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Chen B, Wang J, Huang M, Gui Y, Wei Q, Wang L, Tan BC. C1-FDX is required for the assembly of mitochondrial complex I and subcomplexes of complex V in Arabidopsis. PLoS Genet 2024; 20:e1011419. [PMID: 39356718 PMCID: PMC11446459 DOI: 10.1371/journal.pgen.1011419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 09/05/2024] [Indexed: 10/04/2024] Open
Abstract
C1-FDX (Complex I-ferredoxin) has been defined as a component of CI in a ferredoxin bridge in Arabidopsis mitochondria. However, its full function remains to be addressed. We created two c1-fdx mutants in Arabidopsis using the CRISPR-Cas9 methodology. The mutants show delayed seed germination. Over-expression of C1-FDX rescues the phenotype. Molecular analyses showed that loss of the C1-FDX function decreases the abundance and activity of both CI and subcomplexes of CV. In contrast, the over-expression of C1-FDX-GFP enhances the CI* (a sub-complex of CI) and CV assembly. Immunodetection reveals that the stoichiometric ratio of the α:β subunits in the F1 module of CV is altered in the c1-fdx mutant. In the complemented mutants, C1-FDX-GFP was found to be associated with the F' and α/β sub-complexes of CV. Protein interaction assays showed that C1-FDX could interact with the β, γ, δ, and ε subunits of the F1 module, indicating that C1-FDX, a structural component of CI, also functions as an assembly factor in the assembly of F' and α/β sub-complexes of CV. These results reveal a new role of C1-FDX in the CI and CV assembly and seed germination in Arabidopsis.
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Affiliation(s)
- Baoyin Chen
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai’an, China
| | - Junjun Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Manna Huang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yuanye Gui
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Qingqing Wei
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Le Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
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2
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Zhang X, Ding Z, Lou H, Han R, Ma C, Yang S. A Systematic Review and Developmental Perspective on Origin of CMS Genes in Crops. Int J Mol Sci 2024; 25:8372. [PMID: 39125940 PMCID: PMC11312923 DOI: 10.3390/ijms25158372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Cytoplasmic male sterility (CMS) arises from the incompatibility between the nucleus and cytoplasm as typical representatives of the chimeric structures in the mitochondrial genome (mitogenome), which has been extensively applied for hybrid seed production in various crops. The frequent occurrence of chimeric mitochondrial genes leading to CMS is consistent with the mitochondrial DNA (mtDNA) evolution. The sequence conservation resulting from faithfully maternal inheritance and the chimeric structure caused by frequent sequence recombination have been defined as two major features of the mitogenome. However, when and how these chimeric mitochondrial genes appear in the context of the highly conserved reproduction of mitochondria is an enigma. This review, therefore, presents the critical view of the research on CMS in plants to elucidate the mechanisms of this phenomenon. Generally, distant hybridization is the main mechanism to generate an original CMS source in natural populations and in breeding. Mitochondria and mitogenomes show pleomorphic and dynamic changes at key stages of the life cycle. The promitochondria in dry seeds develop into fully functioning mitochondria during seed imbibition, followed by massive mitochondria or mitogenome fusion and fission in the germination stage along with changes in the mtDNA structure and quantity. The mitogenome stability is controlled by nuclear loci, such as the nuclear gene Msh1. Its suppression leads to the rearrangement of mtDNA and the production of heritable CMS genes. An abundant recombination of mtDNA is also often found in distant hybrids and somatic/cybrid hybrids. Since mtDNA recombination is ubiquitous in distant hybridization, we put forward a hypothesis that the original CMS genes originated from mtDNA recombination during the germination of the hybrid seeds produced from distant hybridizations to solve the nucleo-cytoplasmic incompatibility resulting from the allogenic nuclear genome during seed germination.
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Affiliation(s)
- Xuemei Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China;
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Z.D.); (H.L.)
| | - Zhengpin Ding
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Z.D.); (H.L.)
| | - Hongbo Lou
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Z.D.); (H.L.)
| | - Rui Han
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Cunqiang Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Shengchao Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China;
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3
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Ji J, Lin S, Xin X, Li Y, He J, Xu X, Zhao Y, Su G, Lu X, Yin G. Effects of OsAOX1a Deficiency on Mitochondrial Metabolism at Critical Node of Seed Viability in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2284. [PMID: 37375909 DOI: 10.3390/plants12122284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/29/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Mitochondrial alternative oxidase 1a (AOX1a) plays an extremely important role in the critical node of seed viability during storage. However, the regulatory mechanism is still poorly understood. The aim of this study was to identify the regulatory mechanisms by comparing OsAOX1a-RNAi and wild-type (WT) rice seed during artificial aging treatment. Weight gain and time for the seed germination percentage decreased to 50% (P50) in OsAOX1a-RNAi rice seed, indicating possible impairment in seed development and storability. Compared to WT seeds at 100%, 90%, 80%, and 70% germination, the NADH- and succinate-dependent O2 consumption, the activity of mitochondrial malate dehydrogenase, and ATP contents all decreased in the OsAOX1a-RNAi seeds, indicating that mitochondrial status in the OsAOX1a-RNAi seeds after imbibition was weaker than in the WT seeds. In addition, the reduction in the abundance of Complex I subunits showed that the capacity of the mitochondrial electron transfer chain was significantly inhibited in the OsAOX1a-RNAi seeds at the critical node of seed viability. The results indicate that ATP production was impaired in the OsAOX1a-RNAi seeds during aging. Therefore, we conclude that mitochondrial metabolism and alternative pathways were severely inhibited in the OsAOX1a-RNAi seeds at critical node of viability, which could accelerate the collapse of seed viability. The precise regulatory mechanism of the alternative pathway at the critical node of viability needs to be further analyzed. This finding might provide the basis for developing monitoring and warning indicators when seed viability declines to the critical node during storage.
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Affiliation(s)
- Jing Ji
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuangshuang Lin
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Xia Xin
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Li
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Juanjuan He
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinyue Xu
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yunxia Zhao
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gefei Su
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Biological Science, China Agricultural University, Beijing 100193, China
| | - Xinxiong Lu
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangkun Yin
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Best C, Mizrahi R, Edris R, Tang H, Zer H, Colas des Francs-Small C, Finkel OM, Zhu H, Small ID, Ostersetzer-Biran O. MSP1 encodes an essential RNA-binding pentatricopeptide repeat factor required for nad1 maturation and complex I biogenesis in Arabidopsis mitochondria. THE NEW PHYTOLOGIST 2023; 238:2375-2392. [PMID: 36922396 DOI: 10.1111/nph.18880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/23/2023] [Indexed: 05/19/2023]
Abstract
Mitochondrial biogenesis relies on nuclearly encoded factors, which regulate the expression of the organellar-encoded genes. Pentatricopeptide repeat (PPR) proteins constitute a major gene family in angiosperms that are pivotal in many aspects of mitochondrial (mt)RNA metabolism (e.g. trimming, splicing, or stability). Here, we report the analysis of MITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1 (MSP1, At4g20090), a canonical PPR protein that is necessary for mitochondrial functions and embryo development. Loss-of-function allele of MSP1 leads to seed abortion. Here, we employed an embryo-rescue method for the molecular characterization of msp1 mutants. Our analyses reveal that msp1 embryogenesis fails to proceed beyond the heart/torpedo stage as a consequence of a nad1 pre-RNA processing defect, resulting in the loss of respiratory complex I activity. Functional complementation confirmed that msp1 phenotypes result from a disruption of the MSP1 gene. In Arabidopsis, the maturation of nad1 involves the processing of three RNA fragments, nad1.1, nad1.2, and nad1.3. Based on biochemical analyses and mtRNA profiles of wild-type and msp1 plants, we concluded that MSP1 facilitates the generation of the 3' terminus of nad1.1 transcript, a prerequisite for nad1 exons a-b splicing. Our data substantiate the importance of mtRNA metabolism for the biogenesis of the respiratory system during early plant life.
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Affiliation(s)
- Corinne Best
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ron Mizrahi
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Rana Edris
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Hui Tang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hagit Zer
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Catherine Colas des Francs-Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Omri M Finkel
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Hongliang Zhu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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5
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Pagano A, Macovei A, Balestrazzi A. Molecular dynamics of seed priming at the crossroads between basic and applied research. PLANT CELL REPORTS 2023; 42:657-688. [PMID: 36780009 PMCID: PMC9924218 DOI: 10.1007/s00299-023-02988-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The potential of seed priming is still not fully exploited. Our limited knowledge of the molecular dynamics of seed pre-germinative metabolism is the main hindrance to more effective new-generation techniques. Climate change and other recent global crises are disrupting food security. To cope with the current demand for increased food, feed, and biofuel production, while preserving sustainability, continuous technological innovation should be provided to the agri-food sector. Seed priming, a pre-sowing technique used to increase seed vigor, has become a valuable tool due to its potential to enhance germination and stress resilience under changing environments. Successful priming protocols result from the ability to properly act on the seed pre-germinative metabolism and stimulate events that are crucial for seed quality. However, the technique still requires constant optimization, and researchers are committed to addressing some key open questions to overcome such drawbacks. In this review, an update of the current scientific and technical knowledge related to seed priming is provided. The rehydration-dehydration cycle associated with priming treatments can be described in terms of metabolic pathways that are triggered, modulated, or turned off, depending on the seed physiological stage. Understanding the ways seed priming affects, either positively or negatively, such metabolic pathways and impacts gene expression and protein/metabolite accumulation/depletion represents an essential step toward the identification of novel seed quality hallmarks. The need to expand the basic knowledge on the molecular mechanisms ruling the seed response to priming is underlined along with the strong potential of applied research on primed seeds as a source of seed quality hallmarks. This route will hasten the implementation of seed priming techniques needed to support sustainable agriculture systems.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', Via Ferrata 1, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', Via Ferrata 1, 27100, Pavia, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', Via Ferrata 1, 27100, Pavia, Italy.
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy.
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6
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Ivanova A, O′Leary B, Signorelli S, Falconet D, Moyankova D, Whelan J, Djilianov D, Murcha MW. Mitochondrial activity and biogenesis during resurrection of Haberlea rhodopensis. THE NEW PHYTOLOGIST 2022; 236:943-957. [PMID: 35872573 PMCID: PMC9804507 DOI: 10.1111/nph.18396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/11/2022] [Indexed: 06/01/2023]
Abstract
Haberlea rhodopensis is a resurrection plant that can tolerate extreme and prolonged periods of desiccation with a rapid restoration of physiological function upon rehydration. Specialized mechanisms are required to minimize cellular damage during desiccation and to maintain integrity for rapid recovery following rehydration. In this study we used respiratory activity measurements, electron microscopy, transcript, protein and blue native-PAGE analysis to investigate mitochondrial activity and biogenesis in fresh, desiccated and rehydrated detached H. rhodopensis leaves. We demonstrate that unlike photosynthesis, mitochondrial respiration was almost immediately activated to levels of fresh tissue upon rehydration. The abundance of transcripts and proteins involved in mitochondrial respiration and biogenesis were at comparable levels in fresh, desiccated and rehydrated tissues. Blue native-PAGE analysis revealed fully assembled and equally abundant OXPHOS complexes in mitochondria isolated from fresh, desiccated and rehydrated detached leaves. We observed a high abundance of alternative respiratory components which correlates with the observed high uncoupled respiration capacity in desiccated tissue. Our study reveals that during desiccation of vascular H. rhodopensis tissue, mitochondrial composition is conserved and maintained at a functional state allowing for an almost immediate activation to full capacity upon rehydration. Mitochondria-specific mechanisms were activated during desiccation which probably play a role in maintaining tolerance.
