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Ghanbarpour A, Telusma B, Powell BM, Zhang JJ, Bolstad I, Vargas C, Keller S, Baker T, Sauer RT, Davis JH. An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.604662. [PMID: 39149393 PMCID: PMC11326279 DOI: 10.1101/2024.08.09.604662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
FtsH, a AAA protease, associates with HflK/C subunits to form a megadalton complex that spans the inner membrane and extends into the periplasm of E. coli . How this complex and homologous assemblies in eukaryotic organelles recruit, extract, and degrade membrane-embedded substrates is unclear. Following overproduction of protein components, recent cryo-EM structures reveal symmetric HflK/C cages surrounding FtsH in a manner proposed to inhibit degradation of membrane-embedded substrates. Here, we present structures of native complexes in which HflK/C instead forms an asymmetric nautilus-like assembly with an entryway for membrane-embedded substrates to reach and be engaged by FtsH. Consistent with this nautilus-like structure, proteomic assays suggest that HflK/C enhances FtsH degradation of certain membrane-embedded substrates. The membrane curvature in our FtsH·HflK/C complexes is opposite that of surrounding membrane regions, a property that correlates with lipid-scramblase activity and possibly with FtsH's function in the degradation of membrane-embedded proteins.
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Liu C, Hatzianestis IH, Pfirrmann T, Reza SH, Minina EA, Moazzami A, Stael S, Gutierrez-Beltran E, Pitsili E, Dörmann P, D'Andrea S, Gevaert K, Romero-Campero F, Ding P, Nowack MK, Van Breusegem F, Jones JDG, Bozhkov PV, Moschou PN. Seed longevity is controlled by metacaspases. Nat Commun 2024; 15:6748. [PMID: 39117606 PMCID: PMC11310522 DOI: 10.1038/s41467-024-50848-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
To survive extreme desiccation, seeds enter a period of quiescence that can last millennia. Seed quiescence involves the accumulation of protective storage proteins and lipids through unknown adjustments in protein homeostasis (proteostasis). Here, we show that mutation of all six type-II metacaspase (MCA-II) proteases in Arabidopsis thaliana disturbs proteostasis in seeds. MCA-II mutant seeds fail to restrict the AAA ATPase CELL DIVISION CYCLE 48 (CDC48) at the endoplasmic reticulum to discard misfolded proteins, compromising seed storability. Endoplasmic reticulum (ER) localization of CDC48 relies on the MCA-IIs-dependent cleavage of PUX10 (ubiquitination regulatory X domain-containing 10), the adaptor protein responsible for titrating CDC48 to lipid droplets. PUX10 cleavage enables the shuttling of CDC48 between lipid droplets and the ER, providing an important regulatory mechanism sustaining spatiotemporal proteolysis, lipid droplet dynamics, and protein homeostasis. In turn, the removal of the PUX10 adaptor in MCA-II mutant seeds partially restores proteostasis, CDC48 localization, and lipid droplet dynamics prolonging seed lifespan. Taken together, we uncover a proteolytic module conferring seed longevity.
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Affiliation(s)
- Chen Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Department of Biology, University of Crete, 71500, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71500, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
| | - Ioannis H Hatzianestis
- Department of Biology, University of Crete, 71500, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71500, Heraklion, Greece
| | - Thorsten Pfirrmann
- Department of Medicine, Health and Medical University, 14471, Potsdam, Germany
| | - Salim H Reza
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, 75236, Uppsala, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
| | - Ali Moazzami
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
| | - Simon Stael
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
- VIB-Ugent Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquımica Vegetal y Fotosıntesis, Consejo Superior de Investigaciones Cientıficas (CSIC)-Universidad de Sevilla, 41092, Sevilla, Spain
- Departamento de Bioquımica Vegetal y Biologıa Molecular, Facultad de Biologıa, Universidad de Sevilla, 41012, Sevilla, Spain
| | - Eugenia Pitsili
- VIB-Ugent Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Peter Dörmann
- University of Bonn, Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), Karlrobert Kreiten Straße 13, 53115, Bonn, Germany
| | - Sabine D'Andrea
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052, Ghent, Belgium
| | - Francisco Romero-Campero
- Instituto de Bioquımica Vegetal y Fotosıntesis, Consejo Superior de Investigaciones Cientıficas (CSIC)-Universidad de Sevilla, 41092, Sevilla, Spain
| | - Pingtao Ding
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Moritz K Nowack
- VIB-Ugent Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Frank Van Breusegem
- VIB-Ugent Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Colney Lane, NR47UH, Norwich, UK
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden
| | - Panagiotis N Moschou
- Department of Biology, University of Crete, 71500, Heraklion, Greece.
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 71500, Heraklion, Greece.
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007, Uppsala, Sweden.
