1
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Parvaiz N, Shahbaz M, Azam SS. Role of hinge motion and ATP dynamics in factors for inversion stimulation FIS protein deduced while targeting drug resistant Orientia tsutsugamushi. J Mol Graph Model 2023; 120:108425. [PMID: 36758328 DOI: 10.1016/j.jmgm.2023.108425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023]
Abstract
Orientia tsutsugamushi, the causative agent of scrub typhus has been found resistant to various classes of antibiotics such as penicillins, gentamycin and cephalosporins. Review of current literature suggests that the prevalence of scrub typhus has increased globally. Therefore, the current study has aimed at exploring the genome of O. tsutsugamushi to identify potential drug target proteins that can be used for developing novel antibiotics against the pathogen. Subtractive proteomics approach has revealed FIS as a potential drug target protein involved in two component system (TCS), a signaling pathway crucial for bacteria to survive and adjust in changing environmental conditions. Molecular docking studies have revealed compound-356 (CHEMBRIDGE-10040641-3710.356) as a potential inhibitor in both chains A and B of the FIS protein. Simulation results suggest that the docked complex has remained stable and compact throughout the 200 ns run. Significant conformational changes including the hinge motion was observed in the DNA binding domain. Furthermore, the presence of salt bridge between GLU910 and ARG417, rearrangement of interaction residues and displacement of ATP in the central AAA + domain upon binding to the inhibitor were also observed playing a role in stabilizing the protein structure.
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Affiliation(s)
- Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Maham Shahbaz
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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2
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Singh P, Samanta K, Kebe NM, Michel G, Legrand B, Sitnikova VE, Kajava AV, Pagès M, Bastien P, Pomares C, Coux O, Hernandez JF. The C-terminal segment of Leishmania major HslU: Toward potential inhibitors of LmHslVU activity. Bioorg Chem 2021; 119:105539. [PMID: 34894575 DOI: 10.1016/j.bioorg.2021.105539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/08/2021] [Accepted: 12/01/2021] [Indexed: 01/23/2023]
Abstract
It is urgent to develop less toxic and more efficient treatments for leishmaniases and trypanosomiases. We explore the possibility to target the parasite mitochondrial HslVU protease, which is essential for growth and has no analogue in the human host. For this, we develop compounds potentially inhibiting the complex assembly by mimicking the C-terminal (C-ter) segment of the ATPase HslU. We previously showed that a dodecapeptide derived from Leishmania major HslU C-ter segment (LmC12-U2, Cpd 1) was able to bind to and activate the digestion of a fluorogenic substrate by LmHslV. Here, we present the study of its structure-activity relationships. By replacing each essential residue with related non-proteinogenic residues, we obtained more potent analogues. In particular, a cyclohexylglycine residue at position 11 (cpd 24) allowed a more than three-fold gain in potency while reducing the size of compound 24 from twelve to six residues (cpd 50) without significant loss of potency, opening the way toward short HslU C-ter peptidomimetics as potential inhibitors of HslV proteolytic function. Finally, conjugates constituted of LmC6-U2 analogues and a mitochondrial penetrating peptide were found to penetrate into the promastigote form of L. infantum and to inhibit the parasite growth without showing toxicity toward human THP-1 cells at the same concentration (i.e. 30 μM).
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Affiliation(s)
- Priyanka Singh
- IBMM, CNRS, Univ Montpellier, ENSCM, Montpellier, France
| | | | - Ndeye Mathy Kebe
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), UMR5237, CNRS, Univ Montpellier, 1919, route de Mende, 34000 Montpellier, France
| | - Grégory Michel
- Centre Méditerranéen de Médecine Moléculaire (C3M), U1065, Université Côte d'Azur, Inserm, Archimed Building, 151 route Saint Antoine de Ginestière, 06000 Nice, France
| | | | - Vera E Sitnikova
- International Research Institute of Bioengineering, ITMO University, Kronverksky Pr. 49, 197101 Saint Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), UMR5237, CNRS, Univ Montpellier, 1919, route de Mende, 34000 Montpellier, France
| | - Michel Pagès
- MIVEGEC, Univ Montpellier, CNRS, IRD, CHU, 191 avenue du Doyen Giraud, 34000 Montpellier, France
| | - Patrick Bastien
- MIVEGEC, Univ Montpellier, CNRS, IRD, CHU, 191 avenue du Doyen Giraud, 34000 Montpellier, France
| | - Christelle Pomares
- Centre Méditerranéen de Médecine Moléculaire (C3M), U1065, Université Côte d'Azur, Inserm, Archimed Building, 151 route Saint Antoine de Ginestière, 06000 Nice, France
| | - Olivier Coux
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), UMR5237, CNRS, Univ Montpellier, 1919, route de Mende, 34000 Montpellier, France.
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3
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Yu Y, Liu H, Yu Z, Witkowska HE, Cheng Y. Stoichiometry of Nucleotide Binding to Proteasome AAA+ ATPase Hexamer Established by Native Mass Spectrometry. Mol Cell Proteomics 2020; 19:1997-2015. [PMID: 32883800 PMCID: PMC7710143 DOI: 10.1074/mcp.ra120.002067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/04/2020] [Indexed: 11/06/2022] Open
Abstract
AAA+ ATPases constitute a large family of proteins that are involved in a plethora of cellular processes including DNA disassembly, protein degradation and protein complex disassembly. They typically form a hexametric ring-shaped structure with six subunits in a (pseudo) 6-fold symmetry. In a subset of AAA+ ATPases that facilitate protein unfolding and degradation, six subunits cooperate to translocate protein substrates through a central pore in the ring. The number and type of nucleotides in an AAA+ ATPase hexamer is inherently linked to the mechanism that underlies cooperation among subunits and couples ATP hydrolysis with substrate translocation. We conducted a native MS study of a monodispersed form of PAN, an archaeal proteasome AAA+ ATPase, to determine the number of nucleotides bound to each hexamer of the WT protein. We utilized ADP and its analogs (TNP-ADP and mant-ADP), and a nonhydrolyzable ATP analog (AMP-PNP) to study nucleotide site occupancy within the PAN hexamer in ADP- and ATP-binding states, respectively. Throughout all experiments we used a Walker A mutant (PANK217A) that is impaired in nucleotide binding as an internal standard to mitigate the effects of residual solvation on mass measurement accuracy and to serve as a reference protein to control for nonspecific nucleotide binding. This approach led to the unambiguous finding that a WT PAN hexamer carried - from expression host - six tightly bound ADP molecules that could be exchanged for ADP and ATP analogs. Although the Walker A mutant did not bind ADP analogs, it did bind AMP-PNP, albeit at multiple stoichiometries. We observed variable levels of hexamer dissociation and an appearance of multimeric species with the over-charged molecular ion distributions across repeated experiments. We posit that these phenomena originated during ESI process at the final stages of ESI droplet evolution.
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Affiliation(s)
- Yadong Yu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Haichuan Liu
- Department of OBGYN & Reproductive Sci, Sandler-Moore MS Core Facility, University of California San Francisco, San Francisco, California, USA
| | - Zanlin Yu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - H Ewa Witkowska
- Department of OBGYN & Reproductive Sci, Sandler-Moore MS Core Facility, University of California San Francisco, San Francisco, California, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA.
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4
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Jeong S, Ahn J, Kwon AR, Ha NC. Cleavage-Dependent Activation of ATP-Dependent Protease HslUV from Staphylococcus aureus. Mol Cells 2020; 43:694-704. [PMID: 32694241 PMCID: PMC7468587 DOI: 10.14348/molcells.2020.0074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/19/2020] [Accepted: 06/28/2020] [Indexed: 01/03/2023] Open
Abstract
HslUV is a bacterial heat shock protein complex consisting of the AAA+ ATPase component HslU and the protease component HslV. HslV is a threonine (Thr) protease employing the N-terminal Thr residue in the mature protein as the catalytic residue. To date, HslUV from Gram-negative bacteria has been extensively studied. However, the mechanisms of action and activation of HslUV from Gram-positive bacteria, which have an additional N-terminal sequence before the catalytic Thr residue, remain to be revealed. In this study, we determined the crystal structures of HslV from the Gram-positive bacterium Staphylococcus aureus with and without HslU in the crystallization conditions. The structural comparison suggested that a structural transition to the symmetric form of HslV was triggered by ATP-bound HslU. More importantly, the additional N-terminal sequence was cleaved in the presence of HslU and ATP, exposing the Thr9 residue at the N-terminus and activating the ATP-dependent protease activity. Further biochemical studies demonstrated that the exposed N-terminal Thr residue is critical for catalysis with binding to the symmetric HslU hexamer. Since eukaryotic proteasomes have a similar additional N-terminal sequence, our results will improve our understanding of the common molecular mechanisms for the activation of proteasomes.