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Affiliation(s)
- Aneta Ivanova
- School of Molecular SciencesThe University of Western Australia35 Stirling Highway, CrawleyPerthWA6009Australia
- AgroBioInstituteAgricultural Academy8 Dragan Tzankov Blvd.1164SofiaBulgaria
| | - Brendan O′Leary
- School of Molecular SciencesThe University of Western Australia35 Stirling Highway, CrawleyPerthWA6009Australia
- Saskatoon Research and Development Centre, Agriculture and Agri‐Food Canada107 Science PlaceSaskatoonSKK1A 0C5Canada
| | - Santiago Signorelli
- School of Molecular SciencesThe University of Western Australia35 Stirling Highway, CrawleyPerthWA6009Australia
- Department of Plant Biology, School of AgricultureUniversidad de la RepúblicaE. Garzón 780, Sayago12900MontevideoUruguay
| | - Denis Falconet
- Cell and Plant Physiology Laboratory, CNRS, CEA, INRAE, IRIGUniversité Grenoble Alpes38054GrenobleFrance
| | - Daniela Moyankova
- AgroBioInstituteAgricultural Academy8 Dragan Tzankov Blvd.1164SofiaBulgaria
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy BiologyLa Trobe UniversityBundoora3086VICAustralia
| | - Dimitar Djilianov
- AgroBioInstituteAgricultural Academy8 Dragan Tzankov Blvd.1164SofiaBulgaria
| | - Monika W. Murcha
- School of Molecular SciencesThe University of Western Australia35 Stirling Highway, CrawleyPerthWA6009Australia
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7
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A High-Quality Genome Assembly of the Mitochondrial Genome of the Oil-Tea Tree Camellia gigantocarpa (Theaceae). DIVERSITY 2022. [DOI: 10.3390/d14100850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Camellia gigantocarpa is one of the oil-tea trees whose seeds can be used to extract high-quality vegetable oil. To date, there are no data on the mitochondrial genome of the oil-tea tree, in contrast to the tea-tree C. sinensis, which belongs to the same genus. In this paper, we present the first complete mitochondrial genomes of C. gigantocarpa obtained using PacBio Hi-Fi (high-fidelity) and Hi-C sequencing technologies to anchor the 970,410 bp genome assembly into a single sequence. A set of 44 protein-coding genes, 22 non-coding genes, 746 simple sequence repeats (SSRs), and more than 201 kb of repetitive sequences were annotated in the genome assembly. The high percentage of repetitive sequences in the mitochondrial genome of C. gigantocarpa (20.81%) and C.sinensis (22.15%, tea tree) compared to Arabidopsis thaliana (4.96%) significantly increased the mitogenome size in the genus Camellia. The comparison of the mitochondrial genomes between C. gigantocarpa and C. sinensis revealed genes exhibit high variance in gene order and low substitution rate within the genus Camellia. Information on the mitochondrial genome provides a better understanding of the structure and evolution of the genome in Camellia and may contribute to further study of the after-ripening process of oil-tea trees.
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8
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Racca S, Gras DE, Canal MV, Ferrero LV, Rojas BE, Figueroa CM, Ariel FD, Welchen E, Gonzalez DH. Cytochrome c and the transcription factor ABI4 establish a molecular link between mitochondria and ABA-dependent seed germination. THE NEW PHYTOLOGIST 2022; 235:1780-1795. [PMID: 35637555 DOI: 10.1111/nph.18287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
During germination, seed reserves are mobilised to sustain the metabolic and energetic demands of plant growth. Mitochondrial respiration is presumably required to drive germination in several species, but only recently its role in this process has begun to be elucidated. Using Arabidopsis thaliana lines with changes in the levels of the respiratory chain component cytochrome c (CYTc), we investigated the role of this protein in germination and its relationship with hormonal pathways. Cytochrome c deficiency causes delayed seed germination, which correlates with decreased cyanide-sensitive respiration and ATP production at the onset of germination. In addition, CYTc affects the sensitivity of germination to abscisic acid (ABA), which negatively regulates the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts downstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA and regulates its expression. The results show that CYTc is a main player during seed germination through its role in respiratory metabolism and energy production. In addition, the direct regulation of CYTC-2 by ABI4 and its effect on ABA-responsive germination establishes a link between mitochondrial and hormonal functions during this process.
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Affiliation(s)
- Sofía Racca
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - M Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Lucía V Ferrero
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Bruno E Rojas
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
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9
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Mizrahi R, Shevtsov-Tal S, Ostersetzer-Biran O. Group II Intron-Encoded Proteins (IEPs/Maturases) as Key Regulators of Nad1 Expression and Complex I Biogenesis in Land Plant Mitochondria. Genes (Basel) 2022; 13:genes13071137. [PMID: 35885919 PMCID: PMC9321910 DOI: 10.3390/genes13071137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are semi-autonomous organelles that produce much of the energy required for cellular metabolism. As descendants of a bacterial symbiont, most mitochondria harbor their own genetic system (mtDNA/mitogenome), with intrinsic machineries for transcription and protein translation. A notable feature of plant mitochondria involves the presence of introns (mostly group II-type) that reside in many organellar genes. The splicing of the mtRNAs relies on the activities of various protein cofactors, which may also link organellar functions with cellular or environmental signals. The splicing of canonical group II introns is aided by an ancient class of RT-like enzymes (IEPs/maturases, MATs) that are encoded by the introns themselves and act specifically on their host introns. The plant organellar introns are degenerated in structure and are generally also missing their cognate intron-encoded proteins. The factors required for plant mtRNA processing are mostly nuclearly-encoded, with the exception of a few degenerated MATs. These are in particular pivotal for the maturation of NADH-dehydrogenase transcripts. In the following review we provide an update on the non-canonical MAT factors in angiosperm mitochondria and summarize the current knowledge of their essential roles in regulating Nad1 expression and complex I (CI) biogenesis during embryogenesis and early plant life.
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10
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Tarasenko TA, Koulintchenko MV. Heterogeneity of the Mitochondrial Population in Cells of Plants and Other Organisms. Mol Biol 2022. [DOI: 10.1134/s0026893322020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Xu C, Tao Y, Fu X, Guo L, Xing H, Li C, Yang Z, Su H, Wang X, Hu J, Fan D, Chiang VL, Luo K. The microRNA476a-RFL module regulates adventitious root formation through a mitochondria-dependent pathway in Populus. THE NEW PHYTOLOGIST 2021; 230:2011-2028. [PMID: 33533479 DOI: 10.1111/nph.17252] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/19/2021] [Indexed: 05/25/2023]
Abstract
For woody plants, clonal propagation efficiency is largely determined by adventitious root (AR) formation at the bases of stem cuttings. However, our understanding of the molecular mechanisms contributing to AR morphogenesis in trees remains limited, despite the importance of vegetative propagation, currently the most common practice for tree breeding and commercialization. Here, we identified Populus-specific miR476a as a regulator of wound-induced adventitious rooting that acts by orchestrating mitochondrial homeostasis. MiR476a exhibited inducible expression during AR formation and directly targeted several Restorer of Fertility like (RFL) genes encoding mitochondrion-localized pentatricopeptide repeat proteins. Genetic modification of miR476a-RFL expression revealed that miR476a/RFL-mediated dynamic regulation of mitochondrial homeostasis influences AR formation in poplar. Mitochondrial perturbation via exogenous application of a chemical inhibitor indicated that miR476a/RFL-directed AR formation depends on mitochondrial regulation that acts via auxin signaling. Our results thus establish a microRNA-directed mitochondrion-auxin signaling cascade required for AR development, providing insights into the role of mitochondrial regulation in the developmental plasticity of plants.
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Affiliation(s)
- Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yuanxun Tao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaokang Fu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Li Guo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Haitao Xing
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, 402160, China
| | - Chaofeng Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Ziwei Yang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Huili Su
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xianqiang Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jian Hu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Di Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
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12
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Van Aken O. Mitochondrial redox systems as central hubs in plant metabolism and signaling. PLANT PHYSIOLOGY 2021; 186:36-52. [PMID: 33624829 PMCID: PMC8154082 DOI: 10.1093/plphys/kiab101] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/11/2021] [Indexed: 05/06/2023]
Abstract
Plant mitochondria are indispensable for plant metabolism and are tightly integrated into cellular homeostasis. This review provides an update on the latest research concerning the organization and operation of plant mitochondrial redox systems, and how they affect cellular metabolism and signaling, plant development, and stress responses. New insights into the organization and operation of mitochondrial energy systems such as the tricarboxylic acid cycle and mitochondrial electron transport chain (mtETC) are discussed. The mtETC produces reactive oxygen and nitrogen species, which can act as signals or lead to cellular damage, and are thus efficiently removed by mitochondrial antioxidant systems, including Mn-superoxide dismutase, ascorbate-glutathione cycle, and thioredoxin-dependent peroxidases. Plant mitochondria are tightly connected with photosynthesis, photorespiration, and cytosolic metabolism, thereby providing redox-balancing. Mitochondrial proteins are targets of extensive post-translational modifications, but their functional significance and how they are added or removed remains unclear. To operate in sync with the whole cell, mitochondria can communicate their functional status via mitochondrial retrograde signaling to change nuclear gene expression, and several recent breakthroughs here are discussed. At a whole organism level, plant mitochondria thus play crucial roles from the first minutes after seed imbibition, supporting meristem activity, growth, and fertility, until senescence of darkened and aged tissue. Finally, plant mitochondria are tightly integrated with cellular and organismal responses to environmental challenges such as drought, salinity, heat, and submergence, but also threats posed by pathogens. Both the major recent advances and outstanding questions are reviewed, which may help future research efforts on plant mitochondria.
