartments is mainly caused by reactive oxygen species (ROS). ROS is generated via different cellular pathways and frequently arises in the mitochondrial electron transport chain as a by-product of oxygenic energy transduction. Consequently, mitochondrial proteins are under high risk to become damaged. Perhaps for this reason mitochondria contain a very efficient PQC system that keeps mitochondrial proteins functional as long as damage does not reach a certain threshold and the components of this system themselves are not excessively damaged. The mitochondrial PQC system consists of chaperones that counteract protein aggregation through binding and refolding misfolded polypeptides and of membrane-bound and soluble ATP-dependent proteases that are involved in degradation of damaged proteins. During aging and in neurodegenerative diseases components of this PQC system, including Lon protease present in the mitochondrial matrix, become functionally impaired. In this chapter we summarise the current knowledge of cellular quality control systems with special emphasis on the role of the mitochondrial PQC system and its impact on biological aging and disease.
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Affiliation(s)
- Karin Luce
- Johann Wolfgang Goethe University, Faculty for Biosciences and Cluster of Excellence Macromolecular Complexes, Institute of Molecular Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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188
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Abstract
CtsR is the global transcriptional regulator of the core protein quality networks in low GC, Gram+ bacteria. Balancing these networks during environmental stress is of considerable importance for moderate survival of the bacteria, and also for virulence of pathogenic species. Therefore, inactivation of the CtsR repressor is one of the major cellular responses for fast and efficient adaptation to different protein stress conditions. Historically, CtsR inactivation was mainly studied for the heat stress response, and recently it has been shown that CtsR is an intrinsic thermosensor. Moreover, it has been demonstrated that CtsR degradation is regulated by a two-step mechanism during heat stress, dependent on the arginine kinase activity of McsB. Interestingly, CtsR is also inactivated during oxidative stress, but by a thiol-dependent regulatory pathway. These observations suggest that dual activity control of CtsR activity has developed during the course of evolution.
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Affiliation(s)
- Alexander K W Elsholz
- Ernst-Moritz-Arndt-University Greifswald, Institute of Microbiology, Greifswald, Germany
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189
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Structural basis for the substrate specificity of PepA from Streptococcus pneumoniae, a dodecameric tetrahedral protease. Biochem Biophys Res Commun 2010; 391:431-6. [DOI: 10.1016/j.bbrc.2009.11.075] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 11/10/2009] [Indexed: 11/18/2022]
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190
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ClpP of Streptococcus mutans differentially regulates expression of genomic islands, mutacin production, and antibiotic tolerance. J Bacteriol 2009; 192:1312-23. [PMID: 20038588 DOI: 10.1128/jb.01350-09] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Streptococcus mutans is the primary etiological agent of human dental caries and, at times, of infective endocarditis. Within the oral cavity, the pathogen is subjected to conditions of stress. A well-conserved protein complex named ClpP (caseinolytic protease) plays a vital role in adaptation under stress conditions. To gain a better understanding of the global role of the ClpP protease in cellular homeostasis, a transcriptome analysis was performed using a DeltaclpP mutant strain. The expression levels of more than 100 genes were up- or downregulated in the DeltaclpP mutant compared to the wild type. Notably, the expression of genes in several genomic islands, such as TnSmu1 and TnSmu2, was differentially modulated in the DeltaclpP mutant strain. ClpP deficiency also increased the expression of genes associated with a putative CRISPR locus. Furthermore, several stress-related genes and genes encoding bacteriocin-related peptides and many transcription factors were also found to be altered in the DeltaclpP mutant strain. A comparative analysis of the two-dimensional protein profile of the wild type and the DeltaclpP mutant strains showed altered protein profiles. Comparison of the transcriptome data with the proteomic data identified four common gene products, suggesting that the observed altered protein expression of these genes could be due to altered transcription. The results presented here indicate that ClpP-mediated proteolysis plays an important global role in the regulation of several important traits in this pathogen.
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191
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Barik S, Sureka K, Mukherjee P, Basu J, Kundu M. RseA, the SigE specific anti-sigma factor ofMycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. Mol Microbiol 2009; 75:592-606. [DOI: 10.1111/j.1365-2958.2009.07008.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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192
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Ge Z, Karzai AW. Co-evolution of multipartite interactions between an extended tmRNA tag and a robust Lon protease in Mycoplasma. Mol Microbiol 2009; 74:1083-99. [PMID: 19912542 DOI: 10.1111/j.1365-2958.2009.06923.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Messenger RNAs that lack in-frame stop codons promote ribosome stalling and accumulation of aberrant and potentially harmful polypeptides. The SmpB-tmRNA quality control system has evolved to solve problems associated with non-stop mRNAs, by rescuing stalled ribosomes and directing the addition of a peptide tag to the C-termini of the associated proteins, marking them for proteolysis. In Escherichia coli, the ClpXP system is the major contributor to disposal of tmRNA-tagged proteins. We have shown that the AAA+ Lon protease can also degrade tmRNA-tagged proteins, but with much lower efficiency. Here, we present a unique case of enhanced recognition and degradation of an extended Mycoplasma pneumoniae (MP) tmRNA tag by the MP-Lon protease. We demonstrate that MP-Lon can efficiently and selectively degrade MP-tmRNA-tagged proteins. Most significantly, our studies reveal that the larger (27 amino acids long) MP-tmRNA tag contains multiple discrete signalling motifs for efficient recognition and rapid degradation by Lon. We propose that higher-affinity multipartite interactions between MP-Lon and the extended MP-tmRNA tag have co-evolved from pre-existing weaker interactions, as exhibited by Lon in E. coli, to better fulfil the function of MP-Lon as the sole soluble cytoplasmic protease responsible for the degradation of tmRNA-tagged proteins.