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Affiliation(s)
- Soyeon Jeong
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
| | - Jinsook Ahn
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
| | - Ae-Ran Kwon
- Department of Beauty Care, College of Medical Science, Daegu Haany University, Gyeongsan 38610, Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
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5
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The molecular principles governing the activity and functional diversity of AAA+ proteins. Nat Rev Mol Cell Biol 2019; 21:43-58. [PMID: 31754261 DOI: 10.1038/s41580-019-0183-6] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/26/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+ proteins) are macromolecular machines that convert the chemical energy contained in ATP molecules into powerful mechanical forces to remodel a vast array of cellular substrates, including protein aggregates, macromolecular complexes and polymers. AAA+ proteins have key functionalities encompassing unfolding and disassembly of such substrates in different subcellular localizations and, hence, power a plethora of fundamental cellular processes, including protein quality control, cytoskeleton remodelling and membrane dynamics. Over the past 35 years, many of the key elements required for AAA+ activity have been identified through genetic, biochemical and structural analyses. However, how ATP powers substrate remodelling and whether a shared mechanism underlies the functional diversity of the AAA+ superfamily were uncertain. Advances in cryo-electron microscopy have enabled high-resolution structure determination of AAA+ proteins trapped in the act of processing substrates, revealing a conserved core mechanism of action. It has also become apparent that this common mechanistic principle is structurally adjusted to carry out a diverse array of biological functions. Here, we review how substrate-bound structures of AAA+ proteins have expanded our understanding of ATP-driven protein remodelling.
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6
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The HslV Protease from Leishmania major and Its Activation by C-terminal HslU Peptides. Int J Mol Sci 2019; 20:ijms20051021. [PMID: 30813632 PMCID: PMC6429459 DOI: 10.3390/ijms20051021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/11/2019] [Accepted: 02/20/2019] [Indexed: 12/31/2022] Open
Abstract
HslVU is an ATP-dependent proteolytic complex present in certain bacteria and in the mitochondrion of some primordial eukaryotes, including deadly parasites such as Leishmania. It is formed by the dodecameric protease HslV and the hexameric ATPase HslU, which binds via the C-terminal end of its subunits to HslV and activates it by a yet unclear allosteric mechanism. We undertook the characterization of HslV from Leishmania major (LmHslV), a trypanosomatid that expresses two isoforms for HslU, LmHslU1 and LmHslU2. Using a novel and sensitive peptide substrate, we found that LmHslV can be activated by peptides derived from the C-termini of both LmHslU1 and LmHslU2. Truncations, Ala- and D-scans of the C-terminal dodecapeptide of LmHslU2 (LmC12-U2) showed that five out of the six C-terminal residues of LmHslU2 are essential for binding to and activating HslV. Peptide cyclisation with a lactam bridge allowed shortening of the peptide without loss of potency. Finally, we found that dodecapeptides derived from HslU of other parasites and bacteria are able to activate LmHslV with similar or even higher efficiency. Importantly, using electron microscopy approaches, we observed that the activation of LmHslV was accompanied by a large conformational remodeling, which represents a yet unidentified layer of control of HslV activation.
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7
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Ding Z, Xu C, Sahu I, Wang Y, Fu Z, Huang M, Wong CCL, Glickman MH, Cong Y. Structural Snapshots of 26S Proteasome Reveal Tetraubiquitin-Induced Conformations. Mol Cell 2019; 73:1150-1161.e6. [PMID: 30792173 DOI: 10.1016/j.molcel.2019.01.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/29/2018] [Accepted: 01/11/2019] [Indexed: 11/17/2022]
Abstract
The 26S proteasome is the ATP-dependent protease responsible for regulating the proteome of eukaryotic cells through degradation of mainly ubiquitin-tagged substrates. In order to understand how proteasome responds to ubiquitin signal, we resolved an ensemble of cryo-EM structures of proteasome in the presence of K48-Ub4, with three of them resolved at near-atomic resolution. We identified a conformation with stabilized ubiquitin receptors and a previously unreported orientation of the lid, assigned as a Ub-accepted state C1-b. We determined another structure C3-b with localized K48-Ub4 to the toroid region of Rpn1, assigned as a substrate-processing state. Our structures indicate that tetraUb induced conformational changes in proteasome could initiate substrate degradation. We also propose a CP gate-opening mechanism involving the propagation of the motion of the lid to the gate through the Rpn6-α2 interaction. Our results enabled us to put forward a model of a functional cycle for proteasomes induced by tetraUb and nucleotide.
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Affiliation(s)
- Zhanyu Ding
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China
| | - Cong Xu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Indrajit Sahu
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Yifan Wang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Zhenglin Fu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Min Huang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China
| | - Catherine C L Wong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Yao Cong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China.
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8
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Specific regions of the SulA protein recognized and degraded by the ATP-dependent ClpYQ (HslUV) protease in Escherichia coli. Microbiol Res 2018; 220:21-31. [PMID: 30744816 DOI: 10.1016/j.micres.2018.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/27/2018] [Accepted: 12/09/2018] [Indexed: 10/27/2022]
Abstract
In Escherichia coli, ClpYQ (HslUV) is a two-component ATP-dependent protease, in which ClpQ is the peptidase subunit and ClpY is the ATPase and unfoldase. ClpY functions to recognize protein substrates, and denature and translocate the unfolded polypeptides into the proteolytic site of ClpQ for degradation. However, it is not clear how the natural substrates are recognized by the ClpYQ protease and the mechanism by which the substrates are selected, unfolded and translocated by ClpY into the interior site of ClpQ hexamers. Both Lon and ClpYQ proteases can degrade SulA, a cell division inhibitor, in bacterial cells. In this study, using yeast two-hybrid and in vivo degradation analyses, we first demonstrated that the C-terminal internal hydrophobic region (139th∼149th aa) of SulA is necessary for binding and degradation by ClpYQ. A conserved region, GFIMRP, between 142th and 147th residues of SulA, were identified among various Gram-negative bacteria. By using MBP-SulA(F143Y) (phenylalanine substituted with tyrosine) as a substrate, our results showed that this conserved residue of SulA is necessary for recognition and degradation by ClpYQ. Supporting these data, MBP-SulA(F143Y), MBP-SulA(F143N) (phenylalanine substituted with asparagine) led to a longer half-life with ClpYQ protease in vivo. In contrast, MBP-SulA(F143D) and MBP-SulA(F143S) both have shorter half-lives. Therefore, in the E. coli ClpYQ protease complex, ClpY recognizes the C-terminal region of SulA, and F143 of SulA plays an important role for the recognition and degradation by ClpYQ protease.
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9
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Ma X, Wang Y. Anammox bacteria exhibit capacity to withstand long-term starvation stress: A proteomic-based investigation of survival mechanisms. CHEMOSPHERE 2018; 211:952-961. [PMID: 30119026 DOI: 10.1016/j.chemosphere.2018.07.185] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/04/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Although anammox bacteria are commonly exposed to long-term starvation during transportation and preservation process, physiological changes in these organisms during long-term starvation are not well understood, nor are the molecular bases of their starvation survival strategies. To reveal survival mechanisms during long-term anaerobic and anoxic starvation (60 days at 20 ± 1 °C), metaproteomic technology was utilized to identify differentially expressed proteins in Candidatus Kuenenia stuttgartiensis. Our results showed that Candidatus Kuenenia stuttgartiensis exhibits a capacity to withstand long-term starvation stress. Although activity decay rates of 0.0129 d-1 and 0.0049 d-1 were observed for anammox sludge in anoxic and anaerobic starvation, the relative abundance of Candidatus Kuenenia stuttgartiensis, the shape of anammox granules, and the fraction of viable cells remained constant under both anaerobic and anoxic starvation conditions. Metaproteomics results illustrated that Candidatus Kuenenia stuttgartiensis maintained stable levels of most intracellular proteins, especially enzymes involved in principal metabolic pathways after 60-d of anaerobic or anoxic starvation, thereby allowing cells to regain metabolic activities once substrates became available. Induction of starvation proteins could be a survival strategy employed by Candidatus Kuenenia stuttgartiensis to resist long-term starvation stresses. During anaerobic starvation, 34 proteins were upregulated, five of which were associated with carbohydrate catabolism and oxidation of organic compounds, thereby increasing potential for utilization of endogenous carbon sources to produce energy. During anoxic starvation, only two proteins were upregulated, which may be attributed to insufficient energy for the synthesis of starvation-induced proteins.
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Affiliation(s)
- Xiao Ma
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Insititue of Pollution Contrl and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Insititue of Pollution Contrl and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China.
