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Islam MF, Yamatani H, Takami T, Kusaba M, Sakamoto W. Characterization of organelle DNA degradation mediated by DPD1 exonuclease in the rice genome-edited line. PLANT MOLECULAR BIOLOGY 2024; 114:71. [PMID: 38856917 PMCID: PMC11164812 DOI: 10.1007/s11103-024-01452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/05/2024] [Indexed: 06/11/2024]
Abstract
Mitochondria and plastids, originated as ancestral endosymbiotic bacteria, contain their own DNA sequences. These organelle DNAs (orgDNAs) are, despite the limited genetic information they contain, an indispensable part of the genetic systems but exist as multiple copies, making up a substantial amount of total cellular DNA. Given this abundance, orgDNA is known to undergo tissue-specific degradation in plants. Previous studies have shown that the exonuclease DPD1, conserved among seed plants, degrades orgDNAs during pollen maturation and leaf senescence in Arabidopsis. However, tissue-specific orgDNA degradation was shown to differ among species. To extend our knowledge, we characterized DPD1 in rice in this study. We created a genome-edited (GE) mutant in which OsDPD1 and OsDPD1-like were inactivated. Characterization of this GE plant demonstrated that DPD1 was involved in pollen orgDNA degradation, whereas it had no significant effect on orgDNA degradation during leaf senescence. Comparison of transcriptomes from wild-type and GE plants with different phosphate supply levels indicated that orgDNA had little impact on the phosphate starvation response, but instead had a global impact in plant growth. In fact, the GE plant showed lower fitness with reduced grain filling rate and grain weight in natural light conditions. Taken together, the presented data reinforce the important physiological roles of orgDNA degradation mediated by DPD1.
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Affiliation(s)
- Md Faridul Islam
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Hiroshi Yamatani
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233, Watanuki, Takasaki, Gunma, 370-1292, Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Makoto Kusaba
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-3 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
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2
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Liu M, Yu J, Yang M, Cao L, Chen C. Adaptive evolution of chloroplast division mechanisms during plant terrestrialization. Cell Rep 2024; 43:113950. [PMID: 38489264 DOI: 10.1016/j.celrep.2024.113950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/12/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Despite extensive research, the origin and evolution of the chloroplast division machinery remain unclear. Here, we employ recently sequenced genomes and transcriptomes of Archaeplastida clades to identify the core components of chloroplast division and reconstruct their evolutionary histories, respectively. Our findings show that complete division ring structures emerged in Charophytes. We find that Glaucophytes experienced strong selection pressure, generating diverse variants adapted to the changing terrestrial environments. By integrating the functions of chloroplast division genes (CDGs) annotated in a workflow developed using large-scale multi-omics data, we further show that dispersed duplications acquire more species-specific functions under stronger selection pressures. Notably, PARC6, a dispersed duplicate CDG, regulates leaf color and plant growth in Solanum lycopersicum, demonstrating neofunctionalization. Our findings provide an integrated perspective on the functional evolution of chloroplast division machinery and highlight the potential of dispersed duplicate genes as the primary source of adaptive evolution of chloroplast division.
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Affiliation(s)
- Moyang Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Yu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming Yang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingyan Cao
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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3
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Esch L, Ngai QY, Barclay JE, McNelly R, Hayta S, Smedley MA, Smith AM, Seung D. Increasing amyloplast size in wheat endosperm through mutation of PARC6 affects starch granule morphology. THE NEW PHYTOLOGIST 2023; 240:224-241. [PMID: 37424336 PMCID: PMC10952435 DOI: 10.1111/nph.19118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023]
Abstract
The determination of starch granule morphology in plants is poorly understood. The amyloplasts of wheat endosperm contain large discoid A-type granules and small spherical B-type granules. To study the influence of amyloplast structure on these distinct morphological types, we isolated a mutant in durum wheat (Triticum turgidum) defective in the plastid division protein PARC6, which had giant plastids in both leaves and endosperm. Endosperm amyloplasts of the mutant contained more A- and B-type granules than those of the wild-type. The mutant had increased A- and B-type granule size in mature grains, and its A-type granules had a highly aberrant, lobed surface. This morphological defect was already evident at early stages of grain development and occurred without alterations in polymer structure and composition. Plant growth and grain size, number and starch content were not affected in the mutants despite the large plastid size. Interestingly, mutation of the PARC6 paralog, ARC6, did not increase plastid or starch granule size. We suggest TtPARC6 can complement disrupted TtARC6 function by interacting with PDV2, the outer plastid envelope protein that typically interacts with ARC6 to promote plastid division. We therefore reveal an important role of amyloplast structure in starch granule morphogenesis in wheat.
