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Xie Y, Yu J, Tian F, Li X, Chen X, Li Y, Wu B, Miao Y. MORF9-dependent specific plastid RNA editing inhibits root growth under sugar starvation in Arabidopsis. PLANT, CELL & ENVIRONMENT 2024; 47:1921-1940. [PMID: 38357785 DOI: 10.1111/pce.14856] [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: 08/03/2023] [Revised: 01/23/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Multiple organellar RNA editing factor (MORF) complex was shown to be highly associated with C-to-U RNA editing of vascular plant editosome. However, mechanisms by which MORF9-dependent plastid RNA editing controls plant development and responses to environmental alteration remain obscure. In this study, we found that loss of MORF9 function impaired PSII efficiency, NDH activity, and carbohydrate production, rapidly promoted nuclear gene expression including sucrose transporter and sugar/energy responsive genes, and attenuated root growth under sugar starvation conditions. Sugar repletion increased MORF9 and MORF2 expression in wild-type seedlings and reduced RNA editing of matK-706, accD-794, ndhD-383 and ndhF-290 in the morf9 mutant. RNA editing efficiency of ndhD-383 and ndhF-290 sites was diminished in the gin2/morf9 double mutants, and that of matK-706, accD-794, ndhD-383 and ndhF-290 sites were significantly diminished in the snrk1/morf9 double mutants. In contrast, overexpressing HXK1 or SnRK1 promoted RNA editing rate of matK-706, accD-794, ndhD-383 and ndhF-290 in leaves of morf9 mutants, suggesting that HXK1 partially impacts MORF9 mediated ndhD-383 and ndhF-290 editing, while SnRK1 may only affect MORF9-mediated ndhF-290 site editing. Collectively, these findings suggest that sugar and/or its intermediary metabolites impair MORF9-dependent plastid RNA editing resulting in derangements of plant root development.
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Affiliation(s)
- Yakun Xie
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinfa Yu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Faan Tian
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xue Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinyan Chen
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyun Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binghua Wu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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2
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Shen C, Xu H, Huang WZ, Zhao Q, Zhu RL. Is RNA editing truly absent in the complex thalloid liverworts (Marchantiopsida)? Evidence of extensive RNA editing from Cyathodium cavernarum. THE NEW PHYTOLOGIST 2024; 242:2817-2831. [PMID: 38587065 DOI: 10.1111/nph.19750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024]
Abstract
RNA editing is a crucial modification in plants' organellar transcripts that converts cytidine to uridine (C-to-U; and sometimes uridine to cytidine) in RNA molecules. This post-transcriptional process is controlled by the PLS-class protein with a DYW domain, which belongs to the pentatricopeptide repeat (PPR) protein family. RNA editing is widespread in land plants; however, complex thalloid liverworts (Marchantiopsida) are the only group reported to lack both RNA editing and DYW-PPR protein. The liverwort Cyathodium cavernarum (Marchantiopsida, Cyathodiaceae), typically found in cave habitats, was newly found to have 129 C-to-U RNA editing sites in its chloroplast and 172 sites in its mitochondria. The Cyathodium genus, specifically C. cavernarum, has a large number of PPR editing factor genes, including 251 DYW-type PPR proteins. These DYW-type PPR proteins may be responsible for C-to-U RNA editing in C. cavernarum. Cyathodium cavernarum possesses both PPR DYW proteins and RNA editing. Our analysis suggests that the remarkable RNA editing capability of C. cavernarum may have been acquired alongside the emergence of DYW-type PPR editing factors. These findings provide insight into the evolutionary pattern of RNA editing in land plants.
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Affiliation(s)
- Chao Shen
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Hao Xu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wen-Zhuan Huang
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Qiong Zhao
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Rui-Liang Zhu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
- Tiantong National Station of Forest Ecosystem, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai, 200241, China
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3
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Sayyed A, Chen B, Wang Y, Cao SK, Tan BC. PPR596 Is Required for nad2 Intron Splicing and Complex I Biogenesis in Arabidopsis. Int J Mol Sci 2024; 25:3542. [PMID: 38542518 PMCID: PMC10971677 DOI: 10.3390/ijms25063542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
Mitochondria are essential organelles that generate energy via oxidative phosphorylation. Plant mitochondrial genome encodes some of the respiratory complex subunits, and these transcripts require accurate processing, including C-to-U RNA editing and intron splicing. Pentatricopeptide repeats (PPR) proteins are involved in various organellar RNA processing events. PPR596, a P-type PPR protein, was previously identified to function in the C-to-U editing of mitochondrial rps3 transcripts in Arabidopsis. Here, we demonstrate that PPR596 functions in the cis-splicing of nad2 intron 3 in mitochondria. Loss of the PPR596 function affects the editing at rps3eU1344SS, impairs nad2 intron 3 splicing and reduces the mitochondrial complex I's assembly and activity, while inducing alternative oxidase (AOX) gene expression. This defect in nad2 intron splicing provides a plausible explanation for the slow growth of the ppr595 mutants. Although a few P-type PPR proteins are involved in RNA C-to-U editing, our results suggest that the primary function of PPR596 is intron splicing.
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Affiliation(s)
| | | | | | | | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (A.S.); (B.C.); (Y.W.); (S.-K.C.)
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4
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Zang J, Zhang T, Zhang Z, Liu J, Chen H. DEFECTIVE KERNEL 56 functions in mitochondrial RNA editing and maize seed development. PLANT PHYSIOLOGY 2024; 194:1593-1610. [PMID: 37956067 DOI: 10.1093/plphys/kiad598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
Proper seed development is essential for achieving grain production, successful seed germination, and seedling establishment in maize (Zea mays). In the past few decades, pentatricopeptide repeat (PPR) proteins have been proven to play an essential role in regulating the development of maize kernels through posttranscriptional RNA modification of mitochondrial genes. However, the underlying mechanisms remain largely unknown. Here, we characterized a mutant of DEFECTIVE KERNEL 56 (DEK56) with defective kernels that exhibited arrested development of both the embryo and endosperm. Accordingly, we isolated DEK56 through a map-based cloning strategy and found that it encoded an E subgroup PPR protein located in the mitochondria. Dysfunction of DEK56 resulted in altered cytidine (C)-to-uridine (U) editing efficiency at 48 editing sites across 21 mitochondrial transcripts. Notably, the editing efficiency of the maturase-related (matR)-1124 site was substantially reduced or abolished in the dek56 mutant. Furthermore, we found that the splicing efficiency of NADH dehydrogenase subunit 4 (nad4) Introns 1 and 3 was substantially reduced in dek56 kernels, which might be a consequence of the defective MatR function. Through a protein-protein interaction test, we hypothesized that DEK56 carries out its function by recruiting the PPR-DYW protein PPR motif, coiled-coil, and DYW domain-containing protein 1 (PCW1). This interaction is facilitated by Multiple Organellar RNA Editing Factors (ZmMORFs) and Glutamine-Rich Protein 23 (ZmGRP23). Based on these findings, we developed a working model of PPR-mediated mitochondrial processing that plays an essential role in the development of maize kernels. The present study will further broaden our understanding of PPR-mediated seed development and provide a theoretical basis for maize improvement.
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Affiliation(s)
- Jie Zang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tengfei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100864, China
| | - Zhaogui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juan Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huabang Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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5
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Wei X, Zhu Y, Xie W, Ren W, Zhang Y, Zhang H, Dai S, Huang CF. H2O2 negatively regulates aluminum resistance via oxidation and degradation of the transcription factor STOP1. THE PLANT CELL 2024; 36:688-708. [PMID: 37936326 PMCID: PMC10896299 DOI: 10.1093/plcell/koad281] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023]
Abstract
Aluminum (Al) stress triggers the accumulation of hydrogen peroxide (H2O2) in roots. However, whether H2O2 plays a regulatory role in aluminum resistance remains unclear. In this study, we show that H2O2 plays a crucial role in regulation of Al resistance, which is modulated by the mitochondrion-localized pentatricopeptide repeat protein REGULATION OF ALMT1 EXPRESSION 6 (RAE6). Mutation in RAE6 impairs the activity of complex I of the mitochondrial electron transport chain, resulting in the accumulation of H2O2 and increased sensitivity to Al. Our results suggest that higher H2O2 concentrations promote the oxidation of SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1), an essential transcription factor that promotes Al resistance, thereby promoting its degradation by enhancing the interaction between STOP1 and the F-box protein RAE1. Conversely, decreasing H2O2 levels or blocking the oxidation of STOP1 leads to greater STOP1 stability and increased Al resistance. Moreover, we show that the thioredoxin TRX1 interacts with STOP1 to catalyze its chemical reduction. Thus, our results highlight the importance of H2O2 in Al resistance and regulation of STOP1 stability in Arabidopsis (Arabidopsis thaliana).
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Affiliation(s)
- Xiang Wei
- National Key Laboratory of Plant Molecular Genetics, Key Laboratory of Plant Design, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yifang Zhu
- National Key Laboratory of Plant Molecular Genetics, Key Laboratory of Plant Design, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenxiang Xie
- National Key Laboratory of Plant Molecular Genetics, Key Laboratory of Plant Design, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Weiwei Ren
- Development Center of Plant Germplasm Resources and Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yang Zhang
- National Key Laboratory of Plant Molecular Genetics, Key Laboratory of Plant Design, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hui Zhang
- Development Center of Plant Germplasm Resources and Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources and Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Chao-Feng Huang
- National Key Laboratory of Plant Molecular Genetics, Key Laboratory of Plant Design, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
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6
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Li C, Liu H, Qin M, Tan YJ, Ou XL, Chen XY, Wei Y, Zhang ZJ, Lei M. RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola. FRONTIERS IN PLANT SCIENCE 2024; 15:1332460. [PMID: 38379941 PMCID: PMC10876856 DOI: 10.3389/fpls.2024.1332460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.
