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Brangulis K, Drunka L, Akopjana I, Tars K. Structure of the Borrelia burgdorferi ATP-dependent metalloprotease FtsH in its functionally relevant hexameric form. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140969. [PMID: 37852516 DOI: 10.1016/j.bbapap.2023.140969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
ATP-dependent proteases FtsH are conserved in bacteria, mitochondria, and chloroplasts, where they play an essential role in degradation of misfolded/unneeded membrane and cytosolic proteins. It has also been demonstrated that the FtsH homologous protein BB0789 is crucial for mouse and tick infectivity and in vitro growth of the Lyme disease-causing agent Borrelia burgdorferi. This is not surprising, considering B. burgdorferi complex life cycle, residing in both in mammals and ticks, which requires a wide range of membrane proteins and short-lived cytosolic regulatory proteins to invade and persist in the host organism. In the current study, we have solved the crystal structure of the cytosolic BB0789166-614, lacking both N-terminal transmembrane α-helices and the small periplasmic domain. The structure revealed the arrangement of the AAA+ ATPase and the zinc-dependent metalloprotease domains in a hexamer ring, which is essential for ATPase and proteolytic activity. The AAA+ domain was found in an ADP-bound state, while the protease domain showed coordination of a zinc ion by two histidine residues and one aspartic acid residue. The loop region that forms the central pore in the oligomer was poorly defined in the crystal structure and therefore predicted by AlphaFold to complement the missing structural details, providing a complete picture of the functionally relevant hexameric form of BB0789. We confirmed that BB0789 is functionally active, possessing both protease and ATPase activities, thus providing novel structural-functional insights into the protein, which is known to be absolutely necessary for B. burgdorferi to survive and cause Lyme disease.
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Affiliation(s)
- Kalvis Brangulis
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia; Department of Human Physiology and Biochemistry, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia.
| | - Laura Drunka
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia
| | - Inara Akopjana
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia
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Lei Y, Li B, Wang X, Wei J, Wang P, Zhao J, Yu F, Qi Y. Chloroplast SRP54 and FtsH protease coordinate thylakoid membrane-associated proteostasis in Arabidopsis. PLANT PHYSIOLOGY 2023; 192:2318-2335. [PMID: 36994815 PMCID: PMC10315307 DOI: 10.1093/plphys/kiad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Thylakoid membrane protein quality control (PQC), which requires the coordination of membrane protein translocation and degradation of unassembled proteins, determines chloroplast development during de-etiolation. Despite numerous efforts, the regulation of this process in land plants is largely unknown. Here, we report the isolation and characterization of pale green Arabidopsis4 (pga4) mutants in Arabidopsis (Arabidopsis thaliana) with defects in chloroplast development during de-etiolation. Map-based cloning and complementation assays confirmed that PGA4 encodes the chloroplast Signal Recognition Particle 54 kDa (cpSRP54) protein. A heterogeneous Light-Harvesting Chlorophyll a/b Binding-Green Fluorescent Protein (LhcB2-GFP) fusion protein was generated as an indicative reporter for cpSRP54-mediated thylakoid translocation. LhcB2-GFP was dysfunctional and degraded to a short-form dLhcB2-GFP during de-etiolation through an N-terminal degradation initiated on thylakoid membranes. Further biochemical and genetic evidence demonstrated that the degradation of LhcB2-GFP to dLhcB2-GFP was disrupted in pga4 and yellow variegated2 (var2) mutants caused by mutations in the Filamentous Temperature-Sensitive H2 (VAR2/AtFtsH2) subunit of thylakoid FtsH. The yeast two-hybrid assay showed that the N-terminus of LhcB2-GFP interacts with the protease domain of VAR2/AtFtsH2. Moreover, the over-accumulated LhcB2-GFP in pga4 and var2 formed protein aggregates, which were insoluble in mild nonionic detergents. Genetically, cpSRP54 is a suppressor locus for the leaf variegation phenotype of var2. Together, these results demonstrate the coordination of cpSRP54 and thylakoid FtsH in maintaining thylakoid membrane PQC during the assembly of photosynthetic complexes and provide a trackable substrate and product for monitoring cpSRP54-dependent protein translocation and FtsH-dependent protein degradation.
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Affiliation(s)
- Yang Lei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Bilang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xiaomin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Junyou Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Peiyi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jun Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yafei Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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Qiao Z, Yokoyama T, Yan XF, Beh IT, Shi J, Basak S, Akiyama Y, Gao YG. Cryo-EM structure of the entire FtsH-HflKC AAA protease complex. Cell Rep 2022; 39:110890. [PMID: 35649372 DOI: 10.1016/j.celrep.2022.110890] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/25/2022] [Accepted: 05/06/2022] [Indexed: 11/03/2022] Open
Abstract
The membrane-bound AAA protease FtsH is the key player controlling protein quality in bacteria. Two single-pass membrane proteins, HflK and HflC, interact with FtsH to modulate its proteolytic activity. Here, we present structure of the entire FtsH-HflKC complex, comprising 12 copies of both HflK and HflC, all of which interact reciprocally to form a cage, as well as four FtsH hexamers with periplasmic domains and transmembrane helices enclosed inside the cage and cytoplasmic domains situated at the base of the cage. FtsH K61/D62/S63 in the β2-β3 loop in the periplasmic domain directly interact with HflK, contributing to complex formation. Pull-down and in vivo enzymatic activity assays validate the importance of the interacting interface for FtsH-HflKC complex formation. Structural comparison with the substrate-bound human m-AAA protease AFG3L2 offers implications for the HflKC cage in modulating substrate access to FtsH. Together, our findings provide a better understanding of FtsH-type AAA protease holoenzyme assembly and regulation.
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Affiliation(s)
- Zhu Qiao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 639798, Singapore
| | - Tatsuhiko Yokoyama
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 639798, Singapore
| | - Ing Tsyr Beh
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Jian Shi
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Sandip Basak
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yoshinori Akiyama
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 639798, Singapore.
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Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state. Commun Biol 2022; 5:257. [PMID: 35322207 PMCID: PMC8943139 DOI: 10.1038/s42003-022-03213-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/01/2022] [Indexed: 11/08/2022] Open
Abstract
AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH (TmFtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length TmFtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH.
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Yi L, Liu B, Nixon PJ, Yu J, Chen F. Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases. FRONTIERS IN PLANT SCIENCE 2022; 13:837528. [PMID: 35463435 PMCID: PMC9020784 DOI: 10.3389/fpls.2022.837528] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/24/2022] [Indexed: 05/18/2023]
Abstract
The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologs form homo- and heterocomplexes with specialized functions in maintaining photosynthesis and respiration. The diversification of FtsH homologs combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarize recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.
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Affiliation(s)
- Lanbo Yi
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Bin Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Peter J. Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, London, United Kingdom
- *Correspondence: Peter J. Nixon, ; orcid.org/0000-0003-1952-6937
| | - Jianfeng Yu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, London, United Kingdom
- Jianfeng Yu, ; orcid.org/0000-0001-7174-3803
| | - Feng Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
- Feng Chen, ; orcid.org/0000-0002-9054-943X
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Mishra LS, Funk C. The FtsHi Enzymes of Arabidopsis thaliana: Pseudo-Proteases with an Important Function. Int J Mol Sci 2021; 22:5917. [PMID: 34072887 PMCID: PMC8197885 DOI: 10.3390/ijms22115917] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 01/01/2023] Open
Abstract
FtsH metalloproteases found in eubacteria, animals, and plants are well-known for their vital role in the maintenance and proteolysis of membrane proteins. Their location is restricted to organelles of endosymbiotic origin, the chloroplasts, and mitochondria. In the model organism Arabidopsis thaliana, there are 17 membrane-bound FtsH proteases containing an AAA+ (ATPase associated with various cellular activities) and a Zn2+ metalloprotease domain. However, in five of those, the zinc-binding motif HEXXH is either mutated (FtsHi1, 2, 4, 5) or completely missing (FtsHi3), rendering these enzymes presumably inactive in proteolysis. Still, homozygous null mutants of the pseudo-proteases FtsHi1, 2, 4, 5 are embryo-lethal. Homozygous ftshi3 or a weak point mutant in FTSHi1 are affected in overall plant growth and development. This review will focus on the findings concerning the FtsHi pseudo-proteases and their involvement in protein import, leading to consequences in embryogenesis, seed growth, chloroplast, and leaf development and oxidative stress management.
