1
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Zhu L, Li X, Yang Z, Hao C, Li H, Qin X. The yellow-cotyledon gene (ATYCO) is a crucial factor for thylakoid formation and photosynthesis regulation in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112208. [PMID: 39089330 DOI: 10.1016/j.plantsci.2024.112208] [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: 05/06/2024] [Revised: 07/12/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
Chloroplast development underpins plant growth, by facilitating not only photosynthesis but also other essential biochemical processes. Nonetheless, the regulatory mechanisms and functional components of chloroplast development remain largely uncharacterized due to their complexity. In our study, we identified a plastid-targeted gene, ATYCO/RP8/CDB1, as a critical factor in early chloroplast development in Arabidopsis thaliana. YCO knock-out mutant (yco) exhibited a seedling-lethal, albino phenotype, resulting from dysfunctional chloroplasts lacking thylakoid membranes. Conversely, YCO knock-down mutants produced a chlorophyll-deficient cotyledon and normal leaves when supplemented with sucrose. Transcription analysis also revealed that YCO deficiency could be partially compensated by sucrose supplementation, and that YCO played different roles in the cotyledons and the true leaves. In YCO knock-down mutants, the transcript levels of plastid-encoded RNA polymerase (PEP)-dependent genes and nuclear-encoded photosynthetic genes, as well as the accumulation of photosynthetic proteins, were significantly reduced in the cotyledons. Moreover, the chlorophyll-deficient phenotype in YCO knock-down line can be effectively suppressed by inhibition of PSI cyclic electron transport activity, implying an interaction between YCO and PSI cyclic electron transport. Taken together, our findings de underscore the vital role of YCO in early chloroplast development and photosynthesis.
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Affiliation(s)
- Lixia Zhu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xiuxiu Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China; School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Zonghui Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chenyang Hao
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China; School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xiaochun Qin
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China.
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Hu YX, Huang A, Li Y, Molloy DP, Huang C. Emerging roles of the C-to-U RNA editing in plant stress responses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 349:112263. [PMID: 39299521 DOI: 10.1016/j.plantsci.2024.112263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/08/2024] [Accepted: 09/10/2024] [Indexed: 09/22/2024]
Abstract
RNA editing is an important post-transcriptional event in all living cells. Within chloroplasts and mitochondria of higher plants, RNA editing involves the deamination of specific cytosine (C) residues in precursor RNAs to uracil (U). An increasing number of recent studies detail specificity of C-to-U RNA editing as an essential prerequisite for several plant stress-related responses. In this review, we summarize the current understanding of responses and functions of C-to-U RNA editing in plants under various stress conditions to provide theoretical reference for future research.
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Affiliation(s)
- Yu-Xuan Hu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - An Huang
- College of Communication and Art Design, Swan College, Central South University of Forestry and Technology, Changsha 410128, China.
| | - Yi Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - David P Molloy
- Department of Biochemistry and Molecular Biology, Basic Medical College, Chongqing Medical University, Chongqing 400016, China.
| | - Chao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
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3
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Fan J, Sah SK, Lemes Jorge G, Blanford J, Xie D, Yu L, Thelen J, Shanklin J, Xu C. Arabidopsis trigalactosyldiacylglycerol1 mutants reveal a critical role for phosphtidylcholine remodeling in lipid homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39276345 DOI: 10.1111/tpj.17020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 08/08/2024] [Accepted: 08/27/2024] [Indexed: 09/17/2024]
Abstract
Lipid remodeling plays a critical role in plant response to abiotic stress and metabolic perturbations. Key steps in this process involve modifications of phosphatidylcholine (PC) acyl chains mediated by lysophosphatidylcholine: acyl-CoA acyltransferases (LPCATs) and phosphatidylcholine: diacylglycerol cholinephosphotransferase (ROD1). To assess their importance in lipid homeostasis, we took advantage of the trigalactosyldiacylglycerol1 (tgd1) mutant that exhibits marked increases in fatty acid synthesis and fatty acid flux through PC due to a block in inter-organelle lipid trafficking. Here, we showed that the increased fatty acid synthesis in tgd1 is due to posttranslational activation of the plastidic acetyl-coenzyme A carboxylase. Genetic analysis showed that knockout of LPCAT1 and 2 resulted in a lethal phenotype in tgd1. In addition, plants homozygous for lpcat2 and heterozygous for lpcat1 in the tgd1 background showed reduced levels of PC and triacylglycerols (TAG) and alterations in their fatty acid profiles. We further showed that disruption of ROD1 in tgd1 resulted in changes in fatty acid composition of PC and TAG, decreased leaf TAG content and reduced seedling growth. Together, our results reveal a critical role of LPCATs and ROD1 in maintaining cellular lipid homeostasis under conditions, in which fatty acid production largely exceeds the cellular demand for membrane lipid synthesis.
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Affiliation(s)
- Jilian Fan
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Saroj Kumar Sah
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Gabriel Lemes Jorge
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, 1201 E Rollins, Columbia, Missouri, 65211, USA
| | - Jantana Blanford
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Dongling Xie
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Linhui Yu
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Jay Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, 1201 E Rollins, Columbia, Missouri, 65211, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Changcheng Xu
- Biology Department, Brookhaven National Laboratory, Upton, New York, 11973, USA
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4
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Fang X, Zhu Z, Li J, Wang X, Wei C, Zhang X, Dai Z, Liu S, Luan F. Identification of Chromosomal Regions and Candidate Genes for Round leaf Locus in Cucumis melo L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1134. [PMID: 38674543 PMCID: PMC11054961 DOI: 10.3390/plants13081134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Leaf morphology plays a crucial role in plant classification and provides a significant model for studying plant diversity while directly impacting photosynthetic efficiency. In the case of melons, leaf shape not only influences production and classification but also represents a key genetic trait that requires further exploration. In this study, we utilized forward genetics to pinpoint a recessive locus, dubbed Cmrl (Round leaf), which is responsible for regulating melon leaf shape. Through bulked segregant analysis sequencing and extensive evaluation of a two-year F2 population, we successfully mapped the Cmrl locus to a 537.07 kb region on chromosome 8 of the melon genome. Subsequent genetic fine-mapping efforts, leveraging a larger F2 population encompassing 1322 plants and incorporating F2:3 phenotypic data, further refined the locus to an 80.27 kb interval housing five candidate genes. Promoter analysis and coding sequence cloning confirmed that one of these candidates, MELO3C019152.2 (Cmppr encoding a pentatricopeptide repeat-containing family protein, Cmppr), stands out as a strong candidate gene for the Cmrl locus. Notably, comparisons of Cmrl expressions across various stages of leaf development and different leaf regions suggest a pivotal role of Cmrl in the morphogenesis of melon leaves.
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Affiliation(s)
- Xufeng Fang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Junyan Li
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xuezheng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Chunhua Wei
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (C.W.); (X.Z.)
| | - Xian Zhang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (C.W.); (X.Z.)
| | - Zuyun Dai
- Anhui Jianghuai Horticulture Technology Co., Ltd., Hefei 230031, China;
| | - Shi Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
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5
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Wang L, Di T, Li N, Peng J, Wu Y, He M, Hao X, Huang J, Ding C, Yang Y, Wang X. Transcriptomic analysis of hub genes regulating albinism in light- and temperature-sensitive albino tea cultivars 'Zhonghuang 1' and 'Zhonghuang 2'. PLANT MOLECULAR BIOLOGY 2024; 114:44. [PMID: 38630172 DOI: 10.1007/s11103-024-01430-3] [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: 10/09/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024]
Abstract
Albino tea cultivars have high economic value because their young leaves contain enhanced free amino acids that improve the quality and properties of tea. Zhonghuang 1 (ZH1) and Zhonghuang 2 (ZH2) are two such cultivars widely planted in China; however, the environmental factors and molecular mechanisms regulating their yellow-leaf phenotype remain unclear. In this study, we demonstrated that both ZH1 and ZH2 are light- and temperature-sensitive. Under natural sunlight and low-temperature conditions, their young shoots were yellow with decreased chlorophyll and an abnormal chloroplast ultrastructure. Conversely, young shoots were green with increased chlorophyll and a normal chloroplast ultrastructure under shading and high-temperature conditions. RNA-seq analysis was performed for high light and low light conditions, and pairwise comparisons identified genes exhibiting different light responses between albino and green-leaf cultivars, including transcription factors, cytochrome P450 genes, and heat shock proteins. Weighted gene coexpression network analyses of RNA-seq data identified the modules related to chlorophyll differences between cultivars. Genes involved in chloroplast biogenesis and development, light signaling, and JA biosynthesis and signaling were typically downregulated in albino cultivars, accompanied by a decrease in JA-ILE content in ZH2 during the albino period. Furthermore, we identified the hub genes that may regulate the yellow-leaf phenotype of ZH1 and ZH2, including CsGDC1, CsALB4, CsGUN4, and a TPR gene (TEA010575.1), which were related to chloroplast biogenesis. This study provides new insights into the molecular mechanisms underlying leaf color formation in albino tea cultivars.
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Affiliation(s)
- Lu Wang
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Taimei Di
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Nana Li
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Jing Peng
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Yedie Wu
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Mingming He
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Xinyuan Hao
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Jianyan Huang
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Changqing Ding
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Yajun Yang
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China
| | - Xinchao Wang
- Key laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008, Hangzhou, China.