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Affiliation(s)
- Zhiyun Ge
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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193
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Single-molecule denaturation and degradation of proteins by the AAA+ ClpXP protease. Proc Natl Acad Sci U S A 2009; 106:19340-5. [PMID: 19892734 DOI: 10.1073/pnas.0910484106] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ClpXP is an ATP-fueled molecular machine that unfolds and degrades target proteins. ClpX, an AAA+ enzyme, recognizes specific proteins, and then uses cycles of ATP hydrolysis to denature any native structure and to translocate the unfolded polypeptide into ClpP for degradation. Here, we develop and apply single-molecule fluorescence assays to probe the kinetics of protein denaturation and degradation by ClpXP. These assays employ a single-chain variant of the ClpX hexamer, linked via a single biotin to a streptavidin-coated surface, and fusion substrates with an N-terminal fluorophore and a C-terminal GFP-titin-ssrA module. In the presence of adenosine 5'-[gamma-thio]triphosphate (ATPgammaS), ClpXP degrades the titin-ssrA portion of these substrates but stalls when it encounters GFP. Exchange into ATP then allows synchronous resumption of denaturation and degradation of GFP and any downstream domains. GFP unfolding can be monitored directly, because intrinsic fluorescence is quenched by denaturation. The time required for complete degradation coincides with loss of the substrate fluorophore from the protease complex. Fitting single-molecule data for a set of related substrates provides time constants for ClpX unfolding, translocation, and a terminal step that may involve product release. Comparison of these single-molecule results with kinetics measured in bulk solution indicates similar levels of microscopic and macroscopic ClpXP activity. These results support a stochastic engagement/unfolding mechanism that ultimately results in highly processive degradation and set the stage for more detailed single-molecule studies of machine function.
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194
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Proteolysis in prokaryotes – from molecular machines to a systems perspective. Res Microbiol 2009; 160:615-7. [DOI: 10.1016/j.resmic.2009.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 09/07/2009] [Accepted: 09/07/2009] [Indexed: 11/23/2022]
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195
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Narberhaus F, Obrist M, Führer F, Langklotz S. Degradation of cytoplasmic substrates by FtsH, a membrane-anchored protease with many talents. Res Microbiol 2009; 160:652-9. [DOI: 10.1016/j.resmic.2009.08.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 08/17/2009] [Accepted: 08/17/2009] [Indexed: 12/01/2022]
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196
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Examination of post-transcriptional regulations in prokaryotes by integrative biology. C R Biol 2009; 332:958-73. [DOI: 10.1016/j.crvi.2009.09.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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197
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Escherichia coli glycogen metabolism is controlled by the PhoP-PhoQ regulatory system at submillimolar environmental Mg2+ concentrations, and is highly interconnected with a wide variety of cellular processes. Biochem J 2009; 424:129-41. [PMID: 19702577 DOI: 10.1042/bj20090980] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Using the Keio collection of gene-disrupted mutants of Escherichia coli, we have recently carried out a genome-wide screening of the genes affecting glycogen metabolism. Among the mutants identified in the study, Delta mgtA, Delta phoP and Delta phoQ cells, all lacking genes that are induced under low extracellular Mg2+ conditions, displayed glycogen-deficient phenotypes. In this work we show that these mutants accumulated normal glycogen levels when the culture medium was supplemented with submillimolar Mg2+ concentrations. Expression analyses conducted in wild-type, Delta phoP and Delta phoQ cells showed that the glgCAP operon is under PhoP-PhoQ control in the submillimolar Mg2+ concentration range. Subsequent screening of the Keio collection under non-limiting Mg2+ allowed the identification of 183 knock-out mutants with altered glycogen levels. The stringent and general stress responses, end-turnover of tRNA, intracellular AMP levels, and metabolism of amino acids, iron, carbon and sulfur were major determinants of glycogen levels. glgC::lacZY expression analyses using mutants representing different functional categories revealed that the glgCAP operon belongs to the RelA regulon. We propose an integrated metabolic model wherein glycogen metabolism is (a) tightly controlled by the energy and nutritional status of the cell and (b) finely regulated by changes in environmental Mg2+ occurring at the submillimolar concentration range.
