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Song C, Li Y, Yang M, Li T, Hou Y, Liu Y, Xu C, Liu J, Millar AH, Wang N, Li L. Protein aggregation in plant mitochondria lacking Lon1 inhibits translation and induces unfolded protein responses. PLANT, CELL & ENVIRONMENT 2024; 47:4383-4397. [PMID: 38988259 DOI: 10.1111/pce.15035] [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: 01/25/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
Loss of Lon1 led to stunted plant growth and accumulation of nuclear-encoded mitochondrial proteins including Lon1 substrates. However, an in-depth label-free proteomics quantification of mitochondrial proteins in lon1 revealed that the majority of mitochondrial-encoded proteins decreased in abundance. Additionally, we found that lon1 mutants contained protein aggregates in the mitochondrial that were enriched in metabolic enzymes, ribosomal subunits and PPR-containing proteins of the translation apparatus. These mutants exhibited reduced general mitochondrial translation as well as deficiencies in RNA splicing and editing. These findings support the role of Lon1 in maintaining a functional translational apparatus for mitochondrial-encoded gene translation. Transcriptome analysis of lon1 revealed a mitochondrial unfolded protein response reminiscent of the mitochondrial retrograde signalling dependent on the transcription factor ANAC017. Notably, lon1 mutants exhibited transiently elevated ethylene production, and the shortened hypocotyl observed in lon1 mutants during skotomorphogenesis was partially alleviated by ethylene inhibitors. Furthermore, the short root phenotype was partially ameliorated by introducing a mutation in the ethylene receptor ETR1. Interestingly, the upregulation of only a select few target genes was linked to ETR1-mediated ethylene signalling. Together this provides multiple steps in the link between loss of Lon1 and signalling responses to restore mitochondrial protein homoeostasis in plants.
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Affiliation(s)
- Ce Song
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuanyuan Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Mengmeng Yang
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Tiantian Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuqi Hou
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yinyin Liu
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chang Xu
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jinjian Liu
- Key Laboratory of Radiopharmacokinetics for Innovative Drugs, Chinese Academy of Medical Sciences, and Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Ningning Wang
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Lei Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
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Isono E, Li J, Pulido P, Siao W, Spoel SH, Wang Z, Zhuang X, Trujillo M. Protein degrons and degradation: Exploring substrate recognition and pathway selection in plants. THE PLANT CELL 2024; 36:3074-3098. [PMID: 38701343 PMCID: PMC11371205 DOI: 10.1093/plcell/koae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/27/2024] [Accepted: 04/07/2024] [Indexed: 05/05/2024]
Abstract
Proteome composition is dynamic and influenced by many internal and external cues, including developmental signals, light availability, or environmental stresses. Protein degradation, in synergy with protein biosynthesis, allows cells to respond to various stimuli and adapt by reshaping the proteome. Protein degradation mediates the final and irreversible disassembly of proteins, which is important for protein quality control and to eliminate misfolded or damaged proteins, as well as entire organelles. Consequently, it contributes to cell resilience by buffering against protein or organellar damage caused by stresses. Moreover, protein degradation plays important roles in cell signaling, as well as transcriptional and translational events. The intricate task of recognizing specific proteins for degradation is achieved by specialized systems that are tailored to the substrate's physicochemical properties and subcellular localization. These systems recognize diverse substrate cues collectively referred to as "degrons," which can assume a range of configurations. They are molecular surfaces recognized by E3 ligases of the ubiquitin-proteasome system but can also be considered as general features recognized by other degradation systems, including autophagy or even organellar proteases. Here we provide an overview of the newest developments in the field, delving into the intricate processes of protein recognition and elucidating the pathways through which they are recruited for degradation.
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Affiliation(s)
- Erika Isono
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Jianming Li
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Pablo Pulido
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Wei Siao
- Department of Biology, Aachen RWTH University, Institute of Molecular Plant Physiology, 52074 Aachen, Germany
| | - Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Zhishuo Wang
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Marco Trujillo
- Department of Biology, Aachen RWTH University, Institute of Molecular Plant Physiology, 52074 Aachen, Germany
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3
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Song C, Hou Y, Li T, Liu Y, Wang XA, Qu W, Li L. Lon1 Inactivation Downregulates Autophagic Flux and Brassinosteroid Biogenesis, Modulating Mitochondrial Proportion and Seed Development in Arabidopsis. Int J Mol Sci 2024; 25:5425. [PMID: 38791463 PMCID: PMC11121791 DOI: 10.3390/ijms25105425] [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: 04/02/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial protein homeostasis is crucially regulated by protein degradation processes involving both mitochondrial proteases and cytosolic autophagy. However, it remains unclear how plant cells regulate autophagy in the scenario of lacking a major mitochondrial Lon1 protease. In this study, we observed a notable downregulation of core autophagy proteins in Arabidopsis Lon1 knockout mutant lon1-1 and lon1-2, supporting the alterations in the relative proportions of mitochondrial and vacuolar proteins over total proteins in the plant cells. To delve deeper into understanding the roles of the mitochondrial protease Lon1 and autophagy in maintaining mitochondrial protein homeostasis and plant development, we generated the lon1-2atg5-1 double mutant by incorporating the loss-of-function mutation of the autophagy core protein ATG5, known as atg5-1. The double mutant exhibited a blend of phenotypes, characterized by short plants and early senescence, mirroring those observed in the individual single mutants. Accordingly, distinct transcriptome alterations were evident in each of the single mutants, while the double mutant displayed a unique amalgamation of transcriptional responses. Heightened severity, particularly evident in reduced seed numbers and abnormal embryo development, was observed in the double mutant. Notably, aberrations in protein storage vacuoles (PSVs) and oil bodies were evident in the single and double mutants. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of genes concurrently downregulated in lon1-2, atg5-1, and lon1-2atg5-1 unveiled a significant suppression of genes associated with brassinosteroid (BR) biosynthesis and homeostasis. This downregulation likely contributes to the observed abnormalities in seed and embryo development in the mutants.
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Affiliation(s)
| | | | | | | | | | | | - Lei Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China; (C.S.); (Y.H.); (T.L.); (Y.L.); (X.-A.W.); (W.Q.)
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4
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Borysiuk K, Ostaszewska-Bugajska M, Kryzheuskaya K, Gardeström P, Szal B. Glyoxalase I activity affects Arabidopsis sensitivity to ammonium nutrition. PLANT CELL REPORTS 2022; 41:2393-2413. [PMID: 36242617 PMCID: PMC9700585 DOI: 10.1007/s00299-022-02931-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Elevated methylglyoxal levels contribute to ammonium-induced growth disorders in Arabidopsis thaliana. Methylglyoxal detoxification pathway limitation, mainly the glyoxalase I activity, leads to enhanced sensitivity of plants to ammonium nutrition. Ammonium applied to plants as the exclusive source of nitrogen often triggers multiple phenotypic effects, with severe growth inhibition being the most prominent symptom. Glycolytic flux increase, leading to overproduction of its toxic by-product methylglyoxal (MG), is one of the major metabolic consequences of long-term ammonium nutrition. This study aimed to evaluate the influence of MG metabolism on ammonium-dependent growth restriction in Arabidopsis thaliana plants. As the level of MG in plant cells is maintained by the glyoxalase (GLX) system, we analyzed MG-related metabolism in plants with a dysfunctional glyoxalase pathway. We report that MG detoxification, based on glutathione-dependent glyoxalases, is crucial for plants exposed to ammonium nutrition, and its essential role in ammonium sensitivity relays on glyoxalase I (GLXI) activity. Our results indicated that the accumulation of MG-derived advanced glycation end products significantly contributes to the incidence of ammonium toxicity symptoms. Using A. thaliana frostbite1 as a model plant that overcomes growth repression on ammonium, we have shown that its resistance to enhanced MG levels is based on increased GLXI activity and tolerance to elevated MG-derived advanced glycation end-product (MAGE) levels. Furthermore, our results show that glyoxalase pathway activity strongly affects cellular antioxidative systems. Under stress conditions, the disruption of the MG detoxification pathway limits the functioning of antioxidant defense. However, under optimal growth conditions, a defect in the MG detoxification route results in the activation of antioxidative systems.
