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Fan K, Peng Y, Ren Z, Li D, Zhen S, Hey S, Cui Y, Fu J, Gu R, Wang J, Wang G, Li L. Maize Defective Kernel605 Encodes a Canonical DYW-Type PPR Protein that Edits a Conserved Site of nad1 and Is Essential for Seed Nutritional Quality. PLANT & CELL PHYSIOLOGY 2020; 61:1954-1966. [PMID: 32818255 DOI: 10.1093/pcp/pcaa110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins involved in mitochondrial RNA cytidine (C)-to-uridine (U) editing mostly result in stagnant embryo and endosperm development upon loss of function. However, less is known about PPRs that are involved in farinaceous endosperm formation and maize quality. Here, we cloned a maize DYW-type PPR Defective Kernel605 (Dek605). Mutation of Dek605 delayed seed and seedling development. Mitochondrial transcript analysis of dek605 revealed that loss of DEK605 impaired C-to-U editing at the nad1-608 site and fails to alter Ser203 to Phe203 in NAD1 (dehydrogenase complex I), disrupting complex I assembly and reducing NADH dehydrogenase activity. Meanwhile, complexes III and IV in the cytochrome pathway, as well as AOX2 in the alternative respiratory pathway, are dramatically increased. Interestingly, the dek605 mutation resulted in opaque endosperm and increased levels of the free amino acids alanine, aspartic acid and phenylalanine. The down- and upregulated genes mainly involved in stress response-related and seed dormancy-related pathways, respectively, were observed after transcriptome analysis of dek605 at 12 d after pollination. Collectively, these results indicate that Dek605 specifically affects the single nad1-608 site and is required for normal seed development and resulted in nutritional quality relevant amino acid accumulation.
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Affiliation(s)
- Kaijian Fan
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yixuan Peng
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Zhenjing Ren
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Delin Li
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Sihan Zhen
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Stefan Hey
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Yu Cui
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Junjie Fu
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Riliang Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Jianhua Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
| | - Guoying Wang
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Li Li
- Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China
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Shimada S, Maeda S, Hikita M, Mieda-Higa K, Uene S, Nariai Y, Shinzawa-Itoh K. Solubilization conditions for bovine heart mitochondrial membranes allow selective purification of large quantities of respiratory complexes I, III, and V. Protein Expr Purif 2018; 150:33-43. [PMID: 29702187 DOI: 10.1016/j.pep.2018.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 11/28/2022]
Abstract
Ascertaining the structure and functions of mitochondrial respiratory chain complexes is essential to understanding the biological mechanisms of energy conversion; therefore, numerous studies have examined these complexes. A fundamental part of that research involves devising a method for purifying samples with good reproducibility; the samples obtained need to be stable and their constituents need to retain the same structure and functions they possess when in mitochondrial membranes. Submitochondrial bovine heart particles were isolated using differential centrifugation to adjust to a membrane concentration of 46.0% (w/v) or 31.5% (w/v) based on weight. After 0.7% (w/v) deoxycholic acid, 0.4% (w/v) decyl maltoside, and 7.2% (w/v) potassium chloride were added to the mitochondrial membranes, those membranes were solubilized. At a membrane concentration of 46%, complex V was selectively solubilized, whereas at a concentration of 31.5% (w/v), complexes I and III were solubilized. Two steps-sucrose density gradient centrifugation and anion-exchange chromatography on a POROS HQ 20 μm column-enabled selective purification of samples that retained their structure and functions. These two steps enabled complexes I, III, and V to be purified in two days with a high yield. Complexes I, III, and V were stabilized with n-decyl-β-D-maltoside. A total of 200 mg-300 mg of those complexes from one bovine heart (1.1 kg muscle) was purified with good reproducibility, and the complexes retained the same functions they possessed while in mitochondrial membranes.
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Affiliation(s)
- Satoru Shimada
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Shintaro Maeda
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Masahide Hikita
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Kaoru Mieda-Higa
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Shigefumi Uene
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Yukiko Nariai
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Kyoko Shinzawa-Itoh
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan.
