1
|
Guan J, Jakob U. The Protein Scaffolding Functions of Polyphosphate. J Mol Biol 2024; 436:168504. [PMID: 38423453 DOI: 10.1016/j.jmb.2024.168504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Inorganic polyphosphate (polyP), one of the first high-energy compound on earth, defies its extreme compositional and structural simplicity with an astoundingly wide array of biological activities across all domains of life. However, the underlying mechanism of such functional pleiotropy remains largely elusive. In this review, we will summarize recent studies demonstrating that this simple polyanion stabilizes protein folding intermediates and scaffolds select native proteins. These functions allow polyP to act as molecular chaperone that protects cells against protein aggregation, as pro-amyloidogenic factor that accelerates both physiological and disease-associated amyloid formation, and as a modulator of liquid-liquid phase separation processes. These activities help to explain polyP's known roles in bacterial stress responses and pathogenicity, provide the mechanistic foundation for its potential role in human neurodegenerative diseases, and open a new direction regarding its influence on gene expression through condensate formation. We will highlight critical unanswered questions and point out potential directions that will help to further understand the pleiotropic functions of this ancient and ubiquitous biopolymer.
Collapse
Affiliation(s)
- Jian Guan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
2
|
Structure, Substrate Specificity and Role of Lon Protease in Bacterial Pathogenesis and Survival. Int J Mol Sci 2023; 24:ijms24043422. [PMID: 36834832 PMCID: PMC9961632 DOI: 10.3390/ijms24043422] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Proteases are the group of enzymes that carry out proteolysis in all forms of life and play an essential role in cell survival. By acting on specific functional proteins, proteases affect the transcriptional and post-translational pathways in a cell. Lon, FtsH, HslVU and the Clp family are among the ATP-dependent proteases responsible for intracellular proteolysis in bacteria. In bacteria, Lon protease acts as a global regulator, governs an array of important functions such as DNA replication and repair, virulence factors, stress response and biofilm formation, among others. Moreover, Lon is involved in the regulation of bacterial metabolism and toxin-antitoxin systems. Hence, understanding the contribution and mechanisms of Lon as a global regulator in bacterial pathogenesis is crucial. In this review, we discuss the structure and substrate specificity of the bacterial Lon protease, as well as its ability to regulate bacterial pathogenesis.
Collapse
|
3
|
Gustchina A, Li M, Andrianova AG, Kudzhaev AM, Lountos GT, Sekula B, Cherry S, Tropea JE, Smirnov IV, Wlodawer A, Rotanova TV. Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases. Int J Mol Sci 2022; 23:11425. [PMID: 36232729 PMCID: PMC9569914 DOI: 10.3390/ijms231911425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
ATP-dependent Lon proteases are key participants in the quality control system that supports the homeostasis of the cellular proteome. Based on their unique structural and biochemical properties, Lon proteases have been assigned in the MEROPS database to three subfamilies (A, B, and C). All Lons are single-chain, multidomain proteins containing an ATPase and protease domains, with different additional elements present in each subfamily. LonA and LonC proteases are soluble cytoplasmic enzymes, whereas LonBs are membrane-bound. Based on an analysis of the available sequences of Lon proteases, we identified a number of enzymes currently assigned to the LonB subfamily that, although presumably membrane-bound, include structural features more similar to their counterparts in the LonA subfamily. This observation was confirmed by the crystal structure of the proteolytic domain of the enzyme previously assigned as Bacillus subtilis LonB, combined with the modeled structure of its ATPase domain. Several structural features present in both domains differ from their counterparts in either LonA or LonB subfamilies. We thus postulate that this enzyme is the founding member of a newly identified LonBA subfamily, so far found only in the gene sequences of firmicutes.
Collapse
Affiliation(s)
- Alla Gustchina
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Mi Li
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna G Andrianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Arsen M Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - George T Lountos
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bartosz Sekula
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-573 Lodz, Poland
| | - Scott Cherry
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Joseph E Tropea
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| |
Collapse
|
4
|
Li S, Hsieh KY, Kuo CI, Su SC, Huang KF, Zhang K, Chang CI. Processive cleavage of substrate at individual proteolytic active sites of the Lon protease complex. SCIENCE ADVANCES 2021; 7:eabj9537. [PMID: 34757797 PMCID: PMC8580320 DOI: 10.1126/sciadv.abj9537] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
The Lon protease is the prototype of a family of proteolytic machines with adenosine triphosphatase modules built into a substrate degradation chamber. Lon is known to degrade protein substrates in a processive fashion, cutting a protein chain processively into small peptides before commencing cleavages of another protein chain. Here, we present structural and biochemical evidence demonstrating that processive substrate degradation occurs at each of the six proteolytic active sites of Lon, which forms a deep groove that partially encloses the substrate polypeptide chain by accommodating only the unprimed residues and permits processive cleavage in the C-to-N direction. We identify a universally conserved acidic residue at the exit side of the binding groove indispensable for the proteolytic activity. This noncatalytic residue likely promotes processive proteolysis by carboxyl-carboxylate interactions with cleaved intermediates. Together, these results uncover a previously unrecognized mechanism for processive substrate degradation by the Lon protease.