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Affiliation(s)
| | - Christiane Funk
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden;
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Shin M, Watson ER, Song AS, Mindrebo JT, Novick SJ, Griffin PR, Wiseman RL, Lander GC. Structures of the human LONP1 protease reveal regulatory steps involved in protease activation. Nat Commun 2021; 12:3239. [PMID: 34050165 PMCID: PMC8163871 DOI: 10.1038/s41467-021-23495-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/29/2021] [Indexed: 12/29/2022] Open
Abstract
The human mitochondrial AAA+ protein LONP1 is a critical quality control protease involved in regulating diverse aspects of mitochondrial biology including proteostasis, electron transport chain activity, and mitochondrial transcription. As such, genetic or aging-associated imbalances in LONP1 activity are implicated in pathologic mitochondrial dysfunction associated with numerous human diseases. Despite this importance, the molecular basis for LONP1-dependent proteolytic activity remains poorly defined. Here, we solved cryo-electron microscopy structures of human LONP1 to reveal the underlying molecular mechanisms governing substrate proteolysis. We show that, like bacterial Lon, human LONP1 adopts both an open and closed spiral staircase orientation dictated by the presence of substrate and nucleotide. Unlike bacterial Lon, human LONP1 contains a second spiral staircase within its ATPase domain that engages substrate as it is translocated toward the proteolytic chamber. Intriguingly, and in contrast to its bacterial ortholog, substrate binding within the central ATPase channel of LONP1 alone is insufficient to induce the activated conformation of the protease domains. To successfully induce the active protease conformation in substrate-bound LONP1, substrate binding within the protease active site is necessary, which we demonstrate by adding bortezomib, a peptidomimetic active site inhibitor of LONP1. These results suggest LONP1 can decouple ATPase and protease activities depending on whether AAA+ or both AAA+ and protease domains bind substrate. Importantly, our structures provide a molecular framework to define the critical importance of LONP1 in regulating mitochondrial proteostasis in health and disease.
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Affiliation(s)
- Mia Shin
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Edmond R Watson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Albert S Song
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Jeffrey T Mindrebo
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Scott J Novick
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.
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8
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Wang Y, Cao W, Merritt J, Xie Z, Liu H. Characterization of FtsH Essentiality in Streptococcus mutans via Genetic Suppression. Front Genet 2021; 12:659220. [PMID: 33986772 PMCID: PMC8112672 DOI: 10.3389/fgene.2021.659220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2021] [Indexed: 12/15/2022] Open
Abstract
FtsH belongs to the AAA+ ATP-dependent family of proteases, which participate in diverse cellular processes and are ubiquitous among bacteria, chloroplasts, and mitochondria. FtsH is poorly characterized in most organisms, especially compared to other major housekeeping proteases. In the current study, we examined the source of FtsH essentiality in the human oral microbiome species Streptococcus mutans, one of the primary etiological agents of dental caries. By creating a conditionally lethal ftsH mutant, we were able to identify a secondary suppressor missense mutation in the vicR gene, encoding the response regulator of the essential VicRK two-component system (TCS). Transcriptomic analysis of the vicR (G195R) mutant revealed significantly reduced expression of 46 genes, many of which were located within the genomic island Tnsmu2, which harbors the mutanobactin biosynthetic gene cluster. In agreement with the transcriptomic data, deletion of the mutanobactin biosynthetic gene cluster suppressed ftsH essentiality in S. mutans. We also explored the role of FtsH in S. mutans physiology and demonstrated its critical role in stress tolerance, especially acid stress. The presented results reveal the first insights within S. mutans for the pleiotropic regulatory function of this poorly understood global regulator.
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Affiliation(s)
- Yaqi Wang
- MOE Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Wei Cao
- MOE Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Justin Merritt
- Department of Restorative Dentistry, Oregon Health & Science University, Portland, OR, United States.,Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, United States
| | - Zhoujie Xie
- MOE Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
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Mielke K, Wagner R, Mishra LS, Demir F, Perrar A, Huesgen PF, Funk C. Abundance of metalloprotease FtsH12 modulates chloroplast development in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3455-3473. [PMID: 33216923 PMCID: PMC8042743 DOI: 10.1093/jxb/eraa550] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/19/2020] [Indexed: 05/11/2023]
Abstract
The ATP-dependent metalloprotease FtsH12 (filamentation temperature sensitive protein H 12) has been suggested to participate in a heteromeric motor complex, driving protein translocation into the chloroplast. FtsH12 was immuno-detected in proplastids, seedlings, leaves, and roots. Expression of Myc-tagged FtsH12 under its native promotor allowed identification of FtsHi1, 2, 4, and 5, and plastidic NAD-malate dehydrogenase, five of the six interaction partners in the suggested import motor complex. Arabidopsis thaliana mutant seedlings with reduced FTSH12 abundance exhibited pale cotyledons and small, deformed chloroplasts with altered thylakoid structure. Mature plants retained these chloroplast defects, resulting in slightly variegated leaves and lower chlorophyll content. Label-free proteomics revealed strong changes in the proteome composition of FTSH12 knock-down seedlings, reflecting impaired plastid development. The composition of the translocon on the inner chloroplast membrane (TIC) protein import complex was altered, with coordinated reduction of the FtsH12-FtsHi complex subunits and accumulation of the 1 MDa TIC complex subunits TIC56, TIC214 and TIC22-III. FTSH12 overexpressor lines showed no obvious phenotype, but still displayed distinct differences in their proteome. N-terminome analyses further demonstrated normal proteolytic maturation of plastid-imported proteins irrespective of FTSH12 abundance. Together, our data suggest that FtsH12 has highest impact during seedling development; its abundance alters the plastid import machinery and impairs chloroplast development.
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Affiliation(s)
- Kati Mielke
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Raik Wagner
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, Jülich, Germany
| | - Andreas Perrar
- Central Institute for Engineering, Electronics and Analytics, Jülich, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
- Institute of Biochemistry, University of Cologne, Cologne, Germany
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Carvalho V, Prabudiansyah I, Kovacik L, Chami M, Kieffer R, van der Valk R, de Lange N, Engel A, Aubin-Tam ME. The cytoplasmic domain of the AAA+ protease FtsH is tilted with respect to the membrane to facilitate substrate entry. J Biol Chem 2021; 296:100029. [PMID: 33154162 PMCID: PMC7949044 DOI: 10.1074/jbc.ra120.014739] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/28/2020] [Accepted: 11/05/2020] [Indexed: 11/06/2022] Open
Abstract
AAA+ proteases are degradation machines that use ATP hydrolysis to unfold protein substrates and translocate them through a central pore toward a degradation chamber. FtsH, a bacterial membrane-anchored AAA+ protease, plays a vital role in membrane protein quality control. How substrates reach the FtsH central pore is an open key question that is not resolved by the available atomic structures of cytoplasmic and periplasmic domains. In this work, we used both negative stain TEM and cryo-EM to determine 3D maps of the full-length Aquifex aeolicus FtsH protease. Unexpectedly, we observed that detergent solubilization induces the formation of fully active FtsH dodecamers, which consist of two FtsH hexamers in a single detergent micelle. The striking tilted conformation of the cytosolic domain in the FtsH dodecamer visualized by negative stain TEM suggests a lateral substrate entrance between the membrane and cytosolic domain. Such a substrate path was then resolved in the cryo-EM structure of the FtsH hexamer. By mapping the available structural information and structure predictions for the transmembrane helices to the amino acid sequence we identified a linker of ∼20 residues between the second transmembrane helix and the cytosolic domain. This unique polypeptide appears to be highly flexible and turned out to be essential for proper functioning of FtsH as its deletion fully eliminated the proteolytic activity of FtsH.
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Affiliation(s)
- Vanessa Carvalho
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Irfan Prabudiansyah
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Lubomir Kovacik
- BioEM Lab, C-CINA, Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland
| | - Mohamed Chami
- BioEM Lab, C-CINA, Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland
| | - Roland Kieffer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Ramon van der Valk
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nick de Lange
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Andreas Engel
- BioEM Lab, C-CINA, Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland.
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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Prabudiansyah I, van der Valk R, Aubin-Tam ME. Reconstitution and functional characterization of the FtsH protease in lipid nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183526. [PMID: 33278347 DOI: 10.1016/j.bbamem.2020.183526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 01/09/2023]
Abstract
FtsH is a membrane-bound protease that plays a crucial role in proteolytic regulation of many cellular functions. It is universally conserved in bacteria and responsible for the degradation of misfolded or misassembled proteins. A recent study has determined the structure of bacterial FtsH in detergent micelles. To properly study the function of FtsH in a native-like environment, we reconstituted the FtsH complex into lipid nanodiscs. We found that FtsH in membrane scaffold protein (MSP) nanodiscs maintains its native hexameric conformation and is functionally active. We further investigated the effect of the lipid bilayer composition (acyl chain length, saturation, head group charge and size) on FtsH proteolytic activity. We found that the lipid acyl chain length influences AaFtsH activity in nanodiscs, with the greatest activity in a bilayer of di-C18:1 PC. We conclude that MSP nanodiscs are suitable model membranes for further in vitro studies of the FtsH protease complex.