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Affiliation(s)
- Cui Li
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Han Liu
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Mei Qin
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yao-jing Tan
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Xia-lian Ou
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Xiao-ying Chen
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ying Wei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhan-jiang Zhang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ming Lei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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7
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He Y, Liu W, Wang J. Assembly and comparative analysis of the complete mitochondrial genome of Trigonella foenum-graecum L. BMC Genomics 2023; 24:756. [PMID: 38066419 PMCID: PMC10704837 DOI: 10.1186/s12864-023-09865-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Trigonella foenum-graecum L. is a Leguminosae plant, and the stems, leaves, and seeds of this plant are rich in chemical components that are of high research value. The chloroplast (cp) genome of T. foenum-graecum has been reported, but the mitochondrial (mt) genome remains unexplored. RESULTS In this study, we used second- and third-generation sequencing methods, which have the dual advantage of combining high accuracy and longer read length. The results showed that the mt genome of T. foenum-graecum was 345,604 bp in length and 45.28% in GC content. There were 59 genes, including: 33 protein-coding genes (PCGs), 21 tRNA genes, 4 rRNA genes and 1 pseudo gene. Among them, 11 genes contained introns. The mt genome codons of T. foenum-graecum had a significant A/T preference. A total of 202 dispersed repetitive sequences, 96 simple repetitive sequences (SSRs) and 19 tandem repetitive sequences were detected. Nucleotide diversity (Pi) analysis counted the variation in each gene, with atp6 being the most notable. Both synteny and phylogenetic analyses showed close genetic relationship among Trifolium pratense, Trifolium meduseum, Trifolium grandiflorum, Trifolium aureum, Medicago truncatula and T. foenum-graecum. Notably, in the phylogenetic tree, Medicago truncatula demonstrated the highest level of genetic relatedness to T. foenum-graecum, with a strong support value of 100%. The interspecies non-synonymous substitutions (Ka)/synonymous substitutions (Ks) results showed that 23 PCGs had Ka/Ks < 1, indicating that these genes would continue to evolve under purifying selection pressure. In addition, setting the similarity at 70%, 23 homologous sequences were found in the mt genome of T. foenum-graecum. CONCLUSIONS This study explores the mt genome sequence information of T. foenum-graecum and complements our knowledge of the phylogenetic diversity of Leguminosae plants.
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Affiliation(s)
- Yanfeng He
- College of Pharmacy, Qinghai Minzu University, Xining, 810007, Qinghai, China
| | - Wenya Liu
- College of Pharmacy, Qinghai Minzu University, Xining, 810007, Qinghai, China
| | - Jiuli Wang
- The College of Ecological Environment and Resources, Qinghai Minzu University, Xining, 810007, Qinghai, China.
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8
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Feng LY, Lin PF, Xu RJ, Kang HQ, Gao LZ. Comparative Genomic Analysis of Asian Cultivated Rice and Its Wild Progenitor ( Oryza rufipogon) Has Revealed Evolutionary Innovation of the Pentatricopeptide Repeat Gene Family through Gene Duplication. Int J Mol Sci 2023; 24:16313. [PMID: 38003501 PMCID: PMC10671101 DOI: 10.3390/ijms242216313] [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: 09/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in land plants. However, current knowledge about the evolution of the PPR gene family remains largely limited. In this study, we performed a comparative genomic analysis of the PPR gene family in O. sativa and its wild progenitor, O. rufipogon, and outlined a comprehensive landscape of gene duplications. Our findings suggest that the majority of PPR genes originated from dispersed duplications. Although segmental duplications have only expanded approximately 11.30% and 13.57% of the PPR gene families in the O. sativa and O. rufipogon genomes, we interestingly obtained evidence that segmental duplication promotes the structural diversity of PPR genes through incomplete gene duplications. In the O. sativa and O. rufipogon genomes, 10 (~33.33%) and 22 pairs of gene duplications (~45.83%) had non-PPR paralogous genes through incomplete gene duplication. Segmental duplications leading to incomplete gene duplications might result in the acquisition of domains, thus promoting functional innovation and structural diversification of PPR genes. This study offers a unique perspective on the evolution of PPR gene structures and underscores the potential role of segmental duplications in PPR gene structural diversity.
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Affiliation(s)
- Li-Ying Feng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; (L.-Y.F.); (P.-F.L.)
| | - Pei-Fan Lin
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; (L.-Y.F.); (P.-F.L.)
| | - Rong-Jing Xu
- Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China; (R.-J.X.); (H.-Q.K.)
| | - Hai-Qi Kang
- Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China; (R.-J.X.); (H.-Q.K.)
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; (L.-Y.F.); (P.-F.L.)
- Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China; (R.-J.X.); (H.-Q.K.)
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9
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Wang L, Zhang Z, Han P, Liang Y, Zhang H, Fu Z, Zhao S, E Y, Zhang H, Wu X, Zhang B, Chang Y, Tang K, Zheng W, Chen L, Wang R, Gao W, Hasi A, Li X, Bai C. Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines. Sci Rep 2023; 13:15422. [PMID: 37723186 PMCID: PMC10507079 DOI: 10.1038/s41598-023-42182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023] Open
Abstract
Due to the relatively brief domestication history of sugar beet (Beta vulgaris ssp. vulgaris), our understanding of the genomic diversity and functional genes in its cultivars is limited, resulting in slow breeding progress. To address this issue, a total of 306 germplasm materials of major cultivars and breeding lines from China, the USA, and Europe were selected for genome resequencing. We investigated population structure and genetic diversity and performed selective scanning of genomic regions, identifying six novel genes associated with important agronomic traits: the candidate genes DFAX2 and P5CS for skin roughness; the candidate genes FRO5, GL24, and PPR91 for root yield and sugar yield, and the pleiotropic candidate gene POLX for flourishing growth vigour, plant height, crown size, flesh coarseness, and sugar yield. In addition, we constructed a protein-protein interaction network map and a phenotype-gene network map, which provide valuable information for identifying and characterizing functional genes affecting agronomic traits in sugar beet. Overall, our study sheds light on the future improvement of sugar beet agronomic traits at the molecular level.
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Affiliation(s)
- Liang Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Ziqiang Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Pingan Han
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yahui Liang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Huizhong Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Zengjuan Fu
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Shangmin Zhao
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yuanyuan E
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hui Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Xinrong Wu
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Bizhou Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yue Chang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Kuangang Tang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Wenzhe Zheng
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Li Chen
- College of Modern Agriculture and Ecological Environment, Heilongjiang University, Heilongjiang, China
| | - Ronghua Wang
- Beet Breeding and Seed Processing Laboratory, Institute for Sugar Beet Research, Shihezi Academy of Agricultural Sciences, Shihezi, China
| | - Weishi Gao
- Research Industrial of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumuqi, China
| | - Agula Hasi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Xiaodong Li
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.
| | - Chen Bai
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.
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10
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Oladzad A, Roy J, Mamidi S, Miklas PN, Lee R, Clevenger J, Myers Z, Korani W, McClean PE. Linked candidate genes of different functions for white mold resistance in common bean ( Phaseolus vulgaris L) are identified by multiple QTL mapping approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1233285. [PMID: 37583595 PMCID: PMC10425182 DOI: 10.3389/fpls.2023.1233285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023]
Abstract
White mold (WM) is a major disease in common bean (Phaseolus vulgaris L.), and its complex quantitative genetic control limits the development of WM resistant cultivars. WM2.2, one of the nine meta-QTL with a major effect on WM tolerance, explains up to 35% of the phenotypic variation and was previously mapped to a large genomic interval on Pv02. Our objective was to narrow the interval of this QTL using combined approach of classic QTL mapping and QTL-based bulk segregant analysis (BSA), and confirming those results with Khufu de novo QTL-seq. The phenotypic and genotypic data from two RIL populations, 'Raven'/I9365-31 (R31) and 'AN-37'/PS02-029C-20 (Z0726-9), were used to select resistant and susceptible lines to generate subpopulations for bulk DNA sequencing. The QTL physical interval was determined by considering overlapping interval of the identified QTL or peak region in both populations by three independent QTL mapping analyses. Our findings revealed that meta-QTL WM2.2 consists of three regions, WM2.2a (4.27-5.76 Mb; euchromatic), WM 2.2b (12.19 to 17.61 Mb; heterochromatic), and WM2.2c (23.01-25.74 Mb; heterochromatic) found in both populations. Gene models encoding for gibberellin 2-oxidase 8, pentatricopeptide repeat, and heat-shock proteins are the likely candidate genes associated with WM2.2a resistance. A TIR-NBS-LRR class of disease resistance protein (Phvul.002G09200) and LRR domain containing family proteins are potential candidate genes associated with WM2.2b resistance. Nine gene models encoding disease resistance protein [pathogenesis-related thaumatin superfamily protein and disease resistance-responsive (dirigent-like protein) family protein etc] found within the WM2.2c QTL interval are putative candidate genes. WM2.2a region is most likely associated with avoidance mechanisms while WM2.2b and WM2.2c regions trigger physiological resistance based on putative candidate genes.
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Affiliation(s)
- Atena Oladzad
- Genomics Data Scientist II, Sound Agriculture, Emeryville, CA, United States
| | - Jayanta Roy
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Sujan Mamidi
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Prosser, WA, United States
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Josh Clevenger
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Zachary Myers
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Walid Korani
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Genomics, Phenomics, and Bioinformatics Program, North Dakota State University, Fargo, ND, United States
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11
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Small I, Melonek J, Bohne AV, Nickelsen J, Schmitz-Linneweber C. Plant organellar RNA maturation. THE PLANT CELL 2023; 35:1727-1751. [PMID: 36807982 PMCID: PMC10226603 DOI: 10.1093/plcell/koad049] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 05/30/2023]
Abstract
Plant organellar RNA metabolism is run by a multitude of nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. In chloroplasts and mitochondria, these post-transcriptional processes are vital for the production of a small number of essential components of the photosynthetic and respiratory machinery-and consequently for organellar biogenesis and plant survival. Many organellar RBPs have been functionally assigned to individual steps in RNA maturation, often specific to selected transcripts. While the catalog of factors identified is ever-growing, our knowledge of how they achieve their functions mechanistically is far from complete. This review summarizes the current knowledge of plant organellar RNA metabolism taking an RBP-centric approach and focusing on mechanistic aspects of RBP functions and the kinetics of the processes they are involved in.