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Affiliation(s)
- Lara Esch
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Qi Yang Ngai
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | | | - Rose McNelly
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Sadiye Hayta
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | | | | | - David Seung
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
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4
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Liang J, Zhang Q, Liu Y, Zhang J, Wang W, Zhang Z. Chlorosis seedling lethality 1 encoding a MAP3K protein is essential for chloroplast development in rice. BMC PLANT BIOLOGY 2022; 22:20. [PMID: 34991480 PMCID: PMC8734211 DOI: 10.1186/s12870-021-03404-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/17/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Mitogen-activated protein kinase (MAPK) cascades are conserved signaling modules in eukaryotic organisms and play essential roles in immunity and stress responses. However, the role of MAPKs in chloroplast development remains to be evidently established. RESULTS In this study, a rice chlorosis seedling lethality 1 (csl1) mutant with a Zhonghua11 (ZH11, japonica) background was isolated. Seedlings of the mutant were characterized by chlorotic leaves and death after the trefoil stage, and chloroplasts were observed to contain accumulated starch granules. Molecular cloning revealed that OsCSL1 encoded a MAPK kinase kinase22 (MKKK22) targeted to the endoplasmic reticulum (ER), and functional complementation of OsCSL1 was found to restore the normal phenotype in csl1 plants. The CRISPR/Cas9 technology was used for targeted disruption of OsCSL1, and the OsCSL1-Cas9 lines obtained therein exhibited yellow seedlings which phenocopied the csl1 mutant. CSL1/MKKK22 was observed to establish direct interaction with MKK4, and altered expression of MKK1 and MKK4 was detected in the csl1 mutant. Additionally, disruption of OsCSL1 led to reduced expression of chloroplast-associated genes, including chlorophyll biosynthetic genes, plastid-encoded RNA polymerases, nuclear-encoded RNA polymerase, and nuclear-encoded chloroplast genes. CONCLUSIONS The findings of this study revealed that OsCSL1 played roles in regulating the expression of multiple chloroplast synthesis-related genes, thereby affecting their functions, and leading to wide-ranging defects, including chlorotic seedlings and severely disrupted chloroplasts containing accumulated starch granules.