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Affiliation(s)
- Klaudia Borysiuk
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Monika Ostaszewska-Bugajska
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Katsiaryna Kryzheuskaya
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Per Gardeström
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Bożena Szal
- Department of Plant Bioenergetics, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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5
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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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6
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Zou Y, Bozhkov PV. Chlamydomonas proteases: classification, phylogeny, and molecular mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7680-7693. [PMID: 34468747 PMCID: PMC8643629 DOI: 10.1093/jxb/erab383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/13/2021] [Indexed: 05/08/2023]
Abstract
Proteases can regulate myriad biochemical pathways by digesting or processing target proteins. While up to 3% of eukaryotic genes encode proteases, only a tiny fraction of proteases are mechanistically understood. Furthermore, most of the current knowledge about proteases is derived from studies of a few model organisms, including Arabidopsis thaliana in the case of plants. Proteases in other plant model systems are largely unexplored territory, limiting our mechanistic comprehension of post-translational regulation in plants and hampering integrated understanding of how proteolysis evolved. We argue that the unicellular green alga Chlamydomonas reinhardtii has a number of technical and biological advantages for systematic studies of proteases, including reduced complexity of many protease families and ease of cell phenotyping. With this end in view, we share a genome-wide inventory of proteolytic enzymes in Chlamydomonas, compare the protease degradomes of Chlamydomonas and Arabidopsis, and consider the phylogenetic relatedness of Chlamydomonas proteases to major taxonomic groups. Finally, we summarize the current knowledge of the biochemical regulation and physiological roles of proteases in this algal model. We anticipate that our survey will promote and streamline future research on Chlamydomonas proteases, generating new insights into proteolytic mechanisms and the evolution of digestive and limited proteolysis.
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Affiliation(s)
- Yong Zou
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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7
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Tivendale ND, Belt K, Berkowitz O, Whelan J, Millar AH, Huang S. Knockdown of Succinate Dehydrogenase Assembly Factor 2 Induces Reactive Oxygen Species-Mediated Auxin Hypersensitivity Causing pH-Dependent Root Elongation. PLANT & CELL PHYSIOLOGY 2021; 62:1185-1198. [PMID: 34018557 DOI: 10.1093/pcp/pcab061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/13/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Metabolism, auxin signaling and reactive oxygen species (ROS) all contribute to plant growth, and each is linked to plant mitochondria and the process of respiration. Knockdown of mitochondrial succinate dehydrogenase assembly factor 2 (SDHAF2) in Arabidopsis thaliana lowered succinate dehydrogenase activity and led to pH-inducible root inhibition when the growth medium pH was poised at different points between 7.0 and 5.0, but this phenomenon was not observed in wildtype (WT). Roots of sdhaf2 mutants showed high accumulation of succinate, depletion of citrate and malate and up-regulation of ROS-related and stress-inducible genes at pH 5.5. A change of oxidative status in sdhaf2 roots at low pH was also evidenced by low ROS staining in root tips and altered root sensitivity to H2O2. sdhaf2 had low auxin activity in root tips via DR5-GUS staining but displayed increased indole-3-acetic acid (IAA, auxin) abundance and IAA hypersensitivity, which is most likely caused by the change in ROS levels. On this basis, we conclude that knockdown of SDHAF2 induces pH-related root elongation and auxin hyperaccumulation and hypersensitivity, mediated by altered ROS homeostasis. This observation extends the existing evidence of associations between mitochondrial function and auxin by establishing a cascade of cellular events that link them through ROS formation, metabolism and root growth at different pH values.
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Affiliation(s)
- Nathan D Tivendale
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Katharina Belt
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, School of Life Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University,Plaenty Rd and Kingsburg Dr, Bundoora, VIC 3083, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Life Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University,Plaenty Rd and Kingsburg Dr, Bundoora, VIC 3083, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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8
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Izquierdo Y, Muñiz L, Vicente J, Kulasekaran S, Aguilera V, López Sánchez A, Martínez-Ayala A, López B, Cascón T, Castresana C. Oxylipins From Different Pathways Trigger Mitochondrial Stress Signaling Through Respiratory Complex III. FRONTIERS IN PLANT SCIENCE 2021; 12:705373. [PMID: 34394161 PMCID: PMC8358658 DOI: 10.3389/fpls.2021.705373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Plant oxylipins are signaling molecules produced from fatty acids by oxidative pathways, mainly initiated by 9- and 13-lipoxygenases (9-LOX and 13-LOX), alpha-dioxygenases or non-enzymatic oxidation. Oxylipins from the 9-LOX pathway induce oxidative stress and control root development and plant defense. These activities have been associated with mitochondrial processes, but precise cellular targets and pathways remain unknown. In order to study oxylipin signaling, we previously generated a collection of Arabidopsis thaliana mutants that were insensitive to the 9-LOX products 9(S)-hydroxy-10,12, 15-octadecatrienoic acid (9-HOT) and its ketone derivative 9-KOT (noxy mutants). Here, we describe noxy1, noxy3, noxy5, noxy23, and noxy54 mutants, all affected in nucleus-encoded mitochondrial proteins, and use them to study the role of mitochondria in oxylipin signaling. Functional and phenotypic analyses showed that noxy plants displayed mitochondrial aggregation, reduced respiration rates and resistance to the complex III inhibitor Antimycin A (AA), thus indicating a close similarity of the oxylipin signaling and mitochondrial stress. Application of 9-HOT and 9-KOT protected plants against subsequent mitochondrial stress, whereas they boosted root growth reduction when applied in combination with complex III inhibitors but did not with inhibitors of other respiratory complexes. A similar effect was caused by linear-chain oxylipins from 13-LOX or non-enzymatic pathways having α,β-unsaturated hydroxyl or keto groups in their structure. Studies to investigate 9-HOT and 9-KOT activity indicated that they do not reduce respiration rates, but their action is primarily associated with enhanced ROS responses. This was supported by the results showing that 9-HOT or 9-KOT combined with AA amplified the expression of oxylipin- and ROS-responding genes but not of the AA marker AOX1a, thus implying the activation of a specific mitochondria retrograde signaling pathway. Our results implicate mitochondrial complex III as a hub in the signaling activity of multiple oxylipin pathways and point at downstream ROS responses as components of oxylipin function.