Collapse
Affiliation(s)
- Shanshan Li
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kan-Yen Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chiao-I Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Shih-Chieh Su
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Kaiming Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
5
|
He L, Luo D, Yang F, Li C, Zhang X, Deng H, Zhang JR. Multiple domains of bacterial and human Lon proteases define substrate selectivity. Emerg Microbes Infect 2018; 7:149. [PMID: 30120231 PMCID: PMC6098112 DOI: 10.1038/s41426-018-0148-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/16/2018] [Accepted: 06/23/2018] [Indexed: 02/05/2023]
Abstract
The Lon protease selectively degrades abnormal proteins or certain normal proteins in response to environmental and cellular conditions in many prokaryotic and eukaryotic organisms. However, the mechanism(s) behind the substrate selection of normal proteins remains largely unknown. In this study, we identified 10 new substrates of F. tularensis Lon from a total of 21 candidate substrates identified in our previous work, the largest number of novel Lon substrates from a single study. Cross-species degradation of these and other known Lon substrates revealed that human Lon is unable to degrade many bacterial Lon substrates, suggestive of a “organism-adapted” substrate selection mechanism for the natural Lon variants. However, individually replacing the N, A, and P domains of human Lon with the counterparts of bacterial Lon did not enable the human protease to degrade the same bacterial Lon substrates. This result showed that the “organism-adapted” substrate selection depends on multiple domains of the Lon proteases. Further in vitro proteolysis and mass spectrometry analysis revealed a similar substrate cleavage pattern between the bacterial and human Lon variants, which was exemplified by predominant representation of leucine, alanine, and other hydrophobic amino acids at the P(−1) site within the substrates. These observations suggest that the Lon proteases select their substrates at least in part by fine structural matching with the proteins in the same organisms.
Collapse
Affiliation(s)
- Lihong He
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Dongyang Luo
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Fan Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Chunhao Li
- Philip Research Institute for Oral Health, School of Dentistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China. .,Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.
| |
Collapse
|
6
|
Ding B, Martin DW, Rampello AJ, Glynn SE. Dissecting Substrate Specificities of the Mitochondrial AFG3L2 Protease. Biochemistry 2018; 57:4225-4235. [PMID: 29932645 DOI: 10.1021/acs.biochem.8b00565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. Identifying how AFG3L2 selects substrates from the diverse complement of matrix-localized proteins is essential for understanding mitochondrial protein biogenesis and quality control. Here, we create solubilized forms of AFG3L2 to examine the enzyme's substrate specificity mechanisms. We show that conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form. Moreover, these residues can act as a degron, delivering diverse model proteins to AFG3L2 for degradation. By determining the sequence of degradation products from multiple substrates using mass spectrometry, we construct a peptidase specificity profile that displays constrained product lengths and is dominated by the identity of the residue at the P1' position, with a strong preference for hydrophobic and small polar residues. This specificity profile is validated by examining the cleavage of both fluorogenic reporter peptides and full polypeptide substrates bearing different P1' residues. Together, these results demonstrate that AFG3L2 contains multiple modes of specificity, discriminating between potential substrates by recognizing accessible degron sequences and performing peptide bond cleavage at preferred patterns of residues within the compartmental chamber.
Collapse
|
7
|
Pryde KR, Taanman JW, Schapira AH. A LON-ClpP Proteolytic Axis Degrades Complex I to Extinguish ROS Production in Depolarized Mitochondria. Cell Rep 2017; 17:2522-2531. [PMID: 27926857 PMCID: PMC5177631 DOI: 10.1016/j.celrep.2016.11.027] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 09/28/2016] [Accepted: 11/03/2016] [Indexed: 10/27/2022] Open
Abstract
Mitochondrial dysfunction is implicated in numerous neurodegenerative disorders and in Parkinson's disease (PD) in particular. PINK1 and Parkin gene mutations are causes of autosomal recessive PD, and these respective proteins function cooperatively to degrade depolarized mitochondria (mitophagy). It is widely assumed that impaired mitophagy causes PD, as toxic reactive oxygen species (ROS)-producing mitochondria accumulate and progressively drive neurodegeneration. Instead, we report that a LON-ClpP proteolytic quality control axis extinguishes ROS in depolarized mitochondria by degrading the complex I ROS-generating domain. Complex I deficiency has also been identified in PD brain, and our study provides a compelling non-genetic mechanistic rationale to explain this observation: intact complex I depletes if mitochondrial bioenergetic capacity is robustly attenuated.
Collapse
Affiliation(s)
- Kenneth Robert Pryde
- Department of Clinical Neurosciences, Institute of Neurology, University College London, London WC1E 6BT, UK.
| | - Jan Willem Taanman
- Department of Clinical Neurosciences, Institute of Neurology, University College London, London WC1E 6BT, UK
| | - Anthony Henry Schapira
- Department of Clinical Neurosciences, Institute of Neurology, University College London, London WC1E 6BT, UK
| |
Collapse
|
8
|
Sepuri NBV, Angireddy R, Srinivasan S, Guha M, Spear J, Lu B, Anandatheerthavarada HK, Suzuki CK, Avadhani NG. Mitochondrial LON protease-dependent degradation of cytochrome c oxidase subunits under hypoxia and myocardial ischemia. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:519-528. [PMID: 28442264 PMCID: PMC5507603 DOI: 10.1016/j.bbabio.2017.04.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 04/17/2017] [Accepted: 04/21/2017] [Indexed: 01/08/2023]
Abstract
The mitochondrial ATP dependent matrix protease, Lon, is involved in the maintenance of mitochondrial DNA nucleoids and degradation of abnormal or misfolded proteins. The Lon protease regulates mitochondrial Tfam (mitochondrial transcription factor A) level and thus modulates mitochondrial DNA (mtDNA) content. We have previously shown that hypoxic stress induces the PKA-dependent phosphorylation of cytochrome c oxidase (CcO) subunits I, IVi1, and Vb and a time-dependent reduction of these subunits in RAW 264.7 murine macrophages subjected to hypoxia and rabbit hearts subjected to ischemia/reperfusion. Here, we show that Lon is involved in the preferential turnover of phosphorylated CcO subunits under hypoxic/ischemic stress. Induction of Lon protease occurs at 6 to 12 h of hypoxia and this increase coincides with lower CcO subunit contents. Over-expression of flag-tagged wild type and phosphorylation site mutant Vb and IVi1 subunits (S40A and T52A, respectively) caused marked degradation of wild type protein under hypoxia while the mutant proteins were relatively resistant. Furthermore, the recombinant purified Lon protease degraded the phosphorylated IVi1 and Vb subunits, while the phosphorylation-site mutant proteins were resistant to degradation. 3D structural modeling shows that the phosphorylation sites are exposed to the matrix compartment, accessible to matrix PKA and Lon protease. Hypoxic stress did not alter CcO subunit levels in Lon depleted cells, confirming its role in CcO turnover. Our results therefore suggest that Lon preferentially degrades the phosphorylated subunits of CcO and plays a role in the regulation of CcO activity in hypoxia and ischemia/reperfusion injury.