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Affiliation(s)
- Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | - Joanna Melonek
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley 6009, Australia
| | | | - Jörg Nickelsen
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
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12
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Yang H, Wang Y, Tian Y, Teng X, Lv Z, Lei J, Duan E, Dong H, Yang X, Zhang Y, Sun Y, Chen X, Bao X, Chen R, Gu C, Zhang Y, Jiang X, Ma W, Zhang P, Ji Y, Zhang Y, Wang Y, Wan J. Rice FLOURY ENDOSPERM22, encoding a pentatricopeptide repeat protein, is involved in both mitochondrial RNA splicing and editing and is crucial for endosperm development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:755-771. [PMID: 36333887 DOI: 10.1111/jipb.13402] [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: 07/26/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Most of the reported P-type pentatricopeptide repeat (PPR) proteins play roles in organelle RNA stabilization and splicing. However, P-type PPRs involved in both RNA splicing and editing have rarely been reported, and their underlying mechanism remains largely unknown. Here, we report a rice floury endosperm22 (flo22) mutant with delayed amyloplast development in endosperm cells. Map-based cloning and complementation tests demonstrated that FLO22 encodes a mitochondrion-localized P-type PPR protein. Mutation of FLO22 resulting in defective trans-splicing of mitochondrial nad1 intron 1 and perhaps causing instability of mature transcripts affected assembly and activity of complex Ⅰ, and mitochondrial morphology and function. RNA-seq analysis showed that expression levels of many genes involved in starch and sucrose metabolism were significantly down-regulated in the flo22 mutant compared with the wild type, whereas genes related to oxidative phosphorylation and the tricarboxylic acid cycle were significantly up-regulated. In addition to involvement in splicing as a P-type PPR protein, we found that FLO22 interacted with DYW3, a DYW-type PPR protein, and they may function synergistically in mitochondrial RNA editing. The present work indicated that FLO22 plays an important role in endosperm development and plant growth by participating in nad1 maturation and multi-site editing of mitochondrial messager RNA.
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Affiliation(s)
- Hang Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zehui Lv
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Lei
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erchao Duan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanyan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinglun Sun
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoli Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiuhao Bao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongbo Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chuanwei Gu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yipeng Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaokang Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenyu Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pengcheng Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Ji
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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13
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Zhang L, Ma J, Shen Z, Wang B, Jiang Q, Ma F, Ju Y, Duan G, Zhang Q, Su X. Low copy numbers for mitochondrial DNA moderates the strength of nuclear-cytoplasmic incompatibility in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:739-754. [PMID: 36308719 DOI: 10.1111/jipb.13400] [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: 07/18/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Plant cells contain only small amounts of mitochondrial DNA (mtDNA), with the genomic information shared among multiple mitochondria. The biological relevance and molecular mechanism underlying this hallmark of plant cells has been unclear. Here, we report that Arabidopsis thaliana plants exhibited significantly reduced growth and mitochondrial dysfunction when the mtDNA copy number was increased to the degree that each mitochondrion possessed DNA. The amounts of mitochondrion-encoded transcripts increased several fold in the presence of elevated mtDNA levels. However, the efficiency of RNA editing decreased with this excess of mitochondrion-encoded transcripts, resulting in impaired assembly of mitochondrial complexes containing mtDNA-encoded subunits, such as respiratory complexes I and IV. These observations indicate the occurrence of nuclear-mitochondrial incompatibility in the cells with increased amounts of mtDNA and provide an initial answer to the fundamental question of why plant cells have much lower mtDNA levels than animal cells. We propose that keeping mtDNA levels low moderates nuclear-mitochondrial incompatibility and that this may be a crucial factor driving plant cells to restrict the copy numbers of mtDNA.
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Affiliation(s)
- Liguang Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jin Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhaorui Shen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Bo Wang
- State Key Laboratory of Protein and Plant Gene Research and Biomedical Pioneering Innovation Center (BIOPIC), College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qingling Jiang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Fei Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Ju
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Guangxing Duan
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Quan Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaodong Su
- State Key Laboratory of Protein and Plant Gene Research and Biomedical Pioneering Innovation Center (BIOPIC), College of Life Sciences, Peking University, Beijing, 100871, China
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14
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Carnes J, Gendrin C, McDermott SM, Stuart K. KRGG1 function in RNA editing in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2023; 29:228-240. [PMID: 36400448 PMCID: PMC9891254 DOI: 10.1261/rna.079418.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/11/2022] [Indexed: 05/20/2023]
Abstract
Mitochondrial gene expression in trypanosomes requires numerous multiprotein complexes that are unique to kinetoplastids. Among these, the most well characterized are RNA editing catalytic complexes (RECCs) that catalyze the guide RNA (gRNA)-specified insertion and deletion of uridines during mitochondrial mRNA maturation. This post-transcriptional resequencing of mitochondrial mRNAs can be extensive, involving dozens of different gRNAs and hundreds of editing sites with most of the mature mRNA sequences resulting from the editing process. Proper coordination of the editing with the cognate gRNAs is attributed to RNA editing substrate-binding complexes (RESCs), which are also required for RNA editing. Although the precise mechanism of RESC function is less well understood, their affinity for binding both editing substrates and products suggests that these complexes may provide a scaffold for RECC catalytic processing. KRGG1 has been shown to bind RNAs, and although affinity purification co-isolates RESC complexes, its role in RNA editing remains uncertain. We show here that KRGG1 is essential in BF parasites and required for normal editing. KRGG1 repression results in reduced amounts of edited A6 mRNA and increased amounts of edited ND8 mRNA. Sequence and structure analysis of KRGG1 identified a region of homology with RESC6, and both proteins have predicted tandem helical repeats that resemble ARM/HEAT motifs. The ARM/HEAT-like region is critical for function as exclusive expression of mutated KRGG1 results in growth inhibition and disruption of KRGG1 association with RESCs. These results indicate that KRGG1 is critical for RNA editing and its specific function is associated with RESC activity.
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Affiliation(s)
- Jason Carnes
- Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Claire Gendrin
- Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | | | - Kenneth Stuart
- Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics and Global Health, University of Washington, Seattle, Washington 98105, USA
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15
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McDowell R, Small I, Bond CS. Synthetic PPR proteins as tools for sequence-specific targeting of RNA. Methods 2022; 208:19-26. [DOI: 10.1016/j.ymeth.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
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16
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Loiacono FV, Walther D, Seeger S, Thiele W, Gerlach I, Karcher D, Schöttler MA, Zoschke R, Bock R. Emergence of Novel RNA-Editing Sites by Changes in the Binding Affinity of a Conserved PPR Protein. Mol Biol Evol 2022; 39:6760358. [PMID: 36227729 PMCID: PMC9750133 DOI: 10.1093/molbev/msac222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/07/2023] Open
Abstract
RNA editing converts cytidines to uridines in plant organellar transcripts. Editing typically restores codons for conserved amino acids. During evolution, specific C-to-U editing sites can be lost from some plant lineages by genomic C-to-T mutations. By contrast, the emergence of novel editing sites is less well documented. Editing sites are recognized by pentatricopeptide repeat (PPR) proteins with high specificity. RNA recognition by PPR proteins is partially predictable, but prediction is often inadequate for PPRs involved in RNA editing. Here we have characterized evolution and recognition of a recently gained editing site. We demonstrate that changes in the RNA recognition motifs that are not explainable with the current PPR code allow an ancient PPR protein, QED1, to uniquely target the ndhB-291 site in Brassicaceae. When expressed in tobacco, the Arabidopsis QED1 edits 33 high-confident off-target sites in chloroplasts and mitochondria causing a spectrum of mutant phenotypes. By manipulating the relative expression levels of QED1 and ndhB-291, we show that the target specificity of the PPR protein depends on the RNA:protein ratio. Finally, our data suggest that the low expression levels of PPR proteins are necessary to ensure the specificity of editing site selection and prevent deleterious off-target editing.
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Affiliation(s)
- F Vanessa Loiacono
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Dirk Walther
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stefanie Seeger
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Wolfram Thiele
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ines Gerlach
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Reimo Zoschke
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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17
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Wu C, Chaw S. Evolution of mitochondrial RNA editing in extant gymnosperms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1676-1687. [PMID: 35877596 PMCID: PMC9545813 DOI: 10.1111/tpj.15916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 06/01/2023]
Abstract
To unveil the evolution of mitochondrial RNA editing in gymnosperms, we characterized mitochondrial genomes (mitogenomes), plastid genomes, RNA editing sites, and pentatricopeptide repeat (PPR) proteins from 10 key taxa representing four of the five extant gymnosperm clades. The assembled mitogenomes vary in gene content due to massive gene losses in Gnetum and Conifer II clades. Mitochondrial gene expression levels also vary according to protein function, with the most highly expressed genes involved in the respiratory complex. We identified 9132 mitochondrial C-to-U editing sites, as well as 2846 P-class and 8530 PLS-class PPR proteins. Regains of editing sites were demonstrated in Conifer II rps3 transcripts whose corresponding mitogenomic sequences lack introns due to retroprocessing. Our analyses reveal that non-synonymous editing is efficient and results in more codons encoding hydrophobic amino acids. In contrast, synonymous editing, although performed with variable efficiency, can increase the number of U-ending codons that are preferentially utilized in gymnosperm mitochondria. The inferred loss-to-gain ratio of mitochondrial editing sites in gymnosperms is 2.1:1, of which losses of non-synonymous editing are mainly due to genomic C-to-T substitutions. However, such substitutions only explain a small fraction of synonymous editing site losses, indicating distinct evolutionary mechanisms. We show that gymnosperms have experienced multiple lineage-specific duplications in PLS-class PPR proteins. These duplications likely contribute to accumulated RNA editing sites, as a mechanistic correlation between RNA editing and PLS-class PPR proteins is statistically supported.
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Affiliation(s)
- Chung‐Shien Wu
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
| | - Shu‐Miaw Chaw
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
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18
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Xiang QP, Tang JY, Yu JG, Smith DR, Zhu YM, Wang YR, Kang JS, Yang J, Zhang XC. The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:768-784. [PMID: 35648423 DOI: 10.1111/tpj.15851] [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: 04/06/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Two factors are proposed to account for the unusual features of organellar genomes: the disruptions of organelle-targeted DNA replication, repair, and recombination (DNA-RRR) systems in the nuclear genome and repetitive elements in organellar genomes. Little is known about how these factors affect organellar genome evolution. The deep-branching vascular plant family Selaginellaceae is known to have a deficient DNA-RRR system and convergently evolved organellar genomes. However, we found that the plastid genome (plastome) of Selaginella sinensis has extremely accelerated substitution rates, a low GC content, pervasive repeat elements, a dynamic network structure, and it lacks direct or inverted repeats. Unexpectedly, its organelle DNA-RRR system is short of a plastid-targeted Recombinase A1 (RecA1) and a mitochondrion-targeted RecA3, in line with other explored Selaginella species. The plastome contains a large collection of short- and medium-sized repeats. Given the absence of RecA1 surveillance, we propose that these repeats trigger illegitimate recombination, accelerated mutation rates, and structural instability. The correlations between repeat quantity and architectural complexity in the Selaginella plastomes support these conclusions. We, therefore, hypothesize that the interplay of the deficient DNA-RRR system and the high repeat content has led to the extraordinary divergence of the S. sinensis plastome. Our study not only sheds new light on the mechanism of plastome divergence by emphasizing the power of cytonuclear integration, but it also reconciles the longstanding contradiction on the effects of DNA-RRR system disruption on genome structure evolution.