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Affiliation(s)
- Irfan Prabudiansyah
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, the Netherlands
| | - Ramon van der Valk
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, the Netherlands
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, the Netherlands.
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Shin M, Puchades C, Asmita A, Puri N, Adjei E, Wiseman RL, Karzai AW, Lander GC. Structural basis for distinct operational modes and protease activation in AAA+ protease Lon. SCIENCE ADVANCES 2020; 6:eaba8404. [PMID: 32490208 PMCID: PMC7239648 DOI: 10.1126/sciadv.aba8404] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/09/2020] [Indexed: 05/21/2023]
Abstract
Substrate-bound structures of AAA+ protein translocases reveal a conserved asymmetric spiral staircase architecture wherein a sequential ATP hydrolysis cycle drives hand-over-hand substrate translocation. However, this configuration is unlikely to represent the full conformational landscape of these enzymes, as biochemical studies suggest distinct conformational states depending on the presence or absence of substrate. Here, we used cryo-electron microscopy to determine structures of the Yersinia pestis Lon AAA+ protease in the absence and presence of substrate, uncovering the mechanistic basis for two distinct operational modes. In the absence of substrate, Lon adopts a left-handed, "open" spiral organization with autoinhibited proteolytic active sites. Upon the addition of substrate, Lon undergoes a reorganization to assemble an enzymatically active, right-handed "closed" conformer with active protease sites. These findings define the mechanistic principles underlying the operational plasticity required for processing diverse protein substrates.
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Affiliation(s)
- Mia Shin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cristina Puchades
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ananya Asmita
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Neha Puri
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Eric Adjei
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - R. Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - A. Wali Karzai
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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13
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Fluorescence Methods Applied to the Description of Urea-Dependent YME1L Protease Unfolding. Biomolecules 2020; 10:biom10040656. [PMID: 32340357 PMCID: PMC7226517 DOI: 10.3390/biom10040656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/25/2022] Open
Abstract
ATP-dependent proteases are ubiquitous across all kingdoms of life and are critical to the maintenance of intracellular protein quality control. The enzymatic function of these enzymes requires structural stability under conditions that may drive instability and/or loss of function in potential protein substrates. Thus, these molecular machines must demonstrate greater stability than their substrates in order to ensure continued function in essential quality control networks. We report here a role for ATP in the stabilization of the inner membrane YME1L protease. Qualitative fluorescence data derived from protein unfolding experiments with urea reveal non-standard protein unfolding behavior that is dependent on [ATP]. Using multiple fluorophore systems, stopped-flow fluorescence experiments demonstrate a depletion of the native YME1L ensemble by urea-dependent unfolding and formation of a non-native conformation. Additional stopped-flow fluorescence experiments based on nucleotide binding and unfoldase activities predict that unfolding yields significant loss of active YME1L hexamers from the starting ensemble. Taken together, these data clearly define the stress limits of an important mitochondrial protease.
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14
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AAA+ ATPases in Protein Degradation: Structures, Functions and Mechanisms. Biomolecules 2020; 10:biom10040629. [PMID: 32325699 PMCID: PMC7226402 DOI: 10.3390/biom10040629] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 12/28/2022] Open
Abstract
Adenosine triphosphatases (ATPases) associated with a variety of cellular activities (AAA+), the hexameric ring-shaped motor complexes located in all ATP-driven proteolytic machines, are involved in many cellular processes. Powered by cycles of ATP binding and hydrolysis, conformational changes in AAA+ ATPases can generate mechanical work that unfolds a substrate protein inside the central axial channel of ATPase ring for degradation. Three-dimensional visualizations of several AAA+ ATPase complexes in the act of substrate processing for protein degradation have been resolved at the atomic level thanks to recent technical advances in cryogenic electron microscopy (cryo-EM). Here, we summarize the resulting advances in structural and biochemical studies of AAA+ proteases in the process of proteolysis reactions, with an emphasis on cryo-EM structural analyses of the 26S proteasome, Cdc48/p97 and FtsH-like mitochondrial proteases. These studies reveal three highly conserved patterns in the structure–function relationship of AAA+ ATPase hexamers that were observed in the human 26S proteasome, thus suggesting common dynamic models of mechanochemical coupling during force generation and substrate translocation.
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15
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Botos I, Lountos GT, Wu W, Cherry S, Ghirlando R, Kudzhaev AM, Rotanova TV, de Val N, Tropea JE, Gustchina A, Wlodawer A. Cryo-EM structure of substrate-free E. coli Lon protease provides insights into the dynamics of Lon machinery. Curr Res Struct Biol 2019; 1:13-20. [PMID: 34235464 PMCID: PMC8244335 DOI: 10.1016/j.crstbi.2019.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 11/24/2022] Open
Abstract
Energy-dependent Lon proteases play a key role in cellular regulation by degrading short-lived regulatory proteins and misfolded proteins in the cell. The structure of the catalytically inactive S679A mutant of Escherichia coli LonA protease (EcLon) has been determined by cryo-EM at the resolution of 3.5 Å. EcLonA without a bound substrate adopts a hexameric open-spiral quaternary structure that might represent the resting state of the enzyme. Upon interaction with substrate the open-spiral hexamer undergoes a major conformational change resulting in a compact, closed-circle hexamer as in the recent structure of a complex of Yersinia pestis LonA with a protein substrate. This major change is accomplished by the rigid-body rearrangement of the individual domains within the protomers of the complex around the hinge points in the interdomain linkers. Comparison of substrate-free and substrate-bound Lon structures allows to mark the location of putative pivotal points involved in such conformational changes.
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Affiliation(s)
- Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - George T. Lountos
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Scott Cherry
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Arsen M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Tatyana V. Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Electron Microscopy Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Joseph E. Tropea
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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16
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Puchades C, Ding B, Song A, Wiseman RL, Lander GC, Glynn SE. Unique Structural Features of the Mitochondrial AAA+ Protease AFG3L2 Reveal the Molecular Basis for Activity in Health and Disease. Mol Cell 2019; 75:1073-1085.e6. [PMID: 31327635 PMCID: PMC6731152 DOI: 10.1016/j.molcel.2019.06.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 04/24/2019] [Accepted: 06/13/2019] [Indexed: 12/23/2022]
Abstract
Mitochondrial AAA+ quality-control proteases regulate diverse aspects of mitochondrial biology through specialized protein degradation, but the underlying mechanisms of these enzymes remain poorly defined. The mitochondrial AAA+ protease AFG3L2 is of particular interest, as genetic mutations localized throughout AFG3L2 are linked to diverse neurodegenerative disorders. However, a lack of structural data has limited our understanding of how mutations impact enzymatic function. Here, we used cryoelectron microscopy (cryo-EM) to determine a substrate-bound structure of the catalytic core of human AFG3L2. This structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins. Many disease-relevant mutations localize to these unique structural features of AFG3L2 and distinctly influence its activity and stability. Our results provide a molecular basis for neurological phenotypes associated with different AFG3L2 mutations and establish a structural framework to understand how different members of the AAA+ superfamily achieve specialized biological functions.
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Affiliation(s)
- Cristina Puchades
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bojian Ding
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Albert Song
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Steven E Glynn
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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17
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Steele TE, Glynn SE. Mitochondrial AAA proteases: A stairway to degradation. Mitochondrion 2019; 49:121-127. [PMID: 31377246 DOI: 10.1016/j.mito.2019.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022]
Abstract
Mitochondrial protein quality control requires the action of proteases to remove damaged or unnecessary proteins and perform key regulatory cleavage events. Important components of the quality control network are the mitochondrial AAA proteases, which capture energy from ATP hydrolysis to destabilize and degrade protein substrates on both sides of the inner membrane. Dysfunction of these proteases leads to the breakdown of mitochondrial proteostasis and is linked to the development of severe human diseases. In this review, we will describe recent insights into the structure and motions of the mitochondrial AAA proteases and related enzymes. Together, these studies have revealed the mechanics of ATP-driven protein destruction and significantly advanced our understanding of how these proteases maintain mitochondrial health.