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Affiliation(s)
- Olivier Van Aken
- Department of Biology, Lund University, Lund, Sweden
- Author for communication:
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13
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Tamadaddi C, Sagar V, Verma AK, Afsal F, Sahi C. Expansion of the evolutionarily conserved network of J-domain proteins in the Arabidopsis mitochondrial import complex. PLANT MOLECULAR BIOLOGY 2021; 105:385-403. [PMID: 33206359 DOI: 10.1007/s11103-020-01095-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 11/07/2020] [Indexed: 06/11/2023]
Abstract
We report that discriminate interaction between the expanded mitochondrial chaperone network and variability in their expression might determine their functional specificities and impart robustness to mitochondrial import processes in plants. Mitochondrial Hsp70 (mtHsp70), the central component of the pre-sequence associated motor (PAM) complex, is crucial for the import of proteins to the mitochondrial matrix. Activity of mtHsp70 is regulated by a heterodimeric complex of two J-domain proteins (JDPs), Pam18 and Pam16. Compared to other eukaryotes, plants harbor multiple copies of these JDPs, which posit that plants have an increasingly complex mtHsp70: JDP network in their mitochondrial matrix. Here, we show that although highly similar in sequence, some of the plant JDPs are functionally different. Protein: protein interaction studies including yeast two-hybrid and Bimolecular Fluorescence Complementation revealed that while all the AtPam18s interacted with AtPam16s, the strengths of these promiscuous interactions are variable. Further, down-regulation of AtPAM16L affected seed germination, even in the presence of its seemingly identical paralog, AtPAM16. Knockdown of AtPAM16L caused reduction in mitochondrial number and deregulation of several mitochondrial genes, suggesting towards a specific role of AtPam16L in maintaining mitochondrial homeostasis, especially under stress conditions. Our findings suggest that variations in the spatio-temporal expression, accompanied by discriminate interactions between the JDPs, might be defining the functional specificity of the mtHsp70 co-chaperone machinery and providing resilience to mitochondrial import processes in plants, especially under stress conditions.
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Affiliation(s)
- Chetana Tamadaddi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Room Number 117 AB3, IISER Bhopal, Bhopal Bypass Road, Bhopal, MP, 462066, India
| | - Vinay Sagar
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Room Number 117 AB3, IISER Bhopal, Bhopal Bypass Road, Bhopal, MP, 462066, India
- National Center for Biological Sciences, Rajiv Gandhi Nagar, Kodigehalli, Bengaluru, Karnataka, India
| | - Amit K Verma
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Room Number 117 AB3, IISER Bhopal, Bhopal Bypass Road, Bhopal, MP, 462066, India
- Department of Biochemistry, University of Wisconsin-Madison, Madison, USA
| | - Fathima Afsal
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Room Number 117 AB3, IISER Bhopal, Bhopal Bypass Road, Bhopal, MP, 462066, India
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Room Number 117 AB3, IISER Bhopal, Bhopal Bypass Road, Bhopal, MP, 462066, India.
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14
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Farooq MA, Zhang X, Zafar MM, Ma W, Zhao J. Roles of Reactive Oxygen Species and Mitochondria in Seed Germination. FRONTIERS IN PLANT SCIENCE 2021; 12:781734. [PMID: 34956279 PMCID: PMC8695494 DOI: 10.3389/fpls.2021.781734] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/18/2021] [Indexed: 05/14/2023]
Abstract
Seed germination is crucial for the life cycle of plants and maximum crop production. This critical developmental step is regulated by diverse endogenous [hormones, reactive oxygen species (ROS)] and exogenous (light, temperature) factors. Reactive oxygen species promote the release of seed dormancy by biomolecules oxidation, testa weakening and endosperm decay. Reactive oxygen species modulate metabolic and hormone signaling pathways that induce and maintain seed dormancy and germination. Endosperm provides nutrients and senses environmental signals to regulate the growth of the embryo by secreting timely signals. The growing energy demand of the developing embryo and endosperm is fulfilled by functional mitochondria. Mitochondrial matrix-localized heat shock protein GhHSP24.7 controls seed germination in a temperature-dependent manner. In this review, we summarize comprehensive view of biochemical and molecular mechanisms, which coordinately control seed germination. We also discuss that the accurate and optimized coordination of ROS, mitochondria, heat shock proteins is required to permit testa rupture and subsequent germination.
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Affiliation(s)
- Muhammad Awais Farooq
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Xiaomeng Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | | | - Wei Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- *Correspondence: Wei Ma,
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Jianjun Zhao,
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15
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Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21197404. [PMID: 33036486 PMCID: PMC7584043 DOI: 10.3390/ijms21197404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022] Open
Abstract
Seed germination is a critical process for completion of the plant life cycle and for global food production. Comparing the germination transcriptomes of barley (Hordeum vulgare) to Arabidopsis thaliana revealed the overall pattern was conserved in terms of functional gene ontology; however, many oppositely responsive orthologous genes were identified. Conserved processes included a set of approximately 6000 genes that peaked early in germination and were enriched in processes associated with RNA metabolism, e.g., pentatricopeptide repeat (PPR)-containing proteins. Comparison of orthologous genes revealed more than 3000 orthogroups containing almost 4000 genes that displayed similar expression patterns including functions associated with mitochondrial tricarboxylic acid (TCA) cycle, carbohydrate and RNA/DNA metabolism, autophagy, protein modifications, and organellar function. Biochemical and proteomic analyses indicated mitochondrial biogenesis occurred early in germination, but detailed analyses revealed the timing involved in mitochondrial biogenesis may vary between species. More than 1800 orthogroups representing 2000 genes displayed opposite patterns in transcript abundance, representing functions of energy (carbohydrate) metabolism, photosynthesis, protein synthesis and degradation, and gene regulation. Differences in expression of basic-leucine zippers (bZIPs) and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses.
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16
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Barreto P, Couñago RM, Arruda P. Mitochondrial uncoupling protein-dependent signaling in plant bioenergetics and stress response. Mitochondrion 2020; 53:109-120. [DOI: 10.1016/j.mito.2020.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/06/2020] [Accepted: 05/14/2020] [Indexed: 12/15/2022]
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17
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Best C, Mizrahi R, Ostersetzer-Biran O. Why so Complex? The Intricacy of Genome Structure and Gene Expression, Associated with Angiosperm Mitochondria, May Relate to the Regulation of Embryo Quiescence or Dormancy-Intrinsic Blocks to Early Plant Life. PLANTS (BASEL, SWITZERLAND) 2020; 9:E598. [PMID: 32397140 PMCID: PMC7284508 DOI: 10.3390/plants9050598] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/14/2022]
Abstract
Mitochondria play key roles in cellular-energy metabolism and are vital for plant-life, such as for successful germination and early-seedling establishment. Most mitochondria contain their own genetic system (mtDNA, mitogenome), with an intrinsic protein-synthesis machinery. Although the challenges of maintaining prokaryotic-type structures and functions are common to Eukarya, land plants possess some of the most complex organelle composition of all known organisms. Angiosperms mtDNAs are characteristically the largest and least gene-dense among the eukaryotes. They often contain highly-variable intergenic regions of endogenous or foreign origins and undergo frequent recombination events, which result in different mtDNA configurations, even between closely-related species. The expression of the mitogenome in angiosperms involves extensive mtRNA processing steps, including numerous editing and splicing events. Why do land-plant's mitochondria have to be so complex? The answer to this remains a matter of speculation. We propose that this complexity may have arisen throughout the terrestrialization of plants, as a means to control embryonic mitochondrial functions -a critical adaptive trait to optimize seed germination. The unique characteristics of plant mtDNA may play pivotal roles in the nuclear-regulation of organellar biogenesis and metabolism, possibly to control embryos quiescence or dormancy, essential determinants for the establishment of viable plantlets that can survive post-germination.
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Affiliation(s)
| | | | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus—Givat Ram, Jerusalem 9190401, Israel; (C.B.); (R.M.)
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18
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Wang Y, Selinski J, Mao C, Zhu Y, Berkowitz O, Whelan J. Linking mitochondrial and chloroplast retrograde signalling in plants. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190410. [PMID: 32362265 PMCID: PMC7209950 DOI: 10.1098/rstb.2019.0410] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Retrograde signalling refers to the regulation of nuclear gene expression in response to functional changes in organelles. In plants, the two energy-converting organelles, mitochondria and chloroplasts, are tightly coordinated to balance their activities. Although our understanding of components involved in retrograde signalling has greatly increased in the last decade, studies on the regulation of the two organelle signalling pathways have been largely independent. Thus, the mechanism of how mitochondrial and chloroplastic retrograde signals are integrated is largely unknown. Here, we summarize recent findings on the function of mitochondrial signalling components and their links to chloroplast retrograde responses. From this, a picture emerges showing that the major regulators are integrators of both organellar retrograde signalling pathways. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.
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Affiliation(s)
- Yan Wang
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Jennifer Selinski
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Chunli Mao
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.,Department of Animal Science and Technology, Grassland Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yanqiao Zhu
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.,Department of Animal Science and Technology, Grassland Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
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19
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Lost in Translation: Physiological Roles of Stored mRNAs in Seed Germination. PLANTS 2020; 9:plants9030347. [PMID: 32164149 PMCID: PMC7154877 DOI: 10.3390/plants9030347] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 02/07/2023]
Abstract
Seeds characteristics such as germination ability, dormancy, and storability/longevity are important traits in agriculture, and various genes have been identified that are involved in its regulation at the transcriptional and post-transcriptional level. A particularity of mature dry seeds is a special mechanism that allows them to accumulate more than 10,000 mRNAs during seed maturation and use them as templates to synthesize proteins during germination. Some of these stored mRNAs are also referred to as long-lived mRNAs because they remain translatable even after seeds have been exposed to long-term stressful conditions. Mature seeds can germinate even in the presence of transcriptional inhibitors, and this ability is acquired in mid-seed development. The type of mRNA that accumulates in seeds is affected by the plant hormone abscisic acid and environmental factors, and most of them accumulate in seeds in the form of monosomes. Release of seed dormancy during after-ripening involves the selective oxidation of stored mRNAs and this prevents translation of proteins that function in the suppression of germination after imbibition. Non-selective oxidation and degradation of stored mRNAs occurs during long-term storage of seeds so that the quality of stored RNAs is linked to the degree of seed deterioration. After seed imbibition, a population of stored mRNAs are selectively loaded into polysomes and the mRNAs, involved in processes such as redox, glycolysis, and protein synthesis, are actively translated for germination.
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20
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Liew LC, Narsai R, Wang Y, Berkowitz O, Whelan J, Lewsey MG. Temporal tissue-specific regulation of transcriptomes during barley (Hordeum vulgare) seed germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:700-715. [PMID: 31628689 DOI: 10.1111/tpj.14574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/09/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
The distinct functions of individual cell types require cells to express specific sets of genes. The germinating seed is an excellent model to study genome regulation between cell types since the majority of the transcriptome is differentially expressed in a short period, beginning from a uniform, metabolically inactive state. In this study, we applied laser-capture microdissection RNA-sequencing to small numbers of cells from the plumule, radicle tip and scutellum of germinating barley seeds every 8 h, over a 48 h time course. Tissue-specific gene expression was notably common; 25% (910) of differentially expressed transcripts in plumule, 34% (1876) in radicle tip and 41% (2562) in scutellum were exclusive to that organ. We also determined that tissue-specific storage of transcripts occurs during seed development and maturation. Co-expression of genes had strong spatiotemporal structure, with most co-expression occurring within one organ and at a subset of specific time points during germination. Overlapping and distinct enrichment of functional categories were observed in the tissue-specific profiles. We identified candidate transcription factors amongst these that may be regulators of spatiotemporal gene expression programs. Our findings contribute to the broader goal of generating an integrative model that describes the structure and function of individual cells within seeds during germination.