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10
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Structural determinants for protein unfolding and translocation by the Hsp104 protein disaggregase. Biosci Rep 2017; 37:BSR20171399. [PMID: 29175998 PMCID: PMC5741831 DOI: 10.1042/bsr20171399] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/17/2017] [Accepted: 11/22/2017] [Indexed: 01/23/2023] Open
Abstract
The ring-forming Hsp104 ATPase cooperates with Hsp70 and Hsp40 molecular chaperones to rescue stress-damaged proteins from both amorphous and amyloid-forming aggregates. The ability to do so relies upon pore loops present in the first ATP-binding domain (AAA-1; loop-1 and loop-2 ) and in the second ATP-binding domain (AAA-2; loop-3) of Hsp104, which face the protein translocating channel and couple ATP-driven changes in pore loop conformation to substrate translocation. A hallmark of loop-1 and loop-3 is an invariable and mutational sensitive aromatic amino acid (Tyr257 and Tyr662) involved in substrate binding. However, the role of conserved aliphatic residues (Lys256, Lys258, and Val663) flanking the pore loop tyrosines, and the function of loop-2 in protein disaggregation has not been investigated. Here we present the crystal structure of an N-terminal fragment of Saccharomyces cerevisiae Hsp104 exhibiting molecular interactions involving both AAA-1 pore loops, which resemble contacts with bound substrate. Corroborated by biochemical experiments and functional studies in yeast, we show that aliphatic residues flanking Tyr257 and Tyr662 are equally important for substrate interaction, and abolish Hsp104 function when mutated to glycine. Unexpectedly, we find that loop-2 is sensitive to aspartate substitutions that impair Hsp104 function and abolish protein disaggregation when loop-2 is replaced by four aspartate residues. Our observations suggest that Hsp104 pore loops have non-overlapping functions in protein disaggregation and together coordinate substrate binding, unfolding, and translocation through the Hsp104 hexamer.
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11
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Agbowuro AA, Huston WM, Gamble AB, Tyndall JDA. Proteases and protease inhibitors in infectious diseases. Med Res Rev 2017; 38:1295-1331. [PMID: 29149530 DOI: 10.1002/med.21475] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/10/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022]
Abstract
There are numerous proteases of pathogenic organisms that are currently targeted for therapeutic intervention along with many that are seen as potential drug targets. This review discusses the chemical and biological makeup of some key druggable proteases expressed by the five major classes of disease causing agents, namely bacteria, viruses, fungi, eukaryotes, and prions. While a few of these enzymes including HIV protease and HCV NS3-4A protease have been targeted to a clinically useful level, a number are yet to yield any clinical outcomes in terms of antimicrobial therapy. A significant aspect of this review discusses the chemical and pharmacological characteristics of inhibitors of the various proteases discussed. A total of 25 inhibitors have been considered potent and safe enough to be trialed in humans and are at different levels of clinical application. We assess the mechanism of action and clinical performance of the protease inhibitors against infectious agents with their developmental strategies and look to the next frontiers in the use of protease inhibitors as anti-infective agents.
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Affiliation(s)
| | - Wilhelmina M Huston
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Allan B Gamble
- School of Pharmacy, University of Otago, Dunedin, New Zealand
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12
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Song G. Symmetry in normal modes and its strong dependence on symmetry in structure. J Mol Graph Model 2017; 75:32-41. [DOI: 10.1016/j.jmgm.2017.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 10/19/2022]
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13
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Song G. The finite number of global motion patterns available to symmetric protein complexes. Proteins 2017; 85:1741-1758. [DOI: 10.1002/prot.25331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 05/18/2017] [Accepted: 06/07/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Guang Song
- Graduate Program of Bioinformatics and Computational Biology; Iowa State University; Ames Iowa
- Department of Computer Science; Iowa State University; Ames Iowa
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University; Ames Iowa
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14
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Salunke DM, Nair DT. Macromolecular structures: Quality assessment and biological interpretation. IUBMB Life 2017; 69:563-571. [DOI: 10.1002/iub.1640] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/25/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Dinakar M. Salunke
- International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi India
| | - Deepak T. Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster; 3rd Milestone, Faridabad-Gurgaon Expressway Faridabad Haryana India
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15
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Chang CW, Lee S, Tsai FTF. Structural Elements Regulating AAA+ Protein Quality Control Machines. Front Mol Biosci 2017; 4:27. [PMID: 28523272 PMCID: PMC5415569 DOI: 10.3389/fmolb.2017.00027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/13/2017] [Indexed: 11/13/2022] Open
Abstract
Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines.
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Affiliation(s)
- Chiung-Wen Chang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHouston, TX, USA
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHouston, TX, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHouston, TX, USA.,Departments of Molecular and Cellular Biology, and Molecular Virology and Microbiology, Baylor College of MedicineHouston, TX, USA
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16
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Wu Y, Hu K, Li D, Bai L, Yang S, Jastrab JB, Xiao S, Hu Y, Zhang S, Darwin KH, Wang T, Li H. Mycobacterium tuberculosis proteasomal ATPase Mpa has a β-grasp domain that hinders docking with the proteasome core protease. Mol Microbiol 2017; 105:227-241. [PMID: 28419599 DOI: 10.1111/mmi.13695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2017] [Indexed: 12/21/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has a proteasome system that is essential for its ability to cause lethal infections in mice. A key component of the system is the proteasomal adenosine triphosphatase (ATPase) Mpa, which captures, unfolds, and translocates protein substrates into the Mtb proteasome core particle for degradation. Here, we report the crystal structures of near full-length hexameric Mtb Mpa in apo and ADP-bound forms. Surprisingly, the structures revealed a ubiquitin-like β-grasp domain that precedes the proteasome-activating carboxyl terminus. This domain, which was only found in bacterial proteasomal ATPases, buries the carboxyl terminus of each protomer in the central channel of the hexamer and hinders the interaction of Mpa with the proteasome core protease. Thus, our work reveals the structure of a bacterial proteasomal ATPase in the hexameric form, and the structure finally explains why Mpa is unable to stimulate robust protein degradation in vitro in the absence of other, yet-to-be-identified co-factors.
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Affiliation(s)
- Yujie Wu
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Kuan Hu
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Defeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Lin Bai
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Shaoqing Yang
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Jordan B Jastrab
- Department of Microbiology, New York University School of Medicine, 450 East 29th Street, New York, NY, 10016, USA
| | - Shuhao Xiao
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Yonglin Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Susan Zhang
- Department of Microbiology, New York University School of Medicine, 450 East 29th Street, New York, NY, 10016, USA
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, 450 East 29th Street, New York, NY, 10016, USA
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen, 518055, China.,SZCDC-SUSTech Joint Key Laboratory for Tropical Diseases, Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
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17
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Sysoeva TA. Assessing heterogeneity in oligomeric AAA+ machines. Cell Mol Life Sci 2017; 74:1001-1018. [PMID: 27669691 PMCID: PMC11107579 DOI: 10.1007/s00018-016-2374-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 09/13/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022]
Abstract
ATPases Associated with various cellular Activities (AAA+ ATPases) are molecular motors that use the energy of ATP binding and hydrolysis to remodel their target macromolecules. The majority of these ATPases form ring-shaped hexamers in which the active sites are located at the interfaces between neighboring subunits. Structural changes initiate in an active site and propagate to distant motor parts that interface and reshape the target macromolecules, thereby performing mechanical work. During the functioning cycle, the AAA+ motor transits through multiple distinct states. Ring architecture and placement of the catalytic sites at the intersubunit interfaces allow for a unique level of coordination among subunits of the motor. This in turn results in conformational differences among subunits and overall asymmetry of the motor ring as it functions. To date, a large amount of structural information has been gathered for different AAA+ motors, but even for the most characterized of them only a few structural states are known and the full mechanistic cycle cannot be yet reconstructed. Therefore, the first part of this work will provide a broad overview of what arrangements of AAA+ subunits have been structurally observed focusing on diversity of ATPase oligomeric ensembles and heterogeneity within the ensembles. The second part of this review will concentrate on methods that assess structural and functional heterogeneity among subunits of AAA+ motors, thus bringing us closer to understanding the mechanism of these fascinating molecular motors.