Collapse
Affiliation(s)
- Naresh B V Sepuri
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104-6009, USA
| | - Rajesh Angireddy
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104-6009, USA
| | - Satish Srinivasan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104-6009, USA
| | - Manti Guha
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104-6009, USA
| | - Joseph Spear
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104-6009, USA
| | - Bin Lu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers The State University, New Jersey Medical School, 225 Warren Street, Newark, NJ 17103-3535, USA
| | - Hindupur K Anandatheerthavarada
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104-6009, USA
| | - Carolyn K Suzuki
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers The State University, New Jersey Medical School, 225 Warren Street, Newark, NJ 17103-3535, USA
| | - Narayan G Avadhani
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104-6009, USA.
| |
Collapse
|
9
|
Nishii W, Kukimoto-Niino M, Terada T, Shirouzu M, Muramatsu T, Kojima M, Kihara H, Yokoyama S. A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis. Nat Chem Biol 2014; 11:46-51. [PMID: 25383757 DOI: 10.1038/nchembio.1688] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 09/04/2014] [Indexed: 11/09/2022]
Abstract
The Lon AAA+ protease degrades damaged or misfolded proteins in its intramolecular chamber. Its activity must be precisely controlled, but the mechanism by which Lon is regulated in response to different environments is not known. Facultative anaerobes in the Enterobacteriaceae family, mostly symbionts and pathogens, encounter both anaerobic and aerobic environments inside and outside the host's body, respectively. The bacteria characteristically have two cysteine residues on the Lon protease (P) domain surface that unusually form a disulfide bond. Here we show that the cysteine residues act as a redox switch of Lon. Upon disulfide bond reduction, the exit pore of the P-domain ring narrows by ∼30%, thus interrupting product passage and decreasing activity by 80%; disulfide bonding by oxidation restores the pore size and activity. The redox switch (E°' = -227 mV) is appropriately tuned to respond to variation between anaerobic and aerobic conditions, thus optimizing the cellular proteolysis level for each environment.
Collapse
Affiliation(s)
- Wataru Nishii
- 1] RIKEN Systems and Structural Biology Center, Yokohama, Japan. [2] RIKEN Structural Biology Laboratory, Yokohama, Japan
| | - Mutsuko Kukimoto-Niino
- 1] RIKEN Systems and Structural Biology Center, Yokohama, Japan. [2] Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Takaho Terada
- 1] RIKEN Systems and Structural Biology Center, Yokohama, Japan. [2] RIKEN Structural Biology Laboratory, Yokohama, Japan
| | - Mikako Shirouzu
- 1] RIKEN Systems and Structural Biology Center, Yokohama, Japan. [2] Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Tomonari Muramatsu
- 1] RIKEN Systems and Structural Biology Center, Yokohama, Japan. [2] RIKEN Structural Biology Laboratory, Yokohama, Japan
| | - Masaki Kojima
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | | | - Shigeyuki Yokoyama
- 1] RIKEN Systems and Structural Biology Center, Yokohama, Japan. [2] RIKEN Structural Biology Laboratory, Yokohama, Japan
| |
Collapse
|
10
|
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: 1.3] [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
| |
Collapse
|
11
|
Liao JH, Ihara K, Kuo CI, Huang KF, Wakatsuki S, Wu SH, Chang CI. Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1395-402. [PMID: 23897463 DOI: 10.1107/s0907444913008214] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 03/25/2013] [Indexed: 11/10/2022]
Abstract
The Lon proteases are a unique family of chambered proteases with a built-in AAA+ (ATPases associated with diverse cellular activities) module. Here, crystal structures of a unique member of the Lon family with no intrinsic ATPase activity in the proteolytically active form are reported both alone and in complexes with three covalent inhibitors: two peptidomimetics and one derived from a natural product. This work reveals the unique architectural features of an ATP-independent Lon that selectively degrades unfolded protein substrates. Importantly, these results provide mechanistic insights into the recognition of inhibitors and polypeptide substrates within the conserved proteolytic chamber, which may aid the development of specific Lon-protease inhibitors.
Collapse
Affiliation(s)
- Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | | | | | | | | | | | | |
Collapse
|
12
|
Ngo JK, Pomatto LCD, Davies KJA. Upregulation of the mitochondrial Lon Protease allows adaptation to acute oxidative stress but dysregulation is associated with chronic stress, disease, and aging. Redox Biol 2013; 1:258-64. [PMID: 24024159 PMCID: PMC3757690 DOI: 10.1016/j.redox.2013.01.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 01/18/2013] [Indexed: 11/30/2022] Open
Abstract
The elimination of oxidatively modified proteins is a crucial process in maintaining cellular homeostasis, especially during stress. Mitochondria are protein-dense, high traffic compartments, whose polypeptides are constantly exposed to superoxide, hydrogen peroxide, and other reactive species, generated by 'electron leakage' from the respiratory chain. The level of oxidative stress to mitochondrial proteins is not constant, but instead varies greatly with numerous metabolic and environmental factors. Oxidized mitochondrial proteins must be removed rapidly (by proteolytic degradation) or they will aggregate, cross-link, and cause toxicity. The Lon Protease is a key enzyme in the degradation of oxidized proteins within the mitochondrial matrix. Under conditions of acute stress Lon is highly inducible, possibly with the oxidant acting as the signal inducer, thereby providing increased protection. It seems that under chronic stress conditions, however, Lon levels actually decline. Lon levels also decline with age and with senescence, and senescent cells even lose the ability to induce Lon during acute stress. We propose that the regulation of Lon is biphasic, in that it is up-regulated during transient stress and down-regulated during chronic stress and aging, and we suggest that the loss of Lon responsiveness may be a significant factor in aging, and in age-related diseases.