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6
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Xu C, Li J, Song LY, Guo ZJ, Song SW, Zhang LD, Zheng HL. PlantC2U: deep learning of cross-species sequence landscapes predicts plastid C-to-U RNA editing in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2266-2279. [PMID: 38190348 DOI: 10.1093/jxb/erae007] [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: 10/29/2023] [Accepted: 01/07/2024] [Indexed: 01/10/2024]
Abstract
In plants, C-to-U RNA editing mainly occurs in plastid and mitochondrial transcripts, which contributes to a complex transcriptional regulatory network. More evidence reveals that RNA editing plays critical roles in plant growth and development. However, accurate detection of RNA editing sites using transcriptome sequencing data alone is still challenging. In the present study, we develop PlantC2U, which is a convolutional neural network, to predict plastid C-to-U RNA editing based on the genomic sequence. PlantC2U achieves >95% sensitivity and 99% specificity, which outperforms the PREPACT tool, random forests, and support vector machines. PlantC2U not only further checks RNA editing sites from transcriptome data to reduce possible false positives, but also assesses the effect of different mutations on C-to-U RNA editing based on the flanking sequences. Moreover, we found the patterns of tissue-specific RNA editing in the mangrove plant Kandelia obovata, and observed reduced C-to-U RNA editing rates in the cold stress response of K. obovata, suggesting their potential regulatory roles in plant stress adaptation. In addition, we present RNAeditDB, available online at https://jasonxu.shinyapps.io/RNAeditDB/. Together, PlantC2U and RNAeditDB will help researchers explore the RNA editing events in plants and thus will be of broad utility for the plant research community.
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Affiliation(s)
- Chaoqun Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ling-Yu Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ze-Jun Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Shi-Wei Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Lu-Dan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
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7
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Yang M, Wan S, Chen J, Chen W, Wang Y, Li W, Wang M, Guan R. Mutation to a cytochrome P 450 -like gene alters the leaf color by affecting the heme and chlorophyll biosynthesis pathways in Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:432-445. [PMID: 37421327 DOI: 10.1111/tpj.16382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/04/2023] [Accepted: 07/04/2023] [Indexed: 07/10/2023]
Abstract
The regulated biosynthesis of chlorophyll is important because of its effects on plant photosynthesis and dry biomass production. In this study, a map-based cloning approach was used to isolate the cytochrome P450 -like gene BnaC08g34840D (BnCDE1) from a chlorophyll-deficient mutant (cde1) of Brassica napus obtained by ethyl methanesulfonate (EMS) mutagenization. Sequence analyses revealed that BnaC08g34840D in the cde1 mutant (BnCDE1I320T ) encodes a substitution at amino acid 320 (Ile320Thr) in the conserved region. The over-expression of BnCDE1I320T in ZS11 (i.e., gene-mapping parent with green leaves) recapitulated a yellow-green leaf phenotype. The CRISPR/Cas9 genome-editing system was used to design two single-guide RNAs (sgRNAs) targeting BnCDE1I320T in the cde1 mutant. The knockout of BnCDE1I320T in the cde1 mutant via a gene-editing method restored normal leaf coloration (i.e., green leaves). These results indicate that the substitution in BnaC08g34840D alters the leaf color. Physiological analyses showed that the over-expression of BnCDE1I320T leads to decreases in the number of chloroplasts per mesophyll cell and in the contents of the intermediates of the chlorophyll biosynthesis pathway in leaves, while it increases heme biosynthesis, thereby lowering the photosynthetic efficiency of the cde1 mutant. The Ile320Thr mutation in the highly conserved region of BnaC08g34840D inhibited chlorophyll biosynthesis and disrupted the balance between heme and chlorophyll biosynthesis. Our findings may further reveal how the proper balance between the chlorophyll and heme biosynthesis pathways is maintained.
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Affiliation(s)
- Mao Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shubei Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenjing Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yangming Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiyan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Meihong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongzhan Guan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
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8
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Liu D, Li ZA, Li Y, Molloy DP, Huang C. The DYW domain of RARE1 plays an indispensable role in regulating accD-C794 RNA editing in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 334:111751. [PMID: 37263527 DOI: 10.1016/j.plantsci.2023.111751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023]
Abstract
The Arabidopsis pentatricopeptide repeat (PPR) proteins, required for accD RNA editing 1 (RARE1) and early chloroplast biogenesis 2 (AtECB2), each contain a DYW domain deemed essential for cytosine deamination at the accD-C794 RNA editing site in chloroplasts. Complementation assays using the rare1 mutant investigate the correlation between these PPRs and their respective DYW domain functions in RNA editing of accD-C794. The results demonstrate that the coding sequence of AtECB2 cannot replace that of RARE1. Moreover, rare1 mutants complemented with DYW-deleted RARE1 failed to recover the RNA editing of accD-C794 even in the presence of the highly similar DYW domain of the AtECB2 protein. These findings indicate that RARE1 and AtECB2 possess divergent roles in RNA editing, with specificity for accD-C794 directly attributable to DYW domain within RARE1. Structural modeling data suggest this functioning pertains to a local α-helical motif that residues slightly N-terminal to the consensus glutamate and CXXCH motif in the DYW domain for cytidine deamination during C-to-U editing by RARE1 that is absent within AtECB2.
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Affiliation(s)
- Dan Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Zi-Ang Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yi Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - David P Molloy
- Department of Biochemistry and Molecular Biology, Basic Medical College, Chongqing Medical University, Chongqing 400016, China; Center for Molecular Medicine and Cancer Research, Basic Medical College, Chongqing Medical University, Chongqing 400016, China.
| | - Chao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
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9
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Tian J, Jiang W, Si J, Han Z, Li C, Chen D. Developmental Characteristics and Auxin Response of Epiphytic Root in Dendrobium catenatum. FRONTIERS IN PLANT SCIENCE 2022; 13:935540. [PMID: 35812932 PMCID: PMC9260429 DOI: 10.3389/fpls.2022.935540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Dendrobium catenatum, a traditional precious Chinese herbal medicine, belongs to epiphytic orchids. Its special life mode leads to the specialization of roots, but there is a lack of systematic research. The aerial root in D. catenatum displays diverse unique biological characteristics, and it initially originates from the opposite pole of the shoot meristem within the protocorm. The root development of D. catenatum is not only regulated by internal cues but also adjusts accordingly with the change in growth environments. D. catenatum root is highly tolerant to auxin, which may be closely related to its epiphytic life. Exogenous auxin treatment has dual effects on D. catenatum roots: relatively low concentration promotes root elongation, which is related to the induced expression of cell wall synthesis genes; excessive concentration inhibits the differentiation of velamen and exodermis and promotes the overproliferation of cortical cells, which is related to the significant upregulation of WOX11-WOX5 regeneration pathway genes and cell division regulatory genes. Overexpression of D. catenatum WOX12 (DcWOX12) in Arabidopsis inhibits cell and organ differentiation, but induces cell dedifferentiation and callus production. Therefore, DcWOX12 not only retains the characteristics of ancestors as stem cell regulators, but also obtains stronger cell fate transformation ability than homologous genes of other species. These findings suggest that the aerial root of D. catenatum evolves special structure and developmental characteristics to adapt to epiphytic life, providing insight into ideal root structure breeding of simulated natural cultivation in D. catenatum and a novel target gene for improving the efficiency of monocot plant transformation.
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10
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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: 2] [Impact Index Per Article: 0.7] [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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11
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Joynson R, Molero G, Coombes B, Gardiner L, Rivera‐Amado C, Piñera‐Chávez FJ, Evans JR, Furbank RT, Reynolds MP, Hall A. Uncovering candidate genes involved in photosynthetic capacity using unexplored genetic variation in Spring Wheat. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1537-1552. [PMID: 33638599 PMCID: PMC8384606 DOI: 10.1111/pbi.13568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/26/2021] [Indexed: 05/10/2023]
Abstract
To feed an ever-increasing population we must leverage advances in genomics and phenotyping to harness the variation in wheat breeding populations for traits like photosynthetic capacity which remains unoptimized. Here we survey a diverse set of wheat germplasm containing elite, introgression and synthetic derivative lines uncovering previously uncharacterized variation. We demonstrate how strategic integration of exotic material alleviates the D genome genetic bottleneck in wheat, increasing SNP rate by 62% largely due to Ae. tauschii synthetic wheat donors. Across the panel, 67% of the Ae. tauschii donor genome is represented as introgressions in elite backgrounds. We show how observed genetic variation together with hyperspectral reflectance data can be used to identify candidate genes for traits relating to photosynthetic capacity using association analysis. This demonstrates the value of genomic methods in uncovering hidden variation in wheat and how that variation can assist breeding efforts and increase our understanding of complex traits.
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Affiliation(s)
| | - Gemma Molero
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT)TexcocoMexico
| | | | | | - Carolina Rivera‐Amado
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT)TexcocoMexico
| | | | - John R. Evans
- ARC Centre of Excellence for Translational PhotosynthesisAustralian National UniversityCanberraAustralia
| | - Robert T. Furbank
- ARC Centre of Excellence for Translational PhotosynthesisAustralian National UniversityCanberraAustralia
| | - Matthew P. Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT)TexcocoMexico
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12
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Meng X, Xu J, Zhang M, Du R, Zhao W, Zeng Q, Tu Z, Chen J, Chen B. Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings. BMC Genomics 2021; 22:543. [PMID: 34271866 PMCID: PMC8283932 DOI: 10.1186/s12864-021-07873-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 07/05/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Most plants rely on photosynthesis; therefore, albinism in plants with leaves that are white instead of green causes slow growth, dwarfing, and even death. Although albinism has been characterized in annual model plants, little is known about albino trees. Jackfruit (Artocarpus heterophyllus) is an important tropical fruit tree species. To gain insight into the mechanisms underlying the differential growth and development between albino jackfruit mutants and green seedlings, we analyzed root, stem, and leaf tissues by combining PacBio single-molecule real-time (SMRT) sequencing, high-throughput RNA-sequencing (RNA-seq), and metabolomic analysis. RESULTS We identified 8,202 differentially expressed genes (DEGs), including 225 genes encoding transcription factors (TFs), from 82,572 full-length transcripts. We also identified 298 significantly changed metabolites (SCMs) in albino A. heterophyllus seedlings from a set of 692 metabolites in A. heterophyllus seedlings. Pathway analysis revealed that these DEGs were highly enriched in metabolic pathways such as 'photosynthesis', 'carbon fixation in photosynthetic organisms', 'glycolysis/gluconeogenesis', and 'TCA cycle'. Analysis of the metabolites revealed 76 SCMs associated with metabolic pathways in the albino mutants, including L-aspartic acid, citric acid, succinic acid, and fumaric acid. We selected 225 differentially expressed TF genes, 333 differentially expressed metabolic pathway genes, and 76 SCMs to construct two correlation networks. Analysis of the TF-DEG network suggested that basic helix-loop-helix (bHLH) and MYB-related TFs regulate the expression of genes involved in carbon fixation and energy metabolism to affect light responses or photomorphogenesis and normal growth. Further analysis of the DEG-SCM correlation network and the photosynthetic carbon fixation pathway suggested that NAD-ME2 (encoding a malic enzyme) and L-aspartic acid jointly inhibit carbon fixation in the albino mutants, resulting in reduced photosynthetic efficiency and inhibited plant growth. CONCLUSIONS Our preliminarily screening identified candidate genes and metabolites specifically affected in albino A. heterophyllus seedlings, laying the foundation for further study of the regulatory mechanism of carbon fixation during photosynthesis and energy metabolism. In addition, our findings elucidate the way genes and metabolites respond in albino trees.
