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Prokopchuk G, Butenko A, Dacks JB, Speijer D, Field MC, Lukeš J. Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes. Biol Rev Camb Philos Soc 2023; 98:1910-1927. [PMID: 37336550 PMCID: PMC10952624 DOI: 10.1111/brv.12988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.
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Affiliation(s)
- Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
- Life Science Research Centre, Faculty of ScienceUniversity of OstravaChittussiho 983/10Ostrava71000Czech Republic
| | - Joel B. Dacks
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Division of Infectious Diseases, Department of MedicineUniversity of Alberta1‐124 Clinical Sciences Building, 11350‐83 AvenueEdmontonT6G 2R3AlbertaCanada
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and the EnvironmentUniversity College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMCUniversity of AmsterdamMeibergdreef 15Amsterdam1105 AZThe Netherlands
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
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2
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Ghifari AS, Saha S, Murcha MW. The biogenesis and regulation of the plant oxidative phosphorylation system. PLANT PHYSIOLOGY 2023; 192:728-747. [PMID: 36806687 DOI: 10.1093/plphys/kiad108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 06/01/2023]
Abstract
Mitochondria are central organelles for respiration in plants. At the heart of this process is oxidative phosphorylation (OXPHOS) system, which generates ATP required for cellular energetic needs. OXPHOS complexes comprise of multiple subunits that originated from both mitochondrial and nuclear genome, which requires careful orchestration of expression, translation, import, and assembly. Constant exposure to reactive oxygen species due to redox activity also renders OXPHOS subunits to be more prone to oxidative damage, which requires coordination of disassembly and degradation. In this review, we highlight the composition, assembly, and activity of OXPHOS complexes in plants based on recent biochemical and structural studies. We also discuss how plants regulate the biogenesis and turnover of OXPHOS subunits and the importance of OXPHOS in overall plant respiration. Further studies in determining the regulation of biogenesis and activity of OXPHOS will advances the field, especially in understanding plant respiration and its role to plant growth and development.
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Affiliation(s)
- Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Saurabh Saha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
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3
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Wang G, Wang Y, Ni J, Li R, Zhu F, Wang R, Tian Q, Shen Q, Yang Q, Tang J, Murcha MW, Wang G. An MCIA-like complex is required for mitochondrial complex I assembly and seed development in maize. MOLECULAR PLANT 2022; 15:1470-1487. [PMID: 35957532 DOI: 10.1016/j.molp.2022.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 05/13/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
During adaptive radiation, mitochondria have co-evolved with their hosts, leading to gain or loss of subunits and assembly factors of respiratory complexes. Plant mitochondrial complex I harbors ∼40 nuclear- and 9 mitochondrial-encoded subunits, and is formed by stepwise assembly during which different intermediates are integrated via various assembly factors. In mammals, the mitochondrial complex I intermediate assembly (MCIA) complex is required for building the membrane arm module. However, plants have lost almost all of the MCIA complex components, giving rise to the hypothesis that plants follow an ancestral pathway to assemble the membrane arm subunits. Here, we characterize a maize crumpled seed mutant, crk1, and reveal by map-based cloning that CRK1 encodes an ortholog of human complex I assembly factor 1, zNDUFAF1, the only evolutionarily conserved MCIA subunit in plants. zNDUFAF1 is localized in the mitochondria and accumulates in two intermediate complexes that contain complex I membrane arm subunits. Disruption of zNDUFAF1 results in severe defects in complex I assembly and activity, a cellular bioenergetic shift to aerobic glycolysis, and mitochondrial vacuolation. Moreover, we found that zNDUFAF1, the putative mitochondrial import inner membrane translocase ZmTIM17-1, and the isovaleryl-coenzyme A dehydrogenase ZmIVD1 interact each other, and could be co-precipitated from the mitochondria and co-migrate in the same assembly intermediates. Knockout of either ZmTIM17-1 or ZmIVD1 could lead to the significantly reduced complex I stability and activity as well as defective seeds. These results suggest that zNDUFAF1, ZmTIM17-1 and ZmIVD1 probably form an MCIA-like complex that is essential for the biogenesis of mitochondrial complex I and seed development in maize. Our findings also imply that plants and mammals recruit MCIA subunits independently for mitochondrial complex I assembly, highlighting the importance of parallel evolution in mitochondria adaptation to their hosts.
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Affiliation(s)
- Gang Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yongyan Wang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiacheng Ni
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Rongrong Li
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Fengling Zhu
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruyin Wang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiuzhen Tian
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Qingwen Shen
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Qinghua Yang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The Shennong Laboratory, Zhengzhou, Henan 450002, China
| | - Monika W Murcha
- School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Guifeng Wang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT--China Joint Center of Wheat and Maize, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China.
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4
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Chen Y, Wang Y, Yang J, Zhou W, Dai S. Exploring the diversity of plant proteome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1197-1210. [PMID: 33650765 DOI: 10.1111/jipb.13087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/25/2021] [Indexed: 05/10/2023]
Abstract
The tremendous functional, spatial, and temporal diversity of the plant proteome is regulated by multiple factors that continuously modify protein abundance, modifications, interactions, localization, and activity to meet the dynamic needs of plants. Dissecting the proteome complexity and its underlying genetic variation is attracting increasing research attention. Mass spectrometry (MS)-based proteomics has become a powerful approach in the global study of protein functions and their relationships on a systems level. Here, we review recent breakthroughs and strategies adopted to unravel the diversity of the proteome, with a specific focus on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. We also consider PTM crosstalk and multiple PTMs temporally regulating the life cycle of proteins. Finally, we discuss recent quantitative studies using MS to measure protein turnover rates and examine future directions in the study of the plant proteome.
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Affiliation(s)
- Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Wenbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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5
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Ivanova A, Ghifari AS, Berkowitz O, Whelan J, Murcha MW. The mitochondrial AAA protease FTSH3 regulates Complex I abundance by promoting its disassembly. PLANT PHYSIOLOGY 2021; 186:599-610. [PMID: 33616659 PMCID: PMC8154063 DOI: 10.1093/plphys/kiab074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 06/02/2023]
Abstract
ATP is generated in mitochondria by oxidative phosphorylation. Complex I (NADH:ubiquinone oxidoreductase or NADH dehydrogenase) is the first multisubunit protein complex of this pathway, oxidizing NADH and transferring electrons to the ubiquinone pool. Typically, Complex I mutants display a slow growth rate compared to wild-type plants. Here, using a forward genetic screen approach for restored growth of a Complex I mutant, we have identified the mitochondrial ATP-dependent metalloprotease, Filamentous Temperature Sensitive H 3 (FTSH3), as a factor that is required for the disassembly of Complex I. An ethyl methanesulfonate-induced mutation in FTSH3, named as rmb1 (restoration of mitochondrial biogenesis 1), restored Complex I abundance and plant growth. Complementation could be achieved with FTSH3 lacking proteolytic activity, suggesting the unfoldase function of FTSH3 has a role in Complex I disassembly. The introduction of the rmb1 to an additional, independent, and extensively characterized Complex I mutant, ndufs4, resulted in similar increases to Complex I abundance and a partial restoration of growth. These results show that disassembly or degradation of Complex I plays a role in determining its steady-state abundance and thus turnover may vary under different conditions.
