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Gómez-Baena G, Rangel OA, López-Lozano A, García-Fernández JM, Diez J. Stress responses in Prochlorococcus MIT9313 vs. SS120 involve differential expression of genes encoding proteases ClpP, FtsH and Lon. Res Microbiol 2009; 160:567-75. [PMID: 19732824 DOI: 10.1016/j.resmic.2009.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/27/2009] [Accepted: 08/14/2009] [Indexed: 11/29/2022]
Abstract
Prochlorococcus is a marine cyanobacterium responsible for a significant part of global primary production as well as being one of the most abundant organisms on Earth. Protein turnover is an essential and poorly understood aspect of the cyanobacterial response to environmental stresses. In the present work, cultures of the SS120 and MIT9313 strains were subjected to several conditions, and quantitative real time RT-PCR was used to measure changes in the expression of genes encoding three representative ATP-dependent proteases. We found common responses to conditions such as aging. However, the expression pattern under nutrient starvation was strikingly different in the two strains, probably reflecting the different regulatory backgrounds of the two ecotypes here studied.
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Affiliation(s)
- Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, planta 1, Campus de Rabanales, Universidad de Córdoba, Córdoba 14071, Spain.
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2
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Kang MS, Kim SR, Kwack P, Lim BK, Ahn SW, Rho YM, Seong IS, Park SC, Eom SH, Cheong GW, Chung CH. Molecular architecture of the ATP-dependent CodWX protease having an N-terminal serine active site. EMBO J 2003; 22:2893-902. [PMID: 12805205 PMCID: PMC162141 DOI: 10.1093/emboj/cdg289] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CodWX in Bacillus subtilis is an ATP-dependent, N-terminal serine protease, consisting of CodW peptidase and CodX ATPase. Here we show that CodWX is an alkaline protease and has a distinct molecular architecture. ATP hydrolysis is required for the formation of the CodWX complex and thus for its proteolytic function. Remarkably, CodX has a 'spool-like' structure that is formed by interaction of the intermediate domains of two hexameric or heptameric rings. In the CodWX complex, CodW consisting of two stacked hexameric rings (WW) binds to either or both ends of a CodX double ring (XX), forming asymmetric (WWXX) or symmetric cylindrical particles (WWXXWW). CodWX can also form an elongated particle, in which an additional CodX double ring is bound to the symmetric particle (WWXXWWXX). In addition, CodWX is capable of degrading EzrA, an inhibitor of FtsZ ring formation, implicating it in the regulation of cell division. Thus, CodWX appears to constitute a new type of protease that is distinct from other ATP-dependent proteases in its structure and proteolytic mechanism.
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Affiliation(s)
- Min Suk Kang
- NRL of Protein Biochemistry, School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
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Seong IS, Kang MS, Choi MK, Lee JW, Koh OJ, Wang J, Eom SH, Chung CH. The C-terminal tails of HslU ATPase act as a molecular switch for activation of HslV peptidase. J Biol Chem 2002; 277:25976-82. [PMID: 12011053 DOI: 10.1074/jbc.m202793200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial HslVU ATP-dependent protease is a homolog of the eukaryotic 26 S proteasome. HslU ATPase forms a hexameric ring, and HslV peptidase is a dodecamer consisting of two stacked hexameric rings. In HslVU complex, the HslU and HslV central pores are aligned, and the proteolytic active sites are sequestered in an internal chamber of HslV, with access to this chamber restricted to small axial pores. Here we show that the C-terminal tails of HslU play a critical role in the interaction with and activation of HslV peptidase. A synthetic tail peptide of 10 amino acids could replace HslU in supporting the HslV-mediated hydrolysis of unfolded polypeptide substrates such as alpha-casein, as well as of small peptides, suggesting that the HslU C terminus is involved in the opening of the HslV pore for substrate entry. Moreover, deletion of 7 amino acids from the C terminus prevented the ability of HslU to form an HslVU complex with HslV. In addition, deletion of the C-terminal 10 residues prevented the formation of an HslU hexamer, indicating that the C terminus is required for HslU oligomerization. These results suggest that the HslU C-terminal tails act as a molecular switch for the assembly of HslVU complex and the activation of HslV peptidase.