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Affiliation(s)
- Xiangxu Meng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Jiahong Xu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Maoning Zhang
- School of Agricultural Sciences, Zhengzhou University, 450001, Zhengzhou, People's Republic of China
| | - Ruyue Du
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Wenxiu Zhao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Qing Zeng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Zhihua Tu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Jinhui Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China.
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China.
| | - Beibei Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, 524088, Zhanjiang, People's Republic of China.
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13
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Chen J, Wang L, Jin X, Wan J, Zhang L, Je BI, Zhao K, Kong F, Huang J, Tian M. Oryza sativa ObgC1 Acts as a Key Regulator of DNA Replication and Ribosome Biogenesis in Chloroplast Nucleoids. RICE (NEW YORK, N.Y.) 2021; 14:65. [PMID: 34251486 PMCID: PMC8275814 DOI: 10.1186/s12284-021-00498-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 05/30/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The Spo0B-associated GTP-binding protein (Obg) GTPase, has diverse and important functions in bacteria, including morphological development, DNA replication and ribosome maturation. Homologs of the Bacillus subtilis Obg have been also found in chloroplast of Oryza sativa, but their primary roles remain unknown. RESULTS We clarify that OsObgC1 is a functional homolog of AtObgC. The mutant obgc1-d1 exhibited hypersensitivity to the DNA replication inhibitor hydroxyurea. Quantitative PCR results showed that the ratio of chloroplast DNA to nuclear DNA in the mutants was higher than that of the wild-type plants. After DAPI staining, OsObgC1 mutants showed abnormal nucleoid architectures. The specific punctate staining pattern of OsObgC1-GFP signal suggests that this protein localizes to the chloroplast nucleoids. Furthermore, loss-of-function mutation in OsObgC1 led to a severe suppression of protein biosynthesis by affecting plastid rRNA processing. It was also demonstrated through rRNA profiling that plastid rRNA processing was decreased in obgc1-d mutants, which resulted in impaired ribosome biogenesis. The sucrose density gradient profiles revealed a defective chloroplast ribosome maturation of obgc1-d1 mutants. CONCLUSION Our findings here indicate that the OsObgC1 retains the evolutionarily biological conserved roles of prokaryotic Obg, which acts as a signaling hub that regulates DNA replication and ribosome biogenesis in chloroplast nucleoids.
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Affiliation(s)
- Ji Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Li Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaowan Jin
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Wan
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lang Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Byoung Il Je
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 61005, China
| | - Ke Zhao
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fanlei Kong
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Huang
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 61005, China.
| | - Mengliang Tian
- Institute for New Rural Development, Sichuan Agricultural University, Yaan, 625000, China.
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14
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Yu YH, Li XF, Yang SD, Li SQ, Meng XX, Liu HN, Pei MS, Wei TL, Zhang YJ, Guo DL. Overexpression of VvPPR1, a DYW-type PPR protein in grape, affects the phenotype of Arabidopsis thaliana leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 164:195-204. [PMID: 34004557 DOI: 10.1016/j.plaphy.2021.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins play important roles in plant growth and development. However, little is known about their functions in the leaf morphogenesis of Jingxiu grape (Vitis vinifera L.). Here, we explored the function of VvPPR1, which encodes a DYW-type PPR protein in grape. We showed that VvPPR1 is involved in the regulation of leaf rolling, anthocyanin accumulation, and trichome formation in Arabidopsis thaliana. Analysis of structural characteristics showed that VvPPR1 is a DYW-type PPR gene in the PLS subfamily consisting of 15 PPR motifs. The N-terminal had a targeted chloroplast site, and the C-terminal had a DYW domain. Quantitative PCR analysis revealed that the expression level of VvPPR1 was highest in grape leaves. Subcellular localization revealed that VvPPR1 is localized in the cytoplasm and chloroplast. VvPPR1-overexpressing plants had rolled leaves, high degrees of anthocyanin accumulation, and longer trichomes. The expression levels of genes related to these phenotypes were either significantly up-regulated or down-regulated. These results demonstrate that VvPPR1 is involved in leaf rolling, anthocyanin accumulation, and trichome formation in Arabidopsis; more generally, our findings indicate that VvPPR1 could be a target for improving the cultivation of horticultural crops.
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Affiliation(s)
- Yi-He Yu
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Xu-Fei Li
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Sheng-Di Yang
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Song-Qi Li
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Xiang-Xuan Meng
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Hai-Nan Liu
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Mao-Song Pei
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Tong-Lu Wei
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Yu-Jie Zhang
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Da-Long Guo
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.
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15
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Liu XY, Jiang RC, Wang Y, Tang JJ, Sun F, Yang YZ, Tan BC. ZmPPR26, a DYW-type pentatricopeptide repeat protein, is required for C-to-U RNA editing at atpA-1148 in maize chloroplasts. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4809-4821. [PMID: 33929512 DOI: 10.1093/jxb/erab185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are involved in the C-to-U RNA editing of organellar transcripts. The maize genome contains over 600 PPR proteins and few have been found to function in the C-to-U RNA editing in chloroplasts. Here, we report the function of ZmPPR26 in the C-to-U RNA editing and chloroplast biogenesis in maize. ZmPPR26 encodes a DYW-type PPR protein targeted to chloroplasts. The zmppr26 mutant exhibits albino seedling-lethal phenotype. Loss of function of ZmPPR26 abolishes the editing at atpA-1148 site, and decreases the editing at ndhF-62, rpl20-308, rpl2-2, rpoC2-2774, petB-668, rps8-182, and ndhA-50 sites. Overexpression of ZmPPR26 in zmppr26 restores the editing efficiency and rescues the albino seedling-lethal phenotype. Abolished editing at atpA-1148 causes a Leu to Ser change at AtpA-383 that leads to a reduction in the abundance of chloroplast ATP synthase in zmppr26. The accumulation of photosynthetic complexes are also markedly reduced in zmppr26, providing an explanation for the albino seedling-lethal phenotype. These results indicate that ZmPPR26 is required for the editing at atpA-1148 and is important for editing at the other seven sites in maize chloroplasts. The editing at atpA-1148 is critical for AtpA function, assembly of ATP synthase complex, and chloroplast biogenesis in maize.
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Affiliation(s)
- Xin-Yuan Liu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Rui-Cheng Jiang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yong Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Jiao-Jiao Tang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Feng Sun
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Yan-Zhuo Yang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Bao-Cai Tan
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
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16
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Genetic Polymorphism and Lineage of Pigeon Pea [Cajanus cajan (L.) Millsp.] inferred from Chloroplast and Nuclear DNA gene regions. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2021. [DOI: 10.1007/s13369-020-05036-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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GUN1 and Plastid RNA Metabolism: Learning from Genetics. Cells 2020; 9:cells9102307. [PMID: 33081381 PMCID: PMC7602965 DOI: 10.3390/cells9102307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 11/16/2022] Open
Abstract
GUN1 (genomes uncoupled 1), a chloroplast-localized pentatricopeptide repeat (PPR) protein with a C-terminal small mutS-related (SMR) domain, plays a central role in the retrograde communication of chloroplasts with the nucleus. This flow of information is required for the coordinated expression of plastid and nuclear genes, and it is essential for the correct development and functioning of chloroplasts. Multiple genetic and biochemical findings indicate that GUN1 is important for protein homeostasis in the chloroplast; however, a clear and unified view of GUN1′s role in the chloroplast is still missing. Recently, GUN1 has been reported to modulate the activity of the nucleus-encoded plastid RNA polymerase (NEP) and modulate editing of plastid RNAs upon activation of retrograde communication, revealing a major role of GUN1 in plastid RNA metabolism. In this opinion article, we discuss the recently identified links between plastid RNA metabolism and retrograde signaling by providing a new and extended concept of GUN1 activity, which integrates the multitude of functional genetic interactions reported over the last decade with its primary role in plastid transcription and transcript editing.
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18
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OsCpn60β1 is Essential for Chloroplast Development in Rice ( Oryza sativa L.). Int J Mol Sci 2020; 21:ijms21114023. [PMID: 32512821 PMCID: PMC7313468 DOI: 10.3390/ijms21114023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 01/03/2023] Open
Abstract
The chaperonin 60 (Cpn60) protein is of great importance to plants due to its involvement in modulating the folding of numerous chloroplast protein polypeptides. In chloroplasts, Cpn60 is differentiated into two subunit types—Cpn60α and Cpn60β and the rice genome encodes three α and three β plastid chaperonin subunits. However, the functions of Cpn60 family members in rice were poorly understood. In order to investigate the molecular mechanism of OsCpn60β1, we attempted to disrupt the OsCpn60β1 gene by CRISPR/Cas9-mediated targeted mutagenesis in this study. We succeeded in the production of homozygous OsCpn60β1 knockout rice plants. The OsCpn60β1 mutant displayed a striking albino leaf phenotype and was seedling lethal. Electron microscopy observation demonstrated that chloroplasts were severely disrupted in the OsCpn60β1 mutant. In addition, OsCpn60β1 was located in the chloroplast and OsCpn60β1 is constitutively expressed in various tissues particularly in the green tissues. The label-free qualitative proteomics showed that photosynthesis-related pathways and ribosomal pathways were significantly inhibited in OsCpn60β1 mutants. These results indicate that OsCpn60β1 is essential for chloroplast development in rice.