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Affiliation(s)
- Aneta Ivanova
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Vic, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Vic, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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6
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The composition and turnover of the Arabidopsis thaliana 80S cytosolic ribosome. Biochem J 2021; 477:3019-3032. [PMID: 32744327 PMCID: PMC7452503 DOI: 10.1042/bcj20200385] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/26/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
Cytosolic 80S ribosomes contain proteins of the mature cytosolic ribosome (r-proteins) as well as proteins with roles in ribosome biogenesis, protein folding or modification. Here, we refined the core r-protein composition in Arabidopsis thaliana by determining the abundance of different proteins during enrichment of ribosomes from cell cultures using peptide mass spectrometry. The turnover rates of 26 40S subunit r-proteins and 29 60S subunit r-proteins were also determined, showing that half of the ribosome population is replaced every 3–4 days. Three enriched proteins showed significantly shorter half-lives; a protein annotated as a ribosomal protein uL10 (RPP0D, At1g25260) with a half-life of 0.5 days and RACK1b and c with half-lives of 1–1.4 days. The At1g25260 protein is a homologue of the human Mrt4 protein, a trans-acting factor in the assembly of the pre-60S particle, while RACK1 has known regulatory roles in cell function beyond its role in the 40S subunit. Our experiments also identified 58 proteins that are not from r-protein families but co-purify with ribosomes and co-express with r-proteins; 26 were enriched more than 10-fold during ribosome enrichment. Some of these enriched proteins have known roles in translation, while others are newly proposed ribosome-associated factors in plants. This analysis provides an improved understanding of A. thaliana ribosome protein content, shows that most r-proteins turnover in unison in vivo, identifies a novel set of potential plant translatome components, and how protein turnover can help identify r-proteins involved in ribosome biogenesis or regulation in plants.
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7
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Szczepanowska K, Trifunovic A. Tune instead of destroy: How proteolysis keeps OXPHOS in shape. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148365. [PMID: 33417924 DOI: 10.1016/j.bbabio.2020.148365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023]
Abstract
Mitochondria are highly dynamic and stress-responsive organelles that are renewed, maintained and removed by a number of different mechanisms. Recent findings bring more evidence for the focused, defined, and regulatory function of the intramitochondrial proteases extending far beyond the traditional concepts of damage control and stress responses. Until recently, the macrodegradation processes, such as mitophagy, were promoted as the major regulator of OXPHOS remodelling and turnover. However, the spatiotemporal dynamics of the OXPHOS system can be greatly modulated by the intrinsic mitochondrial mechanisms acting apart from changes in the global mitochondrial dynamics. This, in turn, may substantially contribute to the shaping of the metabolic status of the cell.
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Affiliation(s)
- Karolina Szczepanowska
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), and Institute for Mitochondrial Diseases and Ageing, Medical Faculty, University of Cologne D-50931 Cologne, Germany; Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC), D-50931 Cologne, Germany.
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), and Institute for Mitochondrial Diseases and Ageing, Medical Faculty, University of Cologne D-50931 Cologne, Germany; Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC), D-50931 Cologne, Germany.
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8
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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: 8] [Impact Index Per Article: 2.0] [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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9
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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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10
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Braun HP. The Oxidative Phosphorylation system of the mitochondria in plants. Mitochondrion 2020; 53:66-75. [PMID: 32334143 DOI: 10.1016/j.mito.2020.04.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/26/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022]
Abstract
Mitochondrial Oxidative Phosphorylation (OXPHOS) provides ATP for driving cellular functions. In plants, OXPHOS takes place in the context of photosynthesis. Indeed, metabolism of mitochondria and chloroplasts is tightly linked. OXPHOS has several extra functions in plants. This review takes a view on the OXPHOS system of plants, the electron transfer chain (ETC), the ATP synthase complex and the numerous supplementary enzymes involved. Electron transport pathways are especially branched in plants. Furthermore, the "classical" OXPHOS complexes include extra subunits, some of which introduce side activities into these complexes. Consequently, and to a remarkable degree, OXPHOS is a multi-functional system in plants that needs to be efficiently regulated with respect to all its physiological tasks in the mitochondria, the chloroplasts, and beyond. Regulatory mechanisms based on posttranslational protein modifications and formation of supramolecular protein assemblies are summarized and discussed.
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Affiliation(s)
- Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
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11
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Ivanova A, Gill-Hille M, Huang S, Branca RM, Kmiec B, Teixeira PF, Lehtiö J, Whelan J, Murcha MW. A Mitochondrial LYR Protein Is Required for Complex I Assembly. PLANT PHYSIOLOGY 2019; 181:1632-1650. [PMID: 31601645 PMCID: PMC6878026 DOI: 10.1104/pp.19.00822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 05/04/2023]
Abstract
Complex I biogenesis requires the expression of both nuclear and mitochondrial genes, the import of proteins, cofactor biosynthesis, and the assembly of at least 49 individual subunits. Assembly factors interact with subunits of Complex I but are not part of the final holocomplex. We show that in Arabidopsis (Arabidopsis thaliana), a mitochondrial matrix protein (EMB1793, At1g76060), which we term COMPLEX I ASSEMBLY FACTOR 1 (CIAF1), contains a LYR domain and is required for Complex I assembly. T-DNA insertion mutants of CIAF1 lack Complex I and the Supercomplex I+III. Biochemical characterization shows that the assembly of Complex I is stalled at 650 and 800 kD intermediates in mitochondria isolated from ciaf1 mutant lines.I. Yeast-two-hybrid interaction and complementation assays indicate that CIAF1 specifically interacts with the 23-kD TYKY-1 matrix domain subunit of Complex I and likely plays a role in Fe-S insertion into this subunit. These data show that CIAF1 plays an essential role in assembling the peripheral matrix arm Complex I subunits into the Complex I holoenzyme.