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Affiliation(s)
- Tatyana A Sysoeva
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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18
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Baytshtok V, Chen J, Glynn SE, Nager AR, Grant RA, Baker TA, Sauer RT. Covalently linked HslU hexamers support a probabilistic mechanism that links ATP hydrolysis to protein unfolding and translocation. J Biol Chem 2017; 292:5695-5704. [PMID: 28223361 DOI: 10.1074/jbc.m116.768978] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
The HslUV proteolytic machine consists of HslV, a double-ring self-compartmentalized peptidase, and one or two AAA+ HslU ring hexamers that hydrolyze ATP to power the unfolding of protein substrates and their translocation into the proteolytic chamber of HslV. Here, we use genetic tethering and disulfide bonding strategies to construct HslU pseudohexamers containing mixtures of ATPase active and inactive subunits at defined positions in the hexameric ring. Genetic tethering impairs HslV binding and degradation, even for pseudohexamers with six active subunits, but disulfide-linked pseudohexamers do not have these defects, indicating that the peptide tether interferes with HslV interactions. Importantly, pseudohexamers containing different patterns of hydrolytically active and inactive subunits retain the ability to unfold protein substrates and/or collaborate with HslV in their degradation, supporting a model in which ATP hydrolysis and linked mechanical function in the HslU ring operate by a probabilistic mechanism.
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Affiliation(s)
| | | | | | | | | | - Tania A Baker
- From the Department of Biology and.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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19
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Bittner LM, Arends J, Narberhaus F. Mini review: ATP-dependent proteases in bacteria. Biopolymers 2017; 105:505-17. [PMID: 26971705 DOI: 10.1002/bip.22831] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/11/2016] [Accepted: 03/07/2016] [Indexed: 01/22/2023]
Abstract
AAA(+) proteases are universal barrel-like and ATP-fueled machines preventing the accumulation of aberrant proteins and regulating the proteome according to the cellular demand. They are characterized by two separate operating units, the ATPase and peptidase domains. ATP-dependent unfolding and translocation of a substrate into the proteolytic chamber is followed by ATP-independent degradation. This review addresses the structure and function of bacterial AAA(+) proteases with a focus on the ATP-driven mechanisms and the coordinated movements in the complex mainly based on the knowledge of ClpXP. We conclude by discussing strategies how novel protease substrates can be trapped by mutated AAA(+) protease variants. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 505-517, 2016.
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Affiliation(s)
| | - Jan Arends
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
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20
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Kelch BA. Review: The lord of the rings: Structure and mechanism of the sliding clamp loader. Biopolymers 2017; 105:532-46. [PMID: 26918303 DOI: 10.1002/bip.22827] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/15/2016] [Accepted: 02/23/2016] [Indexed: 12/15/2022]
Abstract
Sliding clamps are ring-shaped polymerase processivity factors that act as master regulators of cellular replication by coordinating multiple functions on DNA to ensure faithful transmission of genetic and epigenetic information. Dedicated AAA+ ATPase machines called clamp loaders actively place clamps on DNA, thereby governing clamp function by controlling when and where clamps are used. Clamp loaders are also important model systems for understanding the basic principles of AAA+ mechanism and function. After nearly 30 years of study, the ATP-dependent mechanism of opening and loading of clamps is now becoming clear. Here I review the structural and mechanistic aspects of the clamp loading process, as well as comment on questions that will be addressed by future studies. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 532-546, 2016.
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Affiliation(s)
- Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
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21
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High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx. Cell Res 2017; 27:373-385. [PMID: 28106073 DOI: 10.1038/cr.2017.12] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/05/2016] [Accepted: 12/23/2016] [Indexed: 12/12/2022] Open
Abstract
The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide. The remaining two subunits, Rpt2 and Rpt6, with empty or only partially occupied nucleotide pocket exhibit pronounced conformational changes in the AAA-ATPase ring, which may represent a collective result of allosteric cooperativity of all the AAA-ATPase subunits responding to ATP hydrolysis. This collective motion of Rpt2 and Rpt6 results in an elevation of their pore loops, which could play an important role in substrate processing of proteasome. Our data also imply that the nucleotide occupancy pattern could be related to the activation status of the complex. Moreover, the HbYX tail insertion may not be sufficient to maintain the gate opening of 20S core particle. Our results provide new insights into the mechanisms of nucleotide-driven allosteric cooperativity of the complex and of the substrate processing by the proteasome.
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22
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Baytshtok V, Fei X, Grant RA, Baker TA, Sauer RT. A Structurally Dynamic Region of the HslU Intermediate Domain Controls Protein Degradation and ATP Hydrolysis. Structure 2016; 24:1766-1777. [PMID: 27667691 DOI: 10.1016/j.str.2016.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/02/2016] [Accepted: 08/06/2016] [Indexed: 11/30/2022]
Abstract
The I domain of HslU sits above the AAA+ ring and forms a funnel-like entry to the axial pore, where protein substrates are engaged, unfolded, and translocated into HslV for degradation. The L199Q I-domain substitution, which was originally reported as a loss-of-function mutation, resides in a segment that appears to adopt multiple conformations as electron density is not observed in HslU and HslUV crystal structures. The L199Q sequence change does not alter the structure of the AAA+ ring or its interactions with HslV but increases I-domain susceptibility to limited endoproteolysis. Notably, the L199Q mutation increases the rate of ATP hydrolysis substantially, results in slower degradation of some proteins but faster degradation of other substrates, and markedly changes the preference of HslUV for initiating degradation at the N or C terminus of model substrates. Thus, a structurally dynamic region of the I domain plays a key role in controlling protein degradation by HslUV.
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Affiliation(s)
- Vladimir Baytshtok
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xue Fei
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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23
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Huang X, Luan B, Wu J, Shi Y. An atomic structure of the human 26S proteasome. Nat Struct Mol Biol 2016; 23:778-85. [PMID: 27428775 DOI: 10.1038/nsmb.3273] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 07/08/2016] [Indexed: 12/12/2022]
Abstract
We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory particle (RP). The C-terminal residues of Rpt3 and Rpt5 subunits in the RP can be seen inserted into surface pockets formed between adjacent α subunits in the CP. Each of the six Rpt subunits contains a bound nucleotide, and the central gate of the CP α-ring is closed despite RP association. The six pore 1 loops in the Rpt ring are arranged similarly to a spiral staircase along the axial channel of substrate transport, which is constricted by the pore 2 loops. We also determined the cryo-EM structure of the human proteasome bound to the deubiquitinating enzyme USP14 at 4.35-Å resolution. Together, our structures provide a framework for mechanistic understanding of eukaryotic proteasome function.
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Affiliation(s)
- Xiuliang Huang
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Bai Luan
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jianping Wu
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yigong Shi
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
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24
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Yu H, Singh Gautam AK, Wilmington SR, Wylie D, Martinez-Fonts K, Kago G, Warburton M, Chavali S, Inobe T, Finkelstein IJ, Babu MM, Matouschek A. Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome. J Biol Chem 2016; 291:14526-39. [PMID: 27226608 PMCID: PMC4938175 DOI: 10.1074/jbc.m116.727578] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 11/23/2022] Open
Abstract
The proteasome has pronounced preferences for the amino acid sequence of its substrates at the site where it initiates degradation. Here, we report that modulating these sequences can tune the steady-state abundance of proteins over 2 orders of magnitude in cells. This is the same dynamic range as seen for inducing ubiquitination through a classic N-end rule degron. The stability and abundance of His3 constructs dictated by the initiation site affect survival of yeast cells and show that variation in proteasomal initiation can affect fitness. The proteasome's sequence preferences are linked directly to the affinity of the initiation sites to their receptor on the proteasome and are conserved between Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human cells. These findings establish that the sequence composition of unstructured initiation sites influences protein abundance in vivo in an evolutionarily conserved manner and can affect phenotype and fitness.
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Affiliation(s)
- Houqing Yu
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | | | - Shameika R Wilmington
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Dennis Wylie
- the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712
| | - Kirby Martinez-Fonts
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Grace Kago
- From the Department of Molecular Biosciences and
| | | | - Sreenivas Chavali
- the Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Tomonao Inobe
- Frontier Research Core for Life Sciences, University of Toyama, 3190 Gofuku, Toyama-shi, Toyama 930-8555, Japan
| | | | - M Madan Babu
- the Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Andreas Matouschek
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208,
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25
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Barthelme D, Sauer RT. Origin and Functional Evolution of the Cdc48/p97/VCP AAA+ Protein Unfolding and Remodeling Machine. J Mol Biol 2015; 428:1861-9. [PMID: 26608813 DOI: 10.1016/j.jmb.2015.11.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/03/2015] [Accepted: 11/16/2015] [Indexed: 01/25/2023]
Abstract
The AAA+ Cdc48 ATPase (alias p97 or VCP) is a key player in multiple ubiquitin-dependent cell signaling, degradation, and quality control pathways. Central to these broad biological functions is the ability of Cdc48 to interact with a large number of adaptor proteins and to remodel macromolecular proteins and their complexes. Different models have been proposed to explain how Cdc48 might couple ATP hydrolysis to forcible unfolding, dissociation, or remodeling of cellular clients. In this review, we provide an overview of possible mechanisms for substrate unfolding/remodeling by this conserved and essential AAA+ protein machine and their adaption and possible biological function throughout evolution.