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Affiliation(s)
- Tyler E Steele
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA; Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Steven E Glynn
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA; Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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18
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Duan J, Lee KP, Dogra V, Zhang S, Liu K, Caceres-Moreno C, Lv S, Xing W, Kato Y, Sakamoto W, Liu R, Macho AP, Kim C. Impaired PSII Proteostasis Promotes Retrograde Signaling via Salicylic Acid. PLANT PHYSIOLOGY 2019; 180:2182-2197. [PMID: 31160506 PMCID: PMC6670100 DOI: 10.1104/pp.19.00483] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/21/2019] [Indexed: 05/18/2023]
Abstract
Photodamage of the PSII reaction center (RC) is an inevitable process in an oxygen-rich environment. The damaged PSII RC proteins (Dam-PSII) undergo degradation via the thylakoid membrane-bound FtsH metalloprotease, followed by posttranslational assembly of PSII. While the effect of Dam-PSII on gene regulation is described for cyanobacteria, its role in land plants is largely unknown. In this study, we reveal an intriguing retrograde signaling pathway by using the Arabidopsis (Arabidopsis thaliana) yellow variegated2-9 mutant, which expresses a mutated FtsH2 (FtsH2G267D) metalloprotease, specifically impairing its substrate-unfolding activity. This lesion leads to the perturbation of PSII protein homeostasis (proteostasis) and the accumulation of Dam-PSII. Subsequently, this results in an up-regulation of salicylic acid (SA)-responsive genes, which is abrogated by inactivation of either an SA transporter in the chloroplast envelope membrane or extraplastidic SA signaling components as well as by removal of SA. These results suggest that the stress hormone SA, which is mainly synthesized via the chloroplast isochorismate pathway in response to the impaired PSII proteostasis, mediates the retrograde signaling. These findings reinforce the emerging view of chloroplast function toward plant stress responses and suggest SA as a potential plastid factor mediating retrograde signaling.
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Affiliation(s)
- Jianli Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Keun Pyo Lee
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Vivek Dogra
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Siyuan Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiwei Liu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Carlos Caceres-Moreno
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Lv
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Weiman Xing
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yusuke Kato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Renyi Liu
- College of Horticulture and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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19
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Yang Y, Gunasekara M, Muhammednazaar S, Li Z, Hong H. Proteolysis mediated by the membrane-integrated ATP-dependent protease FtsH has a unique nonlinear dependence on ATP hydrolysis rates. Protein Sci 2019; 28:1262-1275. [PMID: 31008538 DOI: 10.1002/pro.3629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/17/2019] [Indexed: 12/16/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+) proteases utilize ATP hydrolysis to actively unfold native or misfolded proteins and translocate them into a protease chamber for degradation. This basic mechanism yields diverse cellular consequences, including the removal of misfolded proteins, control of regulatory circuits, and remodeling of protein conformation. Among various bacterial AAA+ proteases, FtsH is only membrane-integrated and plays a key role in membrane protein quality control. Previously, we have shown that FtsH has substantial unfoldase activity for degrading membrane proteins overcoming a dual energetic burden of substrate unfolding and membrane dislocation. Here, we asked how efficiently FtsH utilizes ATP hydrolysis to degrade membrane proteins. To answer this question, we measured degradation rates of the model membrane substrate GlpG at various ATP hydrolysis rates in the lipid bilayers. We find that the dependence of degradation rates on ATP hydrolysis rates is highly nonlinear: (i) FtsH cannot degrade GlpG until it reaches a threshold ATP hydrolysis rate; (ii) after exceeding the threshold, the degradation rates steeply increase and saturate at the ATP hydrolysis rates far below the maxima. During the steep increase, FtsH efficiently utilizes ATP hydrolysis for degradation, consuming only 40-60% of the total ATP cost measured at the maximal ATP hydrolysis rates. This behavior does not fundamentally change against water-soluble substrates as well as upon addition of the macromolecular crowding agent Ficoll 70. The Hill analysis shows that the nonlinearity stems from coupling of three to five ATP hydrolysis events to degradation, which represents unique cooperativity compared to other AAA+ proteases including ClpXP, HslUV, Lon, and proteasomes.
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Affiliation(s)
- Yiqing Yang
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | - Mihiravi Gunasekara
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | | | - Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824
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20
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Abstract
Membranes surrounding the biological cell and its internal compartments host proteins that catalyze chemical reactions essential for the functioning of the cell. Rather than being a passive structural matrix that holds membrane-embedded proteins in place, the membrane can largely shape the conformational energy landscape of membrane proteins and impact the energetics of their chemical reaction. Here, we highlight the challenges in understanding how lipids impact the conformational energy landscape of macromolecular membrane complexes whose functioning involves chemical reactions including proton transfer. We review here advances in our understanding of how chemical reactions occur at membrane interfaces gleaned with both theoretical and experimental advances using simple protein systems as guides. Our perspective is that of bridging experiments with theory to understand general physicochemical principles of membrane reactions, with a long term goal of furthering our understanding of the role of the lipids on the functioning of complex macromolecular assemblies at the membrane interface.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin , Department of Physics, Theoretical Molecular Biophysics Group , Arnimallee 14 , D-14195 Berlin , Germany
| | - M Joanne Lemieux
- University of Alberta , Department of Biochemistry, Membrane Protein Disease Research Group , Edmonton , Alberta T6G 2H7 , Canada
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21
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Mishra LS, Mielke K, Wagner R, Funk C. Reduced expression of the proteolytically inactive FtsH members has impacts on the Darwinian fitness of Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2173-2184. [PMID: 30721974 PMCID: PMC6460958 DOI: 10.1093/jxb/erz004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/04/2019] [Indexed: 05/20/2023]
Abstract
FtsH (filamentation-temperature-sensitive protein H) proteases are a family of membrane-bound enzymes present in eubacteria, animals, and plants. Besides the 12 genes encoding proteolytically active members of the FtsH family in the genome of Arabidopsis, there are five genes coding for members that are assumed to be proteolytically inactive due to mutations in the protease domain; these are termed FtsHi (i for inactive). Despite their lack of proteolytic activity, these FtsHi members seem to be important for chloroplast and plant development as four out of five homozygous knockout-mutants of FtsHis are embryo-lethal. Here, we analysed the Darwinian fitness of weak homozygous (ftshi1,3,4) and heterozygous (ftshi/FTSHi2,4,5) mutants. We compared the growth and development of these mutants to their respective wild-type Arabidopsis plants under controlled laboratory conditions and in the field, and we also evaluated the photosynthetic efficiency by pulse-amplitude modulation fluorescence. Homologous genotypes were subjected to various stress conditions in a greenhouse and gene co-expression as well as phylogenetic analyses were performed. Analysis of the gene-expression network of the five FTSHi genes indicated common clusters with genes encoding FtsH12, OTP51, and methylase. Phylogenetic analyses pointed to a common evolution (and common disappearance in grasses and gymnosperms) of FtsH12 and multiple presumably proteolytically inactive FtsHi enzymes. Our data show that the FtsHi enzymes are highly important during the seedling stage and for Darwinian fitness analyses in semi-natural conditions.
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Affiliation(s)
| | - Kati Mielke
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Raik Wagner
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Christiane Funk
- Department of Chemistry, Umeå University, Umeå, Sweden
- Correspondence:
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22
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Brambley CA, Marsee JD, Halper N, Miller JM. Characterization of Mitochondrial YME1L Protease Oxidative Stress-Induced Conformational State. J Mol Biol 2019; 431:1250-1266. [PMID: 30731091 DOI: 10.1016/j.jmb.2019.01.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/11/2019] [Accepted: 01/27/2019] [Indexed: 10/27/2022]
Abstract
Oxidative stress is a common challenge to mitochondrial function where reactive oxygen species are capable of significant organelle damage. The generation of mitochondrial reactive oxygen species occurs in the inner membrane and matrix compartments as a consequence of subunit function in the electron transport chain and citric acid cycle, respectively. Maintenance of mitochondrial proteostasis and stress response is facilitated by compartmentalized proteases that couple the energy of ATP hydrolysis to unfolding and the regulated removal of damaged, misfolded, or aggregated proteins. The mitochondrial protease YME1L functions in the maintenance of proteostasis in the intermembrane space. YME1L is an inner membrane-anchored hexameric protease with distinct N-terminal, transmembrane, AAA+ (ATPases associated with various cellular activities), and C-terminal M41 zinc-dependent protease domains. The effect of oxidative stress on enzymes such as YME1L tasked with maintaining proteostasis is currently unclear. We report here that recombinant YME1L undergoes a reversible conformational change in response to oxidative stress that involves the interaction of one hydrogen peroxide molecule per YME1L monomer with affinities equal to 31 ± 2 and 26 ± 1 mM for conditions lacking or including nucleotide, respectively. Our data also reveal that oxidative stress does not significantly impact nucleotide binding equilibria, but does stimulate a 2-fold increase in the rate constant for high-affinity ATP binding from (8.9 ± 0.2) × 105 M-1 s-1 to (1.5 ± 0.1) × 106 M-1 s-1. Taken together, these data may suggest a mechanism for the regulated processing of YME1L by other inner membrane proteases such as OMA1.