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Affiliation(s)
- Yovanny Izquierdo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Luis Muñiz
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Jorge Vicente
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Satish Kulasekaran
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Verónica Aguilera
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Ana López Sánchez
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Ada Martínez-Ayala
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Bran López
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Tomás Cascón
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Carmen Castresana
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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9
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Petereit J, Duncan O, Murcha MW, Fenske R, Cincu E, Cahn J, Pružinská A, Ivanova A, Kollipara L, Wortelkamp S, Sickmann A, Lee J, Lister R, Millar AH, Huang S. Mitochondrial CLPP2 Assists Coordination and Homeostasis of Respiratory Complexes. PLANT PHYSIOLOGY 2020; 184:148-164. [PMID: 32571844 PMCID: PMC7479914 DOI: 10.1104/pp.20.00136] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/12/2020] [Indexed: 05/04/2023]
Abstract
Protein homeostasis in eukaryotic organelles and their progenitor prokaryotes is regulated by a series of proteases including the caseinolytic protease (CLPP). CLPP has essential roles in chloroplast biogenesis and maintenance, but the significance of the plant mitochondrial CLPP remains unknown and factors that aid coordination of nuclear- and mitochondrial-encoded subunits for complex assembly in mitochondria await discovery. We generated knockout lines of the single gene for the mitochondrial CLP protease subunit, CLPP2, in Arabidopsis (Arabidopsis thaliana). Mutants showed a higher abundance of transcripts from mitochondrial genes encoding oxidative phosphorylation protein complexes, whereas nuclear genes encoding other subunits of the same complexes showed no change in transcript abundance. By contrast, the protein abundance of specific nuclear-encoded subunits in oxidative phosphorylation complexes I and V increased in CLPP2 knockouts, without accumulation of mitochondrial-encoded counterparts in the same complex. Complexes with subunits mainly or entirely encoded in the nucleus were unaffected. Analysis of protein import and function of complex I revealed that while function was retained, protein homeostasis was disrupted, leading to accumulation of soluble subcomplexes of nuclear-encoded subunits. Therefore, CLPP2 contributes to the mitochondrial protein degradation network through supporting coordination and homeostasis of protein complexes encoded across mitochondrial and nuclear genomes.
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Affiliation(s)
- Jakob Petereit
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Monika W Murcha
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Emilia Cincu
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Jonathan Cahn
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Adriana Pružinská
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Aneta Ivanova
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany
| | - Stefanie Wortelkamp
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen AB24 3FX, Scotland, United Kingdom
- Medizinische Fakultät, Medizinische Proteom-Center, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Jiwon Lee
- Centre for advanced Microscopy, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
- The Harry Perkins Institute of Medical Research, Perth, Washington 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
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10
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Huang S, Li L, Petereit J, Millar AH. Protein turnover rates in plant mitochondria. Mitochondrion 2020; 53:57-65. [DOI: 10.1016/j.mito.2020.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/22/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023]
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11
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López-Vidal O, Olmedilla A, Sandalio LM, Sevilla F, Jiménez A. Is Autophagy Involved in Pepper Fruit Ripening? Cells 2020; 9:cells9010106. [PMID: 31906273 PMCID: PMC7016703 DOI: 10.3390/cells9010106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/23/2019] [Accepted: 12/29/2019] [Indexed: 12/21/2022] Open
Abstract
Autophagy is a universal self-degradation process involved in the removal and recycling of cellular constituents and organelles; however, little is known about its possible role in fruit ripening, in which the oxidation of lipids and proteins and changes in the metabolism of different cellular organelles occur. In this work, we analyzed several markers of autophagy in two critical maturation stages of pepper (Capsicum annuum L.) fruits where variations due to ripening become clearly visible. Using two commercial varieties that ripen to yellow and red fruits respectively, we studied changes in the gene expression and protein content of several autophagy (ATG) components, ATG4 activity, as well as the autophagy receptor NBR1 and the proteases LON1 and LON2. Additionally, the presence of intravacuolar vesicles was analyzed by electron microscopy. Altogether, our data reveal that autophagy plays a role in the metabolic changes which occur during ripening in the two studied varieties, suggesting that this process may be critical to acquiring final optimal quality of pepper fruits.
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Affiliation(s)
- Omar López-Vidal
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Murcia 30100, Spain; (O.L.-V.); (F.S.)
| | - Adela Olmedilla
- Department of Biochemistry, Cellular and Molecular Biology of Plants, EEZ-CSIC, Granada 18160, Spain; (A.O.); (L.M.S.)
| | - Luisa María Sandalio
- Department of Biochemistry, Cellular and Molecular Biology of Plants, EEZ-CSIC, Granada 18160, Spain; (A.O.); (L.M.S.)
| | - Francisca Sevilla
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Murcia 30100, Spain; (O.L.-V.); (F.S.)
| | - Ana Jiménez
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Murcia 30100, Spain; (O.L.-V.); (F.S.)
- Correspondence: ; Tel.: +34-968-396200
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12
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Meyer EH, Welchen E, Carrie C. Assembly of the Complexes of the Oxidative Phosphorylation System in Land Plant Mitochondria. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:23-50. [PMID: 30822116 DOI: 10.1146/annurev-arplant-050718-100412] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant mitochondria play a major role during respiration by producing the ATP required for metabolism and growth. ATP is produced during oxidative phosphorylation (OXPHOS), a metabolic pathway coupling electron transfer with ADP phosphorylation via the formation and release of a proton gradient across the inner mitochondrial membrane. The OXPHOS system is composed of large, multiprotein complexes coordinating metal-containing cofactors for the transfer of electrons. In this review, we summarize the current state of knowledge about assembly of the OXPHOS complexes in land plants. We present the different steps involved in the formation of functional complexes and the regulatory mechanisms controlling the assembly pathways. Because several assembly steps have been found to be ancestral in plants-compared with those described in fungal and animal models-we discuss the evolutionary dynamics that lead to the conservation of ancestral pathways in land plant mitochondria.
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Affiliation(s)
- Etienne H Meyer
- Organelle Biology and Biotechnology Research Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Current affiliation: Institute of Plant Physiology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany;
| | - Elina Welchen
- Cátedra de Biología Celular y Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Chris Carrie
- Plant Sciences Research Group, Department Biologie I, Ludwig-Maximilians-Universität, 82152 Planegg-Martinsried, Germany
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13
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Tsitsekian D, Daras G, Alatzas A, Templalexis D, Hatzopoulos P, Rigas S. Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2185-2197. [PMID: 30590727 PMCID: PMC6460959 DOI: 10.1093/jxb/ery440] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/28/2018] [Indexed: 05/10/2023]
Abstract
The degradation of damaged proteins is essential for cell viability. Lon is a highly conserved ATP-dependent serine-lysine protease that maintains proteostasis. We performed a comparative genome-wide analysis to determine the evolutionary history of Lon proteases. Prokaryotes and unicellular eukaryotes retained a single Lon copy, whereas multicellular eukaryotes acquired a peroxisomal copy, in addition to the mitochondrial gene, to sustain the evolution of higher order organ structures. Land plants developed small Lon gene families. Despite the Lon2 peroxisomal paralog, Lon genes triplicated in the Arabidopsis lineage through sequential evolutionary events including whole-genome and tandem duplications. The retention of Lon1, Lon4, and Lon3 triplicates relied on their differential and even contrasting expression patterns, distinct subcellular targeting mechanisms, and functional divergence. Lon1 seems similar to the pre-duplication ancestral gene unit, whereas the duplication of Lon3 and Lon4 is evolutionarily recent. In the wider context of plant evolution, papaya is the only genome with a single ancestral Lon1-type gene. The evolutionary trend among plants is to acquire Lon copies with ambiguous pre-sequences for dual-targeting to mitochondria and chloroplasts, and a substrate recognition domain that deviates from the ancestral Lon1 type. Lon genes constitute a paradigm of dynamic evolution contributing to understanding the functional fate of gene duplicates.
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Affiliation(s)
- Dikran Tsitsekian
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Gerasimos Daras
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Anastasios Alatzas
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | | | | | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
- Correspondence:
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14
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Rurek M, Czołpińska M, Pawłowski TA, Krzesiński W, Spiżewski T. Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes. Int J Mol Sci 2018; 19:ijms19030877. [PMID: 29547512 PMCID: PMC5877738 DOI: 10.3390/ijms19030877] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 12/11/2022] Open
Abstract
Complex proteomic and physiological approaches for studying cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in relation to mRNA abundance and respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold, major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. In contrast, carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Several transcriptomic and metabolic regulation mechanisms are also suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however, photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse modes (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations at molecular and physiological levels. This implies a more complex model of action of investigated stresses on plant mitochondria.