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Affiliation(s)
- Dominik Barthelme
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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26
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Altered Escherichia coli membrane protein assembly machinery allows proper membrane assembly of eukaryotic protein vitamin K epoxide reductase. Proc Natl Acad Sci U S A 2015; 112:15184-9. [PMID: 26598701 DOI: 10.1073/pnas.1521260112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Functional overexpression of polytopic membrane proteins, particularly when in a foreign host, is often a challenging task. Factors that negatively affect such processes are poorly understood. Using the mammalian membrane protein vitamin K epoxide reductase (VKORc1) as a reporter, we describe a genetic selection approach allowing the isolation of Escherichia coli mutants capable of functionally expressing this blood-coagulation enzyme. The isolated mutants map to components of membrane protein assembly and quality control proteins YidC and HslV. We show that changes in the VKORc1 sequence and in the YidC hydrophilic groove along with the inactivation of HslV promote VKORc1 activity and dramatically increase its expression level. We hypothesize that such changes correct for mismatches in the membrane topogenic signals between E. coli and eukaryotic cells guiding proper membrane integration. Furthermore, the obtained mutants allow the study of VKORc1 reaction mechanisms, inhibition by warfarin, and the high-throughput screening for potential anticoagulants.
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27
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Hazra S, Henderson JN, Liles K, Hilton MT, Wachter RM. Regulation of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) activase: product inhibition, cooperativity, and magnesium activation. J Biol Chem 2015; 290:24222-36. [PMID: 26283786 PMCID: PMC4591810 DOI: 10.1074/jbc.m115.651745] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 08/04/2015] [Indexed: 12/24/2022] Open
Abstract
In many photosynthetic organisms, tight-binding Rubisco inhibitors are released by the motor protein Rubisco activase (Rca). In higher plants, Rca plays a pivotal role in regulating CO2 fixation. Here, the ATPase activity of 0.005 mm tobacco Rca was monitored under steady-state conditions, and global curve fitting was utilized to extract kinetic constants. The kcat was best fit by 22.3 ± 4.9 min(-1), the Km for ATP by 0.104 ± 0.024 mm, and the Ki for ADP by 0.037 ± 0.007 mm. Without ADP, the Hill coefficient for ATP hydrolysis was extracted to be 1.0 ± 0.1, indicating noncooperative behavior of homo-oligomeric Rca assemblies. However, the addition of ADP was shown to introduce positive cooperativity between two or more subunits (Hill coefficient 1.9 ± 0.2), allowing for regulation via the prevailing ATP/ADP ratio. ADP-mediated activation was not observed, although larger amounts led to competitive product inhibition of hydrolytic activity. The catalytic efficiency increased 8.4-fold upon cooperative binding of a second magnesium ion (Hill coefficient 2.5 ± 0.5), suggesting at least three conformational states (ATP-bound, ADP-bound, and empty) within assemblies containing an average of about six subunits. The addition of excess Rubisco (24:1, L8S8/Rca6) and crowding agents did not modify catalytic rates. However, high magnesium provided for thermal Rca stabilization. We propose that magnesium mediates the formation of closed hexameric toroids capable of high turnover rates and amenable to allosteric regulation. We suggest that in vivo, the Rca hydrolytic activity is tuned by fluctuating [Mg(2+)] in response to changes in available light.
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Affiliation(s)
- Suratna Hazra
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
| | - J Nathan Henderson
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
| | - Kevin Liles
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
| | - Matthew T Hilton
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
| | - Rebekka M Wachter
- From the Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287
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28
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Structural Features Reminiscent of ATP-Driven Protein Translocases Are Essential for the Function of a Type III Secretion-Associated ATPase. J Bacteriol 2015; 197:3007-14. [PMID: 26170413 DOI: 10.1128/jb.00434-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/03/2015] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED Many bacterial pathogens and symbionts utilize type III secretion systems to interact with their hosts. These machines have evolved to deliver bacterial effector proteins into eukaryotic target cells to modulate a variety of cellular functions. One of the most conserved components of these systems is an ATPase, which plays an essential role in the recognition and unfolding of proteins destined for secretion by the type III pathway. Here we show that structural features reminiscent of other ATP-driven protein translocases are essential for the function of InvC, the ATPase associated with a Salmonella enterica serovar Typhimurium type III secretion system. Mutational and functional analyses showed that a two-helix-finger motif and a conserved loop located at the entrance of and within the predicted pore formed by the hexameric ATPase are essential for InvC function. These findings provide mechanistic insight into the function of this highly conserved component of type III secretion machines. IMPORTANCE Type III secretion machines are essential for the virulence or symbiotic relationships of many bacteria. These machines have evolved to deliver bacterial effector proteins into host cells to modulate cellular functions, thus facilitating bacterial colonization and replication. An essential component of these machines is a highly conserved ATPase, which is necessary for the recognition and secretion of proteins destined to be delivered by the type III secretion pathway. Using modeling and structure and function analyses, we have identified structural features of one of these ATPases from Salmonella enterica serovar Typhimurium that help to explain important aspects of its function.
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29
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Ciniawsky S, Grimm I, Saffian D, Girzalsky W, Erdmann R, Wendler P. Molecular snapshots of the Pex1/6 AAA+ complex in action. Nat Commun 2015; 6:7331. [PMID: 26066397 PMCID: PMC4490564 DOI: 10.1038/ncomms8331] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/28/2015] [Indexed: 01/23/2023] Open
Abstract
The peroxisomal proteins Pex1 and Pex6 form a heterohexameric type II AAA+ ATPase complex, which fuels essential protein transport across peroxisomal membranes. Mutations in either ATPase in humans can lead to severe peroxisomal disorders and early death. We present an extensive structural and biochemical analysis of the yeast Pex1/6 complex. The heterohexamer forms a trimer of Pex1/6 dimers with a triangular geometry that is atypical for AAA+ complexes. While the C-terminal nucleotide-binding domains (D2) of Pex6 constitute the main ATPase activity of the complex, both D2 harbour essential substrate-binding motifs. ATP hydrolysis results in a pumping motion of the complex, suggesting that Pex1/6 function involves substrate translocation through its central channel. Mutation of the Walker B motif in one D2 domain leads to ATP hydrolysis in the neighbouring domain, giving structural insights into inter-domain communication of these unique heterohexameric AAA+ assemblies. Pex1 and Pex6 form a heterohexameric AAA+ ATPase complex with triangular geometry at the peroxisome membrane. Here the authors use electron microscopy to show that the complex undergoes conformational changes upon ATP hydrolysis, and demonstrate inter-domain communication between neighbouring nucleotide-binding domains.
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Affiliation(s)
- Susanne Ciniawsky
- Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, Munich 81377, Germany
| | - Immanuel Grimm
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Delia Saffian
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Wolfgang Girzalsky
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Petra Wendler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, Munich 81377, Germany
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30
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Kuriata AM, Chakraborty M, Henderson JN, Hazra S, Serban AJ, Pham TVT, Levitus M, Wachter RM. ATP and magnesium promote cotton short-form ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase hexamer formation at low micromolar concentrations. Biochemistry 2014; 53:7232-46. [PMID: 25357088 DOI: 10.1021/bi500968h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report a fluorescence correlation spectroscopy (FCS) study of the assembly pathway of the AAA+ protein ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase (Rca), a ring-forming ATPase responsible for activation of inhibited Rubisco complexes for biological carbon fixation. A thermodynamic characterization of simultaneously populated oligomeric states appears critical in understanding Rca structure and function. Using cotton β-Rca, we demonstrate that apparent diffusion coefficients vary as a function of concentration, nucleotide, and cation. Using manual fitting procedures, we provide estimates for the equilibrium constants for the stepwise assembly and find that in the presence of ATPγS, the Kd for hexamerization is 10-fold lower than with ADP (∼0.1 vs ∼1 μM). Hexamer fractions peak at 30 μM and dominate at 8-70 μM Rca, where they comprise 60-80% of subunits with ATPγS, compared with just 30-40% with ADP. Dimer fractions peak at 1-4 μM Rca, where they comprise 15-18% with ATPγS and 26-28% with ADP. At 30 μM Rca, large aggregates begin to form that comprise ∼10% of total protein with ATPγS and ∼25% with ADP. FCS data collected on the catalytically impaired WalkerB-D173N variant in the presence of ATP provided strong support for these results. Titration with free magnesium ions lead to the disaggregation of larger complexes in favor of hexameric forms, suggesting that a second magnesium binding site with a Kd value of 1-3 mM mediates critical subunit contacts. We propose that closed-ring toroidal hexameric forms are stabilized by binding of Mg·ATP plus Mg2+, whereas Mg·ADP promotes continuous assembly to supramolecular aggregates such as spirals.