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Affiliation(s)
- Ihn Sik Seong
- National Research Laboratory of Protein Biochemistry, School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
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Wang J, Song JJ, Seong IS, Franklin MC, Kamtekar S, Eom SH, Chung CH. Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU. Structure 2001; 9:1107-16. [PMID: 11709174 DOI: 10.1016/s0969-2126(01)00670-0] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND The bacterial heat shock locus ATPase HslU is an AAA(+) protein that has structures known in many nucleotide-free and -bound states. Nucleotide is required for the formation of the biologically active HslU hexameric assembly. The hexameric HslU ATPase binds the dodecameric HslV peptidase and forms an ATP-dependent HslVU protease. RESULTS We have characterized four distinct HslU conformational states, going sequentially from open to closed: the empty, SO(4), ATP, and ADP states. The nucleotide binds at a cleft formed by an alpha/beta domain and an alpha-helical domain in HslU. The four HslU states differ by a rotation of the alpha-helical domain. This classification leads to a correction of nucleotide identity in one structure and reveals the ATP hydrolysis-dependent structural changes in the HslVU complex, including a ring rotation and a conformational change of the HslU C terminus. This leads to an amended protein unfolding-coupled translocation mechanism. CONCLUSIONS The observed nucleotide-dependent conformational changes in HslU and their governing principles provide a framework for the mechanistic understanding of other AAA(+) proteins.
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Affiliation(s)
- J Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
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Kang MS, Lim BK, Seong IS, Seol JH, Tanahashi N, Tanaka K, Chung CH. The ATP-dependent CodWX (HslVU) protease in Bacillus subtilis is an N-terminal serine protease. EMBO J 2001; 20:734-42. [PMID: 11179218 PMCID: PMC145431 DOI: 10.1093/emboj/20.4.734] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2000] [Revised: 10/30/2000] [Accepted: 01/03/2001] [Indexed: 11/13/2022] Open
Abstract
HslVU is a two-component ATP-dependent protease, consisting of HslV peptidase and HslU ATPase. CodW and CodX, encoded by the cod operon in Bacillus subtilis, display 52% identity in their amino acid sequences to HslV and HslU in Escherichia coli, respectively. Here we show that CodW and CodX can function together as a new type of two-component ATP-dependent protease. Remarkably, CodW uses its N-terminal serine hydroxyl group as the catalytic nucleophile, unlike HslV and certain beta-type subunits of the proteasomes, which have N-terminal threonine functioning as an active site residue. The ATP-dependent proteolytic activity of CodWX is strongly inhibited by serine protease inhibitors, unlike that of HslVU. Replacement of the N-terminal serine of CodW by alanine or even threonine completely abolishes the enzyme activity. These results indicate that CodWX in B.subtilis represents the first N-terminal serine protease among all known proteolytic enzymes.
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Affiliation(s)
- Min Suk Kang
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Tokyo Metropolitan Institute of Medical Science, CREST, Japan Science and Technology Corporation, Tokyo 113, Japan Present address: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Corresponding author e-mail:
| | - Byung Kook Lim
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Tokyo Metropolitan Institute of Medical Science, CREST, Japan Science and Technology Corporation, Tokyo 113, Japan Present address: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Corresponding author e-mail:
| | - Ihn Sik Seong
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Tokyo Metropolitan Institute of Medical Science, CREST, Japan Science and Technology Corporation, Tokyo 113, Japan Present address: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Corresponding author e-mail:
| | - Jae Hong Seol
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Tokyo Metropolitan Institute of Medical Science, CREST, Japan Science and Technology Corporation, Tokyo 113, Japan Present address: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Corresponding author e-mail:
| | - Nobuyuki Tanahashi
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Tokyo Metropolitan Institute of Medical Science, CREST, Japan Science and Technology Corporation, Tokyo 113, Japan Present address: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Corresponding author e-mail:
| | - Keiji Tanaka
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Tokyo Metropolitan Institute of Medical Science, CREST, Japan Science and Technology Corporation, Tokyo 113, Japan Present address: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Corresponding author e-mail:
| | - Chin Ha Chung
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Tokyo Metropolitan Institute of Medical Science, CREST, Japan Science and Technology Corporation, Tokyo 113, Japan Present address: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Corresponding author e-mail:
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Wang J, Song JJ, Franklin MC, Kamtekar S, Im YJ, Rho SH, Seong IS, Lee CS, Chung CH, Eom SH. Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism. Structure 2001; 9:177-84. [PMID: 11250202 DOI: 10.1016/s0969-2126(01)00570-6] [Citation(s) in RCA: 207] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BACKGROUND The bacterial heat shock locus HslU ATPase and HslV peptidase together form an ATP-dependent HslVU protease. Bacterial HslVU is a homolog of the eukaryotic 26S proteasome. Crystallographic studies of HslVU should provide an understanding of ATP-dependent protein unfolding, translocation, and proteolysis by this and other ATP-dependent proteases. RESULTS We present a 3.0 A resolution crystal structure of HslVU with an HslU hexamer bound at one end of an HslV dodecamer. The structure shows that the central pores of the ATPase and peptidase are next to each other and aligned. The central pore of HslU consists of a GYVG motif, which is conserved among protease-associated ATPases. The binding of one HslU hexamer to one end of an HslV dodecamer in the 3.0 A resolution structure opens both HslV central pores and induces asymmetric changes in HslV. CONCLUSIONS Analysis of nucleotide binding induced conformational changes in the current and previous HslU structures suggests a protein unfolding-coupled translocation mechanism. In this mechanism, unfolded polypeptides are threaded through the aligned pores of the ATPase and peptidase and translocated into the peptidase central chamber.