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Affiliation(s)
- Jiayan Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiuxin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Yiran Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jingjing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Wenyi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| | - Zemin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Taketa S, Hattori M, Takami T, Himi E, Sakamoto W. Mutations in a�Golden2-Like�Gene Cause Reduced Seed Weight in�Barley�albino lemma 1�Mutants. PLANT & CELL PHYSIOLOGY 2021; 62:447-457. [PMID: 33439257 DOI: 10.1093/pcp/pcab001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
The albino lemma 1 (alm1) mutants of barley (Hordeum vulgare L.) exhibit obvious chlorophyll-deficient hulls. Hulls are seed-enclosing tissues on the spike, consisting of the lemma and palea. The alm1 phenotype is also expressed in the pericarp, culm nodes and basal leaf sheaths, but leaf blades and awns are normal green. A single recessive nuclear gene controls tissue-specific alm1 phenotypic expression. Positional cloning revealed that the ALM1 gene encodes a Golden 2-like (GLK) transcription factor, HvGLK2, belonging to the GARP subfamily of Myb transcription factors. This finding was validated by genetic evidence indicating that all 10 alm1 mutants studied had a lesion in functionally important regions of HvGLK2, including the three alpha-helix domains, an AREAEAA motif and the GCT box. Transmission electron microscopy revealed that, in lemmas of the alm1.g mutant, the chloroplasts lacked thylakoid membranes, instead of stacked thylakoid grana in wild-type chloroplasts. Compared with wild type, alm1.g plants showed similar levels of leaf photosynthesis but reduced spike photosynthesis by 34%. The alm1.g mutant and the alm1.a mutant showed a reduction in 100-grain weight by 15.8% and 23.1%, respectively. As in other plants, barley has HvGLK2 and a paralog, HvGLK1. In flag leaves and awns, HvGLK2 and HvGLK1 are expressed at moderate levels, but in hulls, HvGLK1 expression was barely detectable compared with HvGLK2. Barley alm1/Hvglk2 mutants exhibit more severe phenotypes than glk2 mutants of other plant species reported to date. The severe alm1 phenotypic expression in multiple tissues indicates that HvGLK2 plays some roles that are nonredundant with HvGLK1.
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Affiliation(s)
- Shin Taketa
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Momoko Hattori
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Eiko Himi
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
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6
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Xiong E, Li Z, Zhang C, Zhang J, Liu Y, Peng T, Chen Z, Zhao Q. A study of leaf-senescence genes in rice based on a combination of genomics, proteomics and bioinformatics. Brief Bioinform 2020; 22:5998850. [PMID: 33257942 DOI: 10.1093/bib/bbaa305] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/15/2020] [Accepted: 10/10/2020] [Indexed: 12/14/2022] Open
Abstract
Leaf senescence is a highly complex, genetically regulated and well-ordered process with multiple layers and pathways. Delaying leaf senescence would help increase grain yields in rice. Over the past 15 years, more than 100 rice leaf-senescence genes have been cloned, greatly improving the understanding of leaf senescence in rice. Systematically elucidating the molecular mechanisms underlying leaf senescence will provide breeders with new tools/options for improving many important agronomic traits. In this study, we summarized recent reports on 125 rice leaf-senescence genes, providing an overview of the research progress in this field by analyzing the subcellular localizations, molecular functions and the relationship of them. These data showed that chlorophyll synthesis and degradation, chloroplast development, abscisic acid pathway, jasmonic acid pathway, nitrogen assimilation and ROS play an important role in regulating the leaf senescence in rice. Furthermore, we predicted and analyzed the proteins that interact with leaf-senescence proteins and achieved a more profound understanding of the molecular principles underlying the regulatory mechanisms by which leaf senescence occurs, thus providing new insights for future investigations of leaf senescence in rice.
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Affiliation(s)
- Erhui Xiong
- College of Agriculture, Henan Agricultural University (HAU), China
| | - Zhiyong Li
- Academy for Advanced Interdisciplinary Studies, South University of Science and Technology, Shenzhen, China
| | - Chen Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | | | - Ye Liu
- College of Agriculture, HAU
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7
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Zhang J, Wu S, Boehlein SK, McCarty DR, Song G, Walley JW, Myers A, Settles AM. Maize defective kernel5 is a bacterial TamB homologue required for chloroplast envelope biogenesis. J Cell Biol 2019; 218:2638-2658. [PMID: 31235479 PMCID: PMC6683743 DOI: 10.1083/jcb.201807166] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 05/07/2019] [Accepted: 06/04/2019] [Indexed: 01/10/2023] Open
Abstract
Zhang et al. show that the maize dek5 locus is required for chloroplast envelope biogenesis and encodes a TamB-like protein. Bacterial TamB proteins facilitate insertion of β-barrel outer membrane proteins, indicating plastids have a conserved mechanism for envelope membrane biogenesis. Chloroplasts are of prokaryotic origin with a double-membrane envelope separating plastid metabolism from the cytosol. Envelope membrane proteins integrate chloroplasts with the cell, but envelope biogenesis mechanisms remain elusive. We show that maize defective kernel5 (dek5) is critical for envelope biogenesis. Amyloplasts and chloroplasts are larger and reduced in number in dek5 with multiple ultrastructural defects. The DEK5 protein is homologous to rice SSG4, Arabidopsis thaliana EMB2410/TIC236, and Escherichia coli tamB. TamB functions in bacterial outer membrane biogenesis. DEK5 is localized to the envelope with a topology analogous to TamB. Increased levels of soluble sugars in dek5 developing endosperm and elevated osmotic pressure in mutant leaf cells suggest defective intracellular solute transport. Proteomics and antibody-based analyses show dek5 reduces levels of Toc75 and chloroplast envelope transporters. Moreover, dek5 chloroplasts reduce inorganic phosphate uptake with at least an 80% reduction relative to normal chloroplasts. These data suggest that DEK5 functions in plastid envelope biogenesis to enable transport of metabolites and proteins.