Collapse
Key Words
- 2D-PAGE, two-dimensional polyacrylamide gel electrophoresis
- AAA, ATPases associated with diverse cellular activities
- Aco1, Aconitase 1
- Adaptation
- CDDO, 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid
- CDDO-Me, methyl-2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oate
- COX, cytochrome c oxidase
- COX4-1, cytochrome c oxidase subunit IV isoform 1
- COX4-2, cytochrome c oxidase subunit IV isoform 2
- Ccp1, mitochondrial cytochrome-c peroxidase
- Clp, caseinolytic protease
- ClpP, core catalytic protease unit
- ERAD, endoplasmic reticulum-associated degradation
- FRDA, Friedreich's ataxia
- Fe/S, iron/SULFUR
- HAART, highly active antiretroviral therapy
- HIF-1, hypoxia inducible factor-1
- HSP104, heat shock protein 104
- HSP60, heat shock protein 60
- Hormesis
- HsIVU, bacterial ATP-dependent protease
- Lon Protease
- MELAS, mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes
- MPPβ, mitochondrial processing peptidase beta subunit
- Mitochondria
- NRF-2, nuclear factor (erythroid-derived 2)-like 2
- Nfκb, nuclear factor kappa-light-chain-enhancer of activated B csells
- Oxidative stress
- PRSS15, LON gene
- Pim1, ATP-dependent Lon protease from yeast
- Protease La, ATP-dependent protease
- Protein degradation and oxidation
- Prx1, mitochondrial peroxiredoxin 1
- SLLVY-AMC, N-succinyl-Leu-Leu-Val-Tyr-7-amino-4-methylcoumarin
- SOD, cytosolic superoxide dismutase
- SOD2, mitochondrial superoxide dismutase 2
- SPG13, hereditary spastic paraplegia
- WI-38, human lung fibroblast
- Yjl200c, mitochondrial aconitase isozyme
Collapse
Affiliation(s)
- Jenny K Ngo
- Ethel Percy Andrus Gerontology Center of the Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089-0191, USA
| | | | | |
Collapse
|
13
|
Aseev LV, Chugunov AO, Efremov RG, Boni IV. A single missense mutation in a coiled-coil domain of Escherichia coli ribosomal protein S2 confers a thermosensitive phenotype that can be suppressed by ribosomal protein S1. J Bacteriol 2013; 195:95-104. [PMID: 23104805 PMCID: PMC3536177 DOI: 10.1128/jb.01305-12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 10/21/2012] [Indexed: 01/01/2023] Open
Abstract
Ribosomal protein S2 is an essential component of translation machinery, and its viable mutated variants conferring distinct phenotypes serve as a valuable tool in studying the role of S2 in translation regulation. One of a few available rpsB mutants, rpsB1, shows thermosensitivity and ensures enhanced expression of leaderless mRNAs. In this study, we identified the nature of the rpsB1 mutation. Sequencing of the rpsB1 allele revealed a G-to-A transition in the part of the rpsB gene which encodes a coiled-coil domain of S2. The resulting E132K substitution resides in a highly conserved site, TKKE, a so-called N-terminal capping box, at the beginning of the second alpha helix. The protruding coiled-coil domain of S2 is known to provide binding with 16S rRNA in the head of the 30S subunit and, in addition, to interact with a key mRNA binding protein, S1. Molecular dynamics simulations revealed a detrimental impact of the E132K mutation on the coiled-coil structure and thereby on the interactions between S2 and 16S rRNA, providing a clue for the thermosensitivity of the rpsB1 mutant. Using a strain producing a leaderless lacZ transcript from the chromosomal lac promoter, we demonstrated that not only the rpsB1 mutation generating S2/S1-deficient ribosomes but also the rpsA::IS10 mutation leading to partial deficiency in S1 alone increased translation efficiency of the leaderless mRNA by about 10-fold. Moderate overexpression of S1 relieved all these effects and, moreover, suppressed the thermosensitive phenotype of rpsB1, indicating the role of S1 as an extragenic suppressor of the E132K mutation.
Collapse
Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | | | | | | |
Collapse
|
14
|
Abstract
Lon proteases are a family of ATP-dependent proteases involved in protein quality control, with a unique proteolytic domain and an AAA+ (ATPases associated with various cellular activities) module accommodated within a single polypeptide chain. They were classified into two types as either the ubiquitous soluble LonA or membrane-inserted archaeal LonB. In addition to the energy-dependent forms, a number of medically and ecologically important groups of bacteria encode a third type of Lon-like proteins in which the conserved proteolytic domain is fused to a large N-terminal fragment lacking canonical AAA+ motifs. Here we showed that these Lon-like proteases formed a clade distinct from LonA and LonB. Characterization of one such Lon-like protease from Meiothermus taiwanensis indicated that it formed a hexameric assembly with a hollow chamber similar to LonA/B. The enzyme was devoid of ATPase activity but retained an ability to bind symmetrically six nucleotides per hexamer; accordingly, structure-based alignment suggested possible existence of a non-functional AAA-like domain. The enzyme degraded unstructured or unfolded protein and peptide substrates, but not well-folded proteins, in ATP-independent manner. These results highlight a new type of Lon proteases that may be involved in breakdown of excessive damage or unfolded proteins during stress conditions without consumption of energy.