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Affiliation(s)
- Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun-Yong Tang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Gao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, N6A 5B7, Ontario, Canada
| | - Yan-Mei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Ya-Rong Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jong-Soo Kang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
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19
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Andrade-Marcial M, Pacheco-Arjona R, Góngora-Castillo E, De-la-Peña C. Chloroplastic pentatricopeptide repeat proteins (PPR) in albino plantlets of Agave angustifolia Haw. reveal unexpected behavior. BMC PLANT BIOLOGY 2022; 22:352. [PMID: 35850575 PMCID: PMC9295523 DOI: 10.1186/s12870-022-03742-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pentatricopeptide repeat (PPR) proteins play an essential role in the post-transcriptional regulation of genes in plastid genomes. Although important advances have been made in understanding the functions of these genes, there is little information available on chloroplastic PPR genes in non-model plants and less in plants without chloroplasts. In the present study, a comprehensive and multifactorial bioinformatic strategy was applied to search for putative PPR genes in the foliar and meristematic tissues of green and albino plantlets of the non-model plant Agave angustifolia Haw. RESULTS A total of 1581 PPR transcripts were identified, of which 282 were chloroplastic. Leaf tissue in the albino plantlets showed the highest levels of expression of chloroplastic PPRs. The search for hypothetical targets of 12 PPR sequences in the chloroplast genes of A. angustifolia revealed their action on transcripts related to ribosomes and translation, photosystems, ATP synthase, plastid-encoded RNA polymerase and RuBisCO. CONCLUSIONS Our results suggest that the expression of PPR genes depends on the state of cell differentiation and plastid development. In the case of the albino leaf tissue, which lacks functional chloroplasts, it is possible that anterograde and retrograde signaling networks are severely compromised, leading to a compensatory anterograde response characterized by an increase in the expression of PPR genes.
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Affiliation(s)
- M Andrade-Marcial
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - R Pacheco-Arjona
- Facultad de Medicina Veterinaria y Zootecnia, Consejo Nacional de Ciencia y Tecnología- Universidad Autónoma de Yucatán, Mérida, Mexico
| | - E Góngora-Castillo
- Consejo Nacional de Ciencia y Tecnología-Unidad De Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - C De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico.
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20
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Luo Z, Xiong J, Xia H, Wang L, Hou G, Li Z, Li J, Zhou H, Li T, Luo L. Pentatricopeptide Repeat Gene-Mediated Mitochondrial RNA Editing Impacts on Rice Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:926285. [PMID: 35928709 PMCID: PMC9343880 DOI: 10.3389/fpls.2022.926285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/21/2022] [Indexed: 05/27/2023]
Abstract
Mitochondrial RNA editing plays crucial roles in the plant development and environmental adaptation. Pentatricopeptide repeat (PPR) genes, which are involved in the regulating mitochondrial RNA editing, are potential gene resources in the improvement of rice drought tolerance. In this study, we investigated genome-wide mitochondrial RNA editing in response to drought between upland and lowland rice. Responses of mitochondrial RNA editing to drought exhibit site-specific and genotype-specific patterns. We detected 22 and 57 ecotype-differentiated editing sites under well-watered and drought-treated conditions, respectively. Interestingly, the RNA editing efficiency was positively correlated with many agronomic traits, while it was negatively correlated with drought tolerance. We further selected two mitochondrial-localized PPR proteins, PPR035 and PPR406, to validate their functions in drought tolerance. PPR035 regulated RNA editing at rps4-926 and orfX-406, while PPR406 regulated RNA editing at orfX-355. The defectiveness in RNA editing at these sites had no apparent penalties in rice respiration and vegetative growth. Meanwhile, the knockout mutants of ppr035 and ppr406 show enhanced drought- and salt tolerance. PPR035 and PPR406 were under the balancing selection in upland rice and highly differentiated between upland and lowland rice ecotypes. The upland-dominant haplotypes of PPR035 and PPR406 shall contribute to the better drought tolerance in upland rice. They have great prospective in the improvement of rice drought tolerance.
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Affiliation(s)
- Zhi Luo
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jie Xiong
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hui Xia
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lei Wang
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Guihua Hou
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Zhaoyang Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jing Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hengling Zhou
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Tianfei Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lijun Luo
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
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Rehman O, Uzair M, Chao H, Khan MR, Chen M. Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:892729. [PMID: 35812946 PMCID: PMC9260663 DOI: 10.3389/fpls.2022.892729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Ribonucleic acid editing (RE) is a post-transcriptional process that altered the genetics of RNA which provide the extra level of gene expression through insertion, deletions, and substitutions. In animals, it converts nucleotide residues C-U. Similarly in plants, the role of RNA editing sites (RES) in rice under alkaline stress is not fully studied. Rice is a staple food for most of the world population. Alkaline stress cause reduction in yield. Here, we explored the effect of alkaline stress on RES in the whole mRNA from rice chloroplast and mitochondria. Ribonucleic acid editing sites in both genomes (3336 RESs) including chloroplast (345 RESs) and mitochondria (2991 RESs) with average RES efficiency ∼55% were predicted. Our findings showed that majority of editing events found in non-synonymous codon changes and change trend in amino acids was hydrophobic. Four types of RNA editing A-G (A-I), C-T (C-U), G-A, and T-C were identified in treated and untreated samples. Overall, RNA editing efficiency was increased in the treated samples. Analysis of Gene Ontology revealed that mapped genes were engaged in many biological functions and molecular processes. We also checked the expression of pentatricopeptide repeat (PPR), organelle zinc-finger (OZI), and multiple organellar RNA editing factors/RNA editing factor interacting proteins genes in control and treatment, results revealed upregulation of PPR and OZ1 genes in treated samples. This induction showed the role of these genes in RNA editing. The current findings report that RNA editing increased under alkaline stress which may contribute in adaptation for rice by changing amino acids in edited genes (88 genes). These findings will provide basis for identification of RES in other crops and also will be useful in alkaline tolerance development in rice.
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Affiliation(s)
- Obaid Rehman
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
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22
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Ma S, Yang W, Liu X, Li S, Li Y, Zhu J, Zhang C, Lu X, Zhou X, Chen R. Pentatricopeptide repeat protein CNS1 regulates maize mitochondrial complex III assembly and seed development. PLANT PHYSIOLOGY 2022; 189:611-627. [PMID: 35218364 PMCID: PMC9157079 DOI: 10.1093/plphys/kiac086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/28/2022] [Indexed: 06/02/2023]
Abstract
Mitochondrial function relies on the assembly of electron transport chain complexes, which requires coordination between proteins encoded by the mitochondrion and those of the nucleus. Here, we cloned a maize (Zea mays) cytochrome c maturation FN stabilizer1 (CNS1) and found it encodes a pentatricopeptide repeat (PPR) protein. Members of the PPR family are widely distributed in plants and are associated with RNA metabolism in organelles. P-type PPR proteins play essential roles in stabilizing the 3'-end of RNA in mitochondria; whether a similar process exists for stabilizing the 5'-terminus of mitochondrial RNA remains unclear. The kernels of cns1 exhibited arrested embryo and endosperm development, whereas neither conventional splicing deficiency nor RNA editing difference in mitochondrial genes was observed. Instead, most of the ccmFN transcripts isolated from cns1 mutant plants were 5'-truncated and therefore lacked the start codon. Biochemical and molecular data demonstrated that CNS1 is a P-type PPR protein encoded by nuclear DNA and that it localizes to the mitochondrion. Also, one binding site of CNS1 located upstream of the start codon in the ccmFN transcript. Moreover, abnormal mitochondrial morphology and dramatic upregulation of alternative oxidase genes were observed in the mutant. Together, these results indicate that CNS1 is essential for reaching a suitable level of intact ccmFN transcripts through binding to the 5'-UTR of the RNAs and maintaining 5'-integrity, which is crucial for sustaining mitochondrial complex III function to ensure mitochondrial biogenesis and seed development in maize.
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Affiliation(s)
- Shuai Ma
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenzhu Yang
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoqing Liu
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Suzhen Li
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ye Li
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Chemical and Biological Processing Technology for Farm Products of Zhejiang Province , Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Jiameng Zhu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Chunyi Zhang
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan 250200, China
| | - Xiaojin Zhou
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rumei Chen
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Zheng S, Dong J, Lu J, Li J, Jiang D, Yu H, Ye S, Bu W, Liu Z, Zhou H, Ding Y, Zhuang C. A cytosolic pentatricopeptide repeat protein is essential for tapetal plastid development by regulating OsGLK1 transcript levels in rice. THE NEW PHYTOLOGIST 2022; 234:1678-1695. [PMID: 35306663 DOI: 10.1111/nph.18105] [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: 11/18/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Most plant pentatricopeptide repeat (PPR) proteins localize to and function inside plastids and mitochondria. However, the function of PPRs that only localize to the cytoplasm remains unknown. Here, we demonstrated that the rice (Oryza sativa) PPR protein CYTOPLASM-LOCALIZED PPR1 (OsCPPR1) contributes to pollen development and localizes to the cytoplasm. Knocking down OsCPPR1 led to abnormal plastid development in tapetal cells, prolonged tapetal programmed cell death (PCD) and tapetum degradation, and significantly reduced pollen fertility. Transcriptome analysis revealed that the transcript level of OsGOLDEN-LIKE1 (OsGLK1), which encodes a transcription factor that regulates plastid development and maintenance, was significantly higher in the OsCPPR1 knockdown plants compared to wild-type plants. We further determined that OsCPPR1 downregulates OsGLK1 transcription by directly binding to the single-stranded regions of OsGLK1 mRNAs. Overexpression of OsGLK1 resulted in abnormal tapetum and plastid development, similar to that seen in OsCPPR1 knockdown plants, and suppression of OsGLK1 partially restored pollen fertility in the OsCPPR1 knockdown plants. We therefore conclude that OsCPPR1 suppresses OsGLK1 in the regulation of plastid development and PCD in the tapetum. Our work revealed novel functions for a cytosolic PPR, demonstrating the diverse roles of PPRs in plants and identifying a new regulatory mechanism for regulating pollen development in rice.