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Affiliation(s)
- Chad A Brambley
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN 37132, USA
| | - Justin D Marsee
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN 37132, USA
| | - Neal Halper
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN 37132, USA
| | - Justin M Miller
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN 37132, USA.
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23
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Adam Z, Aviv-Sharon E, Keren-Paz A, Naveh L, Rozenberg M, Savidor A, Chen J. The Chloroplast Envelope Protease FTSH11 - Interaction With CPN60 and Identification of Potential Substrates. FRONTIERS IN PLANT SCIENCE 2019; 10:428. [PMID: 31024594 PMCID: PMC6459962 DOI: 10.3389/fpls.2019.00428] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
FTSH proteases are membrane-bound, ATP-dependent metalloproteases found in bacteria, mitochondria and chloroplasts. The product of one of the 12 genes encoding FTSH proteases in Arabidopsis, FTSH11, has been previously shown to be essential for acquired thermotolerance. However, the substrates of this protease, as well as the mechanism linking it to thermotolerance are largely unknown. To get insight into these, the FTSH11 knockout mutant was complemented with proteolytically active or inactive variants of this protease, tagged with HA-tag, under the control of the native promoter. Using these plants in thermotolerance assay demonstrated that the proteolytic activity, and not only the ATPase one, is essential for conferring thermotolerance. Immunoblot analyses of leaf extracts, isolated organelles and sub-fractionated chloroplast membranes localized FTSH11 mostly to chloroplast envelopes. Affinity purification followed by mass spectrometry analysis revealed interaction between FTSH11 and different components of the CPN60 chaperonin. In affinity enrichment assays, CPN60s as well as a number of envelope, stroma and thylakoid proteins were found associated with proteolytically inactive FTSH11. Comparative proteomic analysis of WT and knockout plants, grown at 20°C or exposed to 30°C for 6 h, revealed a plethora of upregulated chloroplast proteins in the knockout, some of them might be candidate substrates. Among these stood out TIC40, which was stabilized in the knockout line after recovery from heat stress, and three proteins that were found trapped in the affinity enrichment assay: the nucleotide antiporter PAPST2, the fatty acid binding protein FAP1 and the chaperone HSP70. The consistent behavior of these four proteins in different assays suggest that they are potential FTSH11 substrates.
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Affiliation(s)
- Zach Adam
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Zach Adam,
| | - Elinor Aviv-Sharon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alona Keren-Paz
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Leah Naveh
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mor Rozenberg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, United States
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24
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Uthoff M, Baumann U. Conformational flexibility of pore loop-1 gives insights into substrate translocation by the AAA + protease FtsH. J Struct Biol 2018; 204:199-206. [PMID: 30118817 DOI: 10.1016/j.jsb.2018.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/07/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
Abstract
Two crystal structures of a transmembrane helix-lacking FtsH construct from Aquifex aeolicus have been determined at 2.9 Å and 3.3 Å resolution in space groups R32 and P312, respectively. Both structures are virtually identical despite different crystal packing contacts. In both structures, the FtsH hexamer is created from two different subunits of the asymmetric unit by the threefold symmetry of the crystals. Similar to other published structures, all subunits are loaded with ADP and the two subunit in the asymmetric unit resemble the already known open and closed conformations. Within the ATPase cycle while the whole subunit switches from the opened to the closed state, pore loop-1 interacts with the substrate and translocates it into the proteolytic chamber. Unique to our models is a presumably inactive conformation of the pore loop which allows the closed conformation to switch back to the opened state without pushing the substrate out again. Our structures give further insights on how this new pore loop conformation is induced and how it is linked to the intersubunit signalling network.
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Affiliation(s)
- Matthias Uthoff
- Institute of Biochemistry, University of Cologne, Zuelpicher Str. 47, Cologne, North Rhine-Westphalia 50674, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zuelpicher Str. 47, Cologne, North Rhine-Westphalia 50674, Germany.
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25
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ATPase and Protease Domain Movements in the Bacterial AAA+ Protease FtsH Are Driven by Thermal Fluctuations. J Mol Biol 2018; 430:4592-4602. [PMID: 30044948 DOI: 10.1016/j.jmb.2018.07.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 01/27/2023]
Abstract
AAA+ proteases are essential players in cellular pathways of protein degradation. Elucidating their conformational behavior is key for understanding their reaction mechanism and, importantly, for elaborating our understanding of mutation-induced protease deficiencies. Here, we study the structural dynamics of the Thermotoga maritima AAA+ hexameric ring metalloprotease FtsH (TmFtsH). Using a single-molecule Förster resonance energy transfer approach to monitor ATPase and protease inter-domain conformational changes in real time, we show that TmFtsH-even in the absence of nucleotide-is a highly dynamic protease undergoing sequential transitions between five states on the second timescale. Addition of ATP does not influence the number of states or change the timescale of domain motions but affects the state occupancy distribution leading to an inter-domain compaction. These findings suggest that thermal energy, but not chemical energy, provides the major driving force for conformational switching, while ATP, through a state reequilibration, introduces directionality into this process. The TmFtsH A359V mutation, a homolog of the human pathogenic A510V mutation of paraplegin (SPG7) causing hereditary spastic paraplegia, does not affect the dynamic behavior of the protease but impairs the ATP-coupled domain compaction and, thus, may account for protease malfunctioning and pathogenesis in hereditary spastic paraplegia.
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26
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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.
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27
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Yang Y, Guo R, Gaffney K, Kim M, Muhammednazaar S, Tian W, Wang B, Liang J, Hong H. Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-Dependent Protease FtsH. J Am Chem Soc 2018. [PMID: 29528632 DOI: 10.1021/jacs.8b00832] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ATP-dependent protein degradation mediated by AAA+ proteases is one of the major cellular pathways for protein quality control and regulation of functional networks. While a majority of studies of protein degradation have focused on water-soluble proteins, it is not well understood how membrane proteins with abnormal conformation are selectively degraded. The knowledge gap stems from the lack of an in vitro system in which detailed molecular mechanisms can be studied as well as difficulties in studying membrane protein folding in lipid bilayers. To quantitatively define the folding-degradation relationship of membrane proteins, we reconstituted the degradation using the conserved membrane-integrated AAA+ protease FtsH as a model degradation machine and the stable helical-bundle membrane protein GlpG as a model substrate in the lipid bilayer environment. We demonstrate that FtsH possesses a substantial ability to actively unfold GlpG, and the degradation significantly depends on the stability and hydrophobicity near the degradation marker. We find that FtsH hydrolyzes 380-550 ATP molecules to degrade one copy of GlpG. Remarkably, FtsH overcomes the dual-energetic burden of substrate unfolding and membrane dislocation with the ATP cost comparable to that for water-soluble substrates by robust ClpAP/XP proteases. The physical principles elucidated in this study provide general insights into membrane protein degradation mediated by ATP-dependent proteolytic systems.
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Affiliation(s)
| | | | | | | | | | - Wei Tian
- Department of Bioengineering , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Boshen Wang
- Department of Bioengineering , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Jie Liang
- Department of Bioengineering , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
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28
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Puchades C, Rampello AJ, Shin M, Giuliano CJ, Wiseman RL, Glynn SE, Lander GC. Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing. Science 2018; 358:358/6363/eaao0464. [PMID: 29097521 DOI: 10.1126/science.aao0464] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022]
Abstract
We present an atomic model of a substrate-bound inner mitochondrial membrane AAA+ quality control protease in yeast, YME1. Our ~3.4-angstrom cryo-electron microscopy structure reveals how the adenosine triphosphatases (ATPases) form a closed spiral staircase encircling an unfolded substrate, directing it toward the flat, symmetric protease ring. Three coexisting nucleotide states allosterically induce distinct positioning of tyrosines in the central channel, resulting in substrate engagement and translocation to the negatively charged proteolytic chamber. This tight coordination by a network of conserved residues defines a sequential, around-the-ring adenosine triphosphate hydrolysis cycle that results in stepwise substrate translocation. A hingelike linker accommodates the large-scale nucleotide-driven motions of the ATPase spiral relative to the planar proteolytic base. The translocation mechanism is likely conserved for other AAA+ ATPases.