Collapse
|
15
|
Identification of a region in the N-terminus of Escherichia coli Lon that affects ATPase, substrate translocation and proteolytic activity. J Mol Biol 2012; 418:208-25. [PMID: 22387465 DOI: 10.1016/j.jmb.2012.02.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/21/2012] [Accepted: 02/24/2012] [Indexed: 11/24/2022]
Abstract
Lon, also known as protease La, is an AAA+ protease machine that contains the ATPase and proteolytic domain within each enzyme subunit. Three truncated Escherichia coli Lon (ELon) mutants were generated based on a previous limited tryptic digestion result and hydrogen-deuterium exchange mass spectrometry analyses performed in this study. Using methods developed for characterizing wild-type (WT) Lon, we compared the ATPase, ATP-dependent protein degradation and ATP-dependent peptidase activities. With the exception of not degrading a putative structured substrate known as CcrM (cell-cycle-regulated DNA methyltransferase), the mutant lacking the first 239 residues behaved like WT ELon. Comparing the activity data of WT and ELon mutants reveals that the first 239 residues are not needed for minimal enzyme catalysis. The mutants lacking the first 252 residues or residues 232-252 displayed compromised ATPase, protein degradation and ATP-dependent peptide translocation abilities but retained WT-like steady-state peptidase activity. The binding affinities of WT and Lon mutants were evaluated by determining the concentration of λ N (K(λN)) needed to achieve 50% maximal ATPase stimulation. Comparing the K(λN) values reveals that the region encompassing 232-252 of ELon could contribute to λ N binding, but the effect is modest. Taken together, results generated from this study reveal that the region constituting residues 240-252 of ELon is important for ATPase activity, substrate translocation and protein degradation.
Collapse
|
16
|
Venkatesh S, Lee J, Singh K, Lee I, Suzuki CK. Multitasking in the mitochondrion by the ATP-dependent Lon protease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:56-66. [PMID: 22119779 DOI: 10.1016/j.bbamcr.2011.11.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/30/2011] [Accepted: 11/06/2011] [Indexed: 01/13/2023]
Abstract
The AAA(+) Lon protease is a soluble single-ringed homo-oligomer, which represents the most streamlined operational unit mediating ATP-dependent proteolysis. Despite its simplicity, the architecture of Lon proteases exhibits a species-specific diversity. Homology modeling provides insights into the structural features that distinguish bacterial and human Lon proteases as hexameric complexes from yeast Lon, which is uniquely heptameric. The best-understood functions of mitochondrial Lon are linked to maintaining proteostasis under normal metabolic conditions, and preventing proteotoxicity during environmental and cellular stress. An intriguing property of human Lon is its specific binding to G-quadruplex DNA, and its association with the mitochondrial genome in cultured cells. A fraction of Lon preferentially binds to the control region of mitochondrial DNA where transcription and replication are initiated. Here, we present an overview of the diverse functions of mitochondrial Lon, as well as speculative perspectives on its role in protein and mtDNA quality control.
Collapse
Affiliation(s)
- Sundararajan Venkatesh
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, 185 South Orange Avenue, MSB E-633, Newark, New Jersey 07103 USA
| | | | | | | | | |
Collapse
|
17
|
Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber. EMBO J 2010; 29:3520-30. [PMID: 20834233 DOI: 10.1038/emboj.2010.226] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 08/19/2010] [Indexed: 11/08/2022] Open
Abstract
Lon proteases are distributed in all kingdoms of life and are required for survival of cells under stress. Lon is a tandem fusion of an AAA+ molecular chaperone and a protease with a serine-lysine catalytic dyad. We report the 2.0-Å resolution crystal structure of Thermococcus onnurineus NA1 Lon (TonLon). The structure is a three-tiered hexagonal cylinder with a large sequestered chamber accessible through an axial channel. Conserved loops extending from the AAA+ domain combine with an insertion domain containing the membrane anchor to form an apical domain that serves as a gate governing substrate access to an internal unfolding and degradation chamber. Alternating AAA+ domains are in tight- and weak-binding nucleotide states with different domain orientations and intersubunit contacts, reflecting intramolecular dynamics during ATP-driven protein unfolding and translocation. The bowl-shaped proteolytic chamber is contiguous with the chaperone chamber allowing internalized proteins direct access to the proteolytic sites without further gating restrictions.
Collapse
|
18
|
Ugarte N, Petropoulos I, Friguet B. Oxidized mitochondrial protein degradation and repair in aging and oxidative stress. Antioxid Redox Signal 2010; 13:539-49. [PMID: 19958171 DOI: 10.1089/ars.2009.2998] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Proteins are main targets for oxidative damage that occurs during aging and in oxidative stress situations. Since the mitochondria is a major source of reactive oxygen species, mitochondrial proteins are especially exposed to oxidative modification, and elimination of oxidized proteins is crucial for maintaining the integrity of this organelle. Hence, enzymatic reversal of protein oxidation and protein degradation is critical for protein homeostasis while protein maintenance failure has been implicated in the age-related accumulation of oxidized proteins. Within the mitochondrial matrix, the ATP-stimulated mitochondrial Lon protease is believed to play an important role in the degradation of oxidized protein, and age-associated impairment of Lon-like protease activity has been suggested to contribute to oxidized protein buildup in the mitochondria. Oxidized protein repair is limited to certain oxidation products of the sulfur-containing amino acids cysteine and methionine. Oxidized protein repair systems, thioredoxin/thioredoxin reductase or glutaredoxin/glutathione/glutathione reductase that catalytically reduce disulfide bridges or sulfenic acids, and methionine sulfoxide reductase that reverses methionine sulfoxide back to methionine within proteins, are present in the mitochondrial matrix. Thus, the role of the mitochondrial Lon protease and the oxidized protein repair system methionine sulfoxide reductase is further addressed in the context of oxidative stress and aging.