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López B, Izquierdo Y, Cascón T, Zamarreño ÁM, García-Mina JM, Pulido P, Castresana C. Mutant noxy8 exposes functional specificities between the chloroplast chaperones CLPC1 and CLPC2 in the response to organelle stress and plant defence. PLANT, CELL & ENVIRONMENT 2024; 47:2336-2350. [PMID: 38500380 DOI: 10.1111/pce.14882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/20/2024] [Accepted: 03/01/2024] [Indexed: 03/20/2024]
Abstract
Chloroplast function is essential for growth, development, and plant adaptation to stress. Organelle stress and plant defence responses were examined here using noxy8 (nonresponding to oxylipins 8) from a series of Arabidopsis mutants. The noxy8 mutation was located at the CLPC2 gene, encoding a chloroplast chaperone of the protease complex CLP. Although its CLPC1 paralogue is considered to generate redundancy, our data reveal significant differences distinguishing CLPC2 and CLPC1 functions. As such, clpc1 mutants displayed a major defect in housekeeping chloroplast proteostasis, leading to a pronounced reduction in growth and pigment levels, enhanced accumulation of chloroplast and cytosol chaperones, and resistance to fosmidomycin. Conversely, clpc2 mutants showed severe susceptibility to lincomycin inhibition of chloroplast translation and resistance to Antimycin A inhibition of mitochondrial respiration. In the response to Pseudomonas syringae pv. tomato, clpc2 but not clpc1 mutants were resistant to bacterial infection, showing higher salicylic acid levels, defence gene expression and 9-LOX pathway activation. Our findings suggest CLPC2 and CLPC1 functional specificity, with a preferential involvement of CLPC1 in housekeeping processes and of CLPC2 in stress responses.
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Affiliation(s)
- Bran López
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, Spain
| | - Yovanny Izquierdo
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, Spain
| | - Tomás Cascón
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, Spain
| | - Ángel M Zamarreño
- Department of Environmental Biology, Bioma Institute, University of Navarra, Navarra, Spain
| | - José M García-Mina
- Department of Environmental Biology, Bioma Institute, University of Navarra, Navarra, Spain
| | - Pablo Pulido
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, Spain
| | - Carmen Castresana
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, Spain
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4
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Luo J, Yu Y, Wang K, He S, Wang L, Liang F, Chin JW, Tang S. Capturing acyl-enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification. Nat Protoc 2024:10.1038/s41596-024-01006-x. [PMID: 38867073 DOI: 10.1038/s41596-024-01006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 03/29/2024] [Indexed: 06/14/2024]
Abstract
Catalytic mechanism-based, light-activated traps have recently been developed to identify the substrates of cysteine or serine hydrolases. These traps are hydrolase mutants whose catalytic cysteine or serine are replaced with genetically encoded 2,3-diaminopropionic acid (DAP). DAP-containing hydrolases specifically capture the transient thioester- or ester-linked acyl-enzyme intermediates resulting from the first step of the proteolytic reaction as their stable amide analogs. The trapped substrate fragments allow the downstream identification of hydrolase substrates by mass spectrometry and immunoblotting. In this protocol, we provide a detailed step-by-step guide for substrate capture and identification of the peptidase domain of the large tegument protein deneddylase (UL36USP) from human herpesvirus 1, both in mammalian cell lysate and live mammalian cells. Four procedures are included: Procedure 1, DAP-mediated substrate trapping in mammalian cell lysate (~8 d); Procedure 2, DAP-mediated substrate trapping in adherent mammalian cells (~6 d); Procedure 3, DAP-mediated substrate trapping in suspension mammalian cells (~5 d); and Procedure 4, substrate identification and validation (~12-13 d). Basic skills to perform protein expression in bacteria or mammalian cells, affinity enrichment and proteomic analysis are required to implement the protocol. This protocol will be a practical guide for identifying substrates of serine or cysteine hydrolases either in a complex mixture, where genetic manipulation is challenging, or in live cells such as bacteria, yeasts and mammalian cells.
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Affiliation(s)
- Juan Luo
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yao Yu
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Ke Wang
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Sizhe He
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Longjie Wang
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Fangfang Liang
- Department of Medical Oncology, Guangxi Medical University First Affiliated Hospital, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Shan Tang
- Department of Oncology, The First Affiliated Hospital of USTC, Key Laboratory of Immune Response and Immunotherapy, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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5
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Waters ER, Bezanilla M, Vierling E. ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages. PLANT & CELL PHYSIOLOGY 2024; 65:493-502. [PMID: 37859594 DOI: 10.1093/pcp/pcad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
ATPase family AAA domain-containing 3 (ATAD3) proteins are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent in Fungi and Amoebozoa. These ∼600-amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal ATPases Associated with a variety of cellular Activities (AAA+) matrix domain and an ATAD3_N domain, which is located primarily in the inner membrane space but potentially extends to the cytosol to interact with the ER. Sequence and structural alignments indicate that ATAD3 proteins are most similar to classic chaperone unfoldases in the AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here, we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants and the challenges in determining their essential roles in mitochondria.
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Affiliation(s)
- Elizabeth R Waters
- Department of Biology, San Diego State University, 5500 Campanille Dr., San Diego, CA 92182, USA
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, 78 College St., Hanover, NH 03755, USA
| | - Elizabeth Vierling
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003, USA
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Gurung V, Biswas S, Biswas I. Diverse nature of ClpX degradation motifs in Streptococcus mutans. Microbiol Spectr 2024; 12:e0345723. [PMID: 38051052 PMCID: PMC10782952 DOI: 10.1128/spectrum.03457-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Cytoplasmic Clp-related proteases play a major role in maintaining cellular proteome in bacteria. ClpX/P is one such proteolytic complex that is important for conserving protein homeostasis. In this study, we investigated the role of ClpX/P in Streptococcus mutans, an important oral pathogen. We identified several putative substrates whose cellular levels are regulated by ClpX/P in S. mutans and subsequently discovered several recognition motifs that are critical for degradation. Our study is the first comprehensive analysis of determining ClpX/P motifs in streptococci. We believe that identifying the substrates that are regulated by ClpX/P will enhance our understanding about virulence regulation in this important group of pathogens.