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Affiliation(s)
- Michał Rurek
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | - Magdalena Czołpińska
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | | | - Włodzimierz Krzesiński
- Department of Vegetable Crops, Poznan University of Life Sciences, Dąbrowskiego 159, 60-594 Poznań, Poland.
| | - Tomasz Spiżewski
- Department of Vegetable Crops, Poznan University of Life Sciences, Dąbrowskiego 159, 60-594 Poznań, Poland.
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15
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Mansilla N, Racca S, Gras DE, Gonzalez DH, Welchen E. The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants. Int J Mol Sci 2018; 19:ijms19030662. [PMID: 29495437 PMCID: PMC5877523 DOI: 10.3390/ijms19030662] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial respiration is an energy producing process that involves the coordinated action of several protein complexes embedded in the inner membrane to finally produce ATP. Complex IV or Cytochrome c Oxidase (COX) is the last electron acceptor of the respiratory chain, involved in the reduction of O2 to H2O. COX is a multimeric complex formed by multiple structural subunits encoded in two different genomes, prosthetic groups (heme a and heme a3), and metallic centers (CuA and CuB). Tens of accessory proteins are required for mitochondrial RNA processing, synthesis and delivery of prosthetic groups and metallic centers, and for the final assembly of subunits to build a functional complex. In this review, we perform a comparative analysis of COX composition and biogenesis factors in yeast, mammals and plants. We also describe possible external and internal factors controlling the expression of structural proteins and assembly factors at the transcriptional and post-translational levels, and the effect of deficiencies in different steps of COX biogenesis to infer the role of COX in different aspects of plant development. We conclude that COX assembly in plants has conserved and specific features, probably due to the incorporation of a different set of subunits during evolution.
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Affiliation(s)
- Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Sofia Racca
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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16
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Majsec K, Bhuiyan NH, Sun Q, Kumari S, Kumar V, Ware D, van Wijk KJ. The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis. THE PLANT CELL 2017; 29:2687-2710. [PMID: 28947489 PMCID: PMC5728138 DOI: 10.1105/tpc.17.00481] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/29/2017] [Accepted: 09/21/2017] [Indexed: 05/17/2023]
Abstract
Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.
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Affiliation(s)
- Kristina Majsec
- Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Nazmul H Bhuiyan
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853
| | - Sunita Kumari
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Vivek Kumar
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Doreen Ware
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Klaas J van Wijk
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
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17
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Blomme J, Van Aken O, Van Leene J, Jégu T, De Rycke R, De Bruyne M, Vercruysse J, Nolf J, Van Daele T, De Milde L, Vermeersch M, des Francs-Small CC, De Jaeger G, Benhamed M, Millar AH, Inzé D, Gonzalez N. The Mitochondrial DNA-Associated Protein SWIB5 Influences mtDNA Architecture and Homologous Recombination. THE PLANT CELL 2017; 29:1137-1156. [PMID: 28420746 PMCID: PMC5466028 DOI: 10.1105/tpc.16.00899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/04/2017] [Accepted: 04/14/2017] [Indexed: 05/08/2023]
Abstract
In addition to the nucleus, mitochondria and chloroplasts in plant cells also contain genomes. Efficient DNA repair pathways are crucial in these organelles to fix damage resulting from endogenous and exogenous factors. Plant organellar genomes are complex compared with their animal counterparts, and although several plant-specific mediators of organelle DNA repair have been reported, many regulators remain to be identified. Here, we show that a mitochondrial SWI/SNF (nucleosome remodeling) complex B protein, SWIB5, is capable of associating with mitochondrial DNA (mtDNA) in Arabidopsis thaliana Gain- and loss-of-function mutants provided evidence for a role of SWIB5 in influencing mtDNA architecture and homologous recombination at specific intermediate-sized repeats both under normal and genotoxic conditions. SWIB5 interacts with other mitochondrial SWIB proteins. Gene expression and mutant phenotypic analysis of SWIB5 and SWIB family members suggests a link between organellar genome maintenance and cell proliferation. Taken together, our work presents a protein family that influences mtDNA architecture and homologous recombination in plants and suggests a link between organelle functioning and plant development.
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Affiliation(s)
- Jonas Blomme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Olivier Van Aken
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
- Department of Biology, Lund University, 226 52 Lund, Sweden
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Teddy Jégu
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, 91400 Orsay, France
- Molecular Biology Department, Simches Research Center, Boston, Massachusetts 02114
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Michiel De Bruyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jasmien Vercruysse
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Twiggy Van Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | | | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, 91400 Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- INRA, UMR 1332, Biologie du Fruit et Pathologie, CS20032 Villenave d'Ornon, France
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18
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Li L, Millar AH, Huang S. Mitochondrial Lon1 has a role in homeostasis of the mitochondrial ribosome and pentatricopeptide repeat proteins in plants. PLANT SIGNALING & BEHAVIOR 2017; 12:e1276686. [PMID: 28045582 PMCID: PMC5351720 DOI: 10.1080/15592324.2016.1276686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 12/20/2016] [Indexed: 05/28/2023]
Abstract
Lon is a highly conserved protein family in eukaryotes and eubacteria and its members all contain both a chaperone and a proteolytic domain that are important for Lon function. Loss of mitochondrial Lon1 leads to deleterious phenotypes in yeast and plants, and causes developmental disorders and aging-related diseases in humans. In Arabidopsis, we have recently reported the multiple roles of Lon1 in mitochondrial protein homeostasis through an evaluation of changes in protein degradation rates in the absence of Lon1. 1 In this addendum, we extend our discussion to the roles of Lon1 in mitochondrial post-transcriptional regulation by considering the effects of its loss on ribosome proteins required for protein synthesis and mitochondrial PPR proteins required for RNA regulation.
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Affiliation(s)
- Lei Li
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
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19
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Li L, Nelson C, Fenske R, Trösch J, Pružinská A, Millar AH, Huang S. Changes in specific protein degradation rates in Arabidopsis thaliana reveal multiple roles of Lon1 in mitochondrial protein homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:458-471. [PMID: 27726214 DOI: 10.1111/tpj.13392] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 09/29/2016] [Accepted: 10/03/2016] [Indexed: 05/20/2023]
Abstract
Mitochondrial Lon1 loss impairs oxidative phosphorylation complexes and TCA enzymes and causes accumulation of specific mitochondrial proteins. Analysis of over 400 mitochondrial protein degradation rates using 15 N labelling showed that 205 were significantly different between wild type (WT) and lon1-1. Those proteins included ribosomal proteins, electron transport chain subunits and TCA enzymes. For respiratory complexes I and V, decreased protein abundance correlated with higher degradation rate of subunits in total mitochondrial extracts. After blue native separation, however, the assembled complexes had slow degradation, while smaller subcomplexes displayed rapid degradation in lon1-1. In insoluble fractions, a number of TCA enzymes were more abundant but the proteins degraded slowly in lon1-1. In soluble protein fractions, TCA enzymes were less abundant but degraded more rapidly. These observations are consistent with the reported roles of Lon1 as a chaperone aiding the proper folding of newly synthesized/imported proteins to stabilise them and as a protease to degrade mitochondrial protein aggregates. HSP70, prohibitin and enzymes of photorespiration accumulated in lon1-1 and degraded slowly in all fractions, indicating an important role of Lon1 in their clearance from the proteome.