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Affiliation(s)
- Aneta Ivanova
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Mabel Gill-Hille
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Shaobai Huang
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Rui M Branca
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institutet, Stockholm 171 77, Sweden
| | - Beata Kmiec
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm SE-106 91, Sweden
| | - Pedro F Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm SE-106 91, Sweden
| | - Janne Lehtiö
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institutet, Stockholm 171 77, Sweden
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Australia
| | - Monika W Murcha
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
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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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Ligas J, Pineau E, Bock R, Huynen MA, Meyer EH. The assembly pathway of complex I in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:447-459. [PMID: 30347487 DOI: 10.1111/tpj.14133] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 05/23/2023]
Abstract
All present-day mitochondria originate from a single endosymbiotic event that gave rise to the last eukaryotic common ancestor more than a billion years ago. However, to date, many aspects of mitochondrial evolution have remained unresolved. Comparative genomics and proteomics have revealed a complex evolutionary origin for many mitochondrial components. To understand the evolution of the respiratory chain, we have examined both the components and the mechanisms of the assembly pathway of complex I. Complex I represents the first enzyme in the respiratory chain, and complex I deficiencies have dramatic consequences in both animals and plants. The complex is located in the mitochondrial inner membrane and possesses two arms: one embedded in the inner membrane and one protruding in the matrix. Here, we describe the assembly pathway of complex I in the model plant Arabidopsis thaliana. Using a proteomics approach called complexome profiling, we have resolved the different steps in the assembly process in plants. We propose a model for the stepwise assembly of complex I, including every subunit. We then compare this pathway with the corresponding pathway in humans and find that complex I assembly in plants follows a different, and likely ancestral, pathway compared with the one in humans. We show that the main evolutionary changes in complex I structure and assembly in humans occurred at the level of the membrane arm, whereas the matrix arm remained rather conserved.
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Affiliation(s)
- Joanna Ligas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Emmanuelle Pineau
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, 67084, Strasbourg, France
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Centre for Mitochondrial Medicine, Radboud University, Nijmegen, The Netherlands
| | - Etienne H Meyer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, 67084, Strasbourg, France
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Li L, Aro EM, Millar AH. Mechanisms of Photodamage and Protein Turnover in Photoinhibition. TRENDS IN PLANT SCIENCE 2018; 23:667-676. [PMID: 29887276 DOI: 10.1016/j.tplants.2018.05.004] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/05/2018] [Accepted: 05/08/2018] [Indexed: 05/05/2023]
Abstract
Rapid protein degradation and replacement is an important response to photodamage and a means of photoprotection by recovering proteostasis. Protein turnover and translation efficiency studies have discovered fast turnover subunits in cytochrome b6f and the NAD(P)H dehydrogenase (NDH) complex, in addition to PSII subunit D1. Mutations of these complexes have been linked to enhanced photodamage at least partially via cyclic electron flow. Photodamage and photoprotection involving cytochrome b6f, NDH complex, cyclic electron flow, PSI, and nonphotochemical quenching proteins have been reported. Here, we propose that the rapid turnover of specific proteins in cytochrome b6f and the NDH complex need to be characterised and compared with the inhibition of PSII by excess excitation energy and PSI by excess electron flux to expand our understanding of photoinhibition mechanisms.
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Affiliation(s)
- Lei Li
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, 6009, Perth, WA, Australia
| | - Eva-Mari Aro
- Finnish Centre of Excellence in Molecular Biology of Primary Producers, Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, 6009, Perth, WA, Australia.
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15
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Plant mitochondrial protein import: the ins and outs. Biochem J 2018; 475:2191-2208. [PMID: 30018142 DOI: 10.1042/bcj20170521] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 01/29/2023]
Abstract
The majority of the mitochondrial proteome, required to fulfil its diverse range of functions, is cytosolically synthesised and translocated via specialised machinery. The dedicated translocases, receptors, and associated proteins have been characterised in great detail in yeast over the last several decades, yet many of the mechanisms that regulate these processes in higher eukaryotes are still unknown. In this review, we highlight the current knowledge of mitochondrial protein import in plants. Despite the fact that the mechanisms of mitochondrial protein import have remained conserved across species, many unique features have arisen in plants to encompass the developmental, tissue-specific, and stress-responsive regulation in planta. An understanding of unique features and mechanisms in plants provides us with a unique insight into the regulation of mitochondrial biogenesis in higher eukaryotes.
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Senkler J, Senkler M, Braun HP. Structure and function of complex I in animals and plants - a comparative view. PHYSIOLOGIA PLANTARUM 2017; 161:6-15. [PMID: 28261805 DOI: 10.1111/ppl.12561] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
The mitochondrial NADH dehydrogenase complex (complex I) has a molecular mass of about 1000 kDa and includes 40-50 subunits in animals, fungi and plants. It is composed of a membrane arm and a peripheral arm and has a conserved L-like shape in all species investigated. However, in plants and possibly some protists it has a second peripheral domain which is attached to the membrane arm on its matrix exposed side at a central position. The extra domain includes proteins resembling prokaryotic gamma-type carbonic anhydrases. We here present a detailed comparison of complex I from mammals and flowering plants. Forty homologous subunits are present in complex I of both groups of species. In addition, five subunits are present in mammalian complex I, which are absent in plants, and eight to nine subunits are present in plant complex I which do not occur in mammals. Based on the atomic structure of mammalian complex I and biochemical insights into complex I architecture from plants we mapped the species-specific subunits. Interestingly, four of the five animal-specific and five of the eight to nine plant-specific subunits are localized at the inner surface of the membrane arm of complex I in close proximity. We propose that the inner surface of the membrane arm represents a workbench for attaching proteins to complex I, which are not directly related to respiratory electron transport, like nucleoside kinases, acyl-carrier proteins or carbonic anhydrases. We speculate that further enzyme activities might be bound to this micro-location in other groups of organisms.