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19
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Hao Y, Wang Y, Wu M, Zhu X, Teng X, Sun Y, Zhu J, Zhang Y, Jing R, Lei J, Li J, Bao X, Wang C, Wang Y, Wan J. The nuclear-localized PPR protein OsNPPR1 is important for mitochondrial function and endosperm development in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4705-4720. [PMID: 31087099 PMCID: PMC6760278 DOI: 10.1093/jxb/erz226] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/02/2019] [Indexed: 05/06/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants. Recent studies revealed the functions of PPR proteins in organellar RNA metabolism and plant development, but the functions of most PPR proteins, especially PPRs localized in the nucleus, remain largely unknown. Here, we report the isolation and characterization of a rice mutant named floury and growth retardation1 (fgr1). fgr1 showed floury endosperm with loosely arranged starch grains, decreased starch and amylose contents, and retarded seedling growth. Map-based cloning showed that the mutant phenotype was caused by a single nucleotide substitution in the coding region of Os08g0290000. This gene encodes a nuclear-localized PPR protein, which we named OsNPPR1, that affected mitochondrial function. In vitro SELEX and RNA-EMSAs showed that OsNPPR1 was an RNA protein that bound to the CUCAC motif. Moreover, a number of retained intron (RI) events were detected in fgr1. Thus, OsNPPR1 was involved in regulation of mitochondrial development and/or functions that are important for endosperm development. Our results provide novel insights into coordinated interaction between nuclear-localized PPR proteins and mitochondrial function.
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Affiliation(s)
- Yuanyuan Hao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Yunlong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Mingming Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Xiaopin Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Xuan Teng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Yinglun Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Jianping Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Yuanyan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Ruonan Jing
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Jie Lei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Jingfang Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Xiuhao Bao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Chunming Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
| | - Yihua Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
- Correspondence: ; ; or
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, PR China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
- Correspondence: ; ; or
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20
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He P, Wu S, Jiang Y, Zhang L, Tang M, Xiao G, Yu J. GhYGL1d, a pentatricopeptide repeat protein, is required for chloroplast development in cotton. BMC PLANT BIOLOGY 2019; 19:350. [PMID: 31409298 PMCID: PMC6693126 DOI: 10.1186/s12870-019-1945-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/25/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND The pentatricopeptide repeat (PPR) gene family, which contains multiple 35-amino acid repeats, constitutes one of the largest gene families in plants. PPR proteins function in organelles to target specific transcripts and are involved in plant development and growth. However, the function of PPR proteins in cotton is still unknown. RESULTS In this study, we characterized a PPR gene YELLOW-GREEN LEAF (GhYGL1d) that is required for cotton plastid development. The GhYGL1d gene has a DYW domain in C-terminal and is highly express in leaves, localized to the chloroplast fractions. GhYGL1d share high amino acid-sequence homology with AtECB2. In atecb2 mutant, overexpression of GhYGL1d rescued the seedling lethal phenotype and restored the editing of accD and ndhF transcripts. Silencing of GhYGL1d led to the reduction of chlorophyll and phenotypically yellow-green leaves in cotton. Compared with wild type, GhYGL1d-silenced cotton showed significant deformations of thylakoid structures. Furthermore, the transcription levels of plastid-encoded polymerase (PEP) and nuclear-encoded polymerase (NEP) dependent genes were decreased in GhYGL1d-silenced cotton. CONCLUSIONS Our data indicate that GhYGL1d not only contributes to the editing of accD and ndhF genes, but also affects the expression of NEP- and PEP-dependent genes to regulate the development of thylakoids, and therefore regulates leaf variegation in cotton.
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Affiliation(s)
- Peng He
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Shuyin Wu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yanli Jiang
- Shanxi Academy of Agricultural Sciences, Cotton Research Institute, Yucheng, 044000, China
| | - Lihua Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Meiju Tang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Guanghui Xiao
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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21
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Gao S, Gao W, Liao X, Xiong C, Yu G, Yang Q, Yang C, Ye Z. The tomato WV gene encoding a thioredoxin protein is essential for chloroplast development at low temperature and high light intensity. BMC PLANT BIOLOGY 2019; 19:265. [PMID: 31221088 PMCID: PMC6585109 DOI: 10.1186/s12870-019-1829-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 05/13/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Chloroplast biogenesis, a complex process in higher plants, is the key to photoautotrophic growth in plants. White virescent (wv) mutants have been used to unfold the molecular mechanisms underlying the regulation of chloroplast development and chloroplast gene expression in plants. However, most of genes controlling white virescent phenotype still remain unknown. RESULTS In this study, we identified a temperature- and light intensity-sensitive mutant, named as wv. The content of chlorophyll was dramatically decreased in the immature leaves of wv mutant under the conditions of low temperature and high-light intensity. TEM observation showed that the chloroplasts in the young leaves of wv mutant lacked an organized thylakoid membrane, whereas crescent-shaped chloroplasts with well-developed stromal and stacked grana thylakoids in the mature leaves were developed. Immunoblot analyses suggested that proteins of photosynthetic complexes were decreased substantially in wv mutants. Based on map-based cloning and transgenic analysis, we determined that the wv phenotype was caused by single base mutation in the first intron of WV gene, which encoded a thioredoxin protein with 365 amino acids. qRT-PCR analysis revealed that the expression of WV gene was significantly down-regulated in wv mutant. In addition, knockdown of WV gene through RNAi also resulted in white virescent young leaves, suggesting that the mutation possibly blocks the differentiation of chloroplasts through inhibiting the expression of WV gene. Furthermore, the expression of WV peaked in apical buds and gradually decreased along with the developmental stage, which was consistent with the wv mutant phenotype. Expression analysis of chloroplast-encoded genes by qRT-PCR showed that the wv mutation affected the expression pattern of chloroplast-encoded PEP dependent genes. CONCLUSION Our results suggested that wv mutant was sensitive to low temperature and light intensity. WV gene was essential for chloroplast differentiation. A single base mutation in the first intron resulted in down-regulation of WV gene expression, which inhibited the expression of chloroplast-encoded genes, thereby blocking chloroplast formation and chlorophyll synthesis.
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Affiliation(s)
- Shenghua Gao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430070, Hubei, China
| | - Wenjing Gao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiaoli Liao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Cheng Xiong
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Gang Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qihong Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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22
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Transcriptome Analyses Provide Novel Insights into Heat Stress Responses in Chieh-Qua ( Benincasa hispida Cogn. var. Chieh-Qua How). Int J Mol Sci 2019; 20:ijms20040883. [PMID: 30781658 PMCID: PMC6413116 DOI: 10.3390/ijms20040883] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/02/2022] Open
Abstract
Temperature rising caused by global warming has imposed significant negative effects on crop qualities and yields. To get the well-known molecular mechanism upon the higher temperature, we carefully analyzed the RNA sequencing-based transcriptomic responses of two contrasting chieh-qua genotypes: A39 (heat-tolerant) and H5 (heat-sensitive). In this study, twelve cDNA libraries generated from A39 and H5 were performed with a transcriptome assay under normal and heat stress conditions, respectively. A total of 8705 differentially expressed genes (DEGs) were detected under normal conditions (3676 up-regulated and 5029 down-regulated) and 1505 genes under heat stress (914 up-regulated and 591 down-regulated), respectively. A significant positive correlation between RNA-Seq data and qRT-PCR results was identified. DEGs related to heat shock proteins (HSPs), ubiquitin-protein ligase, transcriptional factors, and pentatricopeptide repeat-containing proteins were significantly changed after heat stress. Several genes, which encoded HSPs (CL2311.Contig3 and CL6612.Contig2), cytochrome P450 (CL4517.Contig4 and CL683.Contig7), and bHLH TFs (CL914.Contig2 and CL8321.Contig1) were specifically induced after four days of heat stress. DEGs detected in our study between these two contrasting cultivars would provide a novel basis for isolating useful candidate genes of heat stress responses in chieh-qua.
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23
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Zhang Y, Cui YL, Zhang XL, Yu QB, Wang X, Yuan XB, Qin XM, He XF, Huang C, Yang ZN. A nuclear-encoded protein, mTERF6, mediates transcription termination of rpoA polycistron for plastid-encoded RNA polymerase-dependent chloroplast gene expression and chloroplast development. Sci Rep 2018; 8:11929. [PMID: 30093718 PMCID: PMC6085346 DOI: 10.1038/s41598-018-30166-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 04/20/2018] [Indexed: 12/13/2022] Open
Abstract
The expression of plastid genes is regulated by two types of DNA-dependent RNA polymerases, plastid-encoded RNA polymerase (PEP) and nuclear-encoded RNA polymerase (NEP). The plastid rpoA polycistron encodes a series of essential chloroplast ribosome subunits and a core subunit of PEP. Despite the functional importance, little is known about the regulation of rpoA polycistron. In this work, we show that mTERF6 directly associates with a 3′-end sequence of rpoA polycistron in vitro and in vivo, and that absence of mTERF6 promotes read-through transcription at this site, indicating that mTERF6 acts as a factor required for termination of plastid genes’ transcription in vivo. In addition, the transcriptions of some essential ribosome subunits encoded by rpoA polycistron and PEP-dependent plastid genes are reduced in the mterf6 knockout mutant. RpoA, a PEP core subunit, accumulates to about 50% that of the wild type in the mutant, where early chloroplast development is impaired. Overall, our functional analyses of mTERF6 provide evidence that it is more likely a factor required for transcription termination of rpoA polycistron, which is essential for chloroplast gene expression and chloroplast development.