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Affiliation(s)
- Shaoyan Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jingfang Dong
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jingqin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Dagang Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Haopeng Yu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Simiao Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wenli Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
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24
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Srikakulam N, Guria A, Karanthamalai J, Murugesan V, Krishnan V, Sundaramoorthy K, Saha S, Singh R, Victorathisayam T, Rajapriya V, Sridevi G, Pandi G. An Insight Into Pentatricopeptide-Mediated Chloroplast Necrosis via microRNA395a During Rhizoctonia solani Infection. Front Genet 2022; 13:869465. [PMID: 35706449 PMCID: PMC9189367 DOI: 10.3389/fgene.2022.869465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Sheath blight (ShB) disease, caused by Rhizoctonia solani, is one of the major biotic stress-oriented diseases that adversely affect the rice productivity worldwide. However, the regulatory mechanisms are not understood yet comprehensively. In the current study, we had investigated the potential roles of miRNAs in economically important indica rice variety Pusa Basmati-1 upon R. solani infection by carrying out in-depth, high-throughput small RNA sequencing with a total data size of 435 million paired-end raw reads from rice leaf RNA samples collected at different time points. Detailed data analysis revealed a total of 468 known mature miRNAs and 747 putative novel miRNAs across all the libraries. Target prediction and Gene Ontology functional analysis of these miRNAs were found to be unraveling various cellular, molecular, and biological functions by targeting various plant defense-related genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to validate the miRNAs and their putative target genes. Out of the selected miRNA-specific putative target genes, miR395a binding and its cleavage site on pentatricopeptide were determined by 5’ RACE-PCR. It might be possible that R. solani instigated chloroplast degradation by modulating the pentatricopeptide which led to increased susceptibility to fungal infection.
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25
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Genome-wide investigation and functional analysis of RNA editing sites in wheat. PLoS One 2022; 17:e0265270. [PMID: 35275970 PMCID: PMC8916659 DOI: 10.1371/journal.pone.0265270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
Wheat is an important cereal and half of the world population consumed it. Wheat faces environmental stresses and different techniques (CRISPR, gene silencing, GWAS, etc.) were used to enhance its production but RNA editing (RESs) is not fully explored in wheat. RNA editing has a special role in controlling environmental stresses. The genome-wide identification and functional characterization of RESs in different types of wheat genotypes was done. We employed six wheat genotypes by RNA-seq analyses to achieve RESs. The findings revealed that RNA editing events occurred on all chromosomes equally. RNA editing sites were distributed randomly and 10–12 types of RESs were detected in wheat genotypes. Higher number of RESs were detected in drought-tolerant genotypes. A-to-I RNA editing (2952, 2977, 1916, 2576, 3422, and 3459) sites were also identified in six wheat genotypes. Most of the genes were found to be engaged in molecular processes after a Gene Ontology analysis. PPR (pentatricopeptide repeat), OZ1 (organelle zinc-finger), and MORF/RIP gene expression levels in wheat were also examined. Normal growth conditions diverge gene expression of these three different gene families, implying that normal growth conditions for various genotypes can modify RNA editing events and have an impact on gene expression levels. While the expression of PPR genes was not change. We used Variant Effect Predictor (VEP) to annotate RNA editing sites, and Local White had the highest RESs in the CDS region of the protein. These findings will be useful for prediction of RESs in other crops and will be helpful in drought tolerance development in wheat.
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Zhao J, Cao SK, Li XL, Liu R, Sun F, Jiang RC, Xu C, Tan BC. EMP80 mediates the C-to-U editing of nad7 and atp4 and interacts with ZmDYW2 in maize mitochondria. THE NEW PHYTOLOGIST 2022; 234:1237-1248. [PMID: 35243635 DOI: 10.1111/nph.18067] [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: 01/06/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
RNA C-to-U editing is important to the expression and function of organellar genes in plants. Although several families of proteins have been identified to participate in this process, the underlying mechanism is not fully understood. Here we report the function of EMP80 in the C-to-U editing at the nad7-769 and atp4-118 sites, and the potential recruitment of ZmDYW2 as a trans deaminase in maize (Zea mays) mitochondria. Loss of EMP80 function arrests embryogenesis and endosperm development in maize. EMP80 is a PPR-E+ protein localised to mitochondria. An absence of EMP80 abolishes the C-to-U RNA editing at nad7-769 and atp4-118 sites, resulting in a cysteine-to-arginine (Cys→Arg) change in Nad7 and Atp4 in the emp80 mutant. The amino acid change consequently reduces the assembly of complexes I and V, leading to an accumulation of the F1 subcomplex of complex V. EMP80 was found to interact with atypical DYW-type PPR protein ZmDYW2, which interacts with ZmNUWA. Co-expression of ZmNUWA enhances the interaction between EMP80 and ZmDYW2, suggesting that EMP80 potentially recruits ZmDYW2 as a trans deaminase through protein-protein interaction, and ZmNUWA may function as an enhancer of this interaction.
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Affiliation(s)
- Jiao Zhao
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Shi-Kai Cao
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Xiu-Lan Li
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Rui Liu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Rui-Cheng Jiang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chunhui Xu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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MISF2 Encodes an Essential Mitochondrial Splicing Cofactor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23052670. [PMID: 35269810 PMCID: PMC8910670 DOI: 10.3390/ijms23052670] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/20/2022] Open
Abstract
Mitochondria play key roles in cellular energy metabolism in eukaryotes. Mitochondria of most organisms contain their own genome and specific transcription and translation machineries. The expression of angiosperm mtDNA involves extensive RNA-processing steps, such as RNA trimming, editing, and the splicing of numerous group II-type introns. Pentatricopeptide repeat (PPR) proteins are key players in plant organelle gene expression and RNA metabolism. In the present analysis, we reveal the function of the MITOCHONDRIAL SPLICING FACTOR 2 gene (MISF2, AT3G22670) and show that it encodes a mitochondria-localized PPR protein that is crucial for early embryo development in Arabidopsis. Molecular characterization of embryo-rescued misf2 plantlets indicates that the splicing of nad2 intron 1, and thus respiratory complex I biogenesis, are strongly compromised. Moreover, the molecular function seems conserved between MISF2 protein in Arabidopsis and its orthologous gene (EMP10) in maize, suggesting that the ancestor of MISF2/EMP10 was recruited to function in nad2 processing before the monocot-dicot divergence ~200 million years ago. These data provide new insights into the function of nuclear-encoded factors in mitochondrial gene expression and respiratory chain biogenesis during plant embryo development.
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Kuwabara K, Harada I, Matsuzawa Y, Ariizumi T, Shirasawa K. Organelle genome assembly uncovers the dynamic genome reorganization and cytoplasmic male sterility associated genes in tomato. HORTICULTURE RESEARCH 2021; 8:250. [PMID: 34848681 PMCID: PMC8632925 DOI: 10.1038/s41438-021-00676-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 05/11/2023]
Abstract
To identify cytoplasmic male sterility (CMS)-associated genes in tomato, we determined the genome sequences of mitochondria and chloroplasts in three CMS tomato lines derived from independent asymmetric cell fusions, their nuclear and cytoplasmic donors, and male fertile weedy cultivated tomato and wild relatives. The structures of the CMS mitochondrial genomes were highly divergent from those of the nuclear and cytoplasmic donors, and genes of the donors were mixed up in these genomes. On the other hand, the structures of CMS chloroplast genomes were moderately conserved across the donors, but CMS chloroplast genes were unexpectedly likely derived from the nuclear donors. Comparative analysis of the structures and contents of organelle genes and transcriptome analysis identified three genes that were uniquely present in the CMS lines, but not in the donor or fertile lines. RNA-sequencing analysis indicated that these three genes transcriptionally expressed in anther, and identified different RNA editing levels in one gene, orf265, that was partially similar to ATP synthase subunit 8, between fertile and sterile lines. The orf265 was a highly potential candidate for CMS-associated gene. This study suggests that organelle reorganization mechanisms after cell fusion events differ between mitochondria and chloroplasts, and provides insight into the development of new F1 hybrid breeding programs employing the CMS system in tomato.
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Affiliation(s)
- Kosuke Kuwabara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Issei Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | | | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
- Tsukuba Plant Innovation Research Center, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan.
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CAF Proteins Help SOT1 Regulate the Stability of Chloroplast ndhA Transcripts. Int J Mol Sci 2021; 22:ijms222312639. [PMID: 34884441 PMCID: PMC8657633 DOI: 10.3390/ijms222312639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/20/2021] [Accepted: 11/20/2021] [Indexed: 12/26/2022] Open
Abstract
Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5' ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism.
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Qin T, Zhao P, Sun J, Zhao Y, Zhang Y, Yang Q, Wang W, Chen Z, Mai T, Zou Y, Liu G, Hao W. Research Progress of PPR Proteins in RNA Editing, Stress Response, Plant Growth and Development. Front Genet 2021; 12:765580. [PMID: 34733319 PMCID: PMC8559896 DOI: 10.3389/fgene.2021.765580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
RNA editing is a posttranscriptional phenomenon that includes gene processing and modification at specific nucleotide sites. RNA editing mainly occurs in the genomes of mitochondria and chloroplasts in higher plants. In recent years, pentatricopeptide repeat (PPR) proteins, which may act as trans-acting factors of RNA editing have been identified, and the study of PPR proteins has become a research focus in molecular biology. The molecular functions of these proteins and their physiological roles throughout plant growth and development are widely studied. In this minireview, we summarize the current knowledge of the PPR family, hoping to provide some theoretical reference for future research and applications.