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Affiliation(s)
- Vivek Gurung
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Saswati Biswas
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
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7
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Thakrar FJ, Koladiya GA, Singh SP. Heterologous Expression and Structural Elucidation of a Highly Thermostable Alkaline Serine Protease from Haloalkaliphilic Actinobacterium, Nocardiopsis sp. Mit-7. Appl Biochem Biotechnol 2023; 195:7583-7602. [PMID: 37060510 DOI: 10.1007/s12010-023-04472-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2023] [Indexed: 04/16/2023]
Abstract
A highly thermostable alkaline serine protease gene (SPSPro, MN429015) obtained from haloalkaliphilic actinobacteria, Nocardiopsis sp. Mit-7 (NCIM-5746), was successfully cloned and overexpressed in Escherichia coli BL21 under the control of the T7 promoter in the pET Blue1 vector leading to a 20-kDa gene product. The molecular weight of the recombinant alkaline protease, as determined by SDS-PAGE and the Mass Spectrometer (MALDI-TOF), was 34 kDa. The structural and functional attributes of the recombinant thermostable alkaline serine protease were analyzed by Bioinformatic tools. 3D Monomeric Model and Molecular Docking established the role of the amino acid residues, aspartate, serine, and tryptophan, in the active site of thealkaline protease.The activity of the recombinant alkaline protease was optimal at 65 °C, 5 °C higher than its native protease. The recombinant protease was also active over a wide range of pH 7.0-13.0, with a maximal activity of 6050.47 U/mg at pH 9. Furthermore, the thermodynamic parameters of the immobilized recombinant alkaline protease suggested its reduced vulnerability against adverse conditions under which the enzyme has to undergo varied applications.
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Affiliation(s)
- Foram J Thakrar
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, India
| | - Gopi A Koladiya
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, India
| | - Satya P Singh
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, India.
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8
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Shen BW, Doyle LA, Werther R, Westburg AA, Bies D, Walter S, Luyten Y, Morgan RD, Stoddard B, Kaiser BK. Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor. Nucleic Acids Res 2023; 51:3513-3528. [PMID: 36794719 PMCID: PMC10164562 DOI: 10.1093/nar/gkad083] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/17/2023] Open
Abstract
Bacteriophage exclusion ('BREX') systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been noted to display sequence similarity to various AAA+ protein factors including Lon protease. In this study we describe multiple CryoEM structures of BrxL that demonstrate it to be a chambered, ATP-dependent DNA binding protein. The largest BrxL assemblage corresponds to a dimer of heptamers in the absence of bound DNA, versus a dimer of hexamers when DNA is bound in its central pore. The protein displays DNA-dependent ATPase activity, and ATP binding promotes assembly of the complex on DNA. Point mutations within several regions of the protein-DNA complex alter one or more in vitro behaviors and activities, including ATPase activity and ATP-dependent association with DNA. However, only the disruption of the ATPase active site fully eliminates phage restriction, indicating that other mutations can still complement BrxL function within the context of an otherwise intact BREX system. BrxL displays significant structural homology to MCM subunits (the replicative helicase in archaea and eukaryotes), implying that it and other BREX factors may collaborate to disrupt initiation of phage DNA replication.
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Affiliation(s)
- Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Rachel Werther
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Abigail A Westburg
- Department of Biology, Seattle University, 901 12th Avenue, Seattle, WA 98122, USA
| | - Daniel P Bies
- Department of Biology, Seattle University, 901 12th Avenue, Seattle, WA 98122, USA
| | - Stephanie I Walter
- Department of Biology, Seattle University, 901 12th Avenue, Seattle, WA 98122, USA
| | - Yvette A Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Brett K Kaiser
- Department of Biology, Seattle University, 901 12th Avenue, Seattle, WA 98122, USA
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9
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Winckler LI, Dissmeyer N. Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system. Biol Chem 2023; 404:499-511. [PMID: 36972025 DOI: 10.1515/hsz-2022-0320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
Abstract
Proteolysis is an essential process to maintain cellular homeostasis. One pathway that mediates selective protein degradation and which is in principle conserved throughout the kingdoms of life is the N-degron pathway, formerly called the ‘N-end rule’. In the cytosol of eukaryotes and prokaryotes, N-terminal residues can be major determinants of protein stability. While the eukaryotic N-degron pathway depends on the ubiquitin proteasome system, the prokaryotic counterpart is driven by the Clp protease system. Plant chloroplasts also contain such a protease network, which suggests that they might harbor an organelle specific N-degron pathway similar to the prokaryotic one. Recent discoveries indicate that the N-terminal region of proteins affects their stability in chloroplasts and provides support for a Clp-mediated entry point in an N-degron pathway in plastids. This review discusses structure, function and specificity of the chloroplast Clp system, outlines experimental approaches to test for an N-degron pathway in chloroplasts, relates these aspects into general plastid proteostasis and highlights the importance of an understanding of plastid protein turnover.