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Affiliation(s)
- Yi Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.,Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yong-Lan Cui
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiao-Lei Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qing-Bo Yu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xi Wang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xin-Bo Yuan
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xue-Mei Qin
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiao-Fang He
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chao Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhong-Nan Yang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
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24
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Liu X, Lan J, Huang Y, Cao P, Zhou C, Ren Y, He N, Liu S, Tian Y, Nguyen T, Jiang L, Wan J. WSL5, a pentatricopeptide repeat protein, is essential for chloroplast biogenesis in rice under cold stress. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3949-3961. [PMID: 29893948 PMCID: PMC6054151 DOI: 10.1093/jxb/ery214] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 06/18/2018] [Indexed: 05/18/2023]
Abstract
Chloroplasts play an essential role in plant growth and development, and cold conditions affect chloroplast development. Although many genes or regulators involved in chloroplast biogenesis and development have been isolated and characterized, many other components affecting chloroplast biogenesis under cold conditions have not been characterized. Here, we report the functional characterization of a white stripe leaf 5 (wsl5) mutant in rice. The mutant develops white-striped leaves during early leaf development and is albinic when planted under cold stress. Genetic and molecular analysis revealed that WSL5 encodes a novel chloroplast-targeted pentatricopeptide repeat protein. RNA sequencing analysis showed that expression of nuclear-encoded photosynthetic genes in the mutant was significantly repressed, and expression of many chloroplast-encoded genes was also significantly changed. Notably, the wsl5 mutation causes defects in editing of rpl2 and atpA, and splicing of rpl2 and rps12. wsl5 was impaired in chloroplast ribosome biogenesis under cold stress. We propose that the WSL5 allele is required for normal chloroplast development in maintaining retrograde signaling from plastids to the nucleus under cold stress.
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Affiliation(s)
- Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Jie Lan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Yunshuai Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Penghui Cao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Yaken Ren
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Niqing He
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Thanhliem Nguyen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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25
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Yu QB, Zhao TT, Ye LS, Cheng L, Wu YQ, Huang C, Yang ZN. pTAC10, an S1-domain-containing component of the transcriptionally active chromosome complex, is essential for plastid gene expression in Arabidopsis thaliana and is phosphorylated by chloroplast-targeted casein kinase II. PHOTOSYNTHESIS RESEARCH 2018; 137:69-83. [PMID: 29330702 DOI: 10.1007/s11120-018-0479-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/28/2017] [Indexed: 06/07/2023]
Abstract
In higher plant chloroplasts, the plastid-encoded RNA polymerase (PEP) consists of four catalytic subunits and numerous nuclear-encoded accessory proteins, including pTAC10, an S1-domain-containing protein. In this study, pTAC10 knockout lines were characterized. Two ptac10 mutants had an albino phenotype and severely impaired chloroplast development. The pTAC10 genomic sequence fused to a four-tandem MYC tag driven by its own promoter functionally complemented the ptac10-1 mutant phenotype. pTAC10 was present in both the chloroplast stroma and thylakoids. Two-dimensional blue native polyacrylamide gel electrophoresis (BN-PAGE), and immunoblotting assays showed that pTAC10:MYC co-migrates with one of the PEP core subunits, RpoB. A comprehensive investigation of the plastid gene expression profiles by quantitative RT-PCR revealed that, compared with wild-type plants, the abundance of PEP-dependent plastid transcripts is severely decreased in the ptac10-1 mutant, while the amount of plastid transcripts exclusively transcribed by NEP either barely changes or even increases. RNA blot analysis confirmed that PEP-dependent chloroplast transcripts, including psaB, psbA and rbcL, substantially decrease in the ptac10-1 mutant. Immunoblotting showed reduced accumulation of most chloroplast proteins in the ptac10 mutants. These data indicate the essential role of pTAC10 in plastid gene expression and plastid development. pTAC10 interacts with chloroplast-targeted casein kinase 2 (cpCK2) in vitro and in vivo and can be phosphorylated by Arabidopsis cpCK2 in vitro at sites Ser95, Ser396 and Ser434. RNA-EMSA assays showed that pTAC10 is able to bind to the psbA, atpE and accD transcripts, suggesting a non-specific RNA-binding activity of pTAC10. The RNA affinity of pTAC10 was enhanced by phosphorylation and decreased by the amino acid substitution Ser434-Ala of pTAC10. These data show that pTAC10 is essential for plastid gene expression in Arabidopsis and that it can be phosphorylated by cpCK2.
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Affiliation(s)
- Qing-Bo Yu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Tuan-Tuan Zhao
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lin-Shan Ye
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ling Cheng
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ying-Qian Wu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chao Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhong-Nan Yang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
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26
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Ma F, Hu Y, Ju Y, Jiang Q, Cheng Z, Zhang Q. A novel tetratricopeptide repeat protein, WHITE TO GREEN1, is required for early chloroplast development and affects RNA editing in chloroplasts. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5829-5843. [PMID: 29140512 PMCID: PMC5854136 DOI: 10.1093/jxb/erx383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/05/2017] [Indexed: 05/24/2023]
Abstract
The chloroplast is essential for plant photosynthesis and production, but the regulatory mechanism of chloroplast development is still elusive. Here, a novel gene, WHITE TO GREEN1 (WTG1), was identified to have a function in chloroplast development and plastid gene expression by screening Arabidopsis leaf coloration mutants. WTG1 encodes a chloroplast-localized tetratricopeptide repeat protein that is expressed widely in Arabidopsis cells. Disruption of WTG1 suppresses plant growth, retards leaf greening and chloroplast development, and represses photosynthetic gene expression, but complemented expression of WTG1 restored a normal phenotype. Moreover, WTG1 protein is associated with the organelle RNA editing factors MORF8 and MORF9, and RNA editing of the plastid petL-5 and ndhG-50 transcripts was affected in wtg1 mutants. These results indicate that WTG1 affects both transcriptional and posttranscriptional regulation of plastid gene expression, and provide evidence for the involvement of a tetratricopeptide repeat protein in chloroplast RNA editing in Arabidopsis.
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Affiliation(s)
- Fei Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Yingchun Hu
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Yan Ju
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Qianru Jiang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
| | - Quan Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, China
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27
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Ye LS, Zhang Q, Pan H, Huang C, Yang ZN, Yu QB. EMB2738, which encodes a putative plastid-targeted GTP-binding protein, is essential for embryogenesis and chloroplast development in higher plants. PHYSIOLOGIA PLANTARUM 2017; 161:414-430. [PMID: 28675462 DOI: 10.1111/ppl.12603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
In higher plants, chloroplasts carry out many important functions, and normal chloroplast development is required for embryogenesis. Numerous chloroplast-targeted proteins involved in embryogenesis have been identified. Nevertheless, their functions remain unclear. In this study, a chloroplast-localized protein, EMB2738, was reported to be involved in Arabidopsis embryogenesis. EMB2738 knockout led to defective embryos, and the embryo development in emb2738 was interrupted after the globular stage. Complementation experiments identified the AT3G12080 locus as EMB2738. Cellular observation indicated that severely impaired chloroplast development was observed in these aborted embryos. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis showed that chloroplast-encoded photosynthetic genes, which are transcribed by plastid-encoded RNA polymerase (PEP), are predominantly decreased in defective embryogenesis, compared with those in the wild-type. In contrast, genes encoding PEP core subunits, which are transcribed by nucleus-encoded RNA polymerase (NEP), were increased. These results suggested that the knockout of EMB2738 strongly blocked chloroplast-encoded photosynthesis gene expression in embryos. Silencing of the EMB2738 orthologue in tobacco through a virus-induced genome silencing technique resulted in an albinism phenotype, vacuolated chloroplasts and decreased PEP-dependent plastid transcription. These results suggested that NtEMB2738 might be involved in plastid gene expression. Nevertheless, genetic analysis showed that the NtEMB2738 coding sequence could not fully rescue the defective embryogenesis of the emb2738 mutant, which suggested functional divergence between NtEMB2738 and EMB2738 in embryogenesis. Taken together, these results indicated that both EMB2738 and NtEMB2738 are involved in the expression of plastid genes in higher plants, and there is a functional divergence between NtEMB2738 and EMB2738 in embryogenesis.
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Affiliation(s)
- Lin-Shan Ye
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
- College of Tourism, Shanghai Normal University, Shanghai 200234, China
| | - Qin Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Hui Pan
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Chao Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhong-Nan Yang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
- College of Tourism, Shanghai Normal University, Shanghai 200234, China
| | - Qing-Bo Yu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
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28
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Huang C, Yu QB, Li ZR, Ye LS, Xu L, Yang ZN. Porphobilinogen deaminase HEMC interacts with the PPR-protein AtECB2 for chloroplast RNA editing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:546-556. [PMID: 28850756 DOI: 10.1111/tpj.13672] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 05/10/2023]
Abstract
The pentatricopeptide repeat-DYW protein AtECB2 affects plastid RNA editing at seven sites, including accD-794, accD-1568, ndhF-290, ndhG-50, petL-5, rpoA-200 and rpoC1-488. To understand the mechanism of its involvement in RNA editing, a transgenic line was constructed with AtECB2 fused to a 4xMYC tag that could complement the atecb2 phenotype. RNA immunoprecipitation analysis indicated that AtECB2 is associated with the transcripts of accD, ndhF, ndhG and petL. Co-immunoprecipitation and mass spectrometry experiments showed that multiple organelle RNA editing factor 2 (MORF2) and porphobilinogen deaminase HEMC are associated with AtECB2. Biochemical analysis showed that AtECB2 directly interacts with HEMC through its E domain, while HEMC interacts with MORF8/RIP1. Deletion analysis showed that the E domain is essential for RNA editing. The hemc-1 mutant showed an albino and seedling-lethal phenotype. Of the seven editing sites affected in atecb2, the editing of accD-794 and ndhF-290 was also reduced in hemc-1. RNA immunoprecipitation analysis suggested that HEMC is associated with the editing sites of ndhF transcripts. These results showed that both HEMC and multiple organellar RNA editing factor (MORF) proteins are associated with AtECB2 for RNA editing in plastids.