Collapse
Affiliation(s)
- Nicolas Ugarte
- Laboratoire de Biologie Cellulaire du Vieillissement, Université Pierre et Marie Paris, France
| | | | | |
Collapse
|
19
|
Liao JH, Lin YC, Hsu J, Lee AYL, Chen TA, Hsu CH, Chir JL, Hua KF, Wu TH, Hong LJ, Yen PW, Chiou A, Wu SH. Binding and cleavage of E. coli HUbeta by the E. coli Lon protease. Biophys J 2010; 98:129-37. [PMID: 20085725 DOI: 10.1016/j.bpj.2009.09.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 09/22/2009] [Accepted: 09/24/2009] [Indexed: 10/20/2022] Open
Abstract
The Escherichia coli Lon protease degrades the E. coli DNA-binding protein HUbeta, but not the related protein HUalpha. Here we show that the Lon protease binds to both HUbeta and HUalpha, but selectively degrades only HUbeta in the presence of ATP. Mass spectrometry of HUbeta peptide fragments revealed that region K18-G22 is the preferred cleavage site, followed in preference by L36-K37. The preferred cleavage site was further refined to A20-A21 by constructing and testing mutant proteins; Lon degraded HUbeta-A20Q and HUbeta-A20D more slowly than HUbeta. We used optical tweezers to measure the rupture force between HU proteins and Lon; HUalpha, HUbeta, and HUbeta-A20D can bind to Lon, and in the presence of ATP, the rupture force between each of these proteins and Lon became weaker. Our results support a mechanism of Lon protease cleavage of HU proteins in at least three stages: binding of Lon with the HU protein (HUbeta, HUalpha, or HUbeta-A20D); hydrolysis of ATP by Lon to provide energy to loosen the binding to the HU protein and to allow an induced-fit conformational change; and specific cleavage of only HUbeta.
Collapse
Affiliation(s)
- Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Utilization of synthetic peptides to evaluate the importance of substrate interaction at the proteolytic site of Escherichia coli Lon protease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1355-63. [PMID: 19285157 DOI: 10.1016/j.bbapap.2009.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/24/2009] [Accepted: 02/24/2009] [Indexed: 11/23/2022]
Abstract
Lon, also known as protease La, is an ATP-dependent protease functioning to degrade many unstructured proteins. Currently, very little is known about the substrate determinants of Lon at the proteolytic site. Using synthetic peptides constituting different regions of the endogenous protein substrate lambdaN, we demonstrated that the proteolytic site of Escherichia coli Lon exhibits a certain level of localized sequence specificity. Using an alanine positional scanning approach, we discovered a set of discontinuous substrate determinants surrounding the scissile Lon cleavage site in a model peptide substrate, which function to influence the k(cat) of the peptidase activity of Lon. We further investigated the mode of peptide interaction with the proteolytically inactive Lon mutant S679A in the absence and presence of ADP or AMPPNP by 2-dimensional nuclear magnetic resonance spectroscopy, and discovered that the binding interaction between protein and peptide varies with the nucleotide bound to the enzyme. This observation is suggestive of a substrate translocation step, which likely limits the turnover of the proteolytic reaction. The contribution of the identified substrate determinants towards the kinetics of ATP-dependent degradation of lambdaN and truncated lambdaN mutants by Lon was also examined. Our results indicated that Lon likely recognizes numerous discontinuous substrate determinants throughout lambdaN to achieve substrate promiscuity.
Collapse
|
21
|
Jennings LD, Lun DS, Médard M, Licht S. ClpP hydrolyzes a protein substrate processively in the absence of the ClpA ATPase: mechanistic studies of ATP-independent proteolysis. Biochemistry 2008; 47:11536-46. [PMID: 18839965 DOI: 10.1021/bi801101p] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ATP-dependent proteases are processive, meaning that they degrade full-length proteins into small peptide products without releasing large intermediates along the reaction pathway. In the case of the bacterial ATP-dependent protease ClpAP, ATP hydrolysis by the ClpA component has been proposed to be required for processive proteolysis of full-length protein substrates. We present here data showing that in the absence of the ATPase subunit ClpA, the protease subunit ClpP can degrade full-length protein substrates processively, albeit at a greatly reduced rate. Moreover, the size distribution of peptide products from a ClpP-catalyzed digest is remarkably similar to the size distribution of products from a ClpAP-catalyzed digest. The ClpAP- and ClpP-generated peptide product size distributions are fitted well by a sum of multiple underlying Gaussian peaks with means at integral multiples of approximately 900 Da (7-8 amino acids). Our results are consistent with a mechanism in which ClpP controls product sizes by alternating between translocation in steps of 7-8 (+/-2-3) amino acid residues and proteolysis. On the structural and molecular level, the step size may be controlled by the spacing between the ClpP active sites, and processivity may be achieved by coupling peptide bond hydrolysis to the binding and release of substrate and products in the protease chamber.
Collapse
Affiliation(s)
- Laura D Jennings
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | | | | | | |
Collapse
|
22
|
Aseev LV, Levandovskaya AA, Tchufistova LS, Scaptsova NV, Boni IV. A new regulatory circuit in ribosomal protein operons: S2-mediated control of the rpsB-tsf expression in vivo. RNA (NEW YORK, N.Y.) 2008; 14:1882-94. [PMID: 18648071 PMCID: PMC2525966 DOI: 10.1261/rna.1099108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Accepted: 05/12/2008] [Indexed: 05/09/2023]
Abstract
Autogenous regulation is a general strategy of balancing ribosomal protein synthesis in bacteria. Control mechanisms have been studied in detail for most of ribosomal protein operons, except for rpsB-tsf encoding essential r-protein S2 and elongation factor Ts, where even the promoter has remained unknown. By using single-copy translational fusions with the chromosomal lacZ gene and Western-blot analysis, we demonstrate here that S2 serves as a negative regulator of both rpsB and tsf expression in vivo, acting at a single target within the rpsB 5'-untranslated region (5'-UTR). As determined by primer extension, transcription of the Escherichia coli rpsB-tsf operon starts 162 nucleotides upstream of the rpsB initiation codon at a single promoter TGTGGTATAAA belonging to the extended -10 promoter class. Both the promoter signature and the 5'-UTR structure of the rpsB gene appear to be highly conserved in gamma-proteobacteria. Deletion analysis of the rpsB 5'-UTR within rpsB'-'lacZ fusions has revealed that an operator region involved in the S2 autoregulation comprises conserved structural elements located upstream of the rpsB ribosome binding site. The S2-mediated autogenous control is impaired in rpsB mutants and, more surprisingly, in the rpsA mutant producing decreased amounts of truncated r-protein S1 (rpsAIS10), indicating that S2 might act as a repressor in cooperation with S1.