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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part I. [4Fe-4S] + [2Fe-2S] iron-sulfur proteins. J Struct Biol 2017; 200:1-19. [DOI: 10.1016/j.jsb.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
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Abe K, Fujiyoshi Y. Cryo-electron microscopy for structure analyses of membrane proteins in the lipid bilayer. Curr Opin Struct Biol 2016; 39:71-78. [DOI: 10.1016/j.sbi.2016.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/20/2016] [Accepted: 06/01/2016] [Indexed: 12/12/2022]
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Ostersetzer-Biran O. Respiratory complex I and embryo development. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1205-7. [PMID: 26912908 PMCID: PMC4762395 DOI: 10.1093/jxb/erw051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel 9190401
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Subrahmanian N, Remacle C, Hamel PP. Plant mitochondrial Complex I composition and assembly: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1001-14. [PMID: 26801215 DOI: 10.1016/j.bbabio.2016.01.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/18/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
In the mitochondrial inner membrane, oxidative phosphorylation generates ATP via the operation of several multimeric enzymes. The proton-pumping Complex I (NADH:ubiquinone oxidoreductase) is the first and most complicated enzyme required in this process. Complex I is an L-shaped enzyme consisting of more than 40 subunits, one FMN molecule and eight Fe-S clusters. In recent years, genetic and proteomic analyses of Complex I mutants in various model systems, including plants, have provided valuable insights into the assembly of this multimeric enzyme. Assisted by a number of key players, referred to as "assembly factors", the assembly of Complex I takes place in a sequential and modular manner. Although a number of factors have been identified, their precise function in mediating Complex I assembly still remains to be elucidated. This review summarizes our current knowledge of plant Complex I composition and assembly derived from studies in plant model systems such as Arabidopsis thaliana and Chlamydomonas reinhardtii. Plant Complex I is highly conserved and comprises a significant number of subunits also present in mammalian and fungal Complexes I. Plant Complex I also contains additional subunits absent from the mammalian and fungal counterpart, whose function in enzyme activity and assembly is not clearly understood. While 14 assembly factors have been identified for human Complex I, only two proteins, namely GLDH and INDH, have been established as bona fide assembly factors for plant Complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Nitya Subrahmanian
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Claire Remacle
- Institute of Botany, Department of Life Sciences, University of Liège, 4000 Liège, Belgium
| | - Patrice Paul Hamel
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA; The Ohio State University, Department of Biological Chemistry and Pharmacology, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA.
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Osuda Y, Shinzawa-Itoh K, Tani K, Maeda S, Yoshikawa S, Tsukihara T, Gerle C. Two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes. Microscopy (Oxf) 2016; 65:263-7. [PMID: 26754561 PMCID: PMC4892887 DOI: 10.1093/jmicro/dfv381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/09/2015] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial cytochrome c oxidase utilizes electrons provided by cytochrome c for the active vectorial transport of protons across the inner mitochondrial membrane through the reduction of molecular oxygen to water. Direct structural evidence on the transient cytochrome c oxidase–cytochrome c complex thus far, however, remains elusive and its physiological relevant oligomeric form is unclear. Here, we report on the 2D crystallization of monomeric bovine cytochrome c oxidase with tightly bound cytochrome c at a molar ratio of 1:1 in reconstituted lipid membranes at the basic pH of 8.5 and low ionic strength.
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Affiliation(s)
- Yukiho Osuda
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297, Japan
| | - Kyoko Shinzawa-Itoh
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297, Japan
| | - Kazutoshi Tani
- Cellular and Structural Physiology Institute, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Shintaro Maeda
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shinya Yoshikawa
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297, Japan
| | - Tomitake Tsukihara
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297, Japan Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Japan
| | - Christoph Gerle
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297, Japan Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Japan
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Shinzawa-Itoh K, Shimomura H, Yanagisawa S, Shimada S, Takahashi R, Oosaki M, Ogura T, Tsukihara T. Purification of Active Respiratory Supercomplex from Bovine Heart Mitochondria Enables Functional Studies. J Biol Chem 2015; 291:4178-84. [PMID: 26698328 PMCID: PMC4759192 DOI: 10.1074/jbc.m115.680553] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Indexed: 11/18/2022] Open
Abstract
To understand the roles of mitochondrial respiratory chain supercomplexes, methods for consistently separating and preparing supercomplexes must be established. To this end, we solubilized supercomplexes from bovine heart mitochondria with digitonin and then replaced digitonin with amphipol (A8–35), an amphiphilic polymer. Afterward, supercomplexes were separated from other complexes by sucrose density gradient centrifugation. Twenty-six grams of bovine myocardium yielded 3.2 mg of amphipol-stabilized supercomplex. The purified supercomplexes were analyzed based on their absorption spectra as well as Q10 (ubiquinone with ten isoprene units) and lipid assays. The supercomplex sample did not contain cytochrome c but did contain complexes I, III, and IV at a ratio of 1:2:1, 6 molecules of Q10, and 623 atoms of phosphorus. When cytochrome c was added, the supercomplex exhibited KCN-sensitive NADH oxidation; thus, the purified supercomplex was active. Reduced complex IV absorbs at 444 nm, so we measured the resonance Raman spectrum of the reduced amphipol-solubilized supercomplex and the mixture of amphipol-solubilized complexes I1, III2, and IV1 using an excitation wavelength of 441.6 nm, allowing measurement precision comparable with that obtained for complex IV alone. Use of the purified active sample provides insights into the effects of supercomplex formation.
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Affiliation(s)
- Kyoko Shinzawa-Itoh
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamighori, Akoh, Hyogo, 678-1297, Japan,
| | - Harunobu Shimomura
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Sachiko Yanagisawa
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Satoru Shimada
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamighori, Akoh, Hyogo, 678-1297, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan, and
| | - Ryoko Takahashi
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Marika Oosaki
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Takashi Ogura
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Tomitake Tsukihara
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamighori, Akoh, Hyogo, 678-1297, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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