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Affiliation(s)
- Chao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan, Changsha, 410128, China
- Department of Biology, East China Normal University, Shanghai, 200241, China
| | - Qing-Bo Yu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zi-Ran Li
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lin-Shan Ye
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ling Xu
- Department of Biology, East China Normal University, Shanghai, 200241, China
| | - Zhong-Nan Yang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
- CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
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29
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Tang J, Zhang W, Wen K, Chen G, Sun J, Tian Y, Tang W, Yu J, An H, Wu T, Kong F, Terzaghi W, Wang C, Wan J. OsPPR6, a pentatricopeptide repeat protein involved in editing and splicing chloroplast RNA, is required for chloroplast biogenesis in rice. PLANT MOLECULAR BIOLOGY 2017; 95:345-357. [PMID: 28856519 DOI: 10.1007/s11103-017-0654-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/18/2017] [Indexed: 05/10/2023]
Abstract
OsPPR6, a pentatricopeptide repeat protein involved in editing and splicing chloroplast RNA, is required for chloroplast biogenesis in rice. The chloroplast has its own genetic material and genetic system, but it is also regulated by nuclear-encoded genes. However, little is known about nuclear-plastid regulatory mechanisms underlying early chloroplast biogenesis in rice. In this study, we isolated and characterized a mutant, osppr6, that showed early chloroplast developmental defects leading to albino leaves and seedling death. We found that the osppr6 mutant failed to form thylakoid membranes. Using map-based cloning and complementation tests, we determined that OsPPR6 encoded a new Pentatricopeptide Repeat (PPR) protein localized in plastids. In the osppr6 mutants, mRNA levels of plastidic genes transcribed by the plastid-encoded RNA polymerase decreased, while those of genes transcribed by the nuclear-encoded RNA polymerase increased. Western blot analyses validated these expression results. We further investigated plastidic RNA editing and splicing in the osppr6 mutants and found that the ndhB transcript was mis-edited and the ycf3 transcript was mis-spliced. Therefore, we demonstrate that OsPPR6, a PPR protein, regulates early chloroplast biogenesis and participates in editing of ndhB and splicing of ycf3 transcripts in rice.
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Affiliation(s)
- Jianpeng Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Wenwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weijie Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongzhou An
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingting Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fei Kong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, PA, 18766, USA
| | - Chunming Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Hassani D, Khalid M, Bilal M, Zhang YD, Huang D. Pentatricopeptide Repeat-directed RNA Editing and Their Biomedical Applications. INT J PHARMACOL 2017. [DOI: 10.3923/ijp.2017.762.772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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31
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Bayer-Császár E, Haag S, Jörg A, Glass F, Härtel B, Obata T, Meyer EH, Brennicke A, Takenaka M. The conserved domain in MORF proteins has distinct affinities to the PPR and E elements in PPR RNA editing factors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:813-828. [PMID: 28549935 DOI: 10.1016/j.bbagrm.2017.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/11/2017] [Accepted: 05/14/2017] [Indexed: 11/15/2022]
Abstract
In plant organelles specific nucleotide motifs at C to U RNA editing sites are recognized by the PLS-class of pentatricopeptide repeat (PPR) proteins, which are additionally characterized by a C-terminal E domain. The PPR elements bind the nucleotides in the target RNA, while the function of the E domain has remained unknown. At most sites RNA editing also requires multiple organellar RNA editing factor (MORF) proteins. To understand how these two types of proteins are involved in RNA editing complexes, we systematically analyzed their protein-protein interactions. In vivo pull-down and yeast two-hybrid assays show that MORF proteins connect with selected PPR proteins. In a loss of function mutant of MORF1, a single amino acid alteration in the conserved MORF domain abrogates interactions with many PLS-class PPR proteins, implying the requirement of direct interaction to PPR proteins for the RNA editing function of MORF1. Subfragment analyses show that predominantly the N-terminal/central regions of the MORF domain in MORF1 and MORF3 bind the PPR proteins. Within the PPR proteins, the E domains in addition to PPR elements contact MORF proteins. In chimeric PPR proteins, different E domains alter the specificity of the interaction with MORF proteins. The selective interactions between E domain containing PPR and MORF proteins suggest that the E domains and MORF proteins play a key role for specific protein complexes to assemble at different RNA editing sites.
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Affiliation(s)
| | - Sascha Haag
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
| | - Anja Jörg
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
| | | | | | - Toshihiro Obata
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam, Golm, Germany
| | - Etienne H Meyer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam, Golm, Germany
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32
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Zhu L, Yang Z, Zeng X, Gao J, Liu J, Yi B, Ma C, Shen J, Tu J, Fu T, Wen J. Heme oxygenase 1 defects lead to reduced chlorophyll in Brassica napus. PLANT MOLECULAR BIOLOGY 2017; 93:579-592. [PMID: 28108964 DOI: 10.1007/s11103-017-0583-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/09/2017] [Indexed: 05/08/2023]
Abstract
We previously described a Brassica napus chlorophyll-deficient mutant (ygl) with yellow-green seedling leaves and mapped the related gene, BnaC.YGL, to a 0.35 cM region. However, the molecular mechanisms involved in this chlorophyll defect are still unknown. In this study, the BnaC07.HO1 gene (equivalent to BnaC.YGL) was isolated by the candidate gene approach, and its function was confirmed by genetic complementation. Comparative sequencing analysis suggested that BnaC07.HO1 was lost in the mutant, while a long noncoding-RNA was inserted into the promoter of the homologous gene BnaA07.HO1. This insert was widely present in B. napus cultivars and down-regulated BnaA07.HO1 expression. BnaC07.HO1 was highly expressed in the seedling leaves and encoded heme oxygenase 1, which was localized in the chloroplast. Biochemical analysis showed that BnaC07.HO1 can catalyze heme conversion to form biliverdin IXα. RNA-seq analysis revealed that the loss of BnaC07.HO1 impaired tetrapyrrole metabolism, especially chlorophyll biosynthesis. According, the levels of chlorophyll intermediates were reduced in the ygl mutant. In addition, gene expression in multiple pathways was affected in ygl. These findings provide molecular evidences for the basis of the yellow-green leaf phenotype and further insights into the crucial role of HO1 in B. napus.
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Affiliation(s)
- Lixia Zhu
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zonghui Yang
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xinhua Zeng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops Oil Crops Research the Chinese Institute of Academy of Agricultural Sciences,, Ministry of Agriculture, Wuhan, 430062, China
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China.
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Du L, Zhang J, Qu S, Zhao Y, Su B, Lv X, Li R, Wan Y, Xiao J. The Pentratricopeptide Repeat Protein Pigment-Defective Mutant2 is Involved in the Regulation of Chloroplast Development and Chloroplast Gene Expression in Arabidopsis. PLANT & CELL PHYSIOLOGY 2017; 58:747-759. [PMID: 28158776 DOI: 10.1093/pcp/pcx004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/08/2017] [Indexed: 05/10/2023]
Abstract
The development of functional chloroplasts, which is assisted by a series of nuclear-encoded auxiliary protein factors, is essential for plant autotrophic growth and development. To understand the molecular mechanisms underlying chloroplast development, we isolated and characterized a pigment-defective mutant, pdm2, and its corresponding variegated RNA interference (RNAi) lines in Arabidopsis. Sequence analysis revealed that PDM2 encodes a pentatricopeptide repeat protein that belongs to the P subgroup. Confocal microscopic analysis and immunoblotting of the chloroplast protein fraction showed that PDM2 was located in the stroma. In RNAi plants, protein-related photosynthesis was severely compromised. Furthermore, analysis of the transcript profile of chloroplast genes revealed that plastid-encoded polymerase-dependent transcript levels were markedly reduced, while nuclear-encoded polymerase-dependent transcript levels were increased, in RNAi plants. In addition, PDM2 affects plastid RNA editing efficiency in most editing sites, apparently by directly interacting with multiple organellar RNA editing factor 2 (MORF2) and MORF9. Thus, our results demonstrate that PDM2 is probably involved in the regulation of plastid gene expression required for normal chloroplast development.
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Affiliation(s)
- Liang Du
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jian Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Shaofeng Qu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yuanyuan Zhao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Bodan Su
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xueqin Lv
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ruili Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yinglang Wan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jianwei Xiao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Yang YZ, Ding S, Wang HC, Sun F, Huang WL, Song S, Xu C, Tan BC. The pentatricopeptide repeat protein EMP9 is required for mitochondrial ccmB and rps4 transcript editing, mitochondrial complex biogenesis and seed development in maize. THE NEW PHYTOLOGIST 2017; 214:782-795. [PMID: 28121385 DOI: 10.1111/nph.14424] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/02/2016] [Indexed: 05/02/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins comprise a large family of sequence-specific RNA binding proteins in land plants. Because of its large family size and frequent embryo lethality in the mutants, molecular functions and physiological roles of many PPR proteins are unknown. Through characterization of an empty pericarp9 (emp9) mutant in maize (Zea mays), we defined the functions of EMP9 in mitochondrial RNA editing, respiratory complex formation and seed development. Mu insertions in different regions of Emp9 facilitated dissection of the domain functions of the EMP9. Through genetic and functional analyses of multiple alleles, we showed that deletions of two N-terminal PPR motifs and partial E+ domain do not eliminate the editing function of EMP9. Emp9 encodes an E+ subclass PPR protein that is localized in mitochondria. Loss of EMP9 function abolishes the C-to-U editing of ccmB-43 and rps4-335 sites in mitochondria. The loss of editing at ccmB-43 and rps4-335 affects the maturation of cytochrome c and impairs the biogenesis of mitochondrial respiratory complexes, particularly complex III. This work extends our understanding of PPR-E+ protein in editing function and seed development, and provides insights into the molecular function of mitochondrial CcmB protein in higher plants.