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Affiliation(s)
- Lioba Inken Winckler
- Department of Plant Physiology and Protein Metabolism Laboratory, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
- Center of Cellular Nanoanalytics (CellNanOs), Barbarastrasse 11, D-49076 Osnabruck, Germany
- Faculty of Biology, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
| | - Nico Dissmeyer
- Department of Plant Physiology and Protein Metabolism Laboratory, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
- Center of Cellular Nanoanalytics (CellNanOs), Barbarastrasse 11, D-49076 Osnabruck, Germany
- Faculty of Biology, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
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10
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Dougan DA, Truscott KN. Affinity isolation and biochemical characterization of N-degron ligands using the N-recognin, ClpS. Methods Enzymol 2023. [PMID: 37532398 DOI: 10.1016/bs.mie.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
The N-degron pathways are a set of proteolytic systems that relate the half-life of a protein to its N-terminal (Nt) residue. In Escherichia coli the principal N-degron pathway is known as the Leu/N-degron pathway. Proteins degraded by this pathway contain an Nt degradation signal (N-degron) composed of an Nt primary destabilizing (Nd1) residue (Leu, Phe, Trp or Tyr). All Leu/N-degron substrates are recognized by the adaptor protein, ClpS and delivered to the ClpAP protease for degradation. Although many components of the pathway are well defined, the physiological role of this pathway remains poorly understood. To address this gap in knowledge we developed a biospecific affinity chromatography technique to isolate physiological substrates of the Leu/N-degron pathway. In this chapter we describe the use of peptide arrays to determine the binding specificity of ClpS. We demonstrate how the information obtained from the peptide array, when coupled with ClpS affinity chromatography, can be used to specifically elute physiological Leu/N-degron ligands from a bacterial lysate. These techniques are illustrated using E. coli ClpS (EcClpS), but both are broadly suitable for application to related N-recognins and systems, not only for the determination of N-recognin specificity, but also for the identification of natural Leu/N-degron ligands from various bacterial and plant species that contain ClpS homologs.
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11
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Moloi SJ, Ngara R. The roles of plant proteases and protease inhibitors in drought response: a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1165845. [PMID: 37143877 PMCID: PMC10151539 DOI: 10.3389/fpls.2023.1165845] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/30/2023] [Indexed: 05/06/2023]
Abstract
Upon exposure to drought, plants undergo complex signal transduction events with concomitant changes in the expression of genes, proteins and metabolites. For example, proteomics studies continue to identify multitudes of drought-responsive proteins with diverse roles in drought adaptation. Among these are protein degradation processes that activate enzymes and signalling peptides, recycle nitrogen sources, and maintain protein turnover and homeostasis under stressful environments. Here, we review the differential expression and functional activities of plant protease and protease inhibitor proteins under drought stress, mainly focusing on comparative studies involving genotypes of contrasting drought phenotypes. We further explore studies of transgenic plants either overexpressing or repressing proteases or their inhibitors under drought conditions and discuss the potential roles of these transgenes in drought response. Overall, the review highlights the integral role of protein degradation during plant survival under water deficits, irrespective of the genotypes' level of drought resilience. However, drought-sensitive genotypes exhibit higher proteolytic activities, while drought-tolerant genotypes tend to protect proteins from degradation by expressing more protease inhibitors. In addition, transgenic plant biology studies implicate proteases and protease inhibitors in various other physiological functions under drought stress. These include the regulation of stomatal closure, maintenance of relative water content, phytohormonal signalling systems including abscisic acid (ABA) signalling, and the induction of ABA-related stress genes, all of which are essential for maintaining cellular homeostasis under water deficits. Therefore, more validation studies are required to explore the various functions of proteases and their inhibitors under water limitation and their contributions towards drought adaptation.
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12
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Proteolytic regulation of mitochondrial oxidative phosphorylation components in plants. Biochem Soc Trans 2022; 50:1119-1132. [PMID: 35587610 PMCID: PMC9246333 DOI: 10.1042/bst20220195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/07/2022] [Accepted: 05/03/2022] [Indexed: 11/28/2022]
Abstract
Mitochondrial function relies on the homeostasis and quality control of their proteome, including components of the oxidative phosphorylation (OXPHOS) pathway that generates energy in form of ATP. OXPHOS subunits are under constant exposure to reactive oxygen species due to their oxidation-reduction activities, which consequently make them prone to oxidative damage, misfolding, and aggregation. As a result, quality control mechanisms through turnover and degradation are required for maintaining mitochondrial activity. Degradation of OXPHOS subunits can be achieved through proteomic turnover or modular degradation. In this review, we present multiple protein degradation pathways in plant mitochondria. Specifically, we focus on the intricate turnover of OXPHOS subunits, prior to protein import via cytosolic proteasomal degradation and post import and assembly via intra-mitochondrial proteolysis involving multiple AAA+ proteases. Together, these proteolytic pathways maintain the activity and homeostasis of OXPHOS components.