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Affiliation(s)
- Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
| | - Michael Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
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Han X, Sun N, Xu M, Mi H. Co-ordination of NDH and Cup proteins in CO2 uptake in cyanobacterium Synechocystis sp. PCC 6803. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3869-3877. [PMID: 28911053 PMCID: PMC5853218 DOI: 10.1093/jxb/erx129] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/30/2017] [Indexed: 05/24/2023]
Abstract
High and low affinity CO2-uptake systems containing CupA (NDH-1MS) and CupB (NDH-1MS'), respectively, have been identified in Synechocystis sp. PCC 6803, but it is yet unknown how the complexes function in CO2 uptake. In this work, we found that deletion of cupB significantly lowered the growth of cells, and deletion of both cupA and cupB seriously suppressed the growth below pH 7.0 even under 3% CO2. The rate of photosynthetic oxygen evolution was decreased slightly by deletion of cupA but significantly by deletion of cupB and more severely by deletion of both cupA and cupB, especially in response to changed pH conditions under 3% CO2. Furthermore, we found that assembly of CupB into NDH-1MS' was dependent on NdhD4 and NdhF4. NDH-1MS' was not affected in the NDH-1MS-degradation mutant and NDH-1MS was not affected in the NDH-1MS'-degradation mutants, indicating the existence of independent CO2-uptake systems under high CO2 conditions. The light-induced proton gradient across thylakoid membranes was significantly inhibited in ndhD-deletion mutants, suggesting that NdhDs functions in proton pumping. The carbonic anhydrase activity was suppressed partly in the cupA- or cupB-deletion mutant but severely in the mutant with both cupA and cupB deletion, indicating that CupA and CupB function in conversion of CO2 to HCO3-. In turn, deletion of cup genes lowered the transthylakoid membrane proton gradient and deletion of ndhDs decreased the CO2 hydration. Our results suggest that NDH-1M provides an alkaline region to activate Cup proteins involved in CO2 uptake.
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Affiliation(s)
- Xunling Han
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Nan Sun
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Xu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Hualing Mi
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, China
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Senkler J, Senkler M, Eubel H, Hildebrandt T, Lengwenus C, Schertl P, Schwarzländer M, Wagner S, Wittig I, Braun HP. The mitochondrial complexome of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1079-1092. [PMID: 27943495 DOI: 10.1111/tpj.13448] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/25/2016] [Accepted: 12/02/2016] [Indexed: 05/19/2023]
Abstract
Mitochondria are central to cellular metabolism and energy conversion. In plants they also enable photosynthesis through additional components and functional flexibility. A majority of those processes relies on the assembly of individual proteins to larger protein complexes, some of which operate as large molecular machines. There has been a strong interest in the makeup and function of mitochondrial protein complexes and protein-protein interactions in plants, but the experimental approaches used typically suffer from selectivity or bias. Here, we present a complexome profiling analysis for leaf mitochondria of the model plant Arabidopsis thaliana for the systematic characterization of protein assemblies. Purified organelle extracts were separated by 1D Blue native (BN) PAGE, a resulting gel lane was dissected into 70 slices (complexome fractions) and proteins in each slice were identified by label free quantitative shot-gun proteomics. Overall, 1359 unique proteins were identified, which were, on average, present in 17 complexome fractions each. Quantitative profiles of proteins along the BN gel lane were aligned by similarity, allowing us to visualize protein assemblies. The data allow re-annotating the subunit compositions of OXPHOS complexes, identifying assembly intermediates of OXPHOS complexes and assemblies of alternative respiratory oxidoreductases. Several protein complexes were discovered that have not yet been reported in plants, such as a 530 kDa Tat complex, 460 and 1000 kDa SAM complexes, a calcium ion uniporter complex (150 kDa) and several PPR protein complexes. We have set up a tailored online resource (https://complexomemap.de/at_mito_leaves) to deposit the data and to allow straightforward access and custom data analyses.
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Affiliation(s)
- Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Michael Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Tatjana Hildebrandt
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Christian Lengwenus
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Peter Schertl
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Markus Schwarzländer
- Plant Energy Biology Lab, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, Bonn, 53113, Germany
| | - Stephan Wagner
- Plant Energy Biology Lab, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, Bonn, 53113, Germany
| | - Ilka Wittig
- Functional Proteomics, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt, 60590, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover, 30419, Germany
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Floryszak-Wieczorek J, Arasimowicz-Jelonek M. The multifunctional face of plant carbonic anhydrase. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 112:362-368. [PMID: 28152407 DOI: 10.1016/j.plaphy.2017.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 06/06/2023]
Abstract
Although most studies on the ubiquitous enzyme carbonic anhydrase (CA) have indicated its significant role in plants to facilitate the diffusion of CO2 to the site of inorganic carbon fixation, it is becoming increasingly likely that carbonic anhydrase isoforms also have diverse unexplored functions in plant cells. This review lays emphasis on additional roles of CA associated with many physiological, biochemical and structural changes in plant metabolism. The presented findings have revealed essential functions of CA isoforms in plant adjustment to both abiotic and biotic agents and developmental stimuli. However, sometimes it is difficult to separate the non-photosynthetic from the photosynthetic-related role of CAs during post-stress impaired metabolism, and the preventive CA outcome might be due to the effect of these enzymes on improvement of photosynthetic capacity. Finally, taking into account the experimental evidence, the direct and indirect functional roles of CAs in mitigating negative effects of environmental conditions are presented.
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20
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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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21
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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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Fromm S, Braun HP, Peterhansel C. Mitochondrial gamma carbonic anhydrases are required for complex I assembly and plant reproductive development. THE NEW PHYTOLOGIST 2016; 211:194-207. [PMID: 26889912 DOI: 10.1111/nph.13886] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/04/2016] [Indexed: 05/23/2023]
Abstract
Complex I of the mitochondrial electron transport chain (mETC) in plants contains an extra domain that is made up from proteins homologous to prokaryotic gamma-carbonic anhydrases (γCA). This domain has been suggested to participate in complex I assembly or to support transport of mitochondrial CO2 to the chloroplast. Here, we generated mutants lacking CA1 and CA2 - two out of three CA proteins in Arabidopsis thaliana. Double mutants were characterized at the developmental and physiological levels. Furthermore, the composition and activity of the mETC were determined, and mutated CA versions were used for complementation assays. Embryo development of double mutants was strongly delayed and seed development stopped before maturation. Mutant plants could only be rescued on sucrose media, showed severe stress symptoms and never produced viable seeds. By contrast, callus cultures were only slightly affected in growth. Complex I was undetectable in the double mutants, but complex II and complex IV were upregulated concomitant with increased oxygen consumption in mitochondrial respiration. Ectopic expression of inactive CA variants was sufficient to complement the mutant phenotype. Data indicate that CA proteins are structurally required for complex I assembly and that reproductive development is dependent on the presence of complex I.