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Affiliation(s)
- Agnieszka M Kuriata
- Department of Chemistry and Biochemistry and Center for Bioenergy and Photosynthesis, Arizona State University , Tempe, Arizona 85287, United States
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31
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Abstract
Torsins are membrane-associated ATPases whose activity is dependent on two activating cofactors, lamina-associated polypeptide 1 (LAP1) and luminal domain-like LAP1 (LULL1). The mechanism by which these cofactors regulate Torsin activity has so far remained elusive. In this study, we identify a conserved domain in these activators that is predicted to adopt a fold resembling an AAA+ (ATPase associated with a variety of cellular activities) domain. Within these domains, a strictly conserved Arg residue present in both activating cofactors, but notably missing in Torsins, aligns with a key catalytic Arg found in AAA+ proteins. We demonstrate that cofactors and Torsins associate to form heterooligomeric assemblies with a defined Torsin-activator interface. In this arrangement, the highly conserved Arg residue present in either cofactor comes into close proximity with the nucleotide bound in the neighboring Torsin subunit. Because this invariant Arg is strictly required to stimulate Torsin ATPase activity but is dispensable for Torsin binding, we propose that LAP1 and LULL1 regulate Torsin ATPase activity through an active site complementation mechanism.
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32
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Nakazaki Y, Watanabe YH. ClpB chaperone passively threads soluble denatured proteins through its central pore. Genes Cells 2014; 19:891-900. [PMID: 25288401 DOI: 10.1111/gtc.12188] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/08/2014] [Indexed: 11/27/2022]
Abstract
ClpB disaggregase forms a ring-shaped hexamer that threads substrate proteins through the central pore using energy from ATP. The ClpB protomer consists of an N-terminal domain, a middle domain, and two AAA+ modules. These two AAA+ modules bind and hydrolyze ATP and construct the core of the hexameric ring. Here, we investigated the roles of the two AAA+ modules in substrate threading. BAP is an engineered ClpB that can bind ClpP proteolytic chamber; substrates threaded by BAP are degraded by ClpP. We combined BAP with conserved motif mutations in two AAA+ modules and measured the steady-state rates of threading of soluble denatured proteins by these mutants over a range of substrate concentrations. By fitting the data to the Michaelis-Menten equation, k(cat) and K(m) values were determined. We found that the kinetic parameters of the substrate threading correlate with the type of mutation introduced rather than the ATPase activity of the mutant. Moreover, some mutants having no or marginal ATPase activity could thread denatured proteins significantly. These results indicate that ClpB can passively thread soluble denatured proteins.
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Affiliation(s)
- Yosuke Nakazaki
- Department of Biology, Faculty of Science and Engineering, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan; Institute for Integrative Neurobiology, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan
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33
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Bauer BW, Shemesh T, Chen Y, Rapoport TA. A "push and slide" mechanism allows sequence-insensitive translocation of secretory proteins by the SecA ATPase. Cell 2014; 157:1416-1429. [PMID: 24906156 DOI: 10.1016/j.cell.2014.03.063] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/22/2014] [Accepted: 03/31/2014] [Indexed: 11/16/2022]
Abstract
In bacteria, most secretory proteins are translocated across the plasma membrane by the interplay of the SecA ATPase and the SecY channel. How SecA moves a broad range of polypeptide substrates is only poorly understood. Here we show that SecA moves polypeptides through the SecY channel by a "push and slide" mechanism. In its ATP-bound state, SecA interacts through a two-helix finger with a subset of amino acids in a substrate, pushing them into the channel. A polypeptide can also passively slide back and forth when SecA is in the predominant ADP-bound state or when SecA encounters a poorly interacting amino acid in its ATP-bound state. SecA performs multiple rounds of ATP hydrolysis before dissociating from SecY. The proposed push and slide mechanism is supported by a mathematical model and explains how SecA allows translocation of a wide range of polypeptides. This mechanism may also apply to hexameric polypeptide-translocating ATPases.
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Affiliation(s)
- Benedikt W Bauer
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom Shemesh
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Yu Chen
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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34
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Sung KH, Song HK. Insights into the molecular evolution of HslU ATPase through biochemical and mutational analyses. PLoS One 2014; 9:e103027. [PMID: 25050622 PMCID: PMC4106860 DOI: 10.1371/journal.pone.0103027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 06/26/2014] [Indexed: 11/18/2022] Open
Abstract
The ATP-dependent HslVU complexes are found in all three biological kingdoms. A single HslV protease exists in each species of prokaryotes, archaea, and eukaryotes, but two HslUs (HslU1 and HslU2) are present in the mitochondria of eukaryotes. Previously, a tyrosine residue at the C-terminal tail of HslU2 has been identified as a key determinant of HslV activation in Trypanosoma brucei and a phenylalanine at the equivalent position to E. coli HslU is found in T. brucei HslU1. Unexpectedly, we found that an F441Y mutation in HslU enhanced the peptidase and caseinolytic activity of HslV in E. coli but it showed partially reduced ATPase and SulA degradation activity. Previously, only the C-terminal tail of HslU has been the focus of HslV activation studies. However, the Pro315 residue interacting with Phe441 in free HslU has also been found to be critical for HslV activation. Hence, our current biochemical analyses explore the importance of the loop region just before Pro315 for HslVU complex functionality. The proline and phenylalanine pair in prokaryotic HslU was replaced with the threonine and tyrosine pair from the functional eukaryotic HslU2. Sequence comparisons between multiple HslUs from three different biological kingdoms in combination with biochemical analysis of E. coli mutants have uncovered important new insights into the molecular evolutionary pathway of HslU.
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Affiliation(s)
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul, Korea
- * E-mail:
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35
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Abstract
The ubiquitin proteasome system (UPS) is the main ATP-dependent protein degradation pathway in the cytosol and nucleus of eukaryotic cells. At its centre is the 26S proteasome, which degrades regulatory proteins and misfolded or damaged proteins. In a major breakthrough, several groups have determined high-resolution structures of the entire 26S proteasome particle in different nucleotide conditions and with and without substrate using cryo-electron microscopy combined with other techniques. These structures provide some surprising insights into the functional mechanism of the proteasome and will give invaluable guidance for genetic and biochemical studies of this key regulatory system.
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36
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Mbang-Benet DE, Sterkers Y, Morelle C, Kebe NM, Crobu L, Portalès P, Coux O, Hernandez JF, Meghamla S, Pagès M, Bastien P. The bacterial-like HslVU protease complex subunits are involved in the control of different cell cycle events in trypanosomatids. Acta Trop 2014; 131:22-31. [PMID: 24299926 DOI: 10.1016/j.actatropica.2013.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 11/16/2013] [Accepted: 11/21/2013] [Indexed: 02/08/2023]
Abstract
The trypanosomatid parasites Leishmania and Trypanosoma are responsible for the most important WHO-designated neglected tropical diseases, for which the need for cost-effective new drugs is urgent. In addition to the classical eukaryotic 20S and 26S proteasomes, these unconventional eukaryotes possess a bacterial-like protease complex, HslVU, made of proteolytic (HslV) and regulatory (HslU) subunits. In trypanosomatids, two paralogous genes are co-expressed: HslU1 and HslU2. Conflicting reports have been published with respect to subcellular localization, functional redundancy and putative roles of the different subunits of this complex in trypanosomatids. Here, we definitively established the mitochondrial localization of HslVU in L. major procyclic promastigotes and of HslV in T. brucei bloodstream trypomastigotes, the latter being the form responsible for the disease in the mammalian host. Moreover, our data demonstrate for the first time the essential nature of HslVU in the bloodstream trypomastigotes of T. brucei, in spite of mitochondrial repression at this stage. Interestingly, our work also allows distinguishing a specific role for the different members of the complex, as HslV and HslU1 appear to be involved in the control of different cell cycle events. Finally, these data validate HslVU as a promising drug target against these parasitic diseases of wide medical and economical importance.
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37
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Tracing an allosteric pathway regulating the activity of the HslV protease. Proc Natl Acad Sci U S A 2014; 111:2140-5. [PMID: 24469799 DOI: 10.1073/pnas.1318476111] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The HslU-HslV complex functions as a bacterial proteasome, degrading substrate polypeptides to preserve cellular homeostasis. Here, we use methyl-Transverse Relaxation-Optimized Spectroscopy (TROSY) and highly deuterated, methyl-protonated samples to study the 230 kDa dodecameric HslV protease component that is structurally homologous to the stacked pair of β7-rings of the proteasome. Chemical shift assignments for over 95% of the methyl groups are reported. From the pH dependence of methyl chemical shifts, a pKa of 7.7 is measured for the amine group of the catalytic residue T1, confirming that it can act as a proton acceptor during the initial step in substrate proteolysis. Analyses involving a series of single site mutants in HslV, localized to HslU binding sites or regions undergoing significant changes on HslU binding, have identified hot spots whose perturbation leads to an allosteric pathway of propagated changes in structure and ultimately, substrate proteolysis efficiency. HslV plasticity is explored through methyl-TROSY (13)C relaxation dispersion experiments that are sensitive to millisecond timescale dynamics. The data support a dynamic coupling between residues involved in both HslU and substrate binding and residues localized to the active sites of HslV that facilitate the allostery between these distal sites. An important role for dynamics has also been observed in the archaeal proteasome, suggesting a more generally conserved role of motion in the function of these barrel-like protease structures.