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Affiliation(s)
- Cristina Puchades
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute HZ 175, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anthony J Rampello
- Department of Biochemistry and Cell Biology, Stony Brook University, 450 Life Sciences Building, Stony Brook, NY 11794, USA
| | - Mia Shin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute HZ 175, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher J Giuliano
- Department of Biochemistry and Cell Biology, Stony Brook University, 450 Life Sciences Building, Stony Brook, NY 11794, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven E Glynn
- Department of Biochemistry and Cell Biology, Stony Brook University, 450 Life Sciences Building, Stony Brook, NY 11794, USA.
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute HZ 175, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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29
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Lopes KL, Rodrigues RAO, Silva MC, Braga WGS, Silva-Filho MC. The Zinc-Finger Thylakoid-Membrane Protein FIP Is Involved With Abiotic Stress Response in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:504. [PMID: 29720990 PMCID: PMC5915565 DOI: 10.3389/fpls.2018.00504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/03/2018] [Indexed: 05/15/2023]
Abstract
Many plant genes have their expression modulated by stress conditions. Here, we used Arabidopsis FtsH5 protease, which expression is regulated by light stress, as bait in a yeast two-hybrid screen to search for new proteins involved in the stress response. As a result, we found FIP (FtsH5 Interacting Protein), which possesses an amino proximal cleavable transit peptide, a hydrophobic membrane-anchoring region, and a carboxyl proximal C4-type zinc-finger domain. In vivo experiments using FIP fused to green fluorescent protein (GFP) showed a plastid localization. This finding was corroborated by chloroplast import assays that showed FIP inserted in the thylakoid membrane. FIP expression was down-regulated in plants exposed to high light intensity, oxidative, salt, and osmotic stresses, whereas mutant plants expressing low levels of FIP were more tolerant to these abiotic stresses. Our data shows a new thylakoid-membrane protein involved with abiotic stress response in Arabidopsis thaliana.
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30
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An JY, Sharif H, Kang GB, Park KJ, Lee JG, Lee S, Jin MS, Song JJ, Wang J, Eom SH. Structural insights into the oligomerization of FtsH periplasmic domain from Thermotoga maritima. Biochem Biophys Res Commun 2018; 495:1201-1207. [PMID: 29180014 DOI: 10.1016/j.bbrc.2017.11.158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/23/2017] [Indexed: 11/25/2022]
Abstract
Prompt removal of misfolded membrane proteins and misassembled membrane protein complexes is essential for membrane homeostasis. However, the elimination of these toxic proteins from the hydrophobic membrane environment has high energetic barriers. The transmembrane protein, FtsH, is the only known ATP-dependent protease responsible for this task. The mechanisms by which FtsH recognizes, unfolds, translocates, and proteolyzes its substrates remain unclear. The structure and function of the ATPase and protease domains of FtsH have been previously characterized while the role of the FtsH periplasmic domain has not clearly identified. Here, we report the 1.5-1.95 Å resolution crystal structures of the Thermotoga maritima FtsH periplasmic domain (tmPD) and describe the dynamic features of tmPD oligomerization.
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Affiliation(s)
- Jun Yop An
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Humayun Sharif
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Kyung Jin Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mi Sun Jin
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Ji-Joon Song
- Department of Biological Sciences, KI for the BioCentury, Cancer Metastasis Control Center, KAIST, Daejeon 34141, Republic of Korea
| | - Jimin Wang
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
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31
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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: 15.4] [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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32
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Glynn SE. Multifunctional Mitochondrial AAA Proteases. Front Mol Biosci 2017; 4:34. [PMID: 28589125 PMCID: PMC5438985 DOI: 10.3389/fmolb.2017.00034] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/08/2017] [Indexed: 11/28/2022] Open
Abstract
Mitochondria perform numerous functions necessary for the survival of eukaryotic cells. These activities are coordinated by a diverse complement of proteins encoded in both the nuclear and mitochondrial genomes that must be properly organized and maintained. Misregulation of mitochondrial proteostasis impairs organellar function and can result in the development of severe human diseases. ATP-driven AAA+ proteins play crucial roles in preserving mitochondrial activity by removing and remodeling protein molecules in accordance with the needs of the cell. Two mitochondrial AAA proteases, i-AAA and m-AAA, are anchored to either face of the mitochondrial inner membrane, where they engage and process an array of substrates to impact protein biogenesis, quality control, and the regulation of key metabolic pathways. The functionality of these proteases is extended through multiple substrate-dependent modes of action, including complete degradation, partial processing, or dislocation from the membrane without proteolysis. This review discusses recent advances made toward elucidating the mechanisms of substrate recognition, handling, and degradation that allow these versatile proteases to control diverse activities in this multifunctional organelle.
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Affiliation(s)
- Steven E Glynn
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony Brook, NY, United States
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33
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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: 1.6] [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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34
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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: 30] [Impact Index Per Article: 4.3] [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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35
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Wang F, Qi Y, Malnoë A, Choquet Y, Wollman FA, de Vitry C. The High Light Response and Redox Control of Thylakoid FtsH Protease in Chlamydomonas reinhardtii. MOLECULAR PLANT 2017; 10:99-114. [PMID: 27702692 DOI: 10.1016/j.molp.2016.09.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/07/2016] [Accepted: 09/17/2016] [Indexed: 05/23/2023]
Abstract
In Chlamydomonas reinhardtii, the major protease involved in the maintenance of photosynthetic machinery in thylakoid membranes, the FtsH protease, mostly forms large hetero-oligomers (∼1 MDa) comprising FtsH1 and FtsH2 subunits, whatever the light intensity for growth. Upon high light exposure, the FtsH subunits display a shorter half-life, which is counterbalanced by an increase in FTSH1/2 mRNA levels, resulting in the modest upregulation of FtsH1/2 proteins. Furthermore, we found that high light increases the protease activity through a hitherto unnoticed redox-controlled reduction of intermolecular disulfide bridges. We isolated a Chlamydomonas FTSH1 promoter-deficient mutant, ftsh1-3, resulting from the insertion of a TOC1 transposon, in which the high light-induced upregulation of FTSH1 gene expression is largely lost. In ftsh1-3, the abundance of FtsH1 and FtsH2 proteins are loosely coupled (decreased by 70% and 30%, respectively) with no formation of large and stable homo-oligomers. Using strains exhibiting different accumulation levels of the FtsH1 subunit after complementation of ftsh1-3, we demonstrate that high light tolerance is tightly correlated with the abundance of the FtsH protease. Thus, the response of Chlamydomonas to light stress involves higher levels of FtsH1/2 subunits associated into large complexes with increased proteolytic activity.
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Affiliation(s)
- Fei Wang
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Paris 75005, France
| | - Yafei Qi
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Paris 75005, France
| | - Alizée Malnoë
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Paris 75005, France
| | - Yves Choquet
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Paris 75005, France
| | - Francis-André Wollman
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Paris 75005, France
| | - Catherine de Vitry
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Paris 75005, France.
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36
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Bittner LM, Westphal K, Narberhaus F. Conditional Proteolysis of the Membrane Protein YfgM by the FtsH Protease Depends on a Novel N-terminal Degron. J Biol Chem 2015; 290:19367-78. [PMID: 26092727 DOI: 10.1074/jbc.m115.648550] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/16/2023] Open
Abstract
Regulated proteolysis efficiently and rapidly adapts the bacterial proteome to changing environmental conditions. Many protease substrates contain recognition motifs, so-called degrons, that direct them to the appropriate protease. Here we describe an entirely new degron identified in the cytoplasmic N-terminal end of the membrane-anchored protein YfgM of Escherichia coli. YfgM is stable during exponential growth and degraded in stationary phase by the essential FtsH protease. The alarmone (p)ppGpp, but not the previously described YfgM interactors RcsB and PpiD, influence YfgM degradation. By scanning mutagenesis, we define individual amino acids responsible for turnover of YfgM and find that the degron does not at all comply with the known N-end rule pathway. The YfgM degron is a distinct module that facilitates FtsH-mediated degradation when fused to the N terminus of another monotopic membrane protein but not to that of a cytoplasmic protein. Several lines of evidence suggest that stress-induced degradation of YfgM relieves the response regulator RcsB and thereby permits cellular protection by the Rcs phosphorelay system. On the basis of these and other results in the literature, we propose a model for how the membrane-spanning YfgM protein serves as connector between the stress responses in the periplasm and cytoplasm.