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Affiliation(s)
- Steffanie Fromm
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
- Institute of Botany, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
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Shikanai T. Chloroplast NDH: A different enzyme with a structure similar to that of respiratory NADH dehydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1015-22. [DOI: 10.1016/j.bbabio.2015.10.013] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/21/2015] [Accepted: 10/26/2015] [Indexed: 11/28/2022]
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Fromm S, Senkler J, Zabaleta E, Peterhänsel C, Braun HP. The carbonic anhydrase domain of plant mitochondrial complex I. PHYSIOLOGIA PLANTARUM 2016; 157:289-296. [PMID: 26829901 DOI: 10.1111/ppl.12424] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/06/2015] [Accepted: 12/15/2015] [Indexed: 06/05/2023]
Abstract
The mitochondrial NADH dehydrogenase complex (complex I) consists of several functional domains which independently arose during evolution. In higher plants, it contains an additional domain which includes proteins resembling gamma-type carbonic anhydrases. The Arabidopsis genome codes for five complex I-integrated gamma-type carbonic anhydrases (γCA1, γCA2, γCA3, γCAL1, γCAL2), but only three copies of this group of proteins form an individual extra domain. Biochemical analyses revealed that the domain is composed of one copy of either γCAL1 or γCAL2 plus two copies of the γCA1/γCA2 proteins. Thus, the carbonic anhydrase domain can have six distinct subunit configurations. Single and double mutants with respect to the γCA/γCAL proteins were employed to genetically dissect the function of the domain. New insights into complex I biology in plants will be reviewed and discussed.
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Affiliation(s)
- Steffanie Fromm
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
- Institut für Botanik, Leibniz Universität Hannover, Hannover, 30419, Germany
| | - Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas IIB, CONICET, National University of Mar del Plata, Mar del Plata, 7600, Argentina
| | | | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
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25
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Fromm S, Senkler J, Eubel H, Peterhänsel C, Braun HP. Life without complex I: proteome analyses of an Arabidopsis mutant lacking the mitochondrial NADH dehydrogenase complex. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3079-93. [PMID: 27122571 PMCID: PMC4867900 DOI: 10.1093/jxb/erw165] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The mitochondrial NADH dehydrogenase complex (complex I) is of particular importance for the respiratory chain in mitochondria. It is the major electron entry site for the mitochondrial electron transport chain (mETC) and therefore of great significance for mitochondrial ATP generation. We recently described an Arabidopsis thaliana double-mutant lacking the genes encoding the carbonic anhydrases CA1 and CA2, which both form part of a plant-specific 'carbonic anhydrase domain' of mitochondrial complex I. The mutant lacks complex I completely. Here we report extended analyses for systematically characterizing the proteome of the ca1ca2 mutant. Using various proteomic tools, we show that lack of complex I causes reorganization of the cellular respiration system. Reduced electron entry into the respiratory chain at the first segment of the mETC leads to induction of complexes II and IV as well as alternative oxidase. Increased electron entry at later segments of the mETC requires an increase in oxidation of organic substrates. This is reflected by higher abundance of proteins involved in glycolysis, the tricarboxylic acid cycle and branched-chain amino acid catabolism. Proteins involved in the light reaction of photosynthesis, the Calvin cycle, tetrapyrrole biosynthesis, and photorespiration are clearly reduced, contributing to the significant delay in growth and development of the double-mutant. Finally, enzymes involved in defense against reactive oxygen species and stress symptoms are much induced. These together with previously reported insights into the function of plant complex I, which were obtained by analysing other complex I mutants, are integrated in order to comprehensively describe 'life without complex I'.
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Affiliation(s)
- Steffanie Fromm
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany Institut für Botanik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Christoph Peterhänsel
- Institut für Botanik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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Córdoba JP, Marchetti F, Soto D, Martin MV, Pagnussat GC, Zabaleta E. The CA domain of the respiratory complex I is required for normal embryogenesis in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1589-603. [PMID: 26721503 PMCID: PMC5854192 DOI: 10.1093/jxb/erv556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/10/2015] [Indexed: 05/04/2023]
Abstract
The NADH-ubiquinone oxidoreductase [complex I (CI), EC 1.6.5.3] of the mitochondrial respiratory chain is the principal entry point of electrons, and vital in maintaining metabolism and the redox balance. In a variety of eukaryotic organisms, except animal and fungi (Opisthokonta), it contains an extra domain composed of putative gamma carbonic anhydrases subunits, named the CA domain, which was proposed to be essential for complex I assembly. There are two kinds of carbonic anhydrase subunits: CAs (of which there are three) and carbonic anhydrase-like proteins (CALs) (of which there are two). In plants, the CA domain has been linked to photorespiration. In this work, we report that Arabidopsis mutant plants affected in two specific CA subunits show a lethal phenotype. Double homozygous knockouts ca1ca2 embryos show a significant developmental delay compared to the non-homozygous embryos, which show a wild-type (WT) phenotype in the same silique. Mutant embryos show impaired mitochondrial membrane potential and mitochondrial reactive oxygen species (ROS) accumulation. The characteristic embryo greening does not take place and fewer but larger oil bodies are present. Although seeds look dark brown and wrinkled, they are able to germinate 12 d later than WT seeds. However, they die immediately, most likely due to oxidative stress.Since the CA domain is required for complex I biogenesis, it is predicted that in ca1ca2 mutants no complex I could be formed, triggering the lethal phenotype. The in vivo composition of a functional CA domain is proposed.
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Affiliation(s)
- Juan Pablo Córdoba
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - Fernanda Marchetti
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - Débora Soto
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - María Victoria Martin
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - Gabriela Carolina Pagnussat
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas IIB-CONICET-UNMdP, Funes 3250 3er nivel 7600 Mar del Plata, Argentina Received 6 October 2015; Revised 24 November 2015; Accepted 10 December 2015
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Subrahmanian N, Remacle C, Hamel PP. Plant mitochondrial Complex I composition and assembly: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1001-14. [PMID: 26801215 DOI: 10.1016/j.bbabio.2016.01.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/18/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
In the mitochondrial inner membrane, oxidative phosphorylation generates ATP via the operation of several multimeric enzymes. The proton-pumping Complex I (NADH:ubiquinone oxidoreductase) is the first and most complicated enzyme required in this process. Complex I is an L-shaped enzyme consisting of more than 40 subunits, one FMN molecule and eight Fe-S clusters. In recent years, genetic and proteomic analyses of Complex I mutants in various model systems, including plants, have provided valuable insights into the assembly of this multimeric enzyme. Assisted by a number of key players, referred to as "assembly factors", the assembly of Complex I takes place in a sequential and modular manner. Although a number of factors have been identified, their precise function in mediating Complex I assembly still remains to be elucidated. This review summarizes our current knowledge of plant Complex I composition and assembly derived from studies in plant model systems such as Arabidopsis thaliana and Chlamydomonas reinhardtii. Plant Complex I is highly conserved and comprises a significant number of subunits also present in mammalian and fungal Complexes I. Plant Complex I also contains additional subunits absent from the mammalian and fungal counterpart, whose function in enzyme activity and assembly is not clearly understood. While 14 assembly factors have been identified for human Complex I, only two proteins, namely GLDH and INDH, have been established as bona fide assembly factors for plant Complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Nitya Subrahmanian
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Claire Remacle
- Institute of Botany, Department of Life Sciences, University of Liège, 4000 Liège, Belgium
| | - Patrice Paul Hamel
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA; The Ohio State University, Department of Biological Chemistry and Pharmacology, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA.