Collapse
Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | | | | | | | | |
Collapse
|
23
|
Lee I, Suzuki CK. Functional mechanics of the ATP-dependent Lon protease- lessons from endogenous protein and synthetic peptide substrates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:727-35. [PMID: 18359303 DOI: 10.1016/j.bbapap.2008.02.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 02/17/2008] [Accepted: 02/20/2008] [Indexed: 11/25/2022]
Abstract
Lon, also known as the protease La, is a homo-oligomeric ATP-dependent protease, which is highly conserved in archaea, eubacteria and eukaryotic mitochondria and peroxisomes. Since its discovery, studies have shown that Lon activity is essential for cellular homeostasis, mediating protein quality control and metabolic regulation. This article highlights the discoveries made over the past decade demonstrating that Lon selectively degrades abnormal as well as certain regulatory proteins and thus plays significant roles in maintaining bacterial and mitochondrial function and integrity. In addition, Lon is required in certain pathogenic bacteria, for rendering pathogenicity and host infectivity. Recent research endeavors have been directed toward elucidating the reaction mechanism of the Lon protease by different biochemical and structural biological techniques. In this mini-review, the authors survey the diverse biological roles of Lon, and also place special emphasis on recent findings that clarify the mechanistic aspects of the Lon reaction cycle.
Collapse
Affiliation(s)
- Irene Lee
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-7078, USA.
| | | |
Collapse
|
24
|
Licht S, Lee I. Resolving individual steps in the operation of ATP-dependent proteolytic molecular machines: from conformational changes to substrate translocation and processivity. Biochemistry 2008; 47:3595-605. [PMID: 18311925 DOI: 10.1021/bi800025g] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Clp, Lon, and FtsH proteases are proteolytic molecular machines that use the free energy of ATP hydrolysis to unfold protein substrates and processively present them to protease active sites. Here we review recent biochemical and structural studies relevant to the mechanism of ATP-dependent processive proteolysis. Despite the significant structural differences among the Clp, Lon, and FtsH proteases, these enzymes share important mechanistic features. In these systems, mechanistic studies have provided evidence for ATP binding and hydrolysis-driven conformational changes that drive translocation of substrates, which has significant implications for the processive mechanism of proteolysis. These studies indicate that the nucleotide (ATP, ADP, or nonhydrolyzable ATP analogues) occupancy of the ATPase binding sites can influence the binding mode and/or binding affinity for protein substrates. A general mechanism is proposed in which the communication between ATPase active sites and protein substrate binding regions coordinates a processive cycle of substrate binding, translocation, proteolysis, and product release.
Collapse
Affiliation(s)
- Stuart Licht
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
| | | |
Collapse
|
25
|
Jain R, Chan MK. Support for a potential role of E. coli oligopeptidase A in protein degradation. Biochem Biophys Res Commun 2007; 359:486-90. [PMID: 17553460 DOI: 10.1016/j.bbrc.2007.05.142] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2007] [Accepted: 05/18/2007] [Indexed: 11/28/2022]
Abstract
Protein degradation is an essential quality control and regulatory function in organisms ranging from bacteria to eukaryotes. In bacteria, this process is initiated by ATP-dependent proteases which digest proteins to short peptides that are subsequently hydrolyzed to smaller fragments and free amino acids. While the entire genome of Escherichia coli has been sequenced, identification of endopeptidases that perform this downstream hydrolysis remains incomplete. However, in eukaryotes, thimet oligopeptidases (TOP) has been shown to hydrolyze peptides generated by the degradation of proteins by the 26S proteasome. These findings motivated us to investigate whether E. coli oligopeptidase A (OpdA), a homolog of TOP might play a similar general role in bacterial protein degradation. Herein, we provide initial support for this hypothesis by demonstrating that OpdA efficiently cleaves the peptides generated by the activity of the three primary ATP-dependent proteases from E. coli-Lon, HslUV, and ClpAP.
Collapse
Affiliation(s)
- Rinku Jain
- The Ohio State University Biophysics Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | | |
Collapse
|
26
|
Manes NP, Gustin JK, Rue J, Mottaz HM, Purvine SO, Norbeck AD, Monroe ME, Zimmer JSD, Metz TO, Adkins JN, Smith RD, Heffron F. Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics. Mol Cell Proteomics 2007; 6:717-27. [PMID: 17228056 DOI: 10.1074/mcp.m600282-mcp200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The pathogen Salmonella enterica is known to cause both food poisoning and typhoid fever. Because of the emergence of antibiotic-resistant isolates and the threat of bioterrorism (e.g. contamination of the food supply), there is a growing need to study this bacterium. In this investigation, comparative peptidomics was used to study S. enterica serovar Typhimurium cultured in either a rich medium or in an acidic, low magnesium, and minimal nutrient medium designed to roughly mimic the macrophage phagosomal environment (within which Salmonella are known to survive). Native peptides from cleared cell lysates were enriched by using isopropanol extraction and analyzed by using both LC-MS/MS and LC-FTICR-MS. We identified and quantified 5,163 peptides originating from 682 proteins, and the data clearly indicated that compared with Salmonella cultured in the rich medium, cells cultured in the phagosome-mimicking medium had dramatically higher abundances of a wide variety of protein degradation products, especially from ribosomal proteins. Salmonella from the same cultures were also analyzed using traditional, bottom-up proteomic methods, and when the peptidomics and proteomics data were analyzed together, two clusters of proteins targeted for proteolysis were tentatively identified. Possible roles of targeted proteolysis by phagocytosed Salmonella are discussed.