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Affiliation(s)
- Tengfei Qin
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Pei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jialiang Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Yuping Zhao
- Beijing River and Lake Management Office, Beijing, China
| | - Yaxin Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Qiuyue Yang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Weipeng Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Zhuanqing Chen
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Tengfei Mai
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Yingying Zou
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Guoxiang Liu
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wei Hao
- College of Medical Technology, Beihua University, Jilin City, China
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Møller IM, Rasmusson AG, Van Aken O. Plant mitochondria - past, present and future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:912-959. [PMID: 34528296 DOI: 10.1111/tpj.15495] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) the ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates; (ii) the partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical Complex I NADH dehydrogenase; and (iii) the partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical Complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) plant mitochondrial DNA (mtDNA) is 10-600 times larger than the mammalian mtDNA, yet it only contains approximately 50% more genes; (v) plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity; (vi) mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites); (vii) recombination in mtDNA creates novel reading frames that can produce male sterility; and (viii) plant mitochondria have a large proteome with 2000-3000 different proteins containing many unique proteins such as 200-300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes.
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Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
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Feng X, Yang S, Zhang Y, Zhiyuan C, Tang K, Li G, Yu H, Leng J, Wang Q. GmPGL2, Encoding a Pentatricopeptide Repeat Protein, Is Essential for Chloroplast RNA Editing and Biogenesis in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:690973. [PMID: 34567023 PMCID: PMC8458969 DOI: 10.3389/fpls.2021.690973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
Chloroplast biogenesis and development are highly complex processes requiring interactions between plastids and nuclear genomic products. Pentatricopeptide repeat (PPR) proteins play an essential role in the development of chloroplasts; however, it remains unclear how RNA editing factors influence soybean development. In this study, a Glycine max pale green leaf 2 mutant (Gmpgl2) was identified with decreased chlorophyll contents. Genetic mapping revealed that a single-nucleotide deletion at position 1949 bp in the Glyma.05g132700 gene in the Gmpgl2 mutant, resulting in a truncated GmPGL2 protein. The nuclear-encoded GmPGL2 is a PLS-type PPR protein that localizes to the chloroplasts. The C-to-U editing efficiencies of rps16, rps18, ndhB, ndhD, ndhE, and ndhF were reduced in the Gmpgl2 mutant. RNA electrophoresis mobility shift assay (REMSA) analysis further revealed that GmPGL2 binds to the immediate upstream sequences at RNA editing sites of rps16 and ndhB in vitro, respectively. In addition, GmPGL2 was found to interact with GmMORF8, GmMORF9, and GmORRM6. These results suggest that GmPGL2 participates in C-to-U RNA editing via the formation of a complex RNA editosome in soybean chloroplasts.
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Affiliation(s)
- Xingxing Feng
- College of Food and Biological Engineering, Xuzhou University of Technology, Xuzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Yaohua Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Cheng Zhiyuan
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Kuanqiang Tang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Guang Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Hui Yu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Jiantian Leng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Qingyu Wang
- College of Plant Science, Jilin University, Changchun, China
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Wang Y, Liu XY, Huang ZQ, Li YY, Yang YZ, Sayyed A, Sun F, Gu ZQ, Wang X, Tan BC. PPR-DYW Protein EMP17 Is Required for Mitochondrial RNA Editing, Complex III Biogenesis, and Seed Development in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:693272. [PMID: 34394147 PMCID: PMC8357149 DOI: 10.3389/fpls.2021.693272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/01/2021] [Indexed: 05/31/2023]
Abstract
The conversion of cytidines to uridines (C-to-U) at specific sites in mitochondrial and plastid transcripts is a post-transcriptional processing event that is important to the expression of organellar genes. Pentatricopeptide repeat (PPR) proteins are involved in this process. In this study, we report the function of a previously uncharacterized PPR-DYW protein, Empty pericarp17 (EMP17), in the C-to-U editing and kernel development in maize. EMP17 is targeted to mitochondria. The loss-function of EMP17 arrests maize kernel development, abolishes the editing at ccmF C -799 and nad2-677 sites, and reduces the editing at ccmF C -906 and -966 sites. The absence of editing causes amino acid residue changes in CcmFC-267 (Ser to Pro) and Nad2-226 (Phe to Ser), respectively. As CcmFC functions in cytochrome c (Cytc) maturation, the amount of Cytc and Cytc 1 protein is drastically reduced in emp17, suggesting that the CcmFC-267 (Ser to Pro) change impairs the CcmFC function. As a result, the assembly of complex III is strikingly decreased in emp17. In contrast, the assembly of complex I appears less affected, suggesting that the Nad2-226 (Phe to Ser) change may have less impact on Nad2 function. Together, these results indicate that EMP17 is required for the C-to-U editing at several sites in mitochondrial transcripts, complex III biogenesis, and seed development in maize.
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Affiliation(s)
- Yong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xin-Yuan Liu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Zi-Qin Huang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yan-Yan Li
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yan-Zhuo Yang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Zhi-Qun Gu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaomin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 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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Barik S. An Analytical Review of the Structural Features of Pentatricopeptide Repeats: Strategic Amino Acids, Repeat Arrangements and Superhelical Architecture. Int J Mol Sci 2021; 22:ijms22105407. [PMID: 34065603 PMCID: PMC8160929 DOI: 10.3390/ijms22105407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022] Open
Abstract
Tricopeptide repeats are common in natural proteins, and are exemplified by 34- and 35-residue repeats, known respectively as tetratricopeptide repeats (TPRs) and pentatricopeptide repeats (PPRs). In both classes, each repeat unit forms an antiparallel bihelical structure, so that multiple such units in a polypeptide are arranged in a parallel fashion. The primary structures of the motifs are nonidentical, but amino acids of similar properties occur in strategic positions. The focus of the present work was on PPR, but TPR, its better-studied cousin, is often included for comparison. The analyses revealed that critical amino acids, namely Gly, Pro, Ala and Trp, were placed at distinct locations in the higher order structure of PPR domains. While most TPRs occur in repeats of three, the PPRs exhibited a much greater diversity in repeat numbers, from 1 to 30 or more, separated by spacers of various sequences and lengths. Studies of PPR strings in proteins showed that the majority of PPR units are single, and that the longer tandems (i.e., without space in between) occurred in decreasing order. The multi-PPR domains also formed superhelical vortices, likely governed by interhelical angles rather than the spacers. These findings should be useful in designing and understanding the PPR domains.
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Affiliation(s)
- Sailen Barik
- EonBio, 3780 Pelham Drive, Mobile, AL 36619, USA
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Dai D, Ma Z, Song R. Maize endosperm development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:613-627. [PMID: 33448626 DOI: 10.1111/jipb.13069] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/12/2021] [Indexed: 05/22/2023]
Abstract
Recent breakthroughs in transcriptome analysis and gene characterization have provided valuable resources and information about the maize endosperm developmental program. The high temporal-resolution transcriptome analysis has yielded unprecedented access to information about the genetic control of seed development. Detailed spatial transcriptome analysis using laser-capture microdissection has revealed the expression patterns of specific populations of genes in the four major endosperm compartments: the basal endosperm transfer layer (BETL), aleurone layer (AL), starchy endosperm (SE), and embryo-surrounding region (ESR). Although the overall picture of the transcriptional regulatory network of endosperm development remains fragmentary, there have been some exciting advances, such as the identification of OPAQUE11 (O11) as a central hub of the maize endosperm regulatory network connecting endosperm development, nutrient metabolism, and stress responses, and the discovery that the endosperm adjacent to scutellum (EAS) serves as a dynamic interface for endosperm-embryo crosstalk. In addition, several genes that function in BETL development, AL differentiation, and the endosperm cell cycle have been identified, such as ZmSWEET4c, Thk1, and Dek15, respectively. Here, we focus on current advances in understanding the molecular factors involved in BETL, AL, SE, ESR, and EAS development, including the specific transcriptional regulatory networks that function in each compartment during endosperm development.
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Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Wang Y, Wang Y, Ren Y, Duan E, Zhu X, Hao Y, Zhu J, Chen R, Lei J, Teng X, Zhang Y, Wang D, Zhang X, Guo X, Jiang L, Liu S, Tian Y, Liu X, Chen L, Wang H, Wan J. white panicle2 encoding thioredoxin z, regulates plastid RNA editing by interacting with multiple organellar RNA editing factors in rice. THE NEW PHYTOLOGIST 2021; 229:2693-2706. [PMID: 33119889 PMCID: PMC8027827 DOI: 10.1111/nph.17047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/16/2020] [Indexed: 05/11/2023]
Abstract
Thioredoxins (TRXs) occur in plant chloroplasts as complex disulphide oxidoreductases. Although many biological processes are regulated by thioredoxins, the regulatory mechanism of chloroplast TRXs are largely unknown. Here we report a rice white panicle2 mutant caused by a mutation in the thioredoxin z gene, an orthologue of AtTRX z in Arabidopsis. white panicle2 (wp2) seedlings exhibited a high-temperature-sensitive albinic phenotype. We found that plastid multiple organellar RNA editing factors (MORFs) were the regulatory targets of thioredoxin z. We showed that OsTRX z protein physically interacts with OsMORFs in a redox-dependent manner and that the redox state of a conserved cysteine in the MORF box is essential for MORF-MORF interactions. wp2 and OsTRX z knockout lines show reduced editing efficiencies in many plastidial-encoded genes especially under high-temperature conditions. An Arabidopsis trx z mutant also exhibited significantly reduced chloroplast RNA editing. Our combined results suggest that thioredoxin z regulates chloroplast RNA editing in plants by controlling the redox state of MORFs.