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13
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Whitman BT, Murray CRA, Whitford DS, Paul SS, Fahlman RP, Glover MJN, Owttrim GW. Degron-mediated proteolysis of CrhR-like DEAD-box RNA helicases in cyanobacteria. J Biol Chem 2022; 298:101925. [PMID: 35413287 PMCID: PMC9117542 DOI: 10.1016/j.jbc.2022.101925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 11/18/2022] Open
Abstract
Conditional proteolytic degradation is an irreversible and highly regulated process that fulfills crucial regulatory functions in all organisms. As proteolytic targets tend to be critical metabolic or regulatory proteins, substrates are targeted for degradation only under appropriate conditions through the recognition of an amino acid sequence referred to as a “degron”. DEAD-box RNA helicases mediate all aspects of RNA metabolism, contributing to cellular fitness. However, the mechanism by which abiotic-stress modulation of protein stability regulates bacterial helicase abundance has not been extensively characterized. Here, we provide in vivo evidence that proteolytic degradation of the cyanobacterial DEAD-box RNA helicase CrhR is conditional, being initiated by a temperature upshift from 20 to 30 °C in the model cyanobacterium, Synechocystis sp. PCC 6803. We show degradation requires a unique, highly conserved, inherently bipartite degron located in the C-terminal extension found only in CrhR-related RNA helicases in the phylum Cyanobacteria. However, although necessary, the degron is not sufficient for proteolysis, as disruption of RNA helicase activity and/or translation inhibits degradation. These results suggest a positive feedback mechanism involving a role for CrhR in expression of a crucial factor required for degradation. Furthermore, AlphaFold structural prediction indicated the C-terminal extension is a homodimerization domain with homology to other bacterial RNA helicases, and mass photometry data confirmed that CrhR exists as a dimer in solution at 22 °C. These structural data suggest a model wherein the CrhR degron is occluded at the dimerization interface but could be exposed if dimerization was disrupted by nonpermissive conditions.
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Affiliation(s)
- Brendan T Whitman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Cameron R A Murray
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Denise S Whitford
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Simanta S Paul
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Richard P Fahlman
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mark J N Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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14
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Tang S, Beattie AT, Kafkova L, Petris G, Huguenin-Dezot N, Fiedler M, Freeman M, Chin JW. Mechanism-based traps enable protease and hydrolase substrate discovery. Nature 2022; 602:701-707. [PMID: 35173328 PMCID: PMC8866121 DOI: 10.1038/s41586-022-04414-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/07/2022] [Indexed: 12/28/2022]
Abstract
Hydrolase enzymes, including proteases, are encoded by 2-3% of the genes in the human genome and 14% of these enzymes are active drug targets1. However, the activities and substrate specificities of many proteases-especially those embedded in membranes-and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond2; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs. 3,4). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref. 5) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes.
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Affiliation(s)
- Shan Tang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Adam T Beattie
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Lucie Kafkova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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15
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Rei Liao JY, Friso G, Forsythe ES, Michel EJS, Williams AM, Boguraev SS, Ponnala L, Sloan DB, van Wijk KJ. Proteomics, phylogenetics, and co-expression analyses indicate novel interactions in the plastid CLP chaperone-protease system. J Biol Chem 2022; 298:101609. [PMID: 35065075 PMCID: PMC8889267 DOI: 10.1016/j.jbc.2022.101609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/20/2022] Open
Abstract
The chloroplast chaperone CLPC1 unfolds and delivers substrates to the stromal CLPPRT protease complex for degradation. We previously used an in vivo trapping approach to identify interactors with CLPC1 in Arabidopsis thaliana by expressing a STREPII-tagged copy of CLPC1 mutated in its Walker B domains (CLPC1-TRAP) followed by affinity purification and mass spectrometry. To create a larger pool of candidate substrates, adaptors, or regulators, we carried out a far more sensitive and comprehensive in vivo protein trapping analysis. We identified 59 highly enriched CLPC1 protein interactors, in particular proteins belonging to families of unknown functions (DUF760, DUF179, DUF3143, UVR-DUF151, HugZ/DUF2470), as well as the UVR domain proteins EXE1 and EXE2 implicated in singlet oxygen damage and signaling. Phylogenetic and functional domain analyses identified other members of these families that appear to localize (nearly) exclusively to plastids. In addition, several of these DUF proteins are of very low abundance as determined through the Arabidopsis PeptideAtlas http://www.peptideatlas.org/builds/arabidopsis/ showing that enrichment in the CLPC1-TRAP was extremely selective. Evolutionary rate covariation indicated that the HugZ/DUF2470 family coevolved with the plastid CLP machinery suggesting functional and/or physical interactions. Finally, mRNA-based coexpression networks showed that all 12 CLP protease subunits tightly coexpressed as a single cluster with deep connections to DUF760-3. Coexpression modules for other trapped proteins suggested specific functions in biological processes, e.g., UVR2 and UVR3 were associated with extraplastidic degradation, whereas DUF760-6 is likely involved in senescence. This study provides a strong foundation for discovery of substrate selection by the chloroplast CLP protease system.
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Affiliation(s)
- Jui-Yun Rei Liao
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Evan S Forsythe
- Graduate Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Elena J S Michel
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Alissa M Williams
- Graduate Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sasha S Boguraev
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | | | - Daniel B Sloan
- Graduate Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA.