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Affiliation(s)
| | - Kai Westphal
- From Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Franz Narberhaus
- From Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany
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37
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Vostrukhina M, Popov A, Brunstein E, Lanz MA, Baumgartner R, Bieniossek C, Schacherl M, Baumann U. The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer. ACTA ACUST UNITED AC 2015; 71:1307-18. [PMID: 26057670 DOI: 10.1107/s1399004715005945] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/24/2015] [Indexed: 12/21/2022]
Abstract
The crystal structure of a truncated, soluble quadruple mutant of FtsH from Aquifex aeolicus comprising the AAA and protease domains has been determined at 2.96 Å resolution in space group I222. The protein crystallizes as a hexamer, with the protease domain forming layers in the ab plane. Contacts between these layers are mediated by the AAA domains. These are highly disordered in one crystal form, but are clearly visible in a related form with a shorter c axis. Here, adenosine diphosphate (ADP) is bound to each subunit and the AAA ring exhibits twofold symmetry. The arrangement is different from the ADP-bound state of an analogously truncated, soluble FtsH construct from Thermotoga maritima. The pore is completely closed and the phenylalanine residues in the pore line a contiguous path. The protease hexamer is very similar to those described for other FtsH structures. To resolve certain open issues regarding a conserved glycine in the linker between the AAA and protease domains, as well as the active-site switch β-strand, mutations have been introduced in the full-length membrane-bound protein. Activity analysis of these point mutants reveals the crucial importance of these residues for proteolytic activity and is in accord with previous interpretation of the active-site switch and the importance of the linker glycine residue.
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Affiliation(s)
- Marina Vostrukhina
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Alexander Popov
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, Grenoble, F-38043, France
| | - Elena Brunstein
- Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, Cologne, D-50674, Germany
| | - Martin A Lanz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Renato Baumgartner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Christoph Bieniossek
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Magdalena Schacherl
- Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, Cologne, D-50674, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, Cologne, D-50674, Germany
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38
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Cerdà-Costa N, Gomis-Rüth FX. Architecture and function of metallopeptidase catalytic domains. Protein Sci 2014; 23:123-44. [PMID: 24596965 DOI: 10.1002/pro.2400] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The cleavage of peptide bonds by metallopeptidases (MPs) is essential for life. These ubiquitous enzymes participate in all major physiological processes, and so their deregulation leads to diseases ranging from cancer and metastasis, inflammation, and microbial infection to neurological insults and cardiovascular disorders. MPs cleave their substrates without a covalent intermediate in a single-step reaction involving a solvent molecule, a general base/acid, and a mono- or dinuclear catalytic metal site. Most monometallic MPs comprise a short metal-binding motif (HEXXH), which includes two metal-binding histidines and a general base/acid glutamate, and they are grouped into the zincin tribe of MPs. The latter divides mainly into the gluzincin and metzincin clans. Metzincins consist of globular ∼ 130-270-residue catalytic domains, which are usually preceded by N-terminal pro-segments, typically required for folding and latency maintenance. The catalytic domains are often followed by C-terminal domains for substrate recognition and other protein-protein interactions, anchoring to membranes, oligomerization, and compartmentalization. Metzincin catalytic domains consist of a structurally conserved N-terminal subdomain spanning a five-stranded β-sheet, a backing helix, and an active-site helix. The latter contains most of the metal-binding motif, which is here characteristically extended to HEXXHXXGXX(H,D). Downstream C-terminal subdomains are generally shorter, differ more among metzincins, and mainly share a conserved loop--the Met-turn--and a C-terminal helix. The accumulated structural data from more than 300 deposited structures of the 12 currently characterized metzincin families reviewed here provide detailed knowledge of the molecular features of their catalytic domains, help in our understanding of their working mechanisms, and form the basis for the design of novel drugs.
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Lu X, Li X, Guo K, Wang J, Huang M, Wang JL, Xie TZ, Moorefield CN, Cheng SZD, Wesdemiotis C, Newkome GR. One ligand in dual roles: self-assembly of a bis-rhomboidal-shaped, three-dimensional molecular wheel. Chemistry 2014; 20:13094-8. [PMID: 25155653 DOI: 10.1002/chem.201404358] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 12/22/2022]
Abstract
A facile high yield, self-assembly process that leads to a terpyridine-based, three-dimensional, bis-rhomboidal-shaped, molecular wheel is reported. The desired coordination-driven supramolecular wheel involves eight structurally distorted tristerpyridine (tpy) ligands possessing a 60° angle between the adjacent tpy units and twelve Zn(2+) ions. The tpy ligand plays dual roles in the self-assembly process: two are staggered at 180° to create the internal hub, while six produce the external rim. The wheel can be readily generated by mixing the tpy ligand and Zn(2+) in a stoichiometric ratio of 2:3; full characterization is provided by ESI-MS, NMR spectroscopy, and TEM imaging.
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Affiliation(s)
- Xiaocun Lu
- Department of Polymer Science, Department of Chemistry, The University of Akron, 302 Buchtel Common, Akron, OH 44325 (USA) http://www.dendrimers.com
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Yoshioka-Nishimura M, Nanba D, Takaki T, Ohba C, Tsumura N, Morita N, Sakamoto H, Murata K, Yamamoto Y. Quality control of photosystem II: direct imaging of the changes in the thylakoid structure and distribution of FtsH proteases in spinach chloroplasts under light stress. PLANT & CELL PHYSIOLOGY 2014; 55:1255-65. [PMID: 24891560 DOI: 10.1093/pcp/pcu079] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Under light stress, the reaction center-binding protein D1 of PSII is photo-oxidatively damaged and removed from PSII complexes by proteases located in the chloroplast. A protease considered to be responsible for degradation of the damaged D1 protein is the metalloprotease FtsH. We showed previously that the active hexameric FtsH protease is abundant at the grana margin and the grana end membranes, and this homo-complex removes the photodamaged D1 protein in the grana. Here, we showed a change in the distribution of FtsH in spinach thylakoids during excessive illumination by transmission electron microscopy (TEM) and immunogold labeling of FtsH. The change in distribution of the protease was accompanied by structural changes to the thylakoids, which we detected using spinach leaves by TEM after chemical fixation of the samples. Quantitative analyses showed several characteristic changes in the structure of the thylakoids, including shrinkage of the grana, outward bending of the marginal portions of the thylakoids and an increase in the height of the grana stacks under excessive illumination. The increase in the height of the grana stacks may include swelling of the thylakoids and an increase in the partition gaps between the thylakoids. These data strongly suggest that excessive illumination induces partial unstacking of the thylakoids, which enables FtsH to access easily the photodamaged D1 protein. Finally three-dimensional tomography of the grana was recorded to observe the effect of light stress on the overall structure of the thylakoids.
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Affiliation(s)
- Miho Yoshioka-Nishimura
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530 JapanThese authors contributed equally to this work.
| | - Daisuke Nanba
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530 JapanThese authors contributed equally to this work
| | - Takashi Takaki
- Techinical support center, JEOL, Akishima, 196-0022 Japan
| | - Chikako Ohba
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530 Japan
| | - Nodoka Tsumura
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530 Japan
| | - Noriko Morita
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530 Japan
| | - Hirotaka Sakamoto
- Ushimado Marine Institute, Okayama University, Setouchi, 701-4303 Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, 444-8585 Japan
| | - Yasusi Yamamoto
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530 Japan
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Jana B, Morcos F, Onuchic JN. From structure to function: the convergence of structure based models and co-evolutionary information. Phys Chem Chem Phys 2014; 16:6496-507. [PMID: 24603809 DOI: 10.1039/c3cp55275f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding protein folding and function is one of the most important problems in biological research. Energy landscape theory and the folding funnel concept have provided a framework to investigate the mechanisms associated to these processes. Since protein energy landscapes are in most cases minimally frustrated, structure based models (SMBs) have successfully determined the geometrical features associated with folding and functional transitions. However, structural information is limited, particularly with respect to different functional configurations. This is a major limitation for SBMs. Alternatively, statistical methods to study amino acid co-evolution provide information on residue-residue interactions useful for the study of structure and function. Here, we show how the combination of these two methods gives rise to a novel way to investigate the mechanisms associated with folding and function. We use this methodology to explore the mechanistic aspects of protein translocation in the integral membrane protease FtsH. Dual basin-SBM simulations using the open and closed state of this hexameric motor reveals a functionally important paddling motion in the catalytic cycle. We also find that Direct Coupling Analysis (DCA) predicts physical contacts between AAA and peptidase domains of the motor, which are crucial for the open to close transition. Our combined method, which uses structural information from the open state experimental structure and co-evolutionary couplings, suggests that this methodology can be used to explore the functional landscape of complex biological macromolecules previously inaccessible to methods dependent on experimental structural information. This efficient way to sample the conformational space of large systems creates a theoretical/computational framework capable of better characterizing the functional landscape in large biomolecular assemblies.