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198
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Reuter CJ, Uthandi S, Puentes JA, Maupin-Furlow JA. Hydrophobic carboxy-terminal residues dramatically reduce protein levels in the haloarchaeon Haloferax volcanii. MICROBIOLOGY-SGM 2009; 156:248-255. [PMID: 19850616 DOI: 10.1099/mic.0.032995-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Proteolysis is important not only to cell physiology but also to the successful development of biocatalysts. While a wide-variety of signals are known to trigger protein degradation in bacteria and eukaryotes, these mechanisms are poorly understood in archaea, known for their ability to withstand harsh conditions. Here we present a systematic study in which single C-terminal amino acid residues were added to a reporter protein and shown to influence its levels in an archaeal cell. All 20 amino acid residues were examined for their impact on protein levels, using the reporter protein soluble modified red-shifted GFP (smRS-GFP) expressed in the haloarchaeon Haloferax volcanii as a model system. Addition of hydrophobic residues, including Leu, Cys, Met, Phe, Ala, Tyr, Ile and Val, gave the most pronounced reduction in smRS-GFP levels compared with the addition of either neutral or charged hydrophilic residues. In contrast to the altered protein levels, the C-terminal alterations had no influence on smRS-GFP-specific transcript levels, thus revealing that the effect is post-transcriptional.
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Affiliation(s)
- Christopher J Reuter
- University of Florida, Department of Microbiology and Cell Science, Gainesville, FL 32611-0700, USA
| | - Sivakumar Uthandi
- University of Florida, Department of Microbiology and Cell Science, Gainesville, FL 32611-0700, USA
| | - Jose A Puentes
- University of Florida, Department of Microbiology and Cell Science, Gainesville, FL 32611-0700, USA
| | - Julie A Maupin-Furlow
- University of Florida, Department of Microbiology and Cell Science, Gainesville, FL 32611-0700, USA
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199
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Sakuraba Y, Tanaka R, Yamasato A, Tanaka A. Determination of a chloroplast degron in the regulatory domain of chlorophyllide a oxygenase. J Biol Chem 2009; 284:36689-36699. [PMID: 19843523 DOI: 10.1074/jbc.m109.008144] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chlorophyll b is one of the major photosynthetic pigments of plants. The regulation of chlorophyll b biosynthesis is important for plants in order to acclimate to changing environmental conditions. In the chloroplast, chlorophyll b is synthesized from chlorophyll a by chlorophyllide a oxygenase (CAO), a Rieske-type monooxygenase. The activity of this enzyme is regulated at the level of protein stability via a feedback mechanism through chlorophyll b. The Clp protease and the N-terminal domain (designated the A domain) of CAO are essential for the regulatory mechanism. In this study, we aimed to identify the specific amino acid residue or the sequence within the A domain that is essential for this regulation. To accomplish this goal, we randomly introduced base substitutions into the A domain and searched for potentially important residues by analyzing 1,000 transformants of Arabidopsis thaliana. However, none of the single amino acid substitutions significantly stabilized CAO. Therefore, we generated serial deletions in the A domain and expressed these deletions in the background of CAO-deficient Arabidopsis mutant. We found that the amino acid sequence (97)QDLLTIMILH(106) is essential for the regulation of the protein stability. We furthermore determined that this sequence induces the destabilization of green fluorescent protein. These results suggest that this sequence serves as a degradation signal that is recognized by proteases functioning in the chloroplast.
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Affiliation(s)
- Yasuhito Sakuraba
- Institute of Low Temperature Science, Hokkaido University, N19 W8 Kita-Ku, Sapporo 060-0819, Japan.
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8 Kita-Ku, Sapporo 060-0819, Japan
| | - Akihiro Yamasato
- Research Institute for Biological Sciences Okayama, Okayama 716-1241, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8 Kita-Ku, Sapporo 060-0819, Japan
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200
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Van Melderen L, Aertsen A. Regulation and quality control by Lon-dependent proteolysis. Res Microbiol 2009; 160:645-51. [PMID: 19772918 DOI: 10.1016/j.resmic.2009.08.021] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 08/19/2009] [Accepted: 08/20/2009] [Indexed: 11/17/2022]
Abstract
After their first discovery in Escherichia coli, Lon homologues were found to be widely distributed among prokaryotes to eukaryotes. The ATP-dependent Lon protease belongs to the AAA(+) (ATPases associated with a variety of cellular activities) superfamily, and is involved in both general quality control by degrading abnormal proteins and in the specific control of several regulatory proteins. As such, this enzyme has a pivotal role in quality control and cellular physiology. This review focuses on mechanisms of degradation both from the protease and substrate points of view, and discusses the role of Lon in global regulation, stress response and virulence.
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Affiliation(s)
- Laurence Van Melderen
- Génétique et Physiologie Bactérienne, Université Libre de Bruxelles, Faculté des Sciences, IBMM-DBM, 12 Rue des Professeurs Jeneer et Brachet, B-6041 Gosselies, Belgium.
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