Collapse
Affiliation(s)
- Nathan P Manes
- Fundamental Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Tammenkoski M, Moiseev V, Lahti M, Ugochukwu E, Brondijk THC, White SA, Lahti R, Baykov AA. Kinetic and mutational analyses of the major cytosolic exopolyphosphatase from Saccharomyces cerevisiae. J Biol Chem 2007; 282:9302-9311. [PMID: 17215253 DOI: 10.1074/jbc.m609423200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yeast exopolyphosphatase (scPPX) processively splits off the terminal phosphate group from linear polyphosphates longer than pyrophosphate. scPPX belongs to the DHH phosphoesterase superfamily and is evolutionarily close to the well characterized family II pyrophosphatase (PPase). Here, we used steady-state kinetic and binding measurements to elucidate the metal cofactor requirement for scPPX catalysis over the pH range 4.2-9.5. A single tight binding site for Mg(2+) (K(d) of 24 microm) was detected by equilibrium dialysis. Steady-state kinetic analysis of tripolyphosphate hydrolysis revealed a second site that binds Mg(2+) in the millimolar range and modulates substrate binding. This step requires two protonated and two deprotonated enzyme groups with pK(a) values of 5.0-5.3 and 7.6-8.2, respectively. The catalytic step requiring two deprotonated groups (pK(a) of 4.6 and 5.6) is modulated by ionization of a third group (pK(a) of 8.7). Conservative mutations of Asp(127), His(148), His(149) (conserved in scPPX and PPase), and Asn(35) (His in PPase) reduced activity by a factor of 600-5000. N35H and D127E substitutions reduced the Mg(2+) affinity of the tight binding site by 25-60-fold. Contrary to expectations, the N35H variant was unable to hydrolyze pyrophosphate, but markedly altered metal cofactor specificity, displaying higher catalytic activity with Co(2+) bound to the weak binding site versus the Mg(2+)- or Mn(2+)-bound enzyme. These results provide an initial step toward understanding the dynamics of scPPX catalysis and reveal significant functional differences between structurally similar scPPX and family II PPase.
Collapse
Affiliation(s)
- Marko Tammenkoski
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - ViktorM Moiseev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Matti Lahti
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Emilie Ugochukwu
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - T Harma C Brondijk
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Scott A White
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Reijo Lahti
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland.
| | - Alexander A Baykov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia.
| |
Collapse
|
28
|
Tsilibaris V, Maenhaut-Michel G, Van Melderen L. Biological roles of the Lon ATP-dependent protease. Res Microbiol 2006; 157:701-13. [PMID: 16854568 DOI: 10.1016/j.resmic.2006.05.004] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 05/22/2006] [Accepted: 05/23/2006] [Indexed: 12/24/2022]
Abstract
The Lon ATP-dependent protease plays a major role in protein quality control. An increasing number of regulatory proteins, however, are being identified as Lon substrates, thus indicating that in addition to its housekeeping function, Lon plays an important role in regulating many biological processes in bacteria. This review presents and discusses the involvement of Lon in different aspects of bacterial physiology, including cell differentiation, sporulation, pathogenicity and survival under starvation conditions.
Collapse
Affiliation(s)
- Virginie Tsilibaris
- Laboratoire de Génétique des Procaryotes, IBMM, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
| | | | | |
Collapse
|
29
|
Rotanova TV, Botos I, Melnikov EE, Rasulova F, Gustchina A, Maurizi MR, Wlodawer A. Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains. Protein Sci 2006; 15:1815-28. [PMID: 16877706 PMCID: PMC2242575 DOI: 10.1110/ps.052069306] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
ATP-dependent Lon proteases are multi-domain enzymes found in all living organisms. All Lon proteases contain an ATPase domain belonging to the AAA(+) superfamily of molecular machines and a proteolytic domain with a serine-lysine catalytic dyad. Lon proteases can be divided into two subfamilies, LonA and LonB, exemplified by the Escherichia coli and Archaeoglobus fulgidus paralogs, respectively. The LonA subfamily is defined by the presence of a large N-terminal domain, whereas the LonB subfamily has no such domain, but has a membrane-spanning domain that anchors the protein to the cytoplasmic side of the membrane. The two subfamilies also differ in their consensus sequences. Recent crystal structures for several individual domains and sub-fragments of Lon proteases have begun to illuminate similarities and differences in structure-function relationships between the two subfamilies. Differences in orientation of the active site residues in several isolated Lon protease domains point to possible roles for the AAA(+) domains and/or substrates in positioning the catalytic residues within the active site. Structures of the proteolytic domains have also indicated a possible hexameric arrangement of subunits in the native state of bacterial Lon proteases. The structure of a large segment of the N-terminal domain has revealed a folding motif present in other protein families of unknown function and should lead to new insights regarding ways in which Lon interacts with substrates or other cellular factors. These first glimpses of the structure of Lon are heralding an exciting new era of research on this ancient family of proteases.
Collapse
Affiliation(s)
- Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow
| | | | | | | | | | | | | |
Collapse
|
30
|
Lee I, Berdis AJ, Suzuki CK. Recent developments in the mechanistic enzymology of the ATP-dependent Lon protease from Escherichia coli: highlights from kinetic studies. MOLECULAR BIOSYSTEMS 2006; 2:477-83. [PMID: 17216028 DOI: 10.1039/b609936j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lon protease, also known as protease La, is one of the simplest ATP-dependent proteases that plays vital roles in maintaining cellular functions by selectively eliminating misfolded, damaged and certain short-lived regulatory proteins. Although Lon is a homo-oligomer, each subunit of Lon contains both an ATPase and a protease active site. This relatively simple architecture compared to other hetero-oligomeric ATP-dependent proteases such as the proteasome makes Lon a useful paradigm for studying the mechanism of ATP-dependent proteolysis. In this article, we survey some recent developments in the mechanistic characterization of Lon with an emphasis on the utilization of pre-steady-state enzyme kinetic techniques to determine the timing of the ATPase and peptidase activities of the enzyme.
Collapse
Affiliation(s)
- Irene Lee
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | | | | |
Collapse
|