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Affiliation(s)
- Lei Li
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
| | - Clark Nelson
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
| | - Josua Trösch
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
| | - Adriana Pružinská
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
| | - Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
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20
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Smakowska E, Skibior-Blaszczyk R, Czarna M, Kolodziejczak M, Kwasniak-Owczarek M, Parys K, Funk C, Janska H. Lack of FTSH4 Protease Affects Protein Carbonylation, Mitochondrial Morphology, and Phospholipid Content in Mitochondria of Arabidopsis: New Insights into a Complex Interplay. PLANT PHYSIOLOGY 2016; 171:2516-35. [PMID: 27297677 PMCID: PMC4972270 DOI: 10.1104/pp.16.00370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/06/2016] [Indexed: 05/04/2023]
Abstract
FTSH4 is one of the inner membrane-embedded ATP-dependent metalloproteases in mitochondria of Arabidopsis (Arabidopsis thaliana). In mutants impaired to express FTSH4, carbonylated proteins accumulated and leaf morphology was altered when grown under a short-day photoperiod, at 22°C, and a long-day photoperiod, at 30°C. To provide better insight into the function of FTSH4, we compared the mitochondrial proteomes and oxyproteomes of two ftsh4 mutants and wild-type plants grown under conditions inducing the phenotypic alterations. Numerous proteins from various submitochondrial compartments were observed to be carbonylated in the ftsh4 mutants, indicating a widespread oxidative stress. One of the reasons for the accumulation of carbonylated proteins in ftsh4 was the limited ATP-dependent proteolytic capacity of ftsh4 mitochondria, arising from insufficient ATP amount, probably as a result of an impaired oxidative phosphorylation (OXPHOS), especially complex V. In ftsh4, we further observed giant, spherical mitochondria coexisting among normal ones. Both effects, the increased number of abnormal mitochondria and the decreased stability/activity of the OXPHOS complexes, were probably caused by the lower amount of the mitochondrial membrane phospholipid cardiolipin. We postulate that the reduced cardiolipin content in ftsh4 mitochondria leads to perturbations within the OXPHOS complexes, generating more reactive oxygen species and less ATP, and to the deregulation of mitochondrial dynamics, causing in consequence the accumulation of oxidative damage.
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Affiliation(s)
- Elwira Smakowska
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Renata Skibior-Blaszczyk
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Malgorzata Czarna
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Marta Kolodziejczak
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Malgorzata Kwasniak-Owczarek
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Katarzyna Parys
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Christiane Funk
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Hanna Janska
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
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21
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Kooke R, Kruijer W, Bours R, Becker F, Kuhn A, van de Geest H, Buntjer J, Doeswijk T, Guerra J, Bouwmeester H, Vreugdenhil D, Keurentjes JJB. Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:2187-203. [PMID: 26869705 PMCID: PMC4825126 DOI: 10.1104/pp.15.00997] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 02/11/2016] [Indexed: 05/05/2023]
Abstract
Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified.
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Affiliation(s)
- Rik Kooke
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Willem Kruijer
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Ralph Bours
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Frank Becker
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - André Kuhn
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Henri van de Geest
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Jaap Buntjer
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Timo Doeswijk
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - José Guerra
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Dick Vreugdenhil
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Joost J B Keurentjes
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
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22
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Ströher E, Grassl J, Carrie C, Fenske R, Whelan J, Millar AH. Glutaredoxin S15 Is Involved in Fe-S Cluster Transfer in Mitochondria Influencing Lipoic Acid-Dependent Enzymes, Plant Growth, and Arsenic Tolerance in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:1284-99. [PMID: 26672074 PMCID: PMC4775112 DOI: 10.1104/pp.15.01308] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/14/2015] [Indexed: 05/18/2023]
Abstract
Glutaredoxins (Grxs) are small proteins that function as oxidoreductases with roles in deglutathionylation of proteins, reduction of antioxidants, and assembly of iron-sulfur (Fe-S) cluster-containing enzymes. Which of the 33 Grxs in Arabidopsis (Arabidopsis thaliana) perform roles in Fe-S assembly in mitochondria is unknown. We have examined in detail the function of the monothiol GrxS15 in plants. Our results show its exclusive mitochondrial localization, and we are concluding it is the major or only Grx in this subcellular location. Recombinant GrxS15 has a very low deglutathionylation and dehydroascorbate reductase activity, but it binds a Fe-S cluster. Partially removing GrxS15 from mitochondria slowed whole plant growth and respiration. Native GrxS15 is shown to be especially important for lipoic acid-dependent enzymes in mitochondria, highlighting a putative role in the transfer of Fe-S clusters in this process. The enhanced effect of the toxin arsenic on the growth of GrxS15 knockdown plants compared to wild type highlights the role of mitochondrial glutaredoxin Fe-S-binding in whole plant growth and toxin tolerance.
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Affiliation(s)
- Elke Ströher
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - Julia Grassl
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - Chris Carrie
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
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23
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Huang S, Nelson CJ, Li L, Taylor NL, Ströher E, Peteriet J, Millar AH. INTERMEDIATE CLEAVAGE PEPTIDASE55 Modifies Enzyme Amino Termini and Alters Protein Stability in Arabidopsis Mitochondria. PLANT PHYSIOLOGY 2015; 168:415-27. [PMID: 25862457 PMCID: PMC4453787 DOI: 10.1104/pp.15.00300] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/03/2015] [Indexed: 05/16/2023]
Abstract
Precursor proteins containing mitochondrial peptide signals are cleaved after import by a mitochondrial processing peptidase. In yeast (Saccharomyces cerevisiae) and human (Homo sapiens), intermediate cleavage peptidase55 (ICP55) plays a role in stabilizing mitochondrial proteins by the removal of single amino acids from mitochondrial processing peptidase-processed proteins. We have investigated the role of a metallopeptidase (At1g09300) from Arabidopsis (Arabidopsis thaliana) that has sequence similarity to yeast ICP55. We identified this protein in mitochondria by mass spectrometry and have studied its function in a transfer DNA insertion line (icp55). Monitoring of amino-terminal peptides showed that Arabidopsis ICP55 was responsible for the removal of single amino acids, and its action explained the -3 arginine processing motif of a number of mitochondrial proteins. ICP55 also removed single amino acids from mitochondrial proteins known to be cleaved at nonconserved arginine sites, a subset of mitochondrial proteins specific to plants. Faster mitochondrial protein degradation rates not only for ICP55 cleaved protein but also for some non-ICP55 cleaved proteins were observed in Arabidopsis mitochondrial samples isolated from icp55 than from the wild type, indicating that a complicated protease degradation network has been affected. The lower protein stability of isolated mitochondria and the lack of processing of target proteins in icp55 were complemented by transformation with the full-length ICP55. Analysis of in vitro degradation rates and protein turnover rates in vivo of specific proteins indicated that serine hydroxymethyltransferase was affected in icp55. The maturation of serine hydroxymethyltransferase by ICP55 is unusual, as it involves breaking an amino-terminal diserine that is not known as an ICP55 substrate in other organisms and that is typically considered a sequence that stabilizes rather than destabilizes a protein.