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Affiliation(s)
- Biman Jana
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.
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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: 3.3] [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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Salzano AM, Novi G, Arioli S, Corona S, Mora D, Scaloni A. Mono-dimensional blue native-PAGE and bi-dimensional blue native/urea-PAGE or/SDS-PAGE combined with nLC–ESI-LIT-MS/MS unveil membrane protein heteromeric and homomeric complexes in Streptococcus thermophilus. J Proteomics 2013; 94:240-61. [DOI: 10.1016/j.jprot.2013.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/04/2013] [Accepted: 09/14/2013] [Indexed: 02/06/2023]
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Abstract
UNLABELLED Bacteria organize many membrane-related signaling processes in functional microdomains that are structurally and functionally similar to the lipid rafts of eukaryotic cells. An important structural component of these microdomains is the protein flotillin, which seems to act as a chaperone in recruiting other proteins to lipid rafts to facilitate their interaction. In eukaryotic cells, the occurrence of severe diseases is often observed in combination with an overproduction of flotillin, but a functional link between these two phenomena is yet to be demonstrated. In this work, we used the bacterial model Bacillus subtilis as a tractable system to study the physiological alterations that occur in cells that overproduce flotillin. We discovered that an excess of flotillin altered specific signal transduction pathways that are associated with the membrane microdomains of bacteria. As a consequence of this, we detected significant defects in cell division and cell differentiation. These physiological alterations were in part caused by an unusual stabilization of the raft-associated protease FtsH. This report opens the possibility of using bacteria as a working model to better understand fundamental questions related to the functionality of lipid rafts. IMPORTANCE The identification of signaling platforms in the membrane of bacteria that are functionally and structurally equivalent to eukaryotic lipid rafts reveals a level of sophistication in signal transduction and membrane organization unexpected in bacteria. It opens new and promising venues to address intricate questions related to the functionality of lipid rafts by using bacteria as a more tractable system. This is the first report that uses bacteria as a working model to investigate a fundamental question that was previously raised while studying the role of eukaryotic lipid rafts. It also provides evidence of the critical role of these signaling platforms in orchestrating diverse physiological processes in prokaryotic cells.
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Luciński R, Jackowski G. AtFtsH heterocomplex-mediated degradation of apoproteins of the major light harvesting complex of photosystem II (LHCII) in response to stresses. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:1082-1089. [PMID: 23598180 DOI: 10.1016/j.jplph.2013.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/13/2013] [Accepted: 03/14/2013] [Indexed: 06/02/2023]
Abstract
Chloroplastic heterocomplex consisting of AtFtsH1, 2, 5 and 8 proteases, integrally bound to thylakoid membrane was shown to play a critical role in degradation of photodamaged PsbA molecules, inherent to photosystem II (PSII) repair cycle and in plastid development. As no one thylakoid bound apoproteins besides PsbA has been identified as target for the heterocomplex-mediated degradation we investigated the significance of this protease complex in degradation of apoproteins of the major light harvesting complex of photosystem II (LHCII) in response to various stressing conditions and in stress-related changes in overall composition of LHCII trimers of PSII-enriched membranes (BBY particles). To reach this goal a combination of approaches was applied based on immunoblotting, in vitro degradation and non-denaturing isoelectrofocusing. Exposure of Arabidopsis thaliana leaves to desiccation, cold and high irradiance led to a step-wise disappearance of Lhcb1 and Lhcb2, while Lhcb3 level remained unchanged, except for high irradiance which caused significant Lhcb3 decrease. Furthermore, it was demonstrated that stress-dependent disappearance of Lhcb1-3 is a proteolytic phenomenon for which a metalloprotease is responsible. No changes in Lhcb1-3 level were observed due to exposition of var1-1 mutant leaves to the three stresses clearly pointing to the involvement of AtFtsH heterocomplex in the desiccation, cold and high irradiance-dependent degradation of Lhcb1 and Lhcb2 and in high irradiance-dependent degradation of Lhcb3. Non-denaturing isoelectrofocusing analyses revealed that AtFtsH heterocomplex-dependent differential Lhcb1-3 disappearance behaviour following desiccation stress was accompanied by modulations in abundances of individual LHCII trimers of BBY particles and that LHCII of var1-1 resisted the modulations.
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Affiliation(s)
- Robert Luciński
- Department of Plant Physiology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznań, Poland.
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Lu X, Li X, Cao Y, Schultz A, Wang JL, Moorefield CN, Wesdemiotis C, Cheng SZD, Newkome GR. Self-Assembly of a Supramolecular, Three-Dimensional, Spoked, Bicycle-like Wheel. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302362] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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47
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Lu X, Li X, Cao Y, Schultz A, Wang JL, Moorefield CN, Wesdemiotis C, Cheng SZD, Newkome GR. Self-Assembly of a Supramolecular, Three-Dimensional, Spoked, Bicycle-like Wheel. Angew Chem Int Ed Engl 2013; 52:7728-31. [DOI: 10.1002/anie.201302362] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 01/04/2023]
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48
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Iino R, Noji H. Intersubunit coordination and cooperativity in ring-shaped NTPases. Curr Opin Struct Biol 2013; 23:229-34. [PMID: 23395511 DOI: 10.1016/j.sbi.2013.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/27/2012] [Accepted: 01/17/2013] [Indexed: 01/28/2023]
Abstract
Ring-shaped nucleoside triphosphatases (ring NTPases) are biological molecular machines powered by energy from NTP hydrolysis and are responsible for various cellular activities. These ring NTPases translocate their substrates or rotate their own subunits to/in the hole of the ring. Coordination and cooperativity among subunits in the oligomer ring is a topic of debate focused on understanding the operation mechanism of these protein machines. With the help of X-ray crystallographic structural analysis and optical microscopic single-molecules studies, distinct models, including stochastic, concerted, and rotary catalysis have been proposed. Here, we discuss these models and introduce high-speed atomic force microscopy as a new potent tool for verification of the model, with our recent example of the rotary catalysis of the stator ring of F1-adenosine triphosphatase.
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Affiliation(s)
- Ryota Iino
- Department of Applied Chemistry, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Abstract
This review focuses on organellar AAA/FtsH proteases, whose proteolytic and chaperone-like activity is a crucial component of the protein quality control systems of mitochondrial and chloroplast membranes. We compare the AAA/FtsH proteases from yeast, mammals and plants. The nature of the complexes formed by AAA/FtsH proteases and the current view on their involvement in degradation of non-native organellar proteins or assembly of membrane complexes are discussed. Additional functions of AAA proteases not directly connected with protein quality control found in yeast and mammals but not yet in plants are also described shortly. Following an overview of the molecular functions of the AAA/FtsH proteases we discuss physiological consequences of their inactivation in yeast, mammals and plants. The molecular basis of phenotypes associated with inactivation of the AAA/FtsH proteases is not fully understood yet, with the notable exception of those observed in m-AAA protease-deficient yeast cells, which are caused by impaired maturation of mitochondrial ribosomal protein. Finally, examples of cytosolic events affecting protein quality control in mitochondria and chloroplasts are given. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Hanna Janska
- Department of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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50
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Abstract
FtsH, a member of the AAA (ATPases associated with a variety of cellular activities) family of proteins, is an ATP-dependent protease of ∼71 kDa anchored to the inner membrane. It plays crucial roles in a variety of cellular processes. It is responsible for the degradation of both membrane and cytoplasmic substrate proteins. Substrate proteins are unfolded and translocated through the central pore of the ATPase domain into the proteolytic chamber, where the polypeptide chains are processively degraded into short peptides. FtsH is not only involved in the proteolytic elimination of unnecessary proteins, but also in the proteolytic regulation of a number of cellular functions. Its role in proteolytic regulation is achieved by one of two approaches, either the cellular levels of a regulatory protein are controlled by processive degradation of the entire protein, or the activity of a particular substrate protein is modified by processing. In the latter case, protein processing requires the presence of a stable domain within the substrate. Since FtsH does not have a robust unfolding activity, this stable domain is sufficient to abort processive degradation of the protein - resulting in release of a stable protein fragment.
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Affiliation(s)
- Takashi Okuno
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, 990-8560, Japan,
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