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Affiliation(s)
- Lim Chee Liew
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Yan Wang
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
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21
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Redox-mediated kick-start of mitochondrial energy metabolism drives resource-efficient seed germination. Proc Natl Acad Sci U S A 2019; 117:741-751. [PMID: 31871212 DOI: 10.1073/pnas.1910501117] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Seeds preserve a far developed plant embryo in a quiescent state. Seed metabolism relies on stored resources and is reactivated to drive germination when the external conditions are favorable. Since the switchover from quiescence to reactivation provides a remarkable case of a cell physiological transition we investigated the earliest events in energy and redox metabolism of Arabidopsis seeds at imbibition. By developing fluorescent protein biosensing in intact seeds, we observed ATP accumulation and oxygen uptake within minutes, indicating rapid activation of mitochondrial respiration, which coincided with a sharp transition from an oxidizing to a more reducing thiol redox environment in the mitochondrial matrix. To identify individual operational protein thiol switches, we captured the fast release of metabolic quiescence in organello and devised quantitative iodoacetyl tandem mass tag (iodoTMT)-based thiol redox proteomics. The redox state across all Cys peptides was shifted toward reduction from 27.1% down to 13.0% oxidized thiol. A large number of Cys peptides (412) were redox switched, representing central pathways of mitochondrial energy metabolism, including the respiratory chain and each enzymatic step of the tricarboxylic acid (TCA) cycle. Active site Cys peptides of glutathione reductase 2, NADPH-thioredoxin reductase a/b, and thioredoxin-o1 showed the strongest responses. Germination of seeds lacking those redox proteins was associated with markedly enhanced respiration and deregulated TCA cycle dynamics suggesting decreased resource efficiency of energy metabolism. Germination in aged seeds was strongly impaired. We identify a global operation of thiol redox switches that is required for optimal usage of energy stores by the mitochondria to drive efficient germination.
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22
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Sano N, Takebayashi Y, To A, Mhiri C, Rajjou LC, Nakagami H, Kanekatsu M. Shotgun Proteomic Analysis Highlights the Roles of Long-Lived mRNAs and De Novo Transcribed mRNAs in Rice Seeds upon Imbibition. PLANT & CELL PHYSIOLOGY 2019; 60:2584-2596. [PMID: 31373371 DOI: 10.1093/pcp/pcz152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 07/27/2019] [Indexed: 05/22/2023]
Abstract
During seed germination, proteins are translated not only from mRNAs newly transcribed upon imbibition but also from long-lived mRNAs that are synthesized during seed maturation and stored in the mature dry seeds. To clarify the distinct roles of proteins translated from long-lived mRNAs and de novo transcribed mRNAs in germinating rice embryos, proteome analysis based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) combining the use of a transcriptional inhibitor was performed. We observed that α-amanitin significantly represses transcription in germinating embryos; nevertheless, the embryos could germinate, albeit slowly. The proteomic analysis revealed that a total of 109 proteins were translated from long-lived mRNAs associated with germination as well as 222 proteins whose expression were dependent on de novo transcription upon imbibition. Transcriptomic datasets available in public databases demonstrated that mRNAs of the 222 proteins notably increased during germination while those of the 109 proteins highly accumulated in dry embryos and constitutively expressed upon imbibition. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that many of the 109 proteins from long-lived mRNAs are implicated in energy production such as glycolysis or annotated as nucleotide binding proteins, while the 222 proteins are involved in pathways such as pyruvate metabolism and TCA cycle following glycolysis, and momilactones biosynthesis. We propose that long-lived mRNAs support initial energy production and activation of translational machinery upon imbibition whereas de novo transcription accelerates the energy production after glycolysis, which enables rice seeds to germinate vigorously.
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Affiliation(s)
- Naoto Sano
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Alexandra To
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Corinne Mhiri
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Loï C Rajjou
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, Germany
| | - Motoki Kanekatsu
- Department of Plant Production, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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23
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Ren Z, Fan K, Fang T, Zhang J, Yang L, Wang J, Wang G, Liu Y. Maize Empty Pericarp602 Encodes a P-Type PPR Protein That Is Essential for Seed Development. PLANT & CELL PHYSIOLOGY 2019; 60:1734-1746. [PMID: 31076755 DOI: 10.1093/pcp/pcz083] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/22/2019] [Indexed: 05/23/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins play crucial roles in intron splicing, which is important for RNA maturation. Identification of novel PPR protein with the function of intron splicing would help to understand the RNA splicing mechanism. In this study, we identified the maize empty pericarp602 (emp602) mutants, the mature kernels of which showed empty pericarp phenotype. We cloned the Emp602 gene from emp602 mutants and revealed that Emp602 encodes a mitochondrial-localized P-type PPR protein. We further revealed that Emp602 is specific for the cis-splicing of mitochondrial Nad4 intron 1 and intron 3, and mutation of Emp602 led to the loss of mature Nad4 transcripts. The loss of function of Emp602 nearly damaged the assembly and accumulation of complex I and arrested mitochondria formation, which arrested the seed development. The failed assembly of complex I triggers significant upregulation of Aox expression in emp602 mutants. Transcriptome analysis showed that the expression of mitochondrial-related genes, e.g. the genes associated with mitochondrial inner membrane presequence translocase complex and electron carrier activity, were extensively upregulated in emp602 mutant. These results demonstrate that EMP602 functions in the splicing of Nad4 intron 1 and intron 3, and the loss of function of Emp602 arrested maize seed development by disrupting the mitochondria complex I assembly.
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Affiliation(s)
- Zhenjing Ren
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Center of Seed Science and Technology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Kaijian Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Center of Seed Science and Technology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Ting Fang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaojiao Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Wang
- Center of Seed Science and Technology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Niazi AK, Delannoy E, Iqbal RK, Mileshina D, Val R, Gabryelska M, Wyszko E, Soubigou-Taconnat L, Szymanski M, Barciszewski J, Weber-Lotfi F, Gualberto JM, Dietrich A. Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development. Cells 2019; 8:E583. [PMID: 31200566 PMCID: PMC6627697 DOI: 10.3390/cells8060583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/17/2023] Open
Abstract
We address here organellar genetic regulation and intercompartment genome coordination. We developed earlier a strategy relying on a tRNA-like shuttle to mediate import of nuclear transgene-encoded custom RNAs into mitochondria in plants. In the present work, we used this strategy to drive trans-cleaving hammerhead ribozymes into the organelles, to knock down specific mitochondrial RNAs and analyze the regulatory impact. In a similar approach, the tRNA mimic was used to import into mitochondria in Arabidopsis thaliana the orf77, an RNA associated with cytoplasmic male sterility in maize and possessing sequence identities with the atp9 mitochondrial RNA. In both cases, inducible expression of the transgenes allowed to characterise early regulation and signaling responses triggered by these respective manipulations of the organellar transcriptome. The results imply that the mitochondrial transcriptome is tightly controlled by a "buffering" mechanism at the early and intermediate stages of plant development, a control that is released at later stages. On the other hand, high throughput analyses showed that knocking down a specific mitochondrial mRNA triggered a retrograde signaling and an anterograde nuclear transcriptome response involving a series of transcription factor genes and small RNAs. Our results strongly support transcriptome coordination mechanisms within the organelles and between the organelles and the nucleus.
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Affiliation(s)
- Adnan Khan Niazi
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan.
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France.
| | - Rana Khalid Iqbal
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Daria Mileshina
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Romain Val
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Marta Gabryelska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France.
| | - Maciej Szymanski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, A. Mickiewicz University Poznan, Ul. Umultowska 89, 61-614 Poznan, Poland.
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
- NanoBioMedical Centre of the Adam Mickiewicz University, Umultowska 85, 61614 Poznan, Poland.
| | - Frédérique Weber-Lotfi
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - José Manuel Gualberto
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - André Dietrich
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
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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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Boussardon C, Martin-Magniette ML, Godin B, Benamar A, Vittrant B, Citerne S, Mary-Huard T, Macherel D, Rajjou L, Budar F. Novel Cytonuclear Combinations Modify Arabidopsis thaliana Seed Physiology and Vigor. FRONTIERS IN PLANT SCIENCE 2019; 10:32. [PMID: 30804952 PMCID: PMC6370702 DOI: 10.3389/fpls.2019.00032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/10/2019] [Indexed: 05/10/2023]
Abstract
Dormancy and germination vigor are complex traits of primary importance for adaptation and agriculture. Intraspecific variation in cytoplasmic genomes and cytonuclear interactions were previously reported to affect germination in Arabidopsis using novel cytonuclear combinations that disrupt co-adaptation between natural variants of nuclear and cytoplasmic genomes. However, specific aspects of dormancy and germination vigor were not thoroughly explored, nor the parental contributions to the genetic effects. Here, we specifically assessed dormancy, germination performance and longevity of seeds from Arabidopsis plants with natural and new genomic compositions. All three traits were modified by cytonuclear reshuffling. Both depth and release rate of dormancy could be modified by a changing of cytoplasm. Significant changes on dormancy and germination performance due to specific cytonuclear interacting combinations mainly occurred in opposite directions, consistent with the idea that a single physiological consequence of the new genetic combination affected both traits oppositely. However, this was not always the case. Interestingly, the ability of parental accessions to contribute to significant cytonuclear interactions modifying the germination phenotype was different depending on whether they provided the nuclear or cytoplasmic genetic compartment. The observed deleterious effects of novel cytonuclear combinations (in comparison with the nuclear parent) were consistent with a contribution of cytonuclear interactions to germination adaptive phenotypes. More surprisingly, we also observed favorable effects of novel cytonuclear combinations, suggesting suboptimal genetic combinations exist in natural populations for these traits. Reduced sensitivity to exogenous ABA and faster endogenous ABA decay during germination were observed in a novel cytonuclear combination that also exhibited enhanced longevity and better germination performance, compared to its natural nuclear parent. Taken together, our results strongly support that cytoplasmic genomes represent an additional resource of natural variation for breeding seed vigor traits.