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Affiliation(s)
- Shaobai Huang
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Clark J Nelson
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Lei Li
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Nicolas L Taylor
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Elke Ströher
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jakob Peteriet
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Crawley, Western Australia 6009, Australia
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24
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Cerletti M, Paggi RA, Guevara CR, Poetsch A, De Castro RE. Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii. J Proteomics 2015; 121:1-14. [PMID: 25829260 DOI: 10.1016/j.jprot.2015.03.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/04/2015] [Accepted: 03/12/2015] [Indexed: 02/07/2023]
Abstract
UNLABELLED The membrane-associated LonB protease is essential for viability in Haloferax volcanii, however, the cellular processes affected by this protease in archaea are unknown. In this study, the impact of a lon conditional mutation (down-regulation) on H. volcanii physiology was examined by comparing proteomes of parental and mutant cells using shotgun proteomics. A total of 1778 proteins were identified (44% of H. volcanii predicted proteome) and 142 changed significantly in amount (≥2 fold). Of these, 66 were augmented in response to Lon deficiency suggesting they could be Lon substrates. The "Lon subproteome" included soluble and predicted membrane proteins expected to participate in diverse cellular processes. The dramatic stabilization of phytoene synthase (57 fold) in concert with overpigmentation of lon mutant cells suggests that Lon controls carotenogenesis in H. volcanii. Several hypothetical proteins, which may reveal novel functions and/or be involved in adaptation to extreme environments, were notably increased (300 fold). This study, which represents the first proteome examination of a Lon deficient archaeal cell, shows that Lon has a strong impact on H. volcanii physiology evidencing the cellular processes controlled by this protease in Archaea. Additionally, this work provides a platform for the discovery of novel targets of Lon proteases. BIOLOGICAL SIGNIFICANCE The proteome of a Lon-deficient archaeal cell was examined for the first time showing that Lon has a strong impact on H. volcanii physiology and evidencing the proteins and cellular processes controlled by this protease in Archaea. This work will facilitate future investigations aiming to address Lon function in archaea and provides a platform for the discovery of endogenous targets of the archaeal-type Lon as well as novel targets/processes regulated by Lon proteases. This knowledge will advance the understanding on archaeal physiology and the biological function of membrane proteases in microorganisms.
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Affiliation(s)
- Micaela Cerletti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250 4to nivel, Mar del Plata (7600), Argentina
| | - Roberto A Paggi
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250 4to nivel, Mar del Plata (7600), Argentina
| | | | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Rosana E De Castro
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3250 4to nivel, Mar del Plata (7600), Argentina.
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25
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Strauss KA, Jinks RN, Puffenberger EG, Venkatesh S, Singh K, Cheng I, Mikita N, Thilagavathi J, Lee J, Sarafianos S, Benkert A, Koehler A, Zhu A, Trovillion V, McGlincy M, Morlet T, Deardorff M, Innes AM, Prasad C, Chudley AE, Lee INW, Suzuki CK. CODAS syndrome is associated with mutations of LONP1, encoding mitochondrial AAA+ Lon protease. Am J Hum Genet 2015; 96:121-35. [PMID: 25574826 DOI: 10.1016/j.ajhg.2014.12.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 12/05/2014] [Indexed: 12/30/2022] Open
Abstract
CODAS syndrome is a multi-system developmental disorder characterized by cerebral, ocular, dental, auricular, and skeletal anomalies. Using whole-exome and Sanger sequencing, we identified four LONP1 mutations inherited as homozygous or compound-heterozygous combinations among ten individuals with CODAS syndrome. The individuals come from three different ancestral backgrounds (Amish-Swiss from United States, n = 8; Mennonite-German from Canada, n = 1; mixed European from Canada, n = 1). LONP1 encodes Lon protease, a homohexameric enzyme that mediates protein quality control, respiratory-complex assembly, gene expression, and stress responses in mitochondria. All four pathogenic amino acid substitutions cluster within the AAA(+) domain at residues near the ATP-binding pocket. In biochemical assays, pathogenic Lon proteins show substrate-specific defects in ATP-dependent proteolysis. When expressed recombinantly in cells, all altered Lon proteins localize to mitochondria. The Old Order Amish Lon variant (LONP1 c.2161C>G[p.Arg721Gly]) homo-oligomerizes poorly in vitro. Lymphoblastoid cell lines generated from affected children have (1) swollen mitochondria with electron-dense inclusions and abnormal inner-membrane morphology; (2) aggregated MT-CO2, the mtDNA-encoded subunit II of cytochrome c oxidase; and (3) reduced spare respiratory capacity, leading to impaired mitochondrial proteostasis and function. CODAS syndrome is a distinct, autosomal-recessive, developmental disorder associated with dysfunction of the mitochondrial Lon protease.
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Affiliation(s)
- Kevin A Strauss
- Clinic for Special Children, Strasburg, PA 17579, USA; Lancaster General Hospital, Lancaster, PA 17602, USA; Department of Biology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA 17603, USA.
| | - Robert N Jinks
- Department of Biology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Erik G Puffenberger
- Clinic for Special Children, Strasburg, PA 17579, USA; Department of Biology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Sundararajan Venkatesh
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Kamalendra Singh
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA; Department of Molecular Microbiology and Immunology, Christopher Bond Life Sciences Center, University of Missouri, Columbia, Columbia, MO 65201, USA
| | - Iteen Cheng
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Natalie Mikita
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jayapalraja Thilagavathi
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Jae Lee
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Stefan Sarafianos
- Department of Molecular Microbiology and Immunology, Christopher Bond Life Sciences Center, University of Missouri, Columbia, Columbia, MO 65201, USA
| | - Abigail Benkert
- Clinic for Special Children, Strasburg, PA 17579, USA; Department of Biology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Alanna Koehler
- Department of Biology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Anni Zhu
- Department of Biology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Victoria Trovillion
- Department of Biology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Madeleine McGlincy
- Department of Biology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Thierry Morlet
- Auditory Physiology and Psychoacoustics Research Laboratory, duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Matthew Deardorff
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Chitra Prasad
- Medical Genetics Program, Department of Pediatrics, Children's Health Research Institute and Western University, London, ON N6C 2V5, Canada
| | - Albert E Chudley
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Irene Nga Wing Lee
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Carolyn K Suzuki
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
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26
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van Wijk KJ. Protein maturation and proteolysis in plant plastids, mitochondria, and peroxisomes. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:75-111. [PMID: 25580835 DOI: 10.1146/annurev-arplant-043014-115547] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plastids, mitochondria, and peroxisomes are key organelles with dynamic proteomes in photosynthetic eukaryotes. Their biogenesis and activity must be coordinated and require intraorganellar protein maturation, degradation, and recycling. The three organelles together are predicted to contain ∼200 presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar proteins, such as N-end degrons and tagging systems, have not been identified, but the substrate recognition mechanisms likely share similarities between organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, degrons, and protein lifetime. Intraorganellar proteolysis is complemented by autophagy of whole organelles or selected organellar content, as well as by cytosolic protein ubiquitination and degradation by the proteasome. This review summarizes (putative) plant organellar protease functions and substrate-protease relationships. Examples illustrate key proteolytic events.
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Affiliation(s)
- Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York 14853;
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Geigenberger P, Fernie AR. Metabolic control of redox and redox control of metabolism in plants. Antioxid Redox Signal 2014; 21:1389-421. [PMID: 24960279 PMCID: PMC4158967 DOI: 10.1089/ars.2014.6018] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SIGNIFICANCE Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression. RECENT ADVANCES The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels. CRITICAL ISSUES It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter- and intracellular levels. FUTURE DIRECTIONS Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.
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Affiliation(s)
- Peter Geigenberger
- 1 Department of Biology I, Ludwig Maximilian University Munich , Planegg-Martinsried, Germany
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Daras G, Rigas S, Tsitsekian D, Zur H, Tuller T, Hatzopoulos P. Alternative transcription initiation and the AUG context configuration control dual-organellar targeting and functional competence of Arabidopsis Lon1 protease. MOLECULAR PLANT 2014; 7:989-1005. [PMID: 24646630 DOI: 10.1093/mp/ssu030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Cellular homeostasis relies on components of protein quality control including chaperones and proteases. In bacteria and eukaryotic organelles, Lon proteases play a critical role in removing irreparably damaged proteins and thereby preventing the accumulation of deleterious degradation-resistant aggregates. Gene expression, live-cell imaging, immunobiochemical, and functional complementation approaches provide conclusive evidence for Lon1 dual-targeting to chloroplasts and mitochondria. Dual-organellar deposition of Lon1 isoforms depends on both transcriptional regulation and alternative translation initiation via leaky ribosome scanning from the first AUG sequence context that deviates extensively from the optimum Kozak consensus. Organelle-specific Lon1 targeting results in partial complementation of Arabidopsis lon1-1 mutants, whereas full complementation is solely accomplished by dual-organellar targeting. Both the optimal and non-optimal AUG sequence contexts are functional in yeast and facilitate leaky ribosome scanning complementing the pim1 phenotype when the mitochondrial presequence is used. Bioinformatic search identified a limited number of Arabidopsis genes with Lon1-type dual-targeting sequence organization. Lon4, the paralog of Lon1, has an ambiguous presequence likely evolved from the twin presequences of an ancestral Lon1-like gene, generating a single dual-targeted protein isoform. We postulate that Lon1 and its subfunctional paralog Lon4 evolved complementary subsets of transcriptional and posttranscriptional regulatory components responsive to environmental cues for dual-organellar targeting.