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38
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Nyquist K, Martin A. Marching to the beat of the ring: polypeptide translocation by AAA+ proteases. Trends Biochem Sci 2013; 39:53-60. [PMID: 24316303 DOI: 10.1016/j.tibs.2013.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/07/2013] [Accepted: 11/12/2013] [Indexed: 11/28/2022]
Abstract
ATP-dependent proteases exist in all cells and are crucial regulators of the proteome. These machines consist of a hexameric, ring-shaped motor responsible for engaging, unfolding, and translocating protein substrates into an associated peptidase for degradation. Here, we discuss recent work that has established how the six motor subunits coordinate their ATP-hydrolysis and translocation activities. The closed topology of the ring and the rigidity of subunit/subunit interfaces cause conformational changes within a single subunit to drive motions in other subunits of the hexamer. This structural effect generates allostery between the ATP-binding sites, leading to a preferred order of binding and hydrolysis events among the motor subunits as well as a unique biphasic mechanism of translocation.
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Affiliation(s)
- Kristofor Nyquist
- QB3 Institute, University of California, Berkeley, CA 94720, USA; Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - Andreas Martin
- QB3 Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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39
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Wachter RM, Salvucci ME, Carmo-Silva AE, Barta C, Genkov T, Spreitzer RJ. Activation of interspecies-hybrid Rubisco enzymes to assess different models for the Rubisco-Rubisco activase interaction. PHOTOSYNTHESIS RESEARCH 2013; 117:557-66. [PMID: 23613007 DOI: 10.1007/s11120-013-9827-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/08/2013] [Indexed: 06/02/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is prone to inactivation from non-productive binding of sugar-phosphates. Reactivation of Rubisco requires conformational remodeling by a specific chaperone, Rubisco activase. Rubisco activase from tobacco and other plants in the family Solanaceae is an inefficient activator of Rubisco from non-Solanaceae plants and from the green alga Chlamydomonas reinhardtii. To determine if the Rubisco small subunit plays a role in the interaction with Rubisco activase, a hybrid Rubisco (SSNT) composed of tobacco small subunits and Chlamydomonas large subunits was constructed. The SSNT hybrid, like other hybrid Rubiscos containing plant small subunits, supported photoautotrophic growth in Chlamydomonas, but growth in air was much slower than for cells containing wild-type Rubisco. The kinetic properties of the SSNT hybrid Rubisco were similar to the wild-type enzyme, indicating that the poor growth in air was probably caused by disruption of pyrenoid formation and the consequent impairment of the CO2concentrating mechanism. Recombinant Rubisco activase from Arabidopsis activated the SSNT hybrid Rubisco and hybrid Rubiscos containing spinach and Arabidopsis small subunits at rates similar to the rates with wild-type Rubisco. However, none of the hybrid Rubiscos was activated by tobacco Rubisco activase. That replacement of Chlamydomonas small subunits with plant small subunits does not affect the species-specific interaction between Rubisco and Rubisco activase suggests that the association is not dominated by the small subunits that surround the Rubisco central solvent channel. Therefore, the geometry of a side-on binding mode is more consistent with the data than a top-on or ring-stacking binding mode.
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Affiliation(s)
- Rebekka M Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287, USA
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40
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Saibil H. Chaperone machines for protein folding, unfolding and disaggregation. Nat Rev Mol Cell Biol 2013; 14:630-42. [PMID: 24026055 DOI: 10.1038/nrm3658] [Citation(s) in RCA: 789] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular chaperones are diverse families of multidomain proteins that have evolved to assist nascent proteins to reach their native fold, protect subunits from heat shock during the assembly of complexes, prevent protein aggregation or mediate targeted unfolding and disassembly. Their increased expression in response to stress is a key factor in the health of the cell and longevity of an organism. Unlike enzymes with their precise and finely tuned active sites, chaperones are heavy-duty molecular machines that operate on a wide range of substrates. The structural basis of their mechanism of action is being unravelled (in particular for the heat shock proteins HSP60, HSP70, HSP90 and HSP100) and typically involves massive displacements of 20-30 kDa domains over distances of 20-50 Å and rotations of up to 100°.
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Affiliation(s)
- Helen Saibil
- Department of Crystallography, Institute for Structural and Molecular Biology, Birkbeck College London, UK
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41
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Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase. Nat Struct Mol Biol 2013; 20:1164-72. [PMID: 24013205 PMCID: PMC3869383 DOI: 10.1038/nsmb.2659] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/26/2013] [Indexed: 12/25/2022]
Abstract
The 26S proteasome is the major eukaryotic ATP-dependent protease, yet the detailed mechanisms used by the proteasomal heterohexameric AAA+ unfoldase to drive substrate degradation remain poorly understood. To perform systematic mutational analyses of individual ATPase subunits, we heterologously expressed the unfoldase subcomplex from Saccharomyces cerevisiae in Escherichia coli and reconstituted the proteasome in vitro. Our studies demonstrate that the six ATPases have distinct roles in degradation, corresponding to their positions in the spiral staircases adopted by the AAA+ domains in the absence or presence of substrate. ATP hydrolysis in subunits at the top of the staircases is critical for substrate engagement and translocation. Whereas the unfoldase relies on this vertical asymmetry for substrate processing, interaction with the peptidase exhibits three-fold symmetry with contributions from alternate subunits. These diverse functional asymmetries highlight how the 26S proteasome deviates from simpler, homomeric AAA+ proteases.
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42
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Peng W, Lin Z, Li W, Lu J, Shen Y, Wang C. Structural insights into the unusually strong ATPase activity of the AAA domain of the Caenorhabditis elegans fidgetin-like 1 (FIGL-1) protein. J Biol Chem 2013; 288:29305-12. [PMID: 23979136 DOI: 10.1074/jbc.m113.502559] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The FIGL-1 (fidgetin like-1) protein is a homolog of fidgetin, a protein whose mutation leads to multiple developmental defects. The FIGL-1 protein contains an AAA (ATPase associated with various activities) domain and belongs to the AAA superfamily. However, the biological functions and developmental implications of this protein remain unknown. Here, we show that the AAA domain of the Caenorhabditis elegans FIGL-1 protein (CeFIGL-1-AAA), in clear contrast to homologous AAA domains, has an unusually high ATPase activity and forms a hexamer in solution. By determining the crystal structure of CeFIGL-1-AAA, we found that the loop linking helices α9 and α10 folds into the short helix α9a, which has an acidic surface and interacts with a positively charged surface of the neighboring subunit. Disruption of this charge interaction by mutagenesis diminishes both the ATPase activity and oligomerization capacity of the protein. Interestingly, the acidic residues in helix α9a of CeFIGL-1-AAA are not conserved in other homologous AAA domains that have relatively low ATPase activities. These results demonstrate that the sequence of CeFIGL-1-AAA has adapted to establish an intersubunit charge interaction, which contributes to its strong oligomerization and ATPase activity. These unique properties of CeFIGL-1-AAA distinguish it from other homologous proteins, suggesting that CeFIGL-1 may have a distinct biological function.
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Affiliation(s)
- Wentao Peng
- From the Institute of Protein Research, Tongji University, Shanghai 200092 and
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43
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Park E, Lee JW, Yoo HM, Ha BH, An JY, Jeon YJ, Seol JH, Eom SH, Chung CH. Structural alteration in the pore motif of the bacterial 20S proteasome homolog HslV leads to uncontrolled protein degradation. J Mol Biol 2013; 425:2940-54. [PMID: 23707406 DOI: 10.1016/j.jmb.2013.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/29/2013] [Accepted: 05/15/2013] [Indexed: 11/27/2022]
Abstract
In all cells, ATP-dependent proteases play central roles in the controlled degradation of short-lived regulatory or misfolded proteins. A hallmark of these enzymes is that proteolytic active sites are sequestered within a compartmentalized space, which is accessible to substrates only when they are fed into the cavity by protein-unfolding ATPases. HslVU is a prototype of such enzymes, consisting of the hexameric HslU ATPase and the dodecameric HslV protease. HslV forms a barrel-shaped proteolytic chamber with two constricted axial pores. Here, we report that structural alterations of HslV's pore motif dramatically affect the proteolytic activities of both HslV and HslVU complexes. Mutations of a conserved pore residue in HslV (Leu88 to Ala, Gly, or Ser) led to a tighter binding between HslV and HslU and a dramatic stimulation of both the proteolytic and ATPase activities. Furthermore, the HslV mutants alone showed a marked increase of basal hydrolytic activities toward small peptides and unstructured proteins. A synthetic peptide of the HslU C-terminal tail further stimulated the proteolytic activities of these mutants, even allowing degradation of certain folded proteins in the absence of HslU. Moreover, expression of the L88A mutant in Escherichia coli inhibited cell growth, suggesting that HslV pore mutations dysregulate the protease through relaxing the pore constriction, which normally prevents essential cellular proteins from random degradation. Consistent with these observations, an X-ray crystal structure shows that the pore loop of L88A-HslV is largely disordered. Collectively, these results suggest that substrate degradation by HslV is controlled by gating of its pores.