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Affiliation(s)
- J Wang
- Department of Molecular Biophysics, Biochemistry, 266 Whitney Avenue, Yale University, 06520, New Haven, CT, USA.
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Kim KI, Park SC, Kang SH, Cheong GW, Chung CH. Selective degradation of unfolded proteins by the self-compartmentalizing HtrA protease, a periplasmic heat shock protein in Escherichia coli. J Mol Biol 1999; 294:1363-74. [PMID: 10600391 DOI: 10.1006/jmbi.1999.3320] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
HtrA, which has a high molecular mass of about 500 kDa, is a periplasmic heat shock protein whose proteolytic activity is essential for the survival of Escherichia coli at high temperatures. To determine the structural organization of HtrA, we have used electron microscopy and chemical cross-linking analysis. The averaged image of HtrA with end-on orientation revealed a six-membered, ring-shaped structure with a central cavity, and its side-on view showed a two-layered structure. Thus, HtrA behaves as a dodecamer consisting of two stacks of hexameric ring. HtrA can degrade thermally unfolded citrate synthase and malate dehydrogenase but cannot when in their native form. HtrA degraded partially unfolded casein more rapidly upon increasing the incubation temperature. However, it hydrolyzed oxidized insulin B-chain, which is fully unfolded, at nearly the same rate at all of the temperatures tested. HtrA also rapidly degraded reduced insulin B-chain generated by treatment of insulin with dithiothreitol but not A-chain or intact insulin. Moreover, HtrA degraded fully unfolded alpha-lactalbumin, of which all four disulfide bonds were reduced, but not the native alpha-lactalbumin and its unfolded intermediates containing two or three disulfide bonds. These results indicate that unfolding of the protein substrates, such as by exposure to high temperatures or reduction of disulfide bonds, is essential for their access into the inner chamber of the double ring-shaped HtrA, where cleavage of peptide bonds may occur. Thus, HtrA with a self-compartmentalizing structure may play an important role in elimination of unfolded proteins in the periplasm of Escherichia coli.
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Affiliation(s)
- K I Kim
- Department of Molecular Biology and Research Center for Cell Differentiation, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea
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Yoo SJ, Kim HH, Shin DH, Lee CS, Seong IS, Seol JH, Shimbara N, Tanaka K, Chung CH. Effects of the cys mutations on structure and function of the ATP-dependent HslVU protease in Escherichia coli. The Cys287 to Val mutation in HslU uncouples the ATP-dependent proteolysis by HslvU from ATP hydrolysis. J Biol Chem 1998; 273:22929-35. [PMID: 9722513 DOI: 10.1074/jbc.273.36.22929] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To define the role of the Cys residues in the ATP-dependent HslVU protease, mutagenesis was performed to replace either Cys261 or Cys287 in HslU with Val and Cys159 in HslV with Ser or Ala. Whereas HslU/C261V could hydrolyze ATP and support the ATP-dependent proteolytic activity of HslV as well as the wild-type HslU, HslU/C287V could not hydrolyze ATP. Nevertheless, HslU/C287V could support the HslV-mediated proteolysis by forming the HslVU complex in the presence of ATP but not its absence, indicating that ATP binding but not its hydrolysis is essential for proteolysis. Whereas treatment of N-ethylmaleimide (NEM) resulted in dissociation of the oligomeric HslU into monomers, the C261V mutation, but not C287V, prevented the NEM effect. These results suggest that Cys261 is involved in oligomerization and that Cys287 is related to the ATPase function of HslU. NEM also dissociated the dodecameric HslV into monomers, and this effect could be prevented by either the C159S or C159A mutation, suggesting the involvement of Cys159 in oligomerization of HslV. Moreover, either mutation abolished both the basal and HslU-activated proteolytic activity of HslV and its ability to activate the HslU ATPase and to form the HslVU complex, indicating that Cys159 is essential for the proteolytic activity of HslV and its interaction with HslU. These results suggest that the Cys residues play an important role in maintaining the structure and function of the HslVU protease.
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Affiliation(s)
- S J Yoo
- Department of Molecular Biology and Research Center for Cell Differentiation, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea
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