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Affiliation(s)
- Gerasimos Daras
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Dikran Tsitsekian
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Hadas Zur
- School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Polydefkis Hatzopoulos
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece.
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Smakowska E, Czarna M, Janska H. Mitochondrial ATP-dependent proteases in protection against accumulation of carbonylated proteins. Mitochondrion 2014; 19 Pt B:245-51. [PMID: 24662487 DOI: 10.1016/j.mito.2014.03.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/11/2014] [Accepted: 03/14/2014] [Indexed: 10/25/2022]
Abstract
Carbonylation is an irreversible oxidative modification of proteins induced by reactive oxygen species (ROS) and reactive nitrogen species (RNS) or by-products of oxidative stress. Carbonylation leads to the loss of protein function and is used as a marker of oxidative stress. Recent data indicate that carbonylation is not only an unfavorable chance process but may also play a significant role in the control of diverse physiological processes. In plants, carbonylated proteins have been found in all cellular compartments; however, mitochondria, one of the major sources of reactive species, show the highest levels of oxidatively modified proteins under normal or stress conditions. Carbonylated proteins tend to misfold and have to be removed to prevent the formation of harmful insoluble aggregates. Mitochondria have developed several pathways that continuously monitor and remove oxidatively damaged polypeptides, and the mitochondrial protein quality control (mtPQC) system, comprising chaperones and ATP-dependent proteases, is the first line of defense. The Lon protease has been recognized as a key protease involved in the removal of oxidized proteins in yeast and mammalian mitochondria, but not in plants. Recently, it has been reported that the inner-membrane human i-AAA and m-AAA and Arabidopsis i-AAA proteases are crucial components of the defense against accumulation of carbonylated proteins, but the molecular basis of their action is not yet clear. Altogether, the mitochondrial AAA proteases secure the mitochondrial proteome against accumulation of carbonylated proteins.
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Affiliation(s)
- Elwira Smakowska
- Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, 50-383 Wroclaw, Poland
| | - Malgorzata Czarna
- Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, 50-383 Wroclaw, Poland
| | - Hanna Janska
- Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, 50-383 Wroclaw, Poland.
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Goto-Yamada S, Mano S, Nakamori C, Kondo M, Yamawaki R, Kato A, Nishimura M. Chaperone and Protease Functions of LON Protease 2 Modulate the Peroxisomal Transition and Degradation with Autophagy. ACTA ACUST UNITED AC 2014; 55:482-96. [DOI: 10.1093/pcp/pcu017] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Nelson CJ, Li L, Millar AH. Quantitative analysis of protein turnover in plants. Proteomics 2014; 14:579-92. [DOI: 10.1002/pmic.201300240] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/02/2013] [Accepted: 10/14/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Clark J. Nelson
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
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Verslues PE, Lasky JR, Juenger TE, Liu TW, Kumar MN. Genome-wide association mapping combined with reverse genetics identifies new effectors of low water potential-induced proline accumulation in Arabidopsis. PLANT PHYSIOLOGY 2014; 164:144-59. [PMID: 24218491 PMCID: PMC3875797 DOI: 10.1104/pp.113.224014] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/10/2013] [Indexed: 05/18/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) exhibits natural genetic variation in drought response, including varying levels of proline (Pro) accumulation under low water potential. As Pro accumulation is potentially important for stress tolerance and cellular redox control, we conducted a genome-wide association (GWAS) study of low water potential-induced Pro accumulation using a panel of natural accessions and publicly available single-nucleotide polymorphism (SNP) data sets. Candidate genomic regions were prioritized for subsequent study using metrics considering both the strength and spatial clustering of the association signal. These analyses found many candidate regions likely containing gene(s) influencing Pro accumulation. Reverse genetic analysis of several candidates identified new Pro effector genes, including thioredoxins and several genes encoding Universal Stress Protein A domain proteins. These new Pro effector genes further link Pro accumulation to cellular redox and energy status. Additional new Pro effector genes found include the mitochondrial protease LON1, ribosomal protein RPL24A, protein phosphatase 2A subunit A3, a MADS box protein, and a nucleoside triphosphate hydrolase. Several of these new Pro effector genes were from regions with multiple SNPs, each having moderate association with Pro accumulation. This pattern supports the use of summary approaches that incorporate clusters of SNP associations in addition to consideration of individual SNP probability values. Further GWAS-guided reverse genetics promises to find additional effectors of Pro accumulation. The combination of GWAS and reverse genetics to efficiently identify new effector genes may be especially applicable for traits difficult to analyze by other genetic screening methods.
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Rigas S, Daras G, Tsitsekian D, Alatzas A, Hatzopoulos P. Evolution and significance of the Lon gene family in Arabidopsis organelle biogenesis and energy metabolism. FRONTIERS IN PLANT SCIENCE 2014; 5:145. [PMID: 24782883 PMCID: PMC3990055 DOI: 10.3389/fpls.2014.00145] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/26/2014] [Indexed: 05/18/2023]
Abstract
Lon is the first identified ATP-dependent protease highly conserved across all kingdoms. Model plant species Arabidopsis thaliana has a small Lon gene family of four members. Although these genes share common structural features, they have distinct properties in terms of gene expression profile, subcellular targeting and substrate recognition motifs. This supports the notion that their functions under different environmental conditions are not necessarily redundant. This article intends to unravel the biological role of Lon proteases in energy metabolism and plant growth through an evolutionary perspective. Given that plants are sessile organisms exposed to diverse environmental conditions and plant organelles are semi-autonomous, it is tempting to suggest that Lon genes in Arabidopsis are paralogs. Adaptive evolution through repetitive gene duplication events of a single archaic gene led to Lon genes with complementing sets of subfunctions providing to the organism rapid adaptability for canonical development under different environmental conditions. Lon1 function is adequately characterized being involved in mitochondrial biogenesis, modulating carbon metabolism, oxidative phosphorylation and energy supply, all prerequisites for seed germination and seedling establishment. Lon is not a stand-alone proteolytic machine in plant organelles. Lon in association with other nuclear-encoded ATP-dependent proteases builds up an elegant nevertheless, tight interconnected circuit. This circuitry channels properly and accurately, proteostasis and protein quality control among the distinct subcellular compartments namely mitochondria, chloroplasts, and peroxisomes.