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16
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Rabinovitch E, Mihara K, Sananes A, Zaretsky M, Heyne M, Shifman J, Aharoni A, Hollenberg MD, Papo N. A KLK4 proteinase substrate capture approach to antagonize PAR1. Sci Rep 2021; 11:16170. [PMID: 34373558 PMCID: PMC8352894 DOI: 10.1038/s41598-021-95666-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/29/2021] [Indexed: 11/08/2022] Open
Abstract
Proteinase-activated receptor-1 (PAR1), triggered by thrombin and other serine proteinases such as tissue kallikrein-4 (KLK4), is a key driver of inflammation, tumor invasiveness and tumor metastasis. The PAR1 transmembrane G-protein-coupled receptor therefore represents an attractive target for therapeutic inhibitors. We thus used a computational design to develop a new PAR1 antagonist, namely, a catalytically inactive human KLK4 that acts as a proteinase substrate-capture reagent, preventing receptor cleavage (and hence activation) by binding to and occluding the extracellular R41-S42 canonical PAR1 proteolytic activation site. On the basis of in silico site-saturation mutagenesis, we then generated KLK4S207A,L185D, a first-of-a-kind 'decoy' PAR1 inhibitor, by mutating the S207A and L185D residues in wild-type KLK4, which strongly binds to PAR1. KLK4S207A,L185D markedly inhibited PAR1 cleavage, and PAR1-mediated MAPK/ERK activation as well as the migration and invasiveness of melanoma cells. This 'substrate-capturing' KLK4 variant, engineered to bind to PAR1, illustrates proof of principle for the utility of a KLK4 'proteinase substrate capture' approach to regulate proteinase-mediated PAR1 signaling.
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Affiliation(s)
- Eitan Rabinovitch
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel
| | - Koishiro Mihara
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Amiram Sananes
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel
| | - Marianna Zaretsky
- Department of Life Sciences, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael Heyne
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91906, Jerusalem, Israel
| | - Julia Shifman
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91906, Jerusalem, Israel
| | - Amir Aharoni
- Department of Life Sciences, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Morley D Hollenberg
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Niv Papo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel.
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17
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Iannetta AA, Rogers HT, Al-Mohanna T, O'Brien JN, Wommack AJ, Popescu SC, Hicks LM. Profiling thimet oligopeptidase-mediated proteolysis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:336-350. [PMID: 33481299 DOI: 10.1111/tpj.15165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Protein homeostasis (proteostasis) is crucial for proper cellular function, including the production of peptides with biological functions through controlled proteolysis. Proteostasis has roles in maintenance of cellular functions and plant interactions with the environment under physiological conditions. Plant stress continues to reduce agricultural yields causing substantial economic losses; thus, it is critical to understand how plants perceive stress signals to elicit responses for survival. As previously shown in Arabidopsis thaliana, thimet oligopeptidases (TOPs) TOP1 (also referred to as organellar oligopeptidase) and TOP2 (also referred to as cytosolic oligopeptidase) are essential components in plant response to pathogens, but further characterization of TOPs and their peptide substrates is required to understand their contributions to stress perception and defense signaling. Herein, label-free peptidomics via liquid chromatography-tandem mass spectrometry was used to differentially quantify 1111 peptides, originating from 369 proteins, between the Arabidopsis Col-0 wild type and top1top2 knock-out mutant. This revealed 350 peptides as significantly more abundant in the mutant, representing accumulation of these potential TOP substrates. Ten direct substrates were validated using in vitro enzyme assays with recombinant TOPs and synthetic candidate peptides. These TOP substrates are derived from proteins involved in photosynthesis, glycolysis, protein folding, biogenesis, and antioxidant defense, implicating TOP involvement in processes aside from defense signaling. Sequence motif analysis revealed TOP cleavage preference for non-polar residues in the positions surrounding the cleavage site. Identification of these substrates provides a framework for TOP signaling networks, through which the interplay between proteolytic pathways and defense signaling can be further characterized.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holden T Rogers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, MS, USA
| | | | - Andrew J Wommack
- Department of Chemistry, High Point University, High Point, NC, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, MS, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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18
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Bouchnak I, van Wijk KJ. Structure, function, and substrates of Clp AAA+ protease systems in cyanobacteria, plastids, and apicoplasts: A comparative analysis. J Biol Chem 2021; 296:100338. [PMID: 33497624 PMCID: PMC7966870 DOI: 10.1016/j.jbc.2021.100338] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023] Open
Abstract
ATPases Associated with diverse cellular Activities (AAA+) are a superfamily of proteins that typically assemble into hexameric rings. These proteins contain AAA+ domains with two canonical motifs (Walker A and B) that bind and hydrolyze ATP, allowing them to perform a wide variety of different functions. For example, AAA+ proteins play a prominent role in cellular proteostasis by controlling biogenesis, folding, trafficking, and degradation of proteins present within the cell. Several central proteolytic systems (e.g., Clp, Deg, FtsH, Lon, 26S proteasome) use AAA+ domains or AAA+ proteins to unfold protein substrates (using energy from ATP hydrolysis) to make them accessible for degradation. This allows AAA+ protease systems to degrade aggregates and large proteins, as well as smaller proteins, and feed them as linearized molecules into a protease chamber. This review provides an up-to-date and a comparative overview of the essential Clp AAA+ protease systems in Cyanobacteria (e.g., Synechocystis spp), plastids of photosynthetic eukaryotes (e.g., Arabidopsis, Chlamydomonas), and apicoplasts in the nonphotosynthetic apicomplexan pathogen Plasmodium falciparum. Recent progress and breakthroughs in identifying Clp protease structures, substrates, substrate adaptors (e.g., NblA/B, ClpS, ClpF), and degrons are highlighted. We comment on the physiological importance of Clp activity, including plastid biogenesis, proteostasis, the chloroplast Protein Unfolding Response, and metabolism, across these diverse lineages. Outstanding questions as well as research opportunities and priorities to better understand the essential role of Clp systems in cellular proteostasis are discussed.