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Affiliation(s)
- Clément Boussardon
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Marie-Laure Martin-Magniette
- UMR MIA-Paris, AgroParisTech, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
- Institute of Plant Sciences Paris-Saclay, Université Paris Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Béatrice Godin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Abdelilah Benamar
- Institut de Recherche en Horticulture et Semences, Université d’Angers, Institut National de la Recherche Agronomique, Agrocampus Ouest, UMR 1345, SFR 4207 QUASAV, Angers, France
| | - Benjamin Vittrant
- UMR MIA-Paris, AgroParisTech, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Tristan Mary-Huard
- UMR MIA-Paris, AgroParisTech, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
- GQE – Le Moulon, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - David Macherel
- Institut de Recherche en Horticulture et Semences, Université d’Angers, Institut National de la Recherche Agronomique, Agrocampus Ouest, UMR 1345, SFR 4207 QUASAV, Angers, France
| | - Loïc Rajjou
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Françoise Budar
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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Hu Y, Zou W, Wang Z, Zhang Y, Hu Y, Qian J, Wu X, Ren Y, Zhao J. Translocase of the Outer Mitochondrial Membrane 40 Is Required for Mitochondrial Biogenesis and Embryo Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:389. [PMID: 31001303 PMCID: PMC6455079 DOI: 10.3389/fpls.2019.00389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/13/2019] [Indexed: 05/08/2023]
Abstract
In eukaryotes, mitochondrion is an essential organelle which is surrounded by a double membrane system, including the outer membrane, intermembrane space and the inner membrane. The translocase of the outer mitochondrial membrane (TOM) complex has attracted enormous interest for its role in importing the preprotein from the cytoplasm into the mitochondrion. However, little is understood about the potential biological function of the TOM complex in Arabidopsis. The aim of the present study was to investigate how AtTOM40, a gene encoding the core subunit of the TOM complex, works in Arabidopsis. As a result, we found that lack of AtTOM40 disturbed embryo development and its pattern formation after the globular embryo stage, and finally caused albino ovules and seed abortion at the ratio of a quarter in the homozygous tom40 plants. Further investigation demonstrated that AtTOM40 is wildly expressed in different tissues, especially in cotyledons primordium during Arabidopsis embryogenesis. Moreover, we confirmed that the encoded protein AtTOM40 is localized in mitochondrion, and the observation of the ultrastructure revealed that mitochondrion biogenesis was impaired in tom40-1 embryo cells. Quantitative real-time PCR was utilized to determine the expression of genes encoding outer mitochondrial membrane proteins in the homozygous tom40-1 mutant embryos, including the genes known to be involved in import, assembly and transport of mitochondrial proteins, and the results demonstrated that most of the gene expressions were abnormal. Similarly, the expression of genes relevant to embryo development and pattern formation, such as SAM (shoot apical meristem), cotyledon, vascular primordium and hypophysis, was also affected in homozygous tom40-1 mutant embryos. Taken together, we draw the conclusion that the AtTOM40 gene is essential for the normal structure of the mitochondrion, and participates in early embryo development and pattern formation through maintaining the biogenesis of mitochondria. The findings of this study may provide new insight into the biological function of the TOM40 subunit in higher plants.
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Hou J, Shi X, Chen C, Islam MS, Johnson AF, Kanno T, Huettel B, Yen MR, Hsu FM, Ji T, Chen PY, Matzke M, Matzke AJM, Cheng J, Birchler JA. Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa. Proc Natl Acad Sci U S A 2018; 115:E11321-E11330. [PMID: 30429332 PMCID: PMC6275517 DOI: 10.1073/pnas.1807796115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.
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Affiliation(s)
- Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Xiaowen Shi
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Md Soliman Islam
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Adam F Johnson
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam 550000
| | - Tatsuo Kanno
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding, Cologne, Germany 50829
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Fei-Man Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, MO 65211
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Marjori Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Antonius J M Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211;
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29
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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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Heidorn-Czarna M, Domanski D, Kwasniak-Owczarek M, Janska H. Targeted Proteomics Approach Toward Understanding the Role of the Mitochondrial Protease FTSH4 in the Biogenesis of OXPHOS During Arabidopsis Seed Germination. FRONTIERS IN PLANT SCIENCE 2018; 9:821. [PMID: 29963070 PMCID: PMC6014109 DOI: 10.3389/fpls.2018.00821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/28/2018] [Indexed: 05/23/2023]
Abstract
Seed germination provides an excellent model to study the process of mitochondrial biogenesis. It is a complex and strictly regulated process which requires a proper biogenesis of fully active organelles from existing promitochondrial structures. We have previously reported that the lack of the inner mitochondrial membrane protease FTSH4 delayed Arabidopsis seed germination. Here, we implemented a targeted mass spectrometry-based approach, Multiple Reaction Monitoring (MRM), with stable-isotope-labeled standard peptides for increased sensitivity, to quantify mitochondrial proteins in dry and germinating wild-type and ftsh4 mutant seeds, lacking the FTSH4 protease. Using total seed protein extracts we measured the abundance of the peptide targets belonging to the OXPHOS complexes, AOX1A, transport, and inner membrane scaffold as well as mitochondrial proteins that are highly specific to dry and germinating seeds. The MRM assay showed that the abundance of these proteins in ftsh4 did not differ substantially from that observed in wild-type at the level of dry seed and after stratification, but we observed a reduction in protein abundance in most of the examined OXPHOS subunits in the later stages of germination. These changes in OXPHOS protein levels in ftsh4 mutants were accompanied by a lower cytochrome pathway activity as well as an increased AOX1A amount at the transcript and protein level and alternative pathway activity. The analyses of the steady-state transcript levels of mitochondrial and nuclear genes encoding OXPHOS subunits did not show significant difference in their amount, indicating that the observed changes in the OXPHOS occurred at the post-transcriptional level. At the time when ftsh4 seeds were fully germinated, the abundance of the OXPHOS proteins in the mutant was either slightly lowered or comparable to these amounts in wild-type seeds at the similar developmental stage. By the implementation of an integrative approach combining targeted proteomics, quantitative transcriptomics, and physiological studies we have shown that the FTSH4 protease has an important role in the biogenesis of OXPHOS and thus biogenesis of mitochondria during germination of Arabidopsis seeds.
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Affiliation(s)
- Malgorzata Heidorn-Czarna
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Dominik Domanski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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31
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Mansilla N, Racca S, Gras DE, Gonzalez DH, Welchen E. The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants. Int J Mol Sci 2018; 19:ijms19030662. [PMID: 29495437 PMCID: PMC5877523 DOI: 10.3390/ijms19030662] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial respiration is an energy producing process that involves the coordinated action of several protein complexes embedded in the inner membrane to finally produce ATP. Complex IV or Cytochrome c Oxidase (COX) is the last electron acceptor of the respiratory chain, involved in the reduction of O2 to H2O. COX is a multimeric complex formed by multiple structural subunits encoded in two different genomes, prosthetic groups (heme a and heme a3), and metallic centers (CuA and CuB). Tens of accessory proteins are required for mitochondrial RNA processing, synthesis and delivery of prosthetic groups and metallic centers, and for the final assembly of subunits to build a functional complex. In this review, we perform a comparative analysis of COX composition and biogenesis factors in yeast, mammals and plants. We also describe possible external and internal factors controlling the expression of structural proteins and assembly factors at the transcriptional and post-translational levels, and the effect of deficiencies in different steps of COX biogenesis to infer the role of COX in different aspects of plant development. We conclude that COX assembly in plants has conserved and specific features, probably due to the incorporation of a different set of subunits during evolution.
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Affiliation(s)
- Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Sofia Racca
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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Hameed MW, Juszczak I, Bock R, van Dongen JT. Comparison of mitochondrial gene expression and polysome loading in different tobacco tissues. PLANT METHODS 2017; 13:112. [PMID: 29255478 PMCID: PMC5729415 DOI: 10.1186/s13007-017-0257-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND To investigate translational regulation of gene expression in plant mitochondria, a mitochondrial polysome isolation protocol was established for tobacco to investigate polysomal mRNA loading as a proxy for translational activity. Furthermore, we developed an oligonucleotide based microarray platform to determine the level of Nicotiana tabacum and Arabidopsis thaliana mitochondrial mRNA. RESULTS Microarray analysis of free and polysomal mRNAs was used to characterize differences in the levels of free transcripts and ribosome-bound mRNAs in various organs of tobacco plants. We have observed higher mitochondrial transcript levels in young leaves, flowers and floral buds as compared to fully expanded leaves and roots. A similar pattern of abundance was observed for ribosome-bound mitochondrial mRNAs in these tissues. However, the accumulation of the mitochondrial protein COX2 was found to be inversely related to that of its ribosome-bound mRNA. CONCLUSIONS Our results indicate that the association of mitochondrial mRNAs to ribosomes is largely determined by the total transcript level of a gene. However, at least for Cox2, we demonstrated that the level of ribosome-bound mRNA is not reflected by the amount of COX2 protein.
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Affiliation(s)
- Muhammad Waqar Hameed
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Ilona Juszczak
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Molecular Physiology, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Joost Thomas van Dongen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
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Schwarzländer M, Fuchs P. Plant mitochondrial membranes: adding structure and new functions to respiratory physiology. CURRENT OPINION IN PLANT BIOLOGY 2017; 40:147-157. [PMID: 28992511 DOI: 10.1016/j.pbi.2017.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/31/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
The membranes of mitochondria are focal points of cellular physiology and respiratory energy transformation. Recent discoveries have started painting a refined picture of plant mitochondrial membranes as platforms in which structure and function have evolved in an interconnected and dynamically regulated manner. Hosting ancillary functions that interact with other mitochondrial properties gives mitochondria the characteristics of multitasking and integrated molecular mega machines. We review recent insights into the makeup and the plasticity of the outer and inner mitochondrial membranes, their intimate relationship with respiratory function and regulation, and their properties in mediating solute transport. Synthesizing recent research advances we hypothesize that plant mitochondrial membranes are a privileged location for incorporation of a wide range of processes, some of which collaborate with respiratory function, including plant immunity, metabolic regulation and signal transduction, to underpin flexibility in the acclimation to changing environments.
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Affiliation(s)
- Markus Schwarzländer
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany; Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, D-48143 Münster, Germany.
| | - Philippe Fuchs
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany; Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, D-48143 Münster, Germany
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34
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Narsai R, Gouil Q, Secco D, Srivastava A, Karpievitch YV, Liew LC, Lister R, Lewsey MG, Whelan J. Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination. Genome Biol 2017; 18:172. [PMID: 28911330 PMCID: PMC5599894 DOI: 10.1186/s13059-017-1302-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 08/16/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination. RESULTS We present an integrated analysis of high-resolution RNA sequencing, small RNA sequencing and MethylC sequencing over ten developmental time points in Arabidopsis thaliana seeds, finding extensive transcriptomic and epigenomic transformations associated with seed germination. We identify previously unannotated loci from which messenger RNAs are expressed transiently during germination and find widespread alternative splicing and divergent isoform abundance of genes involved in RNA processing and splicing. We generate the first dynamic transcription factor network model of germination, identifying known and novel regulatory factors. Expression of both microRNA and short interfering RNA loci changes significantly during germination, particularly between the seed and the post-germinative seedling. These are associated with changes in gene expression and large-scale demethylation observed towards the end of germination, as the epigenome transitions from an embryo-like to a vegetative seedling state. CONCLUSIONS This study reveals the complex dynamics and interactions of the transcriptome and epigenome during seed germination, including the extensive remodelling of the seed DNA methylome from an embryo-like to vegetative-like state during the seed-to-seedling transition. Data are available for exploration in a user-friendly browser at https://jbrowse.latrobe.edu.au/germination_epigenome .