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Affiliation(s)
- Yan-Zhuo Yang
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Shuo Ding
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Hong-Chun Wang
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Feng Sun
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Wen-Long Huang
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Shu Song
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Chunhui Xu
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Bao-Cai Tan
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
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Wu L, Wu J, Liu Y, Gong X, Xu J, Lin D, Dong Y. The Rice Pentatricopeptide Repeat Gene TCD10 is Needed for Chloroplast Development under Cold Stress. RICE (NEW YORK, N.Y.) 2016; 9:67. [PMID: 27910002 PMCID: PMC5133210 DOI: 10.1186/s12284-016-0134-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/15/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Chloroplast plays a vital role in plant development and growth. The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in plants. In addition, cold stress affects a broad spectrum of cellular components, e.g. chloroplast, and metabolism in plants. However, the regulatory mechanism for rice PPR genes on chloroplast development still remains elusive under cold stress. RESULT In this paper, we characterized a new rice PPR gene mutant tcd10 (thermo-sensitive chlorophyll-deficient mutant 10) that exhibits the albino phenotype, malformed chloroplast and could not survive after the 5-leaf stage when grown at 20 °C, but does the normal phenotype at 32 °C. Map-based cloning, followed by RNA interference and CRISPR/Cas9 genome editing techniques, revealed that TCD10 encoding a novel PPR protein, mainly localized to the chloroplasts, with 27 PPR motifs, is responsible for the mutant phenotype. In addition, TCD10 is specific expression in tissues. The disruption of TCD10 resulted in an evidently reduced expression of chloroplast-associated genes under cold stress (20 °C), whereas they did recovered to normal levels at high temperature (32 °C). These results showed an important role of TCD10 for chloroplast development under cold stress. CONCLUSIONS The TCD10 encodes a novel rice PPR protein, mainly located in chloroplasts, which is important for chloroplast development, growth and the maintenance of photosynthetic electron transport and its disorder would lead to an aberrant chloroplast and abnormal expressions in these genes for chloroplast development and photosynthesis in rice under cold stress.
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Affiliation(s)
- Lanlan Wu
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jun Wu
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yanxia Liu
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiaodi Gong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Jianlong Xu
- The Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan Cun Street, Beijing, 100081, China
| | - Dongzhi Lin
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Yanjun Dong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China.
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Wang M, Jiang L, Da Q, Liu J, Feng D, Wang J, Wang HB, Jin HL. DELAYED GREENING 238, a Nuclear-Encoded Chloroplast Nucleoid Protein, Is Involved in the Regulation of Early Chloroplast Development and Plastid Gene Expression in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2016; 57:2586-2599. [PMID: 27818379 DOI: 10.1093/pcp/pcw172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
Chloroplast development is an essential process for plant growth that is regulated by numerous proteins. Plastid-encoded plastid RNA polymerase (PEP) is a large complex that regulates plastid gene transcription and chloroplast development. However, many proteins in this complex remain to be identified. Here, through large-scale screening of Arabidopsis mutants by Chl fluorescence imaging, we identified a novel protein, DELAYED GREENING 238 (DG238), which is involved in regulating chloroplast development and plastid gene expression. Loss of DG238 retards plant growth, delays young leaf greening, affects chloroplast development and lowers photosynthetic efficiency. Moreover, blue-native PAGE (BN-PAGE) and Western blot analysis indicated that PSII and PSI protein levels are reduced in dg238 mutants. DG238 is mainly expressed in young tissues and is regulated by light signals. Subcellular localization analysis showed that DG238 is a nuclear-encoded chloroplast nucleoid protein. More interestingly, DG238 was co-expressed with FLN1, which encodes an essential subunit of the PEP complex. Bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP) assays showed that DG238 can also interact with FLN1. Taken together, these results suggest that DG238 may function as a component of the PEP complex that is important for the early stage of chloroplast development and helps regulate PEP-dependent plastid gene expression.
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Affiliation(s)
- Menglong Wang
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Lan Jiang
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Qingen Da
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Jun Liu
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Dongru Feng
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Jinfa Wang
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Hong-Bin Wang
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
| | - Hong-Lei Jin
- State Key Laboratory of Biocontrol and Collaborative Innovation Center of Genetics and Development, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China
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Mishra AK, Duraisamy GS, Matoušek J, Radisek S, Javornik B, Jakse J. Identification and characterization of microRNAs in Humulus lupulus using high-throughput sequencing and their response to Citrus bark cracking viroid (CBCVd) infection. BMC Genomics 2016; 17:919. [PMID: 27846797 PMCID: PMC5109749 DOI: 10.1186/s12864-016-3271-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hop (Humulus lupulus L.) plants are grown primarily for the brewing industry and have been used as a traditional medicinal herb for a long time. Severe hop stunt disease caused by the recently discovered Citrus bark cracking viroid (CBCVd) is one of the most devastating diseases among other viroid infections in hop. MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in gene expression regulation. To identify miRNAs in hop and their response to CBCVd-infection, two small RNA (sRNA) libraries were prepared from healthy and CBCVd-infected hop plants and were investigated by high throughput sequencing. RESULTS A total of 67 conserved and 49 novel miRNAs were identified. Among them, 36 conserved and 37 novel miRNAs were found to be differentially recovered in response to CBCVd-infection. A total of 311 potential targets was predicted for conserved and novel miRNAs based on a sequence homology search using hop transcriptome data. The majority of predicted targets significantly belonged to transcriptional factors that may regulate hop leaf, root and cone growth and development. In addition, the identified miRNAs might also play an important roles in other cellular and metabolic processes, such as signal transduction, stress response and other physiological processes, including prenylflavonoid biosynthesis pathways. Quantitative real time PCR analysis of selected targets revealed their negative correlation with their corresponding CBCVd-responsive miRNAs. CONCLUSIONS Based on the results, we concluded that CBCVd-responsive miRNAs modulate several hormone pathways and transcriptional factors that play important roles in the regulation of metabolism, growth and development. These results provide a framework for further analysis of regulatory roles of sRNAs in plant defense mechanism including other hop infecting viroids in particular.
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Affiliation(s)
- Ajay Kumar Mishra
- Biology Centre ASCR v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, 37005, Czech Republic
| | - Ganesh Selvaraj Duraisamy
- Biology Centre ASCR v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, 37005, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre ASCR v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, 37005, Czech Republic
| | - Sebastjan Radisek
- Slovenian Institute of Hop Research and Brewing, Plant Protection Department, Cesta Zalskega tabora 2, Žalec, SI-3310, Slovenia
| | - Branka Javornik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia.
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Sun T, Bentolila S, Hanson MR. The Unexpected Diversity of Plant Organelle RNA Editosomes. TRENDS IN PLANT SCIENCE 2016; 21:962-973. [PMID: 27491516 DOI: 10.1016/j.tplants.2016.07.005] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/04/2016] [Accepted: 07/05/2016] [Indexed: 05/02/2023]
Abstract
Flowering plants convert many hundreds of organelle cytidines (Cs) to uridines (Us) during post-transcriptional RNA editing. Pentatricopeptide repeat (PPR) proteins dictate specificity by recognizing RNA sequences near C targets. However, the complete mechanism of the editing machinery is not yet understood. Recently, non-PPR editing factors [RNA editing factor interacting proteins (RIPs)/multiple organellar RNA editing factors (MORFs), organelle RNA recognition motif (ORRM) proteins, organelle zinc-finger (OZ) proteins, and protoporphyrinogen oxidase 1 (PPO1)] have been identified as components of the plant RNA editosome, which is a small RNA-protein complex. Surprisingly, plant editosomes are highly diverse not only with regard to the PPR proteins they contain but also in the non-PPR components that are present. Here we review the most recent progress in the field and discuss the implications of the diversity of plant editosomes for the evolution of RNA editing and for possible future applications.
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Affiliation(s)
- Tao Sun
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Stephane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Xie T, Chen D, Wu J, Huang X, Wang Y, Tang K, Li J, Sun M, Peng X. Growing Slowly 1 locus encodes a PLS-type PPR protein required for RNA editing and plant development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5687-5698. [PMID: 27670716 PMCID: PMC5066490 DOI: 10.1093/jxb/erw331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Most pentatricopeptide repeat (PPR) proteins are involved in organelle post-transcriptional processes, including RNA editing. The PPR proteins include the PLS subfamily, containing characteristic triplets of P, L, and S motifs; however, their editing mechanisms and roles in developmental processes are not fully understood. In this study, we isolated the Arabidopsis thaliana Growing slowly 1 (AtGRS1) gene and showed that it functions in RNA editing and plant development. Arabidopsis null mutants of grs1 exhibit slow growth and sterility. Further analysis showed that cell division activity was reduced dramatically in the roots of grs1 plants. We determined that GRS1 is a nuclear-encoded mitochondria-localized PPR protein, and is a member of the PLS subfamily. GRS1 is responsible for the RNA editing at four specific sites of four mitochondrial mRNAs: nad1-265, nad4L-55, nad6-103, and rps4-377 The first three of these mRNAs encode for the subunits of complex I of the electron transport chain in mitochondria. Thus, the activity of complex I is strongly reduced in grs1 Changes in RPS4 editing in grs1 plants affect mitochondrial ribosome biogenesis. Expression of the alternative respiratory pathway and the abscisic acid response gene ABI5 were up-regulated in grs1 mutant plants Genetic analysis revealed that ABI5 is involved in the short root phenotype of grs1 Taken together, our results indicate that AtGRS1 regulates plant development by controlling RNA editing in Arabidopsis.
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Affiliation(s)
- Tingting Xie
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dan Chen
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jian Wu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaorong Huang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yifan Wang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Keli Tang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengxiang Sun
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiongbo Peng
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Leister D, Kleine T. Definition of a core module for the nuclear retrograde response to altered organellar gene expression identifies GLK overexpressors as gun mutants. PHYSIOLOGIA PLANTARUM 2016; 157:297-309. [PMID: 26876646 DOI: 10.1111/ppl.12431] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 12/28/2015] [Accepted: 01/04/2016] [Indexed: 05/03/2023]
Abstract
Retrograde signaling can be triggered by changes in organellar gene expression (OGE) induced by inhibitors such as lincomycin (LIN) or mutations that perturb OGE. Thus, an insufficiency of the organelle-targeted prolyl-tRNA synthetase PRORS1 in Arabidopsis thaliana activates retrograde signaling and reduces the expression of nuclear genes for photosynthetic proteins. Recently, we showed that mTERF6, a member of the so-called mitochondrial transcription termination factor (mTERF) family, is involved in the formation of chloroplast (cp) isoleucine-tRNA. To obtain further insights into its functions, co-expression analysis of MTERF6, PRORS1 and two other genes for organellar aminoacyl-tRNA synthetases was conducted. The results suggest a prominent role of mTERF6 in aminoacylation activity, light signaling and seed storage. Analysis of changes in whole-genome transcriptomes in the mterf6-1 mutant showed that levels of nuclear transcripts for cp OGE proteins were particularly affected. Comparison of the mterf6-1 transcriptome with that of prors1-2 showed that reduced aminoacylation of proline (prors1-2) and isoleucine (mterf6-1) tRNAs alters retrograde signaling in similar ways. Database analyses indicate that comparable gene expression changes are provoked by treatment with LIN, norflurazon or high light. A core OGE response module was defined by identifying genes that were differentially expressed under at least four of six conditions relevant to OGE signaling. Based on this module, overexpressors of the Golden2-like transcription factors GLK1 and GLK2 were identified as genomes uncoupled mutants.