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Affiliation(s)
- Junya Zhang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL
| | - Shan Wu
- Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Susan K Boehlein
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL.,Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Donald R McCarty
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL.,Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Gaoyuan Song
- Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Justin W Walley
- Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Alan Myers
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA
| | - A Mark Settles
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL .,Horticultural Sciences Department, University of Florida, Gainesville, FL
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8
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Zhao Y, Qiang C, Wang X, Chen Y, Deng J, Jiang C, Sun X, Chen H, Li J, Piao W, Zhu X, Zhang Z, Zhang H, Li Z, Li J. New alleles for chlorophyll content and stay-green traits revealed by a genome wide association study in rice (Oryza sativa). Sci Rep 2019; 9:2541. [PMID: 30796281 PMCID: PMC6384888 DOI: 10.1038/s41598-019-39280-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/11/2019] [Indexed: 11/17/2022] Open
Abstract
Higher chlorophyll content (CC) and strong stay-green (SG) traits are conducive for improvement of photosynthetic efficiency in plants. Exploration of natural elite alleles for CC and SG, and highly resolved gene haplotypes are beneficial to rational design of breeding for high-photosynthetic efficiency. Phenotypic analysis of 368 rice accessions showed no significant correlation between CC and SG, and higher CC and stronger SG in japonica than in indica. Genome-wide association studies of six indices for CC and SG identified a large number of association signals, among which 14 were identified as pleiotropic regions for CC and SG. Twenty-five known genes and pleiotropic candidate gene OsSG1 accounted for natural variation in CC and SG. Further analysis indicated that 20 large-effect, non-synonymous SNPs within six known genes around GWAS signals and three SNPs in the promoter of OsSG1 could be functional causing significant phenotypic differences between alleles. Superior haplotypes were identified based on these potentially functional SNPs. Population analyses of 368 cultivated accessions and 446 wild accessions based on SNPs within genes for CC and SG suggested that these genes had been subjected to strong positive selection in japonica in the process of spreading from its subtropical origin to the North China temperate zone. Our studies point to important genes that account for natural variation and provide superior haplotypes of possible functional SNPs that will be beneficial in breeding for high-photosynthetic efficiency in rice.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chenggen Qiang
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xueqiang Wang
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yanfa Chen
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinqiang Deng
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Conghui Jiang
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xingming Sun
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Haiyang Chen
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jin Li
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilan Piao
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Xiaoyang Zhu
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- Key Laboratory of Crop Heterosis and Utilization of the Ministry of Education, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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9
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Niu M, Wang Y, Wang C, Lyu J, Wang Y, Dong H, Long W, Wang D, Kong W, Wang L, Guo X, Sun L, Hu T, Zhai H, Wang H, Wan J. ALR encoding dCMP deaminase is critical for DNA damage repair, cell cycle progression and plant development in rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5773-5786. [PMID: 29186482 DOI: 10.1093/jxb/erx380] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Deoxycytidine monophosphate deaminase (dCMP deaminase, DCD) is crucial to the production of dTTP needed for DNA replication and damage repair. However, the effect of DCD deficiency and its molecular mechanism are poorly understood in plants. Here, we isolated and characterized a rice albinic leaf and growth retardation (alr) mutant that is manifested by albinic leaves, dwarf stature and necrotic lesions. Map-based cloning and complementation revealed that ALR encodes a DCD protein. OsDCD was expressed ubiquitously in all