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Affiliation(s)
- Reena Narsai
- ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Quentin Gouil
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - David Secco
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Akanksha Srivastava
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Yuliya V Karpievitch
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Lim Chee Liew
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
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Betts NS, Berkowitz O, Liu R, Collins HM, Skadhauge B, Dockter C, Burton RA, Whelan J, Fincher GB. Isolation of tissues and preservation of RNA from intact, germinated barley grain. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:754-765. [PMID: 28509349 DOI: 10.1111/tpj.13600] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/05/2017] [Accepted: 05/10/2017] [Indexed: 05/11/2023]
Abstract
Isolated barley (Hordeum vulgare L.) aleurone layers have been widely used as a model system for studying gene expression and hormonal regulation in germinating cereal grains. A serious technological limitation of this approach has been the inability to confidently extrapolate conclusions obtained from isolated tissues back to the whole grain, where the co-location of several living and non-living tissues results in complex tissue-tissue interactions and regulatory pathways coordinated across the multiple tissues. Here we have developed methods for isolating fragments of aleurone, starchy endosperm, embryo, scutellum, pericarp-testa, husk and crushed cell layers from germinated grain. An important step in the procedure involves the rapid fixation of the intact grain to freeze the transcriptional activity of individual tissues while dissection is effected for subsequent transcriptomic analyses. The developmental profiles of 19 611 gene transcripts were precisely defined in the purified tissues and in whole grain during the first 24 h of germination by RNA sequencing. Spatial and temporal patterns of transcription were validated against well-defined data on enzyme activities in both whole grain and isolated tissues. Transcript profiles of genes involved in mitochondrial assembly and function were used to validate the very early stages of germination, while the profiles of genes involved in starch and cell wall mobilisation matched existing data on activities of corresponding enzymes. The data will be broadly applicable for the interrogation of co-expression and differential expression patterns and for the identification of transcription factors that are important in the early stages of grain and seed germination.
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Affiliation(s)
- Natalie S Betts
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Oliver Berkowitz
- School of Life Science and ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Ruijie Liu
- School of Life Science and ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Helen M Collins
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Rachel A Burton
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - James Whelan
- School of Life Science and ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Geoffrey B Fincher
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
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36
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Raveneau MP, Benamar A, Macherel D. Water content, adenylate kinase, and mitochondria drive adenylate balance in dehydrating and imbibing seeds. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3501-3512. [PMID: 28859379 PMCID: PMC5853452 DOI: 10.1093/jxb/erx182] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/04/2017] [Indexed: 05/15/2023]
Abstract
Water and life are inexorably linked, but some organisms are capable of losing almost all cellular water to enter a non-metabolic state of anhydrobiosis. This raises intriguing questions about how energy metabolism is managed during such transitions. Here, we have investigated adenylate metabolism during seed imbibition and drying using intact or fragmented pea (Pisum sativum L.) seeds. AMP was confirmed as the major adenylate stored in dry seeds, and normal adenylate balance was rapidly restored upon rehydration of the tissues. Conversely, re-drying of fully imbibed seeds reversed the balance toward AMP accumulation. The overall analysis, supported by in vitro enzyme mimicking experiments, shows that during tissue dehydration, when oxidative phosphorylation is no longer efficient because of decreasing water content, the ATP metabolic demand is met by adenylate kinase, resulting in accumulation of AMP. During seed imbibition, adenylate balance is rapidly restored from the AMP stock by the concerted action of adenylate kinase and mitochondria. The adenylate balance in orthodox seeds, and probably in other anhydrobiotes, appears to be simply driven by water content throughout the interplay between ATP metabolic demand, adenylate kinase, and oxidative phosphorylation, which requires mitochondria to be energetically efficient from the onset of imbibition.
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Affiliation(s)
- Marie-Paule Raveneau
- USC LEVA, INRA, Ecole Supérieure d’Agricultures, Université Bretagne Loire, SFR QUASAV, rue Rabelais, Angers Cedex, France
| | - Abdelilah Benamar
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR QUASAV, rue Georges Morel, Beaucouzé, France
| | - David Macherel
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR QUASAV, rue Georges Morel, Beaucouzé, France
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37
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Proteomic and Carbonylation Profile Analysis at the Critical Node of Seed Ageing in Oryza sativa. Sci Rep 2017; 7:40611. [PMID: 28094349 PMCID: PMC5240128 DOI: 10.1038/srep40611] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/07/2016] [Indexed: 01/06/2023] Open
Abstract
The critical node (CN), which is the transition from the plateau phase to the rapid decreasing phase of seed ageing, is extremely important for seed conservation. Although numerous studies have investigated the oxidative stress during seed ageing, information on the changes in protein abundance at the CN is limited. In this study, we aimed to investigate the abundance and carbonylation patterns of proteins at the CN of seed ageing in rice. The results showed that the germination rate of seeds decreased by less than 20% at the CN; however, the abundance of 112 proteins and the carbonylation levels of 68 proteins markedly changed, indicating oxidative damage. The abundance and activity of mitochondrial, glycolytic, and pentose phosphate pathway proteins were reduced; consequently, this negatively affected energy production and germination. Proteins related to defense, including antioxidant system and heat shock proteins, also reduced in abundance. Overall, energy metabolism was reduced at the CN, leading to a decrease in the antioxidant capacity, whereas seed storage proteins were up-regulated and carbonylated, indicating that the seed had a lower ability to utilize seed storage proteins for germination. Thus, the significant decrease in metabolic activities at the CN might accelerate the loss of seed viability.
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38
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Paszkiewicz G, Gualberto JM, Benamar A, Macherel D, Logan DC. Arabidopsis Seed Mitochondria Are Bioenergetically Active Immediately upon Imbibition and Specialize via Biogenesis in Preparation for Autotrophic Growth. THE PLANT CELL 2017; 29:109-128. [PMID: 28062752 PMCID: PMC5304351 DOI: 10.1105/tpc.16.00700] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/06/2016] [Accepted: 01/06/2017] [Indexed: 05/14/2023]
Abstract
Seed germination is a vital developmental transition for production of progeny by sexual reproduction in spermatophytes. Quiescent cells in nondormant dry embryos are reawakened first by imbibition and then by perception of germination triggers. Reanimated tissues enter into a germination program requiring energy for expansion growth. However, germination requires that embryonic tissues develop to support the more energy-demanding processes of cell division and organogenesis of the new seedling. Reactivation of mitochondria to supply the required energy is thus a key process underpinning germination and seedling survival. Using live imaging, we investigated reactivation of mitochondrial bioenergetics and dynamics using Arabidopsis thaliana as a model. Bioenergetic reactivation, visualized by presence of a membrane potential, is immediate upon rehydration. However, reactivation of mitochondrial dynamics only occurs after transfer to germination conditions. Reactivation of mitochondrial bioenergetics is followed by dramatic reorganization of the chondriome (all mitochondrial in a cell, collectively) involving massive fusion and membrane biogenesis to form a perinuclear tubuloreticular structure enabling mixing of previously discrete mitochondrial DNA nucleoids. The end of germination coincides with fragmentation of the chondriome, doubling of mitochondrial number, and heterogeneous redistribution of nucleoids among the mitochondria, generating a population of mitochondria tailored to seedling growth.
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Affiliation(s)
- Gaël Paszkiewicz
- IRHS, Université d'Angers, INRA, AGROCAMPUS-Ouest, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
| | - José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Abdelilah Benamar
- IRHS, Université d'Angers, INRA, AGROCAMPUS-Ouest, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
| | - David Macherel
- IRHS, Université d'Angers, INRA, AGROCAMPUS-Ouest, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
| | - David C Logan
- IRHS, Université d'Angers, INRA, AGROCAMPUS-Ouest, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
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39
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Murcha MW, Kubiszewski-Jakubiak S, Teixeira PF, Gügel IL, Kmiec B, Narsai R, Ivanova A, Megel C, Schock A, Kraus S, Berkowitz O, Glaser E, Philippar K, Maréchal-Drouard L, Soll J, Whelan J. Plant-Specific Preprotein and Amino Acid Transporter Proteins Are Required for tRNA Import into Mitochondria. PLANT PHYSIOLOGY 2016; 172:2471-2490. [PMID: 27789739 PMCID: PMC5129730 DOI: 10.1104/pp.16.01519] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/25/2016] [Indexed: 05/03/2023]
Abstract
A variety of eukaryotes, in particular plants, do not contain the required number of tRNAs to support the translation of mitochondria-encoded genes and thus need to import tRNAs from the cytosol. This study identified two Arabidopsis (Arabidopsis thaliana) proteins, Tric1 and Tric2 (for tRNA import component), which on simultaneous inactivation by T-DNA insertion lines displayed a severely delayed and chlorotic growth phenotype and significantly reduced tRNA import capacity into isolated mitochondria. The predicted tRNA-binding domain of Tric1 and Tric2, a sterile-α-motif at the C-terminal end of the protein, was required to restore tRNA uptake ability in mitochondria of complemented plants. The purified predicted tRNA-binding domain binds the T-arm of the tRNA for alanine with conserved lysine residues required for binding. T-DNA inactivation of both Tric proteins further resulted in an increase in the in vitro rate of in organello protein synthesis, which was mediated by a reorganization of the nuclear transcriptome, in particular of genes encoding a variety of proteins required for mitochondrial gene expression at both the transcriptional and translational levels. The characterization of Tric1/2 provides mechanistic insight into the process of tRNA import into mitochondria and supports the theory that the tRNA import pathway resulted from the repurposing of a preexisting protein import apparatus.
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Affiliation(s)
- Monika W Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.);
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.);
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.);
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.);
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.);
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Szymon Kubiszewski-Jakubiak
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Pedro F Teixeira
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Irene L Gügel
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Beata Kmiec
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Reena Narsai
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Aneta Ivanova
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Cyrille Megel
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Annette Schock
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Sabrina Kraus
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Oliver Berkowitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Elzbieta Glaser
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Katrin Philippar
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Laurence Maréchal-Drouard
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - Jürgen Soll
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.)
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.)
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.)
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.)
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (M.W.M., S.K.-J., A.I.);
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden (P.F.T., B.K., E.G.);
- Department Biology 1-Botany, Biocenter Ludwig-Maximilians-University Munich, 82152 Planegg, Germany (I.L.G., A.S., S.K., K.P., J.S.);
- Munich Centre for Integrated Protein Science, Ludwig-Maximilians-University Munich, 81377 Munich, Germany (I.L.G., A.S., S.K., J.S.);
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., O.B., J.W.);
- Center for Human and Molecular Biology, Plant Biology, Saarland University, 66123 Saarbruecken, Germany (K.P.); and
- Institut de Biologie Moléculaire des Plantes-Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (L.M.-D., C.M.)