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Affiliation(s)
| | | | | | | | - Polydefkis Hatzopoulos
- *Correspondence: Polydefkis Hatzopoulos, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece e-mail:
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Bayot A, Gareil M, Chavatte L, Hamon MP, L'Hermitte-Stead C, Beaumatin F, Priault M, Rustin P, Lombès A, Friguet B, Bulteau AL. Effect of Lon protease knockdown on mitochondrial function in HeLa cells. Biochimie 2013; 100:38-47. [PMID: 24355201 DOI: 10.1016/j.biochi.2013.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 12/04/2013] [Indexed: 11/16/2022]
Abstract
ATP-dependent proteases are currently emerging as key regulators of mitochondrial functions. Among these proteolytic systems, Lon protease is involved in the control of selective protein turnover in the mitochondrial matrix. In the absence of Lon, yeast cells have been shown to accumulate electron-dense inclusion bodies in the matrix space, to loose integrity of mitochondrial genome and to be respiratory deficient. In order to address the role of Lon in mitochondrial functionality in human cells, we have set up a HeLa cell line stably transfected with a vector expressing a shRNA under the control of a promoter which is inducible with doxycycline. We have demonstrated that reduction of Lon protease results in a mild phenotype in this cell line in contrast with what have been observed in other cell types such as WI-38 fibroblasts. Nevertheless, deficiency in Lon protease led to an increase in ROS production and to an accumulation of carbonylated protein in the mitochondria. Our study suggests that Lon protease has a wide variety of targets and is likely to play different roles depending of the cell type.
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Affiliation(s)
- Aurélien Bayot
- UR4 - Vieillissement, Stress, Inflammation, Sorbonne Universités, UPMC Univ Paris 06, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France; Inserm, Hopital Robert Debré, 75019 Paris, France
| | - Monique Gareil
- UR4 - Vieillissement, Stress, Inflammation, Sorbonne Universités, UPMC Univ Paris 06, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Laurent Chavatte
- Centre de recherche de Gif-sur-Yvette, FRC 3115, Centre de Génétique Moléculaire, CNRS, UPR3404, 91198 Gif-sur-Yvette Cedex, France
| | - Marie-Paule Hamon
- UR4 - Vieillissement, Stress, Inflammation, Sorbonne Universités, UPMC Univ Paris 06, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | | | - Florian Beaumatin
- Institut de Biochimie et Génétique Cellulaires, UMR 5095, CNRS, Université Bordeaux 2, France
| | - Muriel Priault
- Institut de Biochimie et Génétique Cellulaires, UMR 5095, CNRS, Université Bordeaux 2, France
| | | | - Anne Lombès
- Inserm, Institut Cochin, 75014 Paris, France
| | - Bertrand Friguet
- UR4 - Vieillissement, Stress, Inflammation, Sorbonne Universités, UPMC Univ Paris 06, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France.
| | - Anne-Laure Bulteau
- UR4 - Vieillissement, Stress, Inflammation, Sorbonne Universités, UPMC Univ Paris 06, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
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Sew YS, Ströher E, Holzmann C, Huang S, Taylor NL, Jordana X, Millar AH. Multiplex micro-respiratory measurements of Arabidopsis tissues. THE NEW PHYTOLOGIST 2013; 200:922-932. [PMID: 23834713 DOI: 10.1111/nph.12394] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 05/29/2013] [Indexed: 05/08/2023]
Abstract
Researchers often want to study the respiratory properties of individual parts of plants in response to a range of treatments. Arabidopsis is an obvious model for this work; however, because of its size, it represents a challenge for gas exchange measurements of respiration. The combination of micro-respiratory technologies with multiplex assays has the potential to bridge this gap, and make measurements possible in this model plant species. We show the adaptation of the commercial technology used for mammalian cell respiration analysis to study three critical tissues of interest: leaf sections, root tips and seeds. The measurement of respiration in single leaf discs has allowed the age dependence of the respiration rate in Arabidopsis leaves across the rosette to be observed. The oxygen consumption of single root tips from plate-grown seedlings shows the enhanced respiration of root tips and their time-dependent susceptibility to salinity. The monitoring of single Arabidopsis seeds shows the kinetics of respiration over 48 h post-imbibition, and the effect of the phytohormones gibberellic acid (GA3 ) and abscisic acid (ABA) on respiration during seed germination. These studies highlight the potential for multiplexed micro-respiratory assays to study oxygen consumption in Arabidopsis tissues, and open up new possibilities to screen and study mutants and to identify differences in ecotypes or populations of different plant species.
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Affiliation(s)
- Yun Shin Sew
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Elke Ströher
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Cristián Holzmann
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Millenium Nucleus in Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidád Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Nicolas L Taylor
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Xavier Jordana
- Millenium Nucleus in Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidád Católica de Chile, Casilla 114-D, Santiago, Chile
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
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Vanlerberghe GC. Alternative oxidase: a mitochondrial respiratory pathway to maintain metabolic and signaling homeostasis during abiotic and biotic stress in plants. Int J Mol Sci 2013; 14:6805-47. [PMID: 23531539 PMCID: PMC3645666 DOI: 10.3390/ijms14046805] [Citation(s) in RCA: 415] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 02/07/2023] Open
Abstract
Alternative oxidase (AOX) is a non-energy conserving terminal oxidase in the plant mitochondrial electron transport chain. While respiratory carbon oxidation pathways, electron transport, and ATP turnover are tightly coupled processes, AOX provides a means to relax this coupling, thus providing a degree of metabolic homeostasis to carbon and energy metabolism. Beside their role in primary metabolism, plant mitochondria also act as "signaling organelles", able to influence processes such as nuclear gene expression. AOX activity can control the level of potential mitochondrial signaling molecules such as superoxide, nitric oxide and important redox couples. In this way, AOX also provides a degree of signaling homeostasis to the organelle. Evidence suggests that AOX function in metabolic and signaling homeostasis is particularly important during stress. These include abiotic stresses such as low temperature, drought, and nutrient deficiency, as well as biotic stresses such as bacterial infection. This review provides an introduction to the genetic and biochemical control of AOX respiration, as well as providing generalized examples of how AOX activity can provide metabolic and signaling homeostasis. This review also examines abiotic and biotic stresses in which AOX respiration has been critically evaluated, and considers the overall role of AOX in growth and stress tolerance.
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Affiliation(s)
- Greg C Vanlerberghe
- Department of Biological Sciences and Department of Cell and Systems Biology, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C1A4, Canada.
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Lee CP, Taylor NL, Millar AH. Recent advances in the composition and heterogeneity of the Arabidopsis mitochondrial proteome. FRONTIERS IN PLANT SCIENCE 2013; 4:4. [PMID: 23355843 PMCID: PMC3554846 DOI: 10.3389/fpls.2013.00004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 01/03/2013] [Indexed: 05/04/2023]
Abstract
Mitochondria are important organelles for providing the ATP and carbon skeletons required to sustain cell growth. While these organelles also participate in other key metabolic functions across species, they have a specialized role in plants of optimizing photosynthesis through participating in photorespiration. It is therefore critical to map the protein composition of mitochondria in plants to gain a better understanding of their regulation and define the uniqueness of their metabolic networks. To date, <30% of the predicted number of mitochondrial proteins has been verified experimentally by proteomics and/or GFP localization studies. In this mini-review, we will provide an overview of the advances in mitochondrial proteomics in the model plant Arabidopsis thaliana over the past 5 years. The ultimate goal of mapping the mitochondrial proteome in Arabidopsis is to discover novel mitochondrial components that are critical during development in plants as well as genes involved in developmental abnormalities, such as those implicated in mitochondrial-linked cytoplasmic male sterility.
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Affiliation(s)
- Chun Pong Lee
- Department of Plant Sciences, University of OxfordOxford, UK
- *Correspondence: Chun Pong Lee, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK. e-mail:
| | - Nicolas L. Taylor
- ARC Centre of Excellence in Plant Energy Biology, The University of Western AustraliaCrawley, WA, Australia
- Centre for Comparative Analysis of Biomolecular Networks, The University of Western AustraliaCrawley, WA, Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western AustraliaCrawley, WA, Australia
- Centre for Comparative Analysis of Biomolecular Networks, The University of Western AustraliaCrawley, WA, Australia
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