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Affiliation(s)
- Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yulong Ren
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Erchao Duan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Xiaopin Zhu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yuanyuan Hao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Jianping Zhu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Rongbo Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Jie Lei
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yuanyan Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Di Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Xin Zhang
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Xiuping Guo
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Liangming Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haiyang Wang
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
- National Key Facility for Crop Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
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Du Y, Mo W, Ma T, Tang W, Tian L, Lin R. A pentatricopeptide repeat protein DUA1 interacts with sigma factor 1 to regulate chloroplast gene expression in Rice. PHOTOSYNTHESIS RESEARCH 2021; 147:131-143. [PMID: 33164144 DOI: 10.1007/s11120-020-00793-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Chloroplast gene expression is controlled by both plastid-encoded RNA polymerase (PEP) and nuclear-encoded RNA polymerase and is crucial for chloroplast development and photosynthesis. Environmental factors such as light and temperature can influence transcription in chloroplasts. In this study, we showed that mutation in DUA1, which encodes a pentatricopeptide repeat (PPR) protein in rice (Oryza sativa), led to deficiency in chloroplast development and chlorophyll biosynthesis, impaired photosystems, and reduced expression of PEP-dependent transcripts at low temperature especially under low-light conditions. Furthermore, we demonstrated that sigma factor OsSIG1 interacted with DUA1 in vitro and in vivo. Moreover, the levels of chlorophyll and PEP-dependent gene expression were significantly decreased in the Ossig1 mutants at low-temperature and low-light conditions. Our study reveals that the PPR protein DUA1 plays an important role in regulating PEP-mediated chloroplast gene expression through interacting with OsSIG1, thus modulates chloroplast development in response to environmental signals.
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Affiliation(s)
- Yanxin Du
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiping Mo
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tingting Ma
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Weijiang Tang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lijin Tian
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Dai D, Ma Z, Song R. Maize kernel development. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:2. [PMID: 37309525 PMCID: PMC10231577 DOI: 10.1007/s11032-020-01195-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/03/2020] [Indexed: 06/14/2023]
Abstract
Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.
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Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444 China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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Macedo-Osorio KS, Martínez-Antonio A, Badillo-Corona JA. Pas de Trois: An Overview of Penta-, Tetra-, and Octo-Tricopeptide Repeat Proteins From Chlamydomonas reinhardtii and Their Role in Chloroplast Gene Expression. FRONTIERS IN PLANT SCIENCE 2021; 12:775366. [PMID: 34868174 PMCID: PMC8635915 DOI: 10.3389/fpls.2021.775366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 05/05/2023]
Abstract
Penta-, Tetra-, and Octo-tricopeptide repeat (PPR, TPR, and OPR) proteins are nucleus-encoded proteins composed of tandem repeats of 35, 34, and 38-40 amino acids, respectively. They form helix-turn-helix structures that interact with mRNA or other proteins and participate in RNA stabilization, processing, maturation, and act as translation enhancers of chloroplast and mitochondrial mRNAs. These helical repeat proteins are unevenly present in plants and algae. While PPR proteins are more abundant in plants than in algae, OPR proteins are more abundant in algae. In Arabidopsis, maize, and rice there have been 450, 661, and 477 PPR proteins identified, respectively, which contrasts with only 14 PPR proteins identified in Chlamydomonas reinhardtii. Likewise, more than 120 OPR proteins members have been predicted from the nuclear genome of C. reinhardtii and only one has been identified in Arabidopsis thaliana. Due to their abundance in land plants, PPR proteins have been largely characterized making it possible to elucidate their RNA-binding code. This has even allowed researchers to generate engineered PPR proteins with defined affinity to a particular target, which has served as the basis to develop tools for gene expression in biotechnological applications. However, fine elucidation of the helical repeat proteins code in Chlamydomonas is a pending task. In this review, we summarize the current knowledge on the role PPR, TPR, and OPR proteins play in chloroplast gene expression in the green algae C. reinhardtii, pointing to relevant similarities and differences with their counterparts in plants. We also recapitulate on how these proteins have been engineered and shown to serve as mRNA regulatory factors for biotechnological applications in plants and how this could be used as a starting point for applications in algae.
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Affiliation(s)
- Karla S. Macedo-Osorio
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, México City, México
- Biological Engineering Laboratory, Genetic Engineering Department, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional-Unidad Irapuato, Irapuato, México
- División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Xochimilco, México City, México
- *Correspondence: Karla S. Macedo-Osorio,
| | - Agustino Martínez-Antonio
- Biological Engineering Laboratory, Genetic Engineering Department, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional-Unidad Irapuato, Irapuato, México
| | - Jesús A. Badillo-Corona
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, México City, México
- Jesús A. Badillo-Corona,
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40
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Teramoto T, Kaitany KJ, Kakuta Y, Kimura M, Fierke CA, Hall TMT. Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA. Nucleic Acids Res 2020; 48:11815-11826. [PMID: 32719843 DOI: 10.1093/nar/gkaa627] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
Pentatricopeptide repeat (PPR) motifs are α-helical structures known for their modular recognition of single-stranded RNA sequences with each motif in a tandem array binding to a single nucleotide. Protein-only RNase P 1 (PRORP1) in Arabidopsis thaliana is an endoribonuclease that uses its PPR domain to recognize precursor tRNAs (pre-tRNAs) as it catalyzes removal of the 5'-leader sequence from pre-tRNAs with its NYN metallonuclease domain. To gain insight into the mechanism by which PRORP1 recognizes tRNA, we determined a crystal structure of the PPR domain in complex with yeast tRNAPhe at 2.85 Å resolution. The PPR domain of PRORP1 bound to the structurally conserved elbow of tRNA and recognized conserved structural features of tRNAs using mechanisms that are different from the established single-stranded RNA recognition mode of PPR motifs. The PRORP1 PPR domain-tRNAPhe structure revealed a conformational change of the PPR domain upon tRNA binding and moreover demonstrated the need for pronounced overall flexibility in the PRORP1 enzyme conformation for substrate recognition and catalysis. The PRORP1 PPR motifs have evolved strategies for protein-tRNA interaction analogous to tRNA recognition by the RNA component of ribonucleoprotein RNase P and other catalytic RNAs, indicating convergence on a common solution for tRNA substrate recognition.
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Affiliation(s)
- Takamasa Teramoto
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.,Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Kipchumba J Kaitany
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Makoto Kimura
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Carol A Fierke
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Departments of Chemistry and Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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Feiz L, Strickler SR, van Eck J, Mao L, Movahed N, Taylor C, Gourabathini P, Fei Z, Stern DB. Setaria viridis chlorotic and seedling-lethal mutants define critical functions for chloroplast gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:917-931. [PMID: 32812296 DOI: 10.1111/tpj.14968] [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: 10/01/2018] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Deep insights into chloroplast biogenesis have been obtained by mutant analysis; however, in C4 plants a relevant mutant collection has only been developed and exploited for maize. Here, we report the initial characterization of an ethyl methyl sulfonate-induced mutant population for the C4 model Setaria viridis. Approximately 1000 M2 families were screened for the segregation of pale-green seedlings in the M3 generation, and a subset of these was identified to be deficient in post-transcriptional steps of chloroplast gene expression. Causative mutations were identified for three lines using deep sequencing-based bulked segregant analysis, and in one case confirmed by transgenic complementation. Using chloroplast RNA-sequencing and other molecular assays, we describe phenotypes of mutants deficient in PSRP7, a plastid-specific ribosomal protein, OTP86, an RNA editing factor, and cpPNP, the chloroplast isozyme of polynucleotide phosphorylase. The psrp mutant is globally defective in chloroplast translation, and has varying deficiencies in the accumulation of chloroplast-encoded proteins. The otp86 mutant, like its Arabidopsis counterpart, is specifically defective in editing of the rps14 mRNA; however, the conditional pale-green mutant phenotype contrasts with the normal growth of the Arabidopsis mutant. The pnp mutant exhibited multiple defects in 3' end maturation as well as other qualitative changes in the chloroplast RNA population. Overall, our collection opens the door to global analysis of photosynthesis and early seedling development in an emerging C4 model.
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Affiliation(s)
- Leila Feiz
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | | | - Joyce van Eck
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Linyong Mao
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Department of Biochemistry and Molecular Biology, Howard University, Washington, DC, 20059, USA
| | - Navid Movahed
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Q² Solutions, Ithaca, New York, 14850, USA
| | - Caroline Taylor
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Lansing High School, Lansing, New York, 14882, USA
- Cornell University, Ithaca, New York, New York, 14850, USA
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - David B Stern
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
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Dai D, Jin L, Huo Z, Yan S, Ma Z, Qi W, Song R. Maize pentatricopeptide repeat protein DEK53 is required for mitochondrial RNA editing at multiple sites and seed development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6246-6261. [PMID: 32710615 DOI: 10.1093/jxb/eraa348] [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: 04/30/2020] [Accepted: 07/21/2020] [Indexed: 05/21/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing in plant mitochondria and plastids. In this study, we characterized maize (Zea mays) kernel mutant defective kernel 53 (dek53), which has an embryo lethal and collapsed endosperm phenotype. Dek53 encodes an E-subgroup PPR protein, which possesses a short PLS repeat region of only seven repeats. Subcellular localization analysis indicated that DEK53 is localized in the mitochondrion. Strand- and transcript-specific RNA-seq analysis showed that the dek53 mutation affected C-to-U RNA editing at more than 60 mitochondrial C targets. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the assembly of mitochondrial complex III in dek53. Transmission electron microscopic examination showed severe morphological defects of mitochondria in dek53 endosperm cells. In addition, yeast two-hybrid and luciferase complementation imaging assays indicated that DEK53 can interact with the mitochondrion-targeted non-PPR RNA editing factor ZmMORF1, suggesting that DEK53 might be a functional component of the organellar RNA editosome.
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Affiliation(s)
- Dawei Dai
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Lifang Jin
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Zhenzhen Huo
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Shumei Yan
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Ichinose M, Ishimaru A, Sugita C, Nakajima K, Kawaguchi Y, Sugita M. Two Novel PLS-Class Pentatricopeptide Repeat Proteins Are Involved in the Group II Intron Splicing of Mitochondrial Transcripts in the Moss Physcomitrella patens. PLANT & CELL PHYSIOLOGY 2020; 61:1687-1698. [PMID: 32525534 DOI: 10.1093/pcp/pcaa070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are RNA-binding proteins that function in posttranscriptional regulation as gene-specific regulators of RNA metabolism in plant organelles. Plant PPR proteins are divided into four classes: P, PLS, E and DYW. The E- and DYW-class proteins are mainly implicated in RNA editing, whereas most of the P-class proteins predominantly participate in RNA cleavage, splicing and stabilization. In contrast, the functions of PLS-class proteins still remain obscure. Here, we report the function of PLS-class PpPPR_31 and PpPPR_9 in Physcomitrella patens. The knockout (KO) mutants of PpPPR_31 and PpPPR_9 exhibited slower protonema growth compared to the wild type. The PpPPR_31 KO mutants showed a considerable reduction in the splicing of nad5 intron 3 and atp9 intron 1. The PpPPR_9 KO mutants displayed severely reduced splicing of cox1 intron 3. An RNA electrophoresis mobility shift assay showed that the recombinant PpPPR_31 protein bound to the 5' region of nad5 exon 4 and the bulged A region in domain VI of atp9 group II intron 1 while the recombinant PpPPR_9 bound to the translated region of ORF622 in cox1 intron 3. These results suggest that a certain set of PLS-class PPR proteins may influence the splicing efficiency of mitochondrial group II introns.