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Fromm S, Göing J, Lorenz C, Peterhänsel C, Braun HP. Depletion of the "gamma-type carbonic anhydrase-like" subunits of complex I affects central mitochondrial metabolism in Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:60-71. [PMID: 26482706 DOI: 10.1016/j.bbabio.2015.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/06/2015] [Accepted: 10/15/2015] [Indexed: 11/18/2022]
Abstract
"Gamma-type carbonic anhydrase-like" (CAL) proteins form part of complex I in plants. Together with "gamma carbonic anhydrase" (CA) proteins they form an extra domain which is attached to the membrane arm of complex I on its matrix exposed side. In Arabidopsis two CAL and three CA proteins are present, termed CAL1, CAL2, CA1, CA2 and CA3. It has been proposed that the carbonic anhydrase domain of complex I is involved in a process mediating efficient recycling of mitochondrial CO2 for photosynthetic carbon fixation which is especially important during growth conditions causing increased photorespiration. Depletion of CAL proteins has been shown to significantly affect plant development and photomorphogenesis. To better understand CAL function in plants we here investigated effects of CAL depletion on the mitochondrial compartment. In mutant lines and cell cultures complex I amount was reduced by 90-95% but levels of complexes III and V were unchanged. At the same time, some of the CA transcripts were less abundant. Proteome analysis of CAL depleted cells revealed significant reduction of complex I subunits as well as proteins associated with photorespiration, but increased amounts of proteins participating in amino acid catabolism and stress response reactions. Developmental delay of the mutants was slightly alleviated if plants were cultivated at high CO2. Profiling of selected metabolites revealed defined changes in intermediates of the citric acid cycle and amino acid catabolism. It is concluded that CAL proteins are essential for complex I assembly and that CAL depletion specifically affects central mitochondrial metabolism.
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Affiliation(s)
- Steffanie Fromm
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; Institut für Botanik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Jennifer Göing
- Institut für Botanik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Christin Lorenz
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Christoph Peterhänsel
- Institut für Botanik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
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Soto D, Córdoba JP, Villarreal F, Bartoli C, Schmitz J, Maurino VG, Braun HP, Pagnussat GC, Zabaleta E. Functional characterization of mutants affected in the carbonic anhydrase domain of the respiratory complex I in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:831-844. [PMID: 26148112 DOI: 10.1111/tpj.12930] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 06/04/2023]
Abstract
The NADH-ubiquinone oxidoreductase complex (complex I) (EC 1.6.5.3) is the main entrance site of electrons into the respiratory chain. In a variety of eukaryotic organisms, except animals and fungi (Opisthokonta), it contains an extra domain comprising trimers of putative γ-carbonic anhydrases, named the CA domain, which has been proposed to be essential for assembly of complex I. However, its physiological role in plants is not fully understood. Here, we report that Arabidopsis mutants defective in two CA subunits show an altered photorespiratory phenotype. Mutants grown in ambient air show growth retardation compared to wild-type plants, a feature that is reversed by cultivating plants in a high-CO2 atmosphere. Moreover, under photorespiratory conditions, carbon assimilation is diminished and glycine accumulates, suggesting an imbalance with respect to photorespiration. Additionally, transcript levels of specific CA subunits are reduced in plants grown under non-photorespiratory conditions. Taken together, these results suggest that the CA domain of plant complex I contributes to sustaining efficient photosynthesis under ambient (photorespiratory) conditions.
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Affiliation(s)
- Débora Soto
- Instituto de Investigaciones Biológicas IIB/CONICET, Universidad Nacional de Mar del Plata, cc 1245, 7600, Mar del Plata, Argentina
| | - Juan Pablo Córdoba
- Instituto de Investigaciones Biológicas IIB/CONICET, Universidad Nacional de Mar del Plata, cc 1245, 7600, Mar del Plata, Argentina
| | - Fernando Villarreal
- Instituto de Investigaciones Biológicas IIB/CONICET, Universidad Nacional de Mar del Plata, cc 1245, 7600, Mar del Plata, Argentina
| | - Carlos Bartoli
- Instituto de Fisiología Vegetal, Universidad Nacional de La Plata/CONICET La Plata, cc 327, 1900, La Plata, Argentina
| | - Jessica Schmitz
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Cluster of Excellence on Plant Sciences, Heinrich Heine Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Veronica G Maurino
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Cluster of Excellence on Plant Sciences, Heinrich Heine Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hans Peter Braun
- Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuserstraße 2, D-30419, Hannover, Germany
| | - Gabriela C Pagnussat
- Instituto de Investigaciones Biológicas IIB/CONICET, Universidad Nacional de Mar del Plata, cc 1245, 7600, Mar del Plata, Argentina
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas IIB/CONICET, Universidad Nacional de Mar del Plata, cc 1245, 7600, Mar del Plata, Argentina
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30
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Carrie C, Venne AS, Zahedi RP, Soll J. Identification of cleavage sites and substrate proteins for two mitochondrial intermediate peptidases in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2691-708. [PMID: 25732537 PMCID: PMC4986872 DOI: 10.1093/jxb/erv064] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Most mitochondrial proteins contain an N-terminal targeting signal that is removed by specific proteases following import. In plant mitochondria, only mitochondrial processing peptidase (MPP) has been characterized to date. Therefore, we sought to determine the substrates and cleavage sites of the Arabidopsis thaliana homologues to the yeast Icp55 and Oct1 proteins, using the newly developed ChaFRADIC method for N-terminal protein sequencing. We identified 88 and seven putative substrates for Arabidopsis ICP55 and OCT1, respectively. It was determined that the Arabidopsis ICP55 contains an almost identical cleavage site to that of Icp55 from yeast. However, it can also remove a far greater range of amino acids. The OCT1 substrates from Arabidopsis displayed no consensus cleavage motif, and do not contain the classical -10R motif identified in other eukaryotes. Arabidopsis OCT1 can also cleave presequences independently, without the prior cleavage of MPP. It was concluded that while both OCT1 and ICP55 were probably acquired early on in the evolution of mitochondria, their substrate profiles and cleavage sites have either remained very similar or diverged completely.