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Affiliation(s)
- Eunyong Park
- School of Biological Sciences, Seoul National University, Seoul 151-742, South Korea
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44
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Affiliation(s)
- Artur Gora
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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45
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Mikita N, Cheng I, Fishovitz J, Huang J, Lee I. Processive Degradation of Unstructured Protein by Escherichia coli Lon Occurs via the Slow, Sequential Delivery of Multiple Scissile Sites Followed by Rapid and Synchronized Peptide Bond Cleavage Events. Biochemistry 2013; 52:5629-44. [DOI: 10.1021/bi4008319] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natalie Mikita
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Iteen Cheng
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Jennifer Fishovitz
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Jonathan Huang
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Irene Lee
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
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46
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Sung KH, Lee SY, Song HK. Structural and biochemical analyses of the eukaryotic heat shock locus V (HslV) from Trypanosoma brucei. J Biol Chem 2013; 288:23234-43. [PMID: 23818520 DOI: 10.1074/jbc.m113.484832] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In many bacteria, heat shock locus V (HslV) functions as a protease, which is activated by heat shock locus U (HslU). The primary sequence and structure of HslV are well conserved with those of the β-subunit of the 20 S proteasome core particle in eukaryotes. To date, the HslVU complex has only been characterized in the prokaryotic system. Recently, however, the coexistence of a 20 S proteasome with HslV protease in the same living organism has been reported. In Trypanosoma brucei, a protozoan parasite that causes human sleeping sickness in Africa, HslV is localized in the mitochondria, where it has a novel function in regulating mitochondrial DNA replication. Although the prokaryotic HslVU system has been studied extensively, little is known regarding its eukaryotic counterpart. Here, we report the biochemical characteristics of an HslVU complex from T. brucei. In contrast to the prokaryotic system, T. brucei possesses two potential HslU molecules, and we found that only one of them activates HslV. A key activating residue, Tyr(494), was identified in HslU2 by biochemical and mutational studies. Furthermore, to our knowledge, this study is the first to report the crystal structure of a eukaryotic HslV, determined at 2.4 Å resolution. Drawing on our comparison of the biochemical and structural data, we discuss herein the differences and similarities between eukaryotic and prokaryotic HslVs.
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Affiliation(s)
- Kwang Hoon Sung
- Department of Life Sciences, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-701, Korea
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47
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Ehlinger A, Walters KJ. Structural insights into proteasome activation by the 19S regulatory particle. Biochemistry 2013; 52:3618-28. [PMID: 23672618 DOI: 10.1021/bi400417a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Since its discovery in the late 1970s, the ubiquitin-proteasome system (UPS) has become recognized as the major pathway for regulated cellular proteolysis. Processes such as cell cycle control, pathogen resistance, and protein quality control rely on selective protein degradation at the proteasome for homeostatic function. Perhaps as a consequence of the importance of this pathway, and the genesis of severe diseases upon its dysregulation, protein degradation by the UPS is highly controlled from the level of substrate recognition to proteolysis. Technological advances over the past decade have created an explosion of structural and mechanistic information that has underscored the complexity of the proteasome and its upstream regulatory factors. Significant insights have come from the study of the 19S proteasome regulatory particle (RP) responsible for recognition and processing of ubiquitinated substrates destined for proteolysis. Established as a highly dynamic proteasome activator, the RP has a large number of both permanent and transient components with specialized functional roles that are critical for proteasome function. In this review, we highlight recent mechanistic developments in the study of proteasome activation by the RP and how they provide context to our current understanding of the UPS.
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Affiliation(s)
- Aaron Ehlinger
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States
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Micevski D, Dougan DA. Proteolytic regulation of stress response pathways in Escherichia coli. Subcell Biochem 2013; 66:105-28. [PMID: 23479439 DOI: 10.1007/978-94-007-5940-4_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Maintaining correct cellular function is a fundamental biological process for all forms of life. A critical aspect of this process is the maintenance of protein homeostasis (proteostasis) in the cell, which is largely performed by a group of proteins, referred to as the protein quality control (PQC) network. This network of proteins, comprised of chaperones and proteases, is critical for maintaining proteostasis not only during favourable growth conditions, but also in response to stress. Indeed proteases play a crucial role in the clearance of unwanted proteins that accumulate during stress, but more importantly, in the activation of various different stress response pathways. In bacteria, the cells response to stress is usually orchestrated by a specific transcription factor (sigma factor). In Escherichia coli there are seven different sigma factors, each of which responds to a particular stress, resulting in the rapid expression of a specific set of genes. The cellular concentration of each transcription factor is tightly controlled, at the level of transcription, translation and protein stability. Here we will focus on the proteolytic regulation of two sigma factors (σ(32) and σ(S)), which control the heat and general stress response pathways, respectively. This review will also briefly discuss the role proteolytic systems play in the clearance of unwanted proteins that accumulate during stress.
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Affiliation(s)
- Dimce Micevski
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, 3086, Australia
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Hwang W, Lang MJ. Nucleotide-dependent control of internal strains in ring-shaped AAA+ motors. Cell Mol Bioeng 2012; 6:65-73. [PMID: 23526741 DOI: 10.1007/s12195-012-0264-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The AAA+ (ATPase Associated with various cellular Activities) machinery represents an extremely successful and widely used design plan for biological motors. Recently found crystal structures are beginning to reveal nucleotide-dependent conformational changes in the canonical hexameric rings of the AAA+ motors. However, the physical mechanism by which ATP binding on one subunit allosterically propagates across the entire ring remains to be found. Here we analyze and compare structural organization of three ring-shaped AAA+ motors, ClpX, HslU, and dynein. By constructing multimers using subunits of identical conformations, we find that individual subunits locally possess helical geometries with varying pitch, radius, chirality, and symmetry number. These results suggest that binding of an ATP to a subunit imposes conformational constraint that must be accommodated by more flexible nucleotide-free subunits to relieve mechanical strain on the ring. Local deformation of the ring contour and subsequent propagation of strains may be a general strategy that AAA+ motors adopt to generate force while achieving functional diversity.
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Affiliation(s)
- Wonmuk Hwang
- Department of Biomedical Engineering, Materials Science & Engineering Program, Texas A&M University, College Station, TX 77843, U.S.A
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Brígido C, Robledo M, Menéndez E, Mateos PF, Oliveira S. A ClpB chaperone knockout mutant of Mesorhizobium ciceri shows a delay in the root nodulation of chickpea plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1594-1604. [PMID: 23134119 DOI: 10.1094/mpmi-05-12-0140-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Several molecular chaperones are known to be involved in bacteria stress response. To investigate the role of chaperone ClpB in rhizobia stress tolerance as well as in the rhizobia-plant symbiosis process, the clpB gene from a chickpea microsymbiont, strain Mesorhizobium ciceri LMS-1, was identified and a knockout mutant was obtained. The ClpB knockout mutant was tested to several abiotic stresses, showing that it was unable to grow after a heat shock and it was more sensitive to acid shock than the wild-type strain. A plant-growth assay performed to evaluate the symbiotic performance of the clpB mutant showed a higher proportion of ineffective root nodules obtained with the mutant than with the wild-type strain. Nodulation kinetics analysis showed a 6- to 8-day delay in nodule appearance in plants inoculated with the ΔclpB mutant. Analysis of nodC gene expression showed lower levels of transcript in the ΔclpB mutant strain. Analysis of histological sections of nodules formed by the clpB mutant showed that most of the nodules presented a low number of bacteroids. No differences in the root infection abilities of green fluorescent protein-tagged clpB mutant and wild-type strains were detected. To our knowledge, this is the first study that presents evidence of the involvement of the chaperone ClpB from rhizobia in the symbiotic nodulation process.
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