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Chrobok D, Law SR, Brouwer B, Lindén P, Ziolkowska A, Liebsch D, Narsai R, Szal B, Moritz T, Rouhier N, Whelan J, Gardeström P, Keech O. Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence. PLANT PHYSIOLOGY 2016; 172:2132-2153. [PMID: 27744300 PMCID: PMC5129728 DOI: 10.1104/pp.16.01463] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/13/2016] [Indexed: 05/20/2023]
Abstract
The functions of mitochondria during leaf senescence, a type of programmed cell death aimed at the massive retrieval of nutrients from the senescing organ to the rest of the plant, remain elusive. Here, combining experimental and analytical approaches, we showed that mitochondrial integrity in Arabidopsis (Arabidopsis thaliana) is conserved until the latest stages of leaf senescence, while their number drops by 30%. Adenylate phosphorylation state assays and mitochondrial respiratory measurements indicated that the leaf energy status also is maintained during this time period. Furthermore, after establishing a curated list of genes coding for products targeted to mitochondria, we analyzed in isolation their transcript profiles, focusing on several key mitochondrial functions, such as the tricarboxylic acid cycle, mitochondrial electron transfer chain, iron-sulfur cluster biosynthesis, transporters, as well as catabolic pathways. In tandem with a metabolomic approach, our data indicated that mitochondrial metabolism was reorganized to support the selective catabolism of both amino acids and fatty acids. Such adjustments would ensure the replenishment of α-ketoglutarate and glutamate, which provide the carbon backbones for nitrogen remobilization. Glutamate, being the substrate of the strongly up-regulated cytosolic glutamine synthase, is likely to become a metabolically limiting factor in the latest stages of developmental leaf senescence. Finally, an evolutionary age analysis revealed that, while branched-chain amino acid and proline catabolism are very old mitochondrial functions particularly enriched at the latest stages of leaf senescence, auxin metabolism appears to be rather newly acquired. In summation, our work shows that, during developmental leaf senescence, mitochondria orchestrate catabolic processes by becoming increasingly central energy and metabolic hubs.
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Affiliation(s)
- Daria Chrobok
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Simon R Law
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Bastiaan Brouwer
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Pernilla Lindén
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Agnieszka Ziolkowska
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Daniela Liebsch
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Reena Narsai
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Bozena Szal
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Thomas Moritz
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Nicolas Rouhier
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - James Whelan
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Per Gardeström
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.)
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.)
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.)
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden (D.C., S.R.L., B.B., A.Z., D.L., P.G., O.K.);
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, S-90183 Umea, Sweden (P.L., T.M.);
- Department of Animal, Plant, and Soil Science, School of Life Science, Australian Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (R.N., J.W.);
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw I, 02-096 Warsaw, Poland (B.S.); and
- Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Université de Lorraine/Institut National de la Recherche Agronomique Faculté des Sciences et Technologies, 54506 Vandoeuvre-les-Nancy, France (N.R.)
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Li L, Kubiszewski-Jakubiak S, Radomiljac J, Wang Y, Law SR, Keech O, Narsai R, Berkowitz O, Duncan O, Murcha MW, Whelan J. Characterization of a novel β-barrel protein (AtOM47) from the mitochondrial outer membrane of Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6061-6075. [PMID: 27811077 PMCID: PMC5100019 DOI: 10.1093/jxb/erw366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In plant cells, mitochondria are major providers of energy and building blocks for growth and development as well as abiotic and biotic stress responses. They are encircled by two lipid membranes containing proteins that control mitochondrial function through the import of macromolecules and metabolites. Characterization of a novel β-barrel protein, OUTER MEMBRANE PROTEIN 47 (OM47), unique to the green lineage and related to the voltage-dependent anion channel (VDAC) protein family, showed that OM47 can complement a VDAC mutant in yeast. Mutation of OM47 in Arabidopsis thaliana by T-DNA insertion had no effect on the import of proteins, such as the β-barrel proteins translocase of the outer membrane 40 (TOM40) or sorting and assembly machinery 50 (SAM50), into mitochondria. Molecular and physiological analyses revealed a delay in chlorophyll breakdown, higher levels of starch, and a delay in the induction of senescence marker genes in the mutant lines. While there was a reduction of >90% in OM47 protein in mitochondria isolated from 3-week-old om47 mutants, in mitochondria isolated from 8-week-old plants OM47 levels were similar to that of the wild type. This recovery was achieved by an up-regulation of OM47 transcript abundance in the mutants. Combined, these results highlight a role in leaf senescence for this plant-specific β-barrel protein, probably mediating the recovery and recycling of chloroplast breakdown products by transporting metabolic intermediates into and out of mitochondria.
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Affiliation(s)
- Lu Li
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - 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
| | - Jordan Radomiljac
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Yan Wang
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Simon R Law
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden
| | - Reena Narsai
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Oliver Berkowitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Owen Duncan
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009 Australia
| | - 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
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, 3086, Australia
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Sultan LD, Mileshina D, Grewe F, Rolle K, Abudraham S, Głodowicz P, Niazi AK, Keren I, Shevtsov S, Klipcan L, Barciszewski J, Mower JP, Dietrich A, Ostersetzer-Biran O. The Reverse Transcriptase/RNA Maturase Protein MatR Is Required for the Splicing of Various Group II Introns in Brassicaceae Mitochondria. THE PLANT CELL 2016; 28:2805-2829. [PMID: 27760804 PMCID: PMC5155343 DOI: 10.1105/tpc.16.00398] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/26/2016] [Accepted: 10/19/2016] [Indexed: 05/18/2023]
Abstract
Group II introns are large catalytic RNAs that are ancestrally related to nuclear spliceosomal introns. Sequences corresponding to group II RNAs are found in many prokaryotes and are particularly prevalent within plants organellar genomes. Proteins encoded within the introns themselves (maturases) facilitate the splicing of their own host pre-RNAs. Mitochondrial introns in plants have diverged considerably in sequence and have lost their maturases. In angiosperms, only a single maturase has been retained in the mitochondrial DNA: the matR gene found within NADH dehydrogenase 1 (nad1) intron 4. Its conservation across land plants and RNA editing events, which restore conserved amino acids, indicates that matR encodes a functional protein. However, the biological role of MatR remains unclear. Here, we performed an in vivo investigation of the roles of MatR in Brassicaceae. Directed knockdown of matR expression via synthetically designed ribozymes altered the processing of various introns, including nad1 i4. Pull-down experiments further indicated that MatR is associated with nad1 i4 and several other intron-containing pre-mRNAs. MatR may thus represent an intermediate link in the gradual evolutionary transition from the intron-specific maturases in bacteria into their versatile spliceosomal descendants in the nucleus. The similarity between maturases and the core spliceosomal Prp8 protein further supports this intriguing theory.
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Affiliation(s)
- Laure D Sultan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Daria Mileshina
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 67084 Strasbourg, France
| | - Felix Grewe
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - Katarzyna Rolle
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Sivan Abudraham
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Paweł Głodowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Adnan Khan Niazi
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 67084 Strasbourg, France
| | - Ido Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Sofia Shevtsov
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Liron Klipcan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 67084 Strasbourg, France
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
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A multi-step peptidolytic cascade for amino acid recovery in chloroplasts. Nat Chem Biol 2016; 13:15-17. [PMID: 27820795 DOI: 10.1038/nchembio.2227] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/24/2016] [Indexed: 12/28/2022]
Abstract
Plastids (including chloroplasts) are subcellular sites for a plethora of proteolytic reactions, required in functions ranging from protein biogenesis to quality control. Here we show that peptides generated from pre-protein maturation within chloroplasts of Arabidopsis thaliana are degraded to amino acids by a multi-step peptidolytic cascade consisting of oligopeptidases and aminopeptidases, effectively allowing the recovery of single amino acids within these organelles.
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Van Aken O, De Clercq I, Ivanova A, Law SR, Van Breusegem F, Millar AH, Whelan J. Mitochondrial and Chloroplast Stress Responses Are Modulated in Distinct Touch and Chemical Inhibition Phases. PLANT PHYSIOLOGY 2016; 171:2150-65. [PMID: 27208304 PMCID: PMC4936557 DOI: 10.1104/pp.16.00273] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/04/2016] [Indexed: 05/20/2023]
Abstract
Previous studies have identified a range of transcription factors that modulate retrograde regulation of mitochondrial and chloroplast functions in Arabidopsis (Arabidopsis thaliana). However, the relative importance of these regulators and whether they act downstream of separate or overlapping signaling cascades is still unclear. Here, we demonstrate that multiple stress-related signaling pathways, with distinct kinetic signatures, converge on overlapping gene sets involved in energy organelle function. The transcription factor ANAC017 is almost solely responsible for transcript induction of marker genes around 3 to 6 h after chemical inhibition of organelle function and is a key regulator of mitochondrial and specific types of chloroplast retrograde signaling. However, an independent and highly transient gene expression phase, initiated within 10 to 30 min after treatment, also targets energy organelle functions, and is related to touch and wounding responses. Metabolite analysis demonstrates that this early response is concurrent with rapid changes in tricarboxylic acid cycle intermediates and large changes in transcript abundance of genes encoding mitochondrial dicarboxylate carrier proteins. It was further demonstrated that transcription factors AtWRKY15 and AtWRKY40 have repressive regulatory roles in this touch-responsive gene expression. Together, our results show that several regulatory systems can independently affect energy organelle function in response to stress, providing different means to exert operational control.
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Affiliation(s)
- Olivier Van Aken
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, The University of Western Australia, Crawley 6009, Western Australia, Australia (O.V.A., A.I., A.H.M.);Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Victoria 3086, Australia (I.D.C., S.R.L.);Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.); andDepartment of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden (S.R.L.)
| | - Inge De Clercq
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, The University of Western Australia, Crawley 6009, Western Australia, Australia (O.V.A., A.I., A.H.M.);Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Victoria 3086, Australia (I.D.C., S.R.L.);Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.); andDepartment of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden (S.R.L.)
| | - Aneta Ivanova
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, The University of Western Australia, Crawley 6009, Western Australia, Australia (O.V.A., A.I., A.H.M.);Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Victoria 3086, Australia (I.D.C., S.R.L.);Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.); andDepartment of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden (S.R.L.)
| | - Simon R Law
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, The University of Western Australia, Crawley 6009, Western Australia, Australia (O.V.A., A.I., A.H.M.);Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Victoria 3086, Australia (I.D.C., S.R.L.);Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.); andDepartment of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden (S.R.L.)
| | - Frank Van Breusegem
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, The University of Western Australia, Crawley 6009, Western Australia, Australia (O.V.A., A.I., A.H.M.);Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Victoria 3086, Australia (I.D.C., S.R.L.);Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.); andDepartment of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden (S.R.L.)
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, The University of Western Australia, Crawley 6009, Western Australia, Australia (O.V.A., A.I., A.H.M.);Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Victoria 3086, Australia (I.D.C., S.R.L.);Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.); andDepartment of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden (S.R.L.)
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, The University of Western Australia, Crawley 6009, Western Australia, Australia (O.V.A., A.I., A.H.M.);Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Victoria 3086, Australia (I.D.C., S.R.L.);Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium (I.D.C., F.V.B.); andDepartment of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden (S.R.L.)
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Mitochondrial Proteome Studies in Seeds during Germination. Proteomes 2016; 4:proteomes4020019. [PMID: 28248229 PMCID: PMC5217346 DOI: 10.3390/proteomes4020019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 01/25/2023] Open
Abstract
Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications. The aim of this review is to give a comprehensive summary of seed mitochondrial proteome studies during germination of various plant model organisms. We describe different gel-based and gel-free proteomic approaches used to characterize mitochondrial proteomes of germinating seeds as well as challenges and limitations of these proteomic studies. Furthermore, the dynamic changes in the abundance of the mitochondrial proteomes of germinating seeds are illustrated, highlighting numerous mitochondrial proteins involved in respiration, tricarboxycylic acid (TCA) cycle, metabolism, import, and stress response as potentially important for seed germination. We then review seed mitochondrial protein carbonylation, phosphorylation, and S-nitrosylation as well as discuss the possible link between these post-translational modifications (PTMs) and the regulation of seed germination.