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Affiliation(s)
- Chris Carrie
- Department of Biology I, Botany, Ludwig-Maximilians Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany
| | - A Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 11, D-44139 Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 11, D-44139 Dortmund, Germany
| | - Jürgen Soll
- Department of Biology I, Botany, Ludwig-Maximilians Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany Munich Centre for Integrated Protein Science, CiPSM, Ludwig-Maximilians Universität München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany
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31
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Abstract
The protein content of plant cells is constantly being updated. This process is driven by the opposing actions of protein degradation, which defines the half-life of each polypeptide, and protein synthesis. Our understanding of the processes that regulate protein synthesis and degradation in plants has advanced significantly over the past decade. Post-transcriptional modifications that influence features of the mRNA populations, such as poly(A) tail length and secondary structure, contribute to the regulation of protein synthesis. Post-translational modifications such as phosphorylation, ubiquitination and non-enzymatic processes such as nitrosylation and carbonylation, govern the rate of degradation. Regulators such as the plant TOR kinase, and effectors such as the E3 ligases, allow plants to balance protein synthesis and degradation under developmental and environmental change. Establishing an integrated understanding of the processes that underpin changes in protein abundance under various physiological and developmental scenarios will accelerate our ability to model and rationally engineer plants.
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Affiliation(s)
- Clark J Nelson
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Hwy, Crawley 6009, Perth, Western Australia, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Hwy, Crawley 6009, Perth, Western Australia, Australia
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32
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Murcha MW, Kmiec B, Kubiszewski-Jakubiak S, Teixeira PF, Glaser E, Whelan J. Protein import into plant mitochondria: signals, machinery, processing, and regulation. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6301-35. [PMID: 25324401 DOI: 10.1093/jxb/eru399] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The majority of more than 1000 proteins present in mitochondria are imported from nuclear-encoded, cytosolically synthesized precursor proteins. This impressive feat of transport and sorting is achieved by the combined action of targeting signals on mitochondrial proteins and the mitochondrial protein import apparatus. The mitochondrial protein import apparatus is composed of a number of multi-subunit protein complexes that recognize, translocate, and assemble mitochondrial proteins into functional complexes. While the core subunits involved in mitochondrial protein import are well conserved across wide phylogenetic gaps, the accessory subunits of these complexes differ in identity and/or function when plants are compared with Saccharomyces cerevisiae (yeast), the model system for mitochondrial protein import. These differences include distinct protein import receptors in plants, different mechanistic operation of the intermembrane protein import system, the location and activity of peptidases, the function of inner-membrane translocases in linking the outer and inner membrane, and the association/regulation of mitochondrial protein import complexes with components of the respiratory chain. Additionally, plant mitochondria share proteins with plastids, i.e. dual-targeted proteins. Also, the developmental and cell-specific nature of mitochondrial biogenesis is an aspect not observed in single-celled systems that is readily apparent in studies in plants. This means that plants provide a valuable model system to study the various regulatory processes associated with protein import and mitochondrial biogenesis.
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Affiliation(s)
- Monika W Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Beata Kmiec
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden
| | - Szymon Kubiszewski-Jakubiak
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Pedro F Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden
| | - Elzbieta Glaser
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, Victoria, 3086, Australia
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Nelson CJ, Alexova R, Jacoby RP, Millar AH. Proteins with high turnover rate in barley leaves estimated by proteome analysis combined with in planta isotope labeling. PLANT PHYSIOLOGY 2014; 166:91-108. [PMID: 25082890 PMCID: PMC4149734 DOI: 10.1104/pp.114.243014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein turnover is a key component in cellular homeostasis; however, there is little quantitative information on degradation kinetics for individual plant proteins. We have used (15)N labeling of barley (Hordeum vulgare) plants and gas chromatography-mass spectrometry analysis of free amino acids and liquid chromatography-mass spectrometry analysis of proteins to track the enrichment of (15)N into the amino acid pools in barley leaves and then into tryptic peptides derived from newly synthesized proteins. Using information on the rate of growth of barley leaves combined with the rate of degradation of (14)N-labeled proteins, we calculate the turnover rates of 508 different proteins in barley and show that they vary by more than 100-fold. There was approximately a 9-h lag from label application until (15)N incorporation could be reliably quantified in extracted peptides. Using this information and assuming constant translation rates for proteins during the time course, we were able to quantify degradation rates for several proteins that exhibit half-lives on the order of hours. Our workflow, involving a stringent series of mass spectrometry filtering steps, demonstrates that (15)N labeling can be used for large-scale liquid chromatography-mass spectrometry studies of protein turnover in plants. We identify a series of abundant proteins in photosynthesis, photorespiration, and specific subunits of chlorophyll biosynthesis that turn over significantly more rapidly than the average protein involved in these processes. We also highlight a series of proteins that turn over as rapidly as the well-known D1 subunit of photosystem II. While these proteins need further verification for rapid degradation in vivo, they cluster in chlorophyll and thiamine biosynthesis.
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Affiliation(s)
- 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, Perth, Western Australia 6009, Australia
| | - Ralitza Alexova
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Richard P Jacoby
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, 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, Perth, Western Australia 6009, Australia
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Stitt M, Gibon Y. Why measure enzyme activities in the era of systems biology? TRENDS IN PLANT SCIENCE 2014; 19:256-65. [PMID: 24332227 DOI: 10.1016/j.tplants.2013.11.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/05/2013] [Accepted: 11/08/2013] [Indexed: 05/22/2023]
Abstract
Information about the abundance and biological activities of proteins is essential to reveal how genes affect phenotypes. Over the past decade, mass spectrometry (MS)-based proteomics has revolutionized the identification and quantification of proteins, and the detection of post-translational modifications. Interpretation of proteomics data depends on information about the biological activities of proteins, which has created a bottleneck in research. This review focuses on enzymes in central metabolism. We examine the methods used for measuring enzyme activities, and discuss how these methods provide information about the kinetic and regulatory properties of enzymes, their turnover, and how this information can be integrated into metabolic models. We also discuss how robotized assays could enable the genetic networks that control enzyme abundance to be analyzed.