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Affiliation(s)
- Imen Bouchnak
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA.
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19
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Burgos R, Weber M, Martinez S, Lluch‐Senar M, Serrano L. Protein quality control and regulated proteolysis in the genome-reduced organism Mycoplasma pneumoniae. Mol Syst Biol 2020; 16:e9530. [PMID: 33320415 PMCID: PMC7737663 DOI: 10.15252/msb.20209530] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Protein degradation is a crucial cellular process in all-living systems. Here, using Mycoplasma pneumoniae as a model organism, we defined the minimal protein degradation machinery required to maintain proteome homeostasis. Then, we conditionally depleted the two essential ATP-dependent proteases. Whereas depletion of Lon results in increased protein aggregation and decreased heat tolerance, FtsH depletion induces cell membrane damage, suggesting a role in quality control of membrane proteins. An integrative comparative study combining shotgun proteomics and RNA-seq revealed 62 and 34 candidate substrates, respectively. Cellular localization of substrates and epistasis studies supports separate functions for Lon and FtsH. Protein half-life measurements also suggest a role for Lon-modulated protein decay. Lon plays a key role in protein quality control, degrading misfolded proteins and those not assembled into functional complexes. We propose that regulating complex assembly and degradation of isolated proteins is a mechanism that coordinates important cellular processes like cell division. Finally, by considering the entire set of proteases and chaperones, we provide a fully integrated view of how a minimal cell regulates protein folding and degradation.
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Affiliation(s)
- Raul Burgos
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Marc Weber
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sira Martinez
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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20
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Hofsetz E, Demir F, Szczepanowska K, Kukat A, Kizhakkedathu JN, Trifunovic A, Huesgen PF. The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis. Mol Cell Proteomics 2020; 19:1330-1345. [PMID: 32467259 PMCID: PMC8014998 DOI: 10.1074/mcp.ra120.002082] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/24/2020] [Indexed: 12/29/2022] Open
Abstract
The mammalian mitochondrial proteome consists of more than 1100 annotated proteins and their proteostasis is regulated by only a few ATP-dependent protease complexes. Technical advances in protein mass spectrometry allowed for detailed description of the mitoproteome from different species and tissues and their changes under specific conditions. However, protease-substrate relations within mitochondria are still poorly understood. Here, we combined Terminal Amine Isotope Labeling of Substrates (TAILS) N termini profiling of heart mitochondria proteomes isolated from wild type and Clpp-/- mice with a classical substrate-trapping screen using FLAG-tagged proteolytically active and inactive CLPP variants to identify new ClpXP substrates in mammalian mitochondria. Using TAILS, we identified N termini of more than 200 mitochondrial proteins. Expected N termini confirmed sequence determinants for mitochondrial targeting signal (MTS) cleavage and subsequent N-terminal processing after import, but the majority were protease-generated neo-N termini mapping to positions within the proteins. Quantitative comparison revealed widespread changes in protein processing patterns, including both strong increases or decreases in the abundance of specific neo-N termini, as well as an overall increase in the abundance of protease-generated neo-N termini in CLPP-deficient mitochondria that indicated altered mitochondrial proteostasis. Based on the combination of altered processing patterns, protein accumulation and stabilization in CLPP-deficient mice and interaction with CLPP, we identified OAT, HSPA9 and POLDIP2 and as novel bona fide ClpXP substrates. Finally, we propose that ClpXP participates in the cooperative degradation of UQCRC1. Together, our data provide the first landscape of the heart mitochondria N terminome and give further insights into regulatory and assisted proteolysis mediated by ClpXP.
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Affiliation(s)
- Eduard Hofsetz
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Karolina Szczepanowska
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Alexandra Kukat
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, School of Biomedical Engineering, Department of Pathology & Laboratory Medicine, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aleksandra Trifunovic
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Pitter F Huesgen
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany; Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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21
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Protective Roles of Cytosolic and Plastidal Proteasomes on Abiotic Stress and Pathogen Invasion. PLANTS 2020; 9:plants9070832. [PMID: 32630761 PMCID: PMC7412383 DOI: 10.3390/plants9070832] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 01/18/2023]
Abstract
Protein malfunction is typically caused by abiotic stressors. To ensure cell survival during conditions of stress, it is important for plant cells to maintain proteins in their respective functional conformation. Self-compartmentalizing proteases, such as ATP-dependent Clp proteases and proteasomes are designed to act in the crowded cellular environment, and they are responsible for degradation of misfolded or damaged proteins within the cell. During different types of stress conditions, the levels of misfolded or orphaned proteins that are degraded by the 26S proteasome in the cytosol and nucleus and by the Clp proteases in the mitochondria and chloroplasts increase. This allows cells to uphold feedback regulations to cellular-level signals and adjust to altered environmental conditions. In this review, we summarize recent findings on plant proteolytic complexes with respect to their protective functions against abiotic and biotic stressors.