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Berkowitz O, De Clercq I, Van Breusegem F, Whelan J. Interaction between hormonal and mitochondrial signalling during growth, development and in plant defence responses. PLANT, CELL & ENVIRONMENT 2016; 39:1127-39. [PMID: 26763171 DOI: 10.1111/pce.12712] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/22/2015] [Accepted: 12/30/2015] [Indexed: 05/23/2023]
Abstract
Mitochondria play a central role in plant metabolism as they are a major source of ATP through synthesis by the oxidative phosphorylation pathway and harbour key metabolic reactions such as the TCA cycle. The energy and building blocks produced by mitochondria are essential to drive plant growth and development as well as to provide fuel for responses to abiotic and biotic stresses. The majority of mitochondrial proteins are encoded in the nuclear genome and have to be imported into the organelle. For the regulation of the corresponding genes intricate signalling pathways exist to adjust their expression. Signals directly regulate nuclear gene expression (anterograde signalling) to adjust the protein composition of the mitochondria to the needs of the cell. In parallel, mitochondria communicate back their functional status to the nucleus (retrograde signalling) to prompt transcriptional regulation of responsive genes via largely unknown signalling mechanisms. Plant hormones are the major signalling components regulating all layers of plant development and cellular functions. Increasing evidence is now becoming available that plant hormones are also part of signalling networks controlling mitochondrial function and their biogenesis. This review summarizes recent advances in understanding the interaction of mitochondrial and hormonal signalling pathways.
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Affiliation(s)
- Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Inge De Clercq
- Department of Animal, Plant and Soil Sciences, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
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Yin G, Whelan J, Wu S, Zhou J, Chen B, Chen X, Zhang J, He J, Xin X, Lu X. Comprehensive Mitochondrial Metabolic Shift during the Critical Node of Seed Ageing in Rice. PLoS One 2016; 11:e0148013. [PMID: 27124767 PMCID: PMC4849721 DOI: 10.1371/journal.pone.0148013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/12/2016] [Indexed: 11/19/2022] Open
Abstract
The critical node (CN) in seed aging in rice (Oryza sativa) is the transformation from Phase I (P-I) to Phase II (P-II) of the reverse S-shaped curve (RS-SC). Although mitochondrial dysfunction plays a key role in seed ageing, the metabolic shift in the CN remains poorly understood. Here, we investigated the mitochondrial regulatory mechanisms during the CN of rice seed ageing. We showed that during the CN of seed ageing, the mitochondrial ultrastructure was impaired, causing oxygen consumption to decrease, along with cytochrome c (cyt c) oxidase and malate dehydrogenase (MDH) activity. In addition, the transcript levels for the alternative pathway of the electron transport chain (ETC) were significantly induced, whereas the transcripts of the cytochrome oxidase (COX) pathway were inhibited. These changes were concomitant with the down-regulation of mitochondrial protein levels related to carbon and nitrogen metabolism, ATP synthase (ATPase) complex, tricarboxylic acid cycle (TCA) cycle, mitochondrial oxidative enzymes, and a variety of other proteins. Therefore, while these responses inhibit the production of ATP and its intermediates, signals from mitochondria (such as the decrease of cyt c and accumulation of reactive oxygen species (ROS)) may also induce oxidative damage. These events provide considerable information about the mitochondrial metabolic shifts involved in the progression of seed ageing in the CN.
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Affiliation(s)
- Guangkun Yin
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Shuhua Wu
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Zhou
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Baoyin Chen
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaoling Chen
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinmei Zhang
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Juanjuan He
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Xin
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- * E-mail: (XL); (XX)
| | - Xinxiong Lu
- National Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- * E-mail: (XL); (XX)
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Silva AT, Ribone PA, Chan RL, Ligterink W, Hilhorst HWM. A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in Arabidopsis thaliana. PLANT PHYSIOLOGY 2016; 170:2218-31. [PMID: 26888061 PMCID: PMC4825141 DOI: 10.1104/pp.15.01704] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/15/2016] [Indexed: 05/18/2023]
Abstract
The transition from a quiescent dry seed to an actively growing photoautotrophic seedling is a complex and crucial trait for plant propagation. This study provides a detailed description of global gene expression in seven successive developmental stages of seedling establishment in Arabidopsis (Arabidopsis thaliana). Using the transcriptome signature from these developmental stages, we obtained a coexpression gene network that highlights interactions between known regulators of the seed-to-seedling transition and predicts the functions of uncharacterized genes in seedling establishment. The coexpressed gene data sets together with the transcriptional module indicate biological functions related to seedling establishment. Characterization of the homeodomain leucine zipper I transcription factor AtHB13, which is expressed during the seed-to-seedling transition, demonstrated that this gene regulates some of the network nodes and affects late seedling establishment. Knockout mutants for athb13 showed increased primary root length as compared with wild-type (Columbia-0) seedlings, suggesting that this transcription factor is a negative regulator of early root growth, possibly repressing cell division and/or cell elongation or the length of time that cells elongate. The signal transduction pathways present during the early phases of the seed-to-seedling transition anticipate the control of important events for a vigorous seedling, such as root growth. This study demonstrates that a gene coexpression network together with transcriptional modules can provide insights that are not derived from comparative transcript profiling alone.
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Affiliation(s)
- Anderson Tadeu Silva
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
| | - Pamela A Ribone
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
| | - Raquel L Chan
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
| | - Wilco Ligterink
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
| | - Henk W M Hilhorst
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
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Karniely S, Weekes MP, Antrobus R, Rorbach J, van Haute L, Umrania Y, Smith DL, Stanton RJ, Minczuk M, Lehner PJ, Sinclair JH. Human Cytomegalovirus Infection Upregulates the Mitochondrial Transcription and Translation Machineries. mBio 2016; 7:e00029. [PMID: 27025248 PMCID: PMC4807356 DOI: 10.1128/mbio.00029-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/25/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Infection with human cytomegalovirus (HCMV) profoundly affects cellular metabolism. Like in tumor cells, HCMV infection increases glycolysis, and glucose carbon is shifted from the mitochondrial tricarboxylic acid cycle to the biosynthesis of fatty acids. However, unlike in many tumor cells, where aerobic glycolysis is accompanied by suppression of mitochondrial oxidative phosphorylation, HCMV induces mitochondrial biogenesis and respiration. Here, we affinity purified mitochondria and used quantitative mass spectrometry to determine how the mitochondrial proteome changes upon HCMV infection. We found that the mitochondrial transcription and translation systems are induced early during the viral replication cycle. Specifically, proteins involved in biogenesis of the mitochondrial ribosome were highly upregulated by HCMV infection. Inhibition of mitochondrial translation with chloramphenicol or knockdown of HCMV-induced ribosome biogenesis factor MRM3 abolished the HCMV-mediated increase in mitochondrially encoded proteins and significantly impaired viral growth under bioenergetically restricting conditions. Our findings demonstrate how HCMV manipulates mitochondrial biogenesis to support its replication. IMPORTANCE Human cytomegalovirus (HCMV), a betaherpesvirus, is a leading cause of morbidity and mortality during congenital infection and among immunosuppressed individuals. HCMV infection significantly changes cellular metabolism. Akin to tumor cells, in HCMV-infected cells, glycolysis is increased and glucose carbon is shifted from the tricarboxylic acid cycle to fatty acid biosynthesis. However, unlike in tumor cells, HCMV induces mitochondrial biogenesis even under aerobic glycolysis. Here, we have affinity purified mitochondria and used quantitative mass spectrometry to determine how the mitochondrial proteome changes upon HCMV infection. We find that the mitochondrial transcription and translation systems are induced early during the viral replication cycle. Specifically, proteins involved in biogenesis of the mitochondrial ribosome were highly upregulated by HCMV infection. Inhibition of mitochondrial translation with chloramphenicol or knockdown of HCMV-induced ribosome biogenesis factor MRM3 abolished the HCMV-mediated increase in mitochondrially encoded proteins and significantly impaired viral growth. Our findings demonstrate how HCMV manipulates mitochondrial biogenesis to support its replication.
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Affiliation(s)
- S Karniely
- Department of Medicine, University of Cambridge Clinical School, Addenbrookes Hospital, Cambridge, United Kingdom
| | - M P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - R Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - J Rorbach
- MRC, Mitochondrial Biology Unit, Cambridge, United Kingdom
| | - L van Haute
- MRC, Mitochondrial Biology Unit, Cambridge, United Kingdom
| | - Y Umrania
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - D L Smith
- Paterson Institute for Cancer Research, University of Manchester, Withington, Manchester, United Kingdom
| | - R J Stanton
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - M Minczuk
- MRC, Mitochondrial Biology Unit, Cambridge, United Kingdom
| | - P J Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - J H Sinclair
- Department of Medicine, University of Cambridge Clinical School, Addenbrookes Hospital, Cambridge, United Kingdom
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Ströher E, Grassl J, Carrie C, Fenske R, Whelan J, Millar AH. Glutaredoxin S15 Is Involved in Fe-S Cluster Transfer in Mitochondria Influencing Lipoic Acid-Dependent Enzymes, Plant Growth, and Arsenic Tolerance in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:1284-99. [PMID: 26672074 PMCID: PMC4775112 DOI: 10.1104/pp.15.01308] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/14/2015] [Indexed: 05/18/2023]
Abstract
Glutaredoxins (Grxs) are small proteins that function as oxidoreductases with roles in deglutathionylation of proteins, reduction of antioxidants, and assembly of iron-sulfur (Fe-S) cluster-containing enzymes. Which of the 33 Grxs in Arabidopsis (Arabidopsis thaliana) perform roles in Fe-S assembly in mitochondria is unknown. We have examined in detail the function of the monothiol GrxS15 in plants. Our results show its exclusive mitochondrial localization, and we are concluding it is the major or only Grx in this subcellular location. Recombinant GrxS15 has a very low deglutathionylation and dehydroascorbate reductase activity, but it binds a Fe-S cluster. Partially removing GrxS15 from mitochondria slowed whole plant growth and respiration. Native GrxS15 is shown to be especially important for lipoic acid-dependent enzymes in mitochondria, highlighting a putative role in the transfer of Fe-S clusters in this process. The enhanced effect of the toxin arsenic on the growth of GrxS15 knockdown plants compared to wild type highlights the role of mitochondrial glutaredoxin Fe-S-binding in whole plant growth and toxin tolerance.
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Affiliation(s)
- Elke Ströher
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - Julia Grassl
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - Chris Carrie
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, M316, Faculty of Science, The University of Western Australia, Crawley, 6009 Western Australia, Australia (E.S., J.G., C.C., R.F., A.H.M.); and ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, LaTrobe University, Bundoora, 3086 Victoria, Australia (J.W.)
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