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Affiliation(s)
- Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Yves Gibon
- INRA, University of Bordeaux, UMR 1332 Fruit Biology and Pathology, F-33883 Villenave d'Ornon, France
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35
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Gehl B, Lee CP, Bota P, Blatt MR, Sweetlove LJ. An Arabidopsis stomatin-like protein affects mitochondrial respiratory supercomplex organization. PLANT PHYSIOLOGY 2014; 164:1389-400. [PMID: 24424325 PMCID: PMC3938628 DOI: 10.1104/pp.113.230383] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Stomatins belong to the band-7 protein family, a diverse group of conserved eukaryotic and prokaryotic membrane proteins involved in the formation of large protein complexes as protein-lipid scaffolds. The Arabidopsis (Arabidopsis thaliana) genome contains two paralogous genes encoding stomatin-like proteins (SLPs; AtSLP1 and AtSLP2) that are phylogenetically related to human SLP2, a protein involved in mitochondrial fusion and protein complex formation in the mitochondrial inner membrane. We used reverse genetics in combination with biochemical methods to investigate the function of AtSLPs. We demonstrate that both SLPs localize to mitochondrial membranes. SLP1 migrates as a large (approximately 3 MDa) complex in blue-native gel electrophoresis. Remarkably, slp1 knockout mutants have reduced protein and activity levels of complex I and supercomplexes, indicating that SLP affects the assembly and/or stability of these complexes. These findings point to a role for SLP1 in the organization of respiratory supercomplexes in Arabidopsis.
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36
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Braun HP, Binder S, Brennicke A, Eubel H, Fernie AR, Finkemeier I, Klodmann J, König AC, Kühn K, Meyer E, Obata T, Schwarzländer M, Takenaka M, Zehrmann A. The life of plant mitochondrial complex I. Mitochondrion 2014; 19 Pt B:295-313. [PMID: 24561573 DOI: 10.1016/j.mito.2014.02.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/28/2014] [Accepted: 02/12/2014] [Indexed: 12/29/2022]
Abstract
The mitochondrial NADH dehydrogenase complex (complex I) of the respiratory chain has several remarkable features in plants: (i) particularly many of its subunits are encoded by the mitochondrial genome, (ii) its mitochondrial transcripts undergo extensive maturation processes (e.g. RNA editing, trans-splicing), (iii) its assembly follows unique routes, (iv) it includes an additional functional domain which contains carbonic anhydrases and (v) it is, indirectly, involved in photosynthesis. Comprising about 50 distinct protein subunits, complex I of plants is very large. However, an even larger number of proteins are required to synthesize these subunits and assemble the enzyme complex. This review aims to follow the complete "life cycle" of plant complex I from various molecular perspectives. We provide arguments that complex I represents an ideal model system for studying the interplay of respiration and photosynthesis, the cooperation of mitochondria and the nucleus during organelle biogenesis and the evolution of the mitochondrial oxidative phosphorylation system.
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Affiliation(s)
- Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Stefan Binder
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Axel Brennicke
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Iris Finkemeier
- Plant Sciences, Ludwig Maximilians Universität München, Grosshadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Jennifer Klodmann
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Ann-Christine König
- Plant Sciences, Ludwig Maximilians Universität München, Grosshadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Kristina Kühn
- Institut für Biologie/Molekulare Zellbiologie der Pflanzen, Humboldt Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Etienne Meyer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Markus Schwarzländer
- INRES - Chemical Signalling, Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
| | - Mizuki Takenaka
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Anja Zehrmann
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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37
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Wydro MM, Sharma P, Foster JM, Bych K, Meyer EH, Balk J. The evolutionarily conserved iron-sulfur protein INDH is required for complex I assembly and mitochondrial translation in Arabidopsis [corrected]. THE PLANT CELL 2013; 25:4014-27. [PMID: 24179128 PMCID: PMC3877808 DOI: 10.1105/tpc.113.117283] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The assembly of respiratory complexes is a multistep process, requiring coordinate expression of mitochondrial and nuclear genes and cofactor biosynthesis. We functionally characterized the iron-sulfur protein required for NADH dehydrogenase (INDH) in the model plant Arabidopsis thaliana. An indh knockout mutant lacked complex I but had low levels of a 650-kD assembly intermediate, similar to mutations in the homologous NUBPL (nucleotide binding protein-like) in Homo sapiens. However, heterozygous indh/+ mutants displayed unusual phenotypes during gametogenesis and resembled mutants in mitochondrial translation more than mutants in complex I. Gradually increased expression of INDH in indh knockout plants revealed a significant delay in reassembly of complex I, suggesting an indirect role for INDH in the assembly process. Depletion of INDH protein was associated with decreased (35)S-Met labeling of translation products in isolated mitochondria, whereas the steady state levels of several mitochondrial transcripts were increased. Mitochondrially encoded proteins were differentially affected, with near normal levels of cytochrome c oxidase subunit2 and Nad7 but little Nad6 protein in the indh mutant. These data suggest that INDH has a primary role in mitochondrial translation that underlies its role in complex I assembly.
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Affiliation(s)
- Mateusz M. Wydro
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Pia Sharma
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Jonathan M. Foster
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Katrine Bych
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Etienne H. Meyer
- Max Planck Institute for Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Janneke Balk
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
- Address correspondence to
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Nelson CJ, Li L, Jacoby RP, Millar AH. Degradation Rate of Mitochondrial Proteins in Arabidopsis thaliana Cells. J Proteome Res 2013; 12:3449-59. [DOI: 10.1021/pr400304r] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Clark J. Nelson
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Richard P. Jacoby
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
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Peters K, Belt K, Braun HP. 3D Gel Map of Arabidopsis Complex I. FRONTIERS IN PLANT SCIENCE 2013; 4:153. [PMID: 23761796 PMCID: PMC3671202 DOI: 10.3389/fpls.2013.00153] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 05/04/2013] [Indexed: 05/20/2023]
Abstract
Complex I has a unique structure in plants and includes extra subunits. Here, we present a novel study to define its protein constituents. Mitochondria were isolated from Arabidopsis thaliana cell cultures, leaves, and roots. Subunits of complex I were resolved by 3D blue-native (BN)/SDS/SDS-PAGE and identified by mass spectrometry. Overall, 55 distinct proteins were found, seven of which occur in pairs of isoforms. We present evidence that Arabidopsis complex I consists of 49 distinct types of subunits, 40 of which represent homologs of bovine complex I. The nine other subunits represent special proteins absent in the animal linage of eukaryotes, most prominently a group of subunits related to bacterial gamma-type carbonic anhydrases. A GelMap http://www.gelmap.de/arabidopsis-3d-complex-i/ is presented for promoting future complex I research in Arabidopsis thaliana.
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Affiliation(s)
- Katrin Peters
- Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, Hannover, Germany
| | - Katharina Belt
- Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, Hannover, Germany
| | - Hans-Peter Braun
- Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, Hannover, Germany
- *Correspondence: Hans-Peter Braun, Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany e-mail:
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