tissues. Enzyme activity assays showed that OsDCD catalyses conversion of dCMP to dUMP, and the ΔDCD protein in the alr mutant is a loss-of-function protein that lacks binding ability. We report that alr plants have typical DCD-mediated imbalanced dNTP pools with decreased dTTP; exogenous dTTP recovers the wild-type phenotype. A comet assay and Trypan Blue staining showed that OsDCD deficiency causes accumulation of DNA damage in the alr mutant, sometimes leading to cell apoptosis. Moreover, OsDCD deficiency triggered cell cycle checkpoints and arrested cell progression at the G1/S-phase. The expression of nuclear and plastid genome replication genes was down-regulated under decreased dTTP, and together with decreased cell proliferation and defective chloroplast development in the alr mutant this demonstrated the molecular and physiological roles of DCD-mediated dNTP pool balance in plant development.
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Affiliation(s)
- Mei Niu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Chunming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Jia Lyu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Wuhua Long
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Di Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Weiyi Kong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Liwei Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Xiuping Guo
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
| | - Liting Sun
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Tingting Hu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Huqu Zhai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
| | - Haiyang Wang
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
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10
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Rice gene SDL / RNRS1 , encoding the small subunit of ribonucleotide reductase, is required for chlorophyll synthesis and plant growth development. Gene 2017; 627:351-362. [DOI: 10.1016/j.gene.2017.05.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/18/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022]
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11
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Matsushima R, Maekawa M, Kusano M, Tomita K, Kondo H, Nishimura H, Crofts N, Fujita N, Sakamoto W. Amyloplast Membrane Protein SUBSTANDARD STARCH GRAIN6 Controls Starch Grain Size in Rice Endosperm. PLANT PHYSIOLOGY 2016; 170:1445-59. [PMID: 26792122 PMCID: PMC4775137 DOI: 10.1104/pp.15.01811] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/18/2016] [Indexed: 05/18/2023]
Abstract
Starch is a biologically and commercially important polymer of glucose. Starch is organized into starch grains (SGs) inside amyloplasts. The SG size differs depending on the plant species and is one of the most important factors for industrial applications of starch. There is limited information on genetic factors regulating SG sizes. In this study, we report the rice (Oryza sativa) mutant substandard starch grain6 (ssg6), which develops enlarged SGs in endosperm. Enlarged SGs are observed starting at 3 d after flowering. During endosperm development, a number of smaller SGs appear and coexist with enlarged SGs in the same cells. The ssg6 mutation also affects SG morphologies in pollen. The SSG6 gene was identified by map-based cloning and microarray analysis. SSG6 encodes a protein homologous to aminotransferase. SSG6 differs from other rice homologs in that it has a transmembrane domain. SSG6-green fluorescent protein is localized in the amyloplast membrane surrounding SGs in rice endosperm, pollen, and pericarp. The results of this study suggest that SSG6 is a novel protein that controls SG size. SSG6 will be a useful molecular tool for future starch breeding and applications.
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Affiliation(s)
- Ryo Matsushima
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Masahiko Maekawa
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Miyako Kusano
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Katsura Tomita
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Hideki Nishimura
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Naoko Crofts
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Naoko Fujita
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M., M.M., H.K., H.N., W.S.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (M.K.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K.);Fukui Agricultural Experiment Station, Fukui 918-8215, Japan (K.T.); andDepartment of Biological Production, Akita Prefectural University, Akita 010-0195, Japan (N.C., N.F.)
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