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Affiliation(s)
- Mizuho Ichinose
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601 Japan
- Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Airi Ishimaru
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
| | - Chieko Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
| | - Kensaku Nakajima
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
| | | | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan
- Graduate School of Information Science, Nagoya University, Nagoya, 464-8601 Japan
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Liu R, Cao SK, Sayyed A, Xu C, Sun F, Wang X, Tan BC. The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the cis-Splicing of nad4 Intron 1 and Essential to Seed Development in Maize. Int J Mol Sci 2020; 21:ijms21114047. [PMID: 32516991 PMCID: PMC7312232 DOI: 10.3390/ijms21114047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 11/16/2022] Open
Abstract
Pentatricopeptide repeat (PPR) protein comprises a large family, participating in various aspects of organellar RNA metabolism in land plants. There are approximately 600 PPR proteins in maize, but the functions of many PPR proteins remain unknown. In this study, we defined the function of PPR18 in the cis-splicing of nad4 intron 1 in mitochondria and seed development in maize. Loss function of PPR18 seriously impairs embryo and endosperm development, resulting in the empty pericarp (emp) phenotype in maize. PPR18 encodes a mitochondrion-targeted P-type PPR protein with 18 PPR motifs. Transcripts analysis indicated that the splicing of nad4 intron 1 is impaired in the ppr18 mutant, resulting in the absence of nad4 transcript, leading to severely reduced assembly and activity of mitochondrial complex I and dramatically reduced respiration rate. These results demonstrate that PPR18 is required for the cis-splicing of nad4 intron 1 in mitochondria, and critical to complex I assembly and seed development in maize.
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Affiliation(s)
- Rui Liu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Shi-Kai Cao
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Chunhui Xu
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Feng Sun
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
| | - Xiaomin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, China;
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (R.L.); (S.-K.C.); (A.S.); (C.X.); (F.S.)
- Correspondence:
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45
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Rodrigues NF, Nogueira FCS, Domont GB, Margis R. Identification of soybean trans-factors associated with plastid RNA editing sites. Genet Mol Biol 2020; 43:e20190067. [PMID: 32459826 PMCID: PMC7231544 DOI: 10.1590/1678-4685-gmb-2019-0067] [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: 03/12/2019] [Accepted: 08/09/2019] [Indexed: 12/05/2022] Open
Abstract
RNA editing is a posttranscriptional process that changes nucleotide sequences, among which cytosine-to-uracil by a deamination reaction can revert non-neutral codon mutations. Pentatricopeptide repeat (PPR) proteins comprise a family of RNA-binding proteins, with members acting as editing trans-factors that recognize specific RNA cis-elements and perform the deamination reaction. PPR proteins are classified into P and PLS subfamilies. In this work, we have designed RNA biotinylated probes based in soybean plastid RNA editing sites to perform trans-factor specific protein isolation. Soybean cis-elements from these three different RNA probes show differences in respect to other species. Pulldown samples were submitted to mass spectrometry for protein identification. Among detected proteins, five corresponded to PPR proteins. More than one PPR protein, with distinct functional domains, was pulled down with each one of the RNA probes. Comparison of the soybean PPR proteins to Arabidopsis allowed identification of the closest homologous. Differential gene expression analysis demonstrated that the PPR locus Glyma.02G174500 doubled its expression under salt stress, which correlates with the increase of its potential rps14 editing. The present study represents the first identification of RNA editing trans-factors in soybean. Data also indicated that potential multiple trans-factors should interact with RNA cis-elements to perform the RNA editing.
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Affiliation(s)
- Nureyev F. Rodrigues
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
| | - Fábio C. S. Nogueira
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Laboratório de Apoio ao Desenvolvimento Tecnológico (LADETEC), Rio de Janeiro, RJ,
Brazil
| | - Gilberto B. Domont
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de
Biofísica, Porto Alegre, RS, Brazil
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46
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Searing AM, Satyanarayan MB, O′Donnell JP, Lu Y. Two organelle RNA recognition motif proteins affect distinct sets of RNA editing sites in the Arabidopsis thaliana plastid. PLANT DIRECT 2020; 4:e00213. [PMID: 32259001 PMCID: PMC7132558 DOI: 10.1002/pld3.213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/12/2019] [Accepted: 03/13/2020] [Indexed: 06/01/2023]
Abstract
Plastid and mitochondrial RNAs in vascular plants are subjected to cytidine-to-uridine editing. The model plant species Arabidopsis thaliana (Arabidopsis) has two nuclear-encoded plastid-targeted organelle RNA recognition motif (ORRM) proteins: ORRM1 and ORRM6. In the orrm1 mutant, 21 plastid RNA editing sites were affected but none are essential to photosynthesis. In the orrm6 mutants, two plastid RNA editing sites were affected: psbF-C77 and accD-C794. Because psbF encodes the β subunit of cytochrome b 559 in photosystem II, which is essential to photosynthesis, the orrm6 mutants were much smaller than the wild type. In addition, the orrm6 mutants had pale green leaves and reduced photosynthetic efficiency. To investigate the functional relationship between ORRM1 and ORRM6, we generated orrm1 orrm6 double homozygous mutants. Morphological and physiological analyses showed that the orrm1 orrm6 double mutants had a smaller plant size, reduced chlorophyll contents, and decreased photosynthetic efficiency, similar to the orrm6 single mutants. Although the orrm1 orrm6 double mutants adopted the phenotype of the orrm6 single mutants, the total number of plastid RNA editing sites affected in the orrm1 orrm6 double mutants was the sum of the sites affected in the orrm1 and orrm6 single mutants. These data suggest that ORRM1 and ORRM6 are in charge of distinct sets of plastid RNA editing sites and that simultaneous mutations in ORRM1 and ORRM6 genes do not cause additional reduction in editing extent at other plastid RNA editing sites.
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Affiliation(s)
- Audrey M. Searing
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
| | | | - James P. O′Donnell
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
| | - Yan Lu
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
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47
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Dong S, Zhao C, Zhang S, Wu H, Mu W, Wei T, Li N, Wan T, Liu H, Cui J, Zhu R, Goffinet B, Liu Y. The Amount of RNA Editing Sites in Liverwort Organellar Genes Is Correlated with GC Content and Nuclear PPR Protein Diversity. Genome Biol Evol 2020; 11:3233-3239. [PMID: 31651960 PMCID: PMC6865856 DOI: 10.1093/gbe/evz232] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2019] [Indexed: 02/06/2023] Open
Abstract
RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded pentatricopeptide repeat (PPR) proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059 PPR protein sequences. The abundance of organellar RNA editing sites varies greatly among liverwort lineages, genes, and codon positions, and shows strong positive correlations with the GC content of protein-coding genes, and the diversity of the PLS class of nuclear PPR proteins.
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Affiliation(s)
- Shanshan Dong
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Chaoxian Zhao
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.,Department of Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Shouzhou Zhang
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | | | | | - Na Li
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Tao Wan
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | | | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Ruiliang Zhu
- Department of Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut
| | - Yang Liu
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
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48
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Small ID, Schallenberg-Rüdinger M, Takenaka M, Mireau H, Ostersetzer-Biran O. Plant organellar RNA editing: what 30 years of research has revealed. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1040-1056. [PMID: 31630458 DOI: 10.1111/tpj.14578] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/25/2019] [Accepted: 10/08/2019] [Indexed: 05/21/2023]
Abstract
The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.
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Affiliation(s)
- Ian D Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
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Gutmann B, Royan S, Schallenberg-Rüdinger M, Lenz H, Castleden IR, McDowell R, Vacher MA, Tonti-Filippini J, Bond CS, Knoop V, Small ID. The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants. MOLECULAR PLANT 2020; 13:215-230. [PMID: 31760160 DOI: 10.1016/j.molp.2019.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/10/2019] [Accepted: 11/11/2019] [Indexed: 05/08/2023]
Abstract
The RNA-binding pentatricopeptide repeat (PPR) family comprises hundreds to thousands of genes in most plants, but only a few dozen in algae, indicating massive gene expansions during land plant evolution. The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant lineages. In this study, we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family, focusing on the proteins typically associated with RNA editing, which show the most spectacular variation in numbers and domain composition across the plant kingdom. We characterize over 2 250 000 PPR motifs in over 400 000 proteins. In lycophytes, polypod ferns, and hornworts, nearly 10% of expressed protein-coding genes encode putative PPR editing factors, whereas they are absent from algae and complex-thalloid liverworts. We show that rather than a single expansion, most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity. We identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing co-factors. Finally, using the sequence variations across the datasets, we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors, given their phylogenetic distribution and sequence characteristics.
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Affiliation(s)
- Bernard Gutmann
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Santana Royan
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Henning Lenz
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Ian R Castleden
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Rose McDowell
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Michael A Vacher
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Julian Tonti-Filippini
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia.
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50
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Zhang J, Fu XX, Li RQ, Zhao X, Liu Y, Li MH, Zwaenepoel A, Ma H, Goffinet B, Guan YL, Xue JY, Liao YY, Wang QF, Wang QH, Wang JY, Zhang GQ, Wang ZW, Jia Y, Wang MZ, Dong SS, Yang JF, Jiao YN, Guo YL, Kong HZ, Lu AM, Yang HM, Zhang SZ, Van de Peer Y, Liu ZJ, Chen ZD. The hornwort genome and early land plant evolution. NATURE PLANTS 2020; 6:107-118. [PMID: 32042158 PMCID: PMC7027989 DOI: 10.1038/s41477-019-0588-4] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/20/2019] [Indexed: 05/10/2023]
Abstract
Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xing Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Yan-Long Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-Yu Xue
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yi-Ying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jie-Yu Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Zhi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shan-Shan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Jian-Fen Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Zhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - An-Ming Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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