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22
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Lon Protease Removes Excess Signal Recognition Particle Protein in Escherichia coli. J Bacteriol 2020; 202:JB.00161-20. [PMID: 32366590 DOI: 10.1128/jb.00161-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Correct targeting of membrane proteins is essential for membrane integrity, cell physiology, and viability. Cotranslational targeting depends on the universally conserved signal recognition particle (SRP), which is a ribonucleoprotein complex comprised of the protein component Ffh and the 4.5S RNA in Escherichia coli About 25 years ago it was reported that Ffh is an unstable protein, but the underlying mechanism has never been explored. Here, we show that Lon is the primary protease responsible for adjusting the cellular Ffh level. When overproduced, Ffh is particularly prone to degradation during transition from exponential to stationary growth and the cellular Ffh amount is lowest in stationary phase. The Ffh protein consists of two domains, the NG domain, responsible for GTP hydrolysis and docking to the membrane receptor FtsY, and the RNA-binding M domain. We find that the NG domain alone is stable, whereas the isolated M domain is degraded. Consistent with the importance of Lon in this process, the M domain confers synthetic lethality to the lon mutant. The Ffh homolog from the model plant Arabidopsis thaliana, which forms a protein-protein complex rather than a protein-RNA complex, is stable, suggesting that the RNA-binding ability residing in the M domain of E. coli Ffh is important for proteolysis. Our results support a model in which excess Ffh not bound to 4.5S RNA is subjected to proteolysis until an appropriate Ffh concentration is reached. The differential proteolysis adjusts Ffh levels to the cellular demand and maintains cotranslational protein transport and membrane integrity.IMPORTANCE Since one-third of all bacterial proteins reside outside the cytoplasm, protein targeting to the appropriate address is an essential process. Cotranslational targeting to the membrane relies on the signal recognition particle (SRP), which is a protein-RNA complex in bacteria. We report that the protein component Ffh is a substrate of the Lon protease. Regulated proteolysis of Ffh provides a simple mechanism to adjust the concentration of the essential protein to the cellular demand. This is important because elevated or depleted SRP levels negatively impact protein targeting and bacterial fitness.
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23
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Huang M, Zhao Y, Feng L, Zhu L, Zhan L, Chen X. Role of the ClpX from Corynebacterium crenatum involved in stress responses and energy metabolism. Appl Microbiol Biotechnol 2020; 104:5505-5517. [PMID: 32300856 DOI: 10.1007/s00253-020-10597-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 02/04/2023]
Abstract
ClpX and ClpP are involved in many important functions, including stress responses and energy metabolism, in microorganisms. However, the ClpX and ClpP of microbes used in industrial scale have rarely been studied. Industrial bacterial fermentation experiences a variety of stresses, and energy metabolism is extremely important for industrial bacteria. Thus, the role played by the ClpX and ClpP of industrial bacteria in fermentation should be investigated. Most microorganisms have a single clpP gene, while Corynebacterium crenatum AS 1.542 possesses two clpPs. Herein, the clpX, clpP1, and clpP2 of C. crenatum were cloned, and its fusion protein was expressed and characterized. We also constructed clpX deletion mutant and complementation strain. Results indicate that ClpX serves an important function in thermal, pH, and ethanol stresses. It is also involved in NADPH synthesis and glucose consumption during fermentation.
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Affiliation(s)
- Mingzhu Huang
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China.,School of Life Science, Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330096, People's Republic of China
| | - Yue Zhao
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Lin Feng
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Lingfeng Zhu
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Li Zhan
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Xuelan Chen
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China. .,School of Life Science, Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330096, People's Republic of China.
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24
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Bouchnak I, van Wijk KJ. N-Degron Pathways in Plastids. TRENDS IN PLANT SCIENCE 2019; 24:917-926. [PMID: 31300194 DOI: 10.1016/j.tplants.2019.06.013] [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: 04/26/2019] [Revised: 06/12/2019] [Accepted: 06/19/2019] [Indexed: 06/10/2023]
Abstract
Protein amino (N) termini are major determinants of protein stability in the cytosol of eukaryotes and prokaryotes, conceptualized in the N-end rule pathway, lately referred to as N-degron pathways. Here we argue for the existence of N-degron pathways in plastids of apicomplexa, algae, and plants. The prokaryotic N-degron pathway depends on a caseinolytic protease (CLP) S recognin (adaptor) for the recognition and delivery of N-degron-bearing substrates to CLP chaperone-protease systems. Diversified CLP systems are found in chloroplasts and nonphotosynthetic plastids, including CLPS homologs that specifically interact with a subset of N-terminal residues and stromal proteins. Chloroplast N-terminome data show enrichment of classic stabilizing residues [Ala (A), Ser (S), Val (V), Thr (T)] and avoidance of charged and large hydrophobic residues. We outline experimental test strategies for plastid N-degron pathways.
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Affiliation(s)
- Imen Bouchnak
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14850, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14850, USA.
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25
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Montandon C, Friso G, Liao JYR, Choi J, van Wijk KJ. In Vivo Trapping of Proteins Interacting with the Chloroplast CLPC1 Chaperone: Potential Substrates and Adaptors. J Proteome Res 2019; 18:2585-2600. [DOI: 10.1021/acs.jproteome.9b00112] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Cyrille Montandon
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Jui-Yun Rei Liao
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Junsik Choi
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Klaas J. van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
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26
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Stael S, Van Breusegem F, Gevaert K, Nowack MK. Plant proteases and programmed cell death. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1991-1995. [PMID: 31222306 PMCID: PMC6460956 DOI: 10.1093/jxb/erz126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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