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Affiliation(s)
- Dario Leister
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität, Planegg-Martinsried, Munich, Germany
| | - Tatjana Kleine
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität, Planegg-Martinsried, Munich, Germany
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Goto S, Kawaguchi Y, Sugita C, Ichinose M, Sugita M. P-class pentatricopeptide repeat protein PTSF1 is required for splicing of the plastid pre-tRNA(I) (le) in Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:493-503. [PMID: 27117879 DOI: 10.1111/tpj.13184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/31/2016] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins are widely distributed in eukaryotes and are mostly localized in mitochondria or plastids. PPR proteins play essential roles in various RNA processing steps in organelles; however, the function of the majority of PPR proteins remains unknown. To examine the function of plastid PPR proteins, PpPPR_4 gene knock-out mutants were characterized in Physcomitrella patens. The knock-out mosses displayed severe growth retardation and reduced effective quantum yield of photosystem II. Immunoblot analysis showed that knock-out of PpPPR_4 resulted in a strongly reduced level of plastid-encoded proteins, such as photosystem II reaction center protein D1, the β subunit of ATP synthase, and the stromal enzyme, Rubisco. To further investigate whether knock-out of the PpPPR_4 gene affects plastid gene expression, we analyzed steady-state transcript levels of protein- and rRNA-coding genes by quantitative RT-PCR. This analysis showed that the level of many protein-coding transcripts increased in the mutants. In contrast, splicing of a spacer tRNA(I) (le) precursor encoded by the rrn operon was specifically impaired in the mutants, whereas the accumulation of other plastid tRNAs and rRNAs was not largely affected. Thus, the defect in tRNA(I) (le) splicing leads to a considerable reduction of mature tRNA(I) (le) , which may be accountable for the reduced protein level. An RNA mobility shift assay showed that the recombinant PpPPR_4 bound preferentially to domain III of the tRNA(I) (le) group-II intron. These results provide evidence that PpPPR_4 functions in RNA splicing of the tRNA(I) (le) intron, and hence PpPPR_4 was named plastid tRNA splicing factor 1 (PTSF1).
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Affiliation(s)
- Seiya Goto
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | | | - Chieko Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | - Mizuho Ichinose
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya, 464-8602, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
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Guan H, Xu X, He C, Liu C, Liu Q, Dong R, Liu T, Wang L. Fine Mapping and Candidate Gene Analysis of the Leaf-Color Gene ygl-1 in Maize. PLoS One 2016; 11:e0153962. [PMID: 27100184 PMCID: PMC4839758 DOI: 10.1371/journal.pone.0153962] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 04/06/2016] [Indexed: 11/24/2022] Open
Abstract
A novel yellow-green leaf mutant yellow-green leaf-1 (ygl-1) was isolated in self-pollinated progenies from the cross of maize inbred lines Ye478 and Yuanwu02. The mutant spontaneously showed yellow-green character throughout the lifespan. Meanwhile, the mutant reduced contents of chlorophyll and Car, arrested chloroplast development and lowered the capacity of photosynthesis compared with the wild-type Lx7226. Genetic analysis revealed that the mutant phenotype was controlled by a recessive nuclear gene. The ygl-1 locus was initially mapped to an interval of about 0.86 Mb in bin 1.01 on the short arm of chromosome 1 using 231 yellow-green leaf individuals of an F2 segregating population from ygl-1/Lx7226. Utilizing four new polymorphic SSR markers, the ygl-1 locus was narrowed down to a region of about 48 kb using 2930 and 2247 individuals of F2 and F3 mapping populations, respectively. Among the three predicted genes annotated within this 48 kb region, GRMZM2G007441, which was predicted to encode a cpSRP43 protein, had a 1-bp nucleotide deletion in the coding region of ygl-1 resulting in a frame shift mutation. Semi-quantitative RT-PCR analysis revealed that YGL-1 was constitutively expressed in all tested tissues and its expression level was not significantly affected in the ygl-1 mutant from early to mature stages, while light intensity regulated its expression both in the ygl-1 mutant and wild type seedlings. Furthermore, the mRNA levels of some genes involved in chloroplast development were affected in the six-week old ygl-1 plants. These findings suggested that YGL-1 plays an important role in chloroplast development of maize.
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Affiliation(s)
- Haiying Guan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of North Summer Maize, Ministry of Agriculture, Jinan, China
- National Maize Improvement Sub-Center, Jinan, China
| | - Xiangbo Xu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of North Summer Maize, Ministry of Agriculture, Jinan, China
- National Maize Improvement Sub-Center, Jinan, China
| | - Chunmei He
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of North Summer Maize, Ministry of Agriculture, Jinan, China
- National Maize Improvement Sub-Center, Jinan, China
| | - Chunxiao Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of North Summer Maize, Ministry of Agriculture, Jinan, China
- National Maize Improvement Sub-Center, Jinan, China
| | - Qiang Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of North Summer Maize, Ministry of Agriculture, Jinan, China
- National Maize Improvement Sub-Center, Jinan, China
| | - Rui Dong
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of North Summer Maize, Ministry of Agriculture, Jinan, China
- National Maize Improvement Sub-Center, Jinan, China
| | - Tieshan Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of North Summer Maize, Ministry of Agriculture, Jinan, China
- National Maize Improvement Sub-Center, Jinan, China
- * E-mail: (TSL); (LMW)
| | - Liming Wang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of North Summer Maize, Ministry of Agriculture, Jinan, China
- National Maize Improvement Sub-Center, Jinan, China
- * E-mail: (TSL); (LMW)
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Salie MJ, Thelen JJ. Regulation and structure of the heteromeric acetyl-CoA carboxylase. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1207-1213. [PMID: 27091637 DOI: 10.1016/j.bbalip.2016.04.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 11/16/2022]
Abstract
The enzyme acetyl-CoA carboxylase (ACCase) catalyzes the committed step of the de novo fatty acid biosynthesis (FAS) pathway by converting acetyl-CoA to malonyl-CoA. Two forms of ACCase exist in nature, a homomeric and heteromic form. The heteromeric form of this enzyme requires four different subunits for activity: biotin carboxylase; biotin carboxyl carrier protein; and α- and β-carboxyltransferases. Heteromeric ACCases (htACCase) can be found in prokaryotes and the plastids of most plants. The plant htACCase is regulated by diverse mechanisms reflected by the biochemical and genetic complexity of this multienzyme complex and the plastid stroma where it resides. In this review we summarize the regulation of the plant htACCase and also describe the structural characteristics of this complex from both prokaryotes and plants. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
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Affiliation(s)
- Matthew J Salie
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, 1201 E. Rollins, Columbia, MO 65201, USA.
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, 1201 E. Rollins, Columbia, MO 65201, USA.
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Hein A, Polsakiewicz M, Knoop V. Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors. BMC Evol Biol 2016; 16:23. [PMID: 26809609 PMCID: PMC4727281 DOI: 10.1186/s12862-016-0589-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/12/2016] [Indexed: 11/11/2022] Open
Abstract
Background RNA editing by cytidine-to-uridine conversions is an essential step of RNA maturation in plant organelles. Some 30–50 sites of C-to-U RNA editing exist in chloroplasts of flowering plant models like Arabidopsis, rice or tobacco. We now predicted significantly more RNA editing in chloroplasts of early-branching angiosperm genera like Amborella, Calycanthus, Ceratophyllum, Chloranthus, Illicium, Liriodendron, Magnolia, Nuphar and Zingiber. Nuclear-encoded RNA-binding pentatricopeptide repeat (PPR) proteins are key editing factors expected to coevolve with their cognate RNA editing sites in the organelles. Results With an extensive chloroplast transcriptome study we identified 138 sites of RNA editing in Amborella trichopoda, approximately the 3- to 4-fold of cp editing in Arabidopsis thaliana or Oryza sativa. Selected cDNA studies in the other early-branching flowering plant taxa furthermore reveal a high diversity of early angiosperm RNA editomes. Many of the now identified editing sites in Amborella have orthologues in ferns, lycophytes or hornworts. We investigated the evolution of CRR28 and RARE1, two known Arabidopsis RNA editing factors responsible for cp editing events ndhBeU467PL, ndhDeU878SL and accDeU794SL, respectively, all of which we now found conserved in Amborella. In a phylogenetically wide sampling of 65 angiosperm genomes we find evidence for only one single loss of CRR28 in chickpea but several independent losses of RARE1, perfectly congruent with the presence of their cognate editing sites in the respective cpDNAs. Conclusion Chloroplast RNA editing is much more abundant in early-branching than in widely investigated model flowering plants. RNA editing specificity factors can be traced back for more than 120 million years of angiosperm evolution and show highly divergent patterns of evolutionary losses, matching the presence of their target editing events. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0589-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anke Hein
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Monika Polsakiewicz
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany.
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Brehme N, Bayer-Császár E, Glass F, Takenaka M. The DYW Subgroup PPR Protein MEF35 Targets RNA Editing Sites in the Mitochondrial rpl16, nad4 and cob mRNAs in Arabidopsis thaliana. PLoS One 2015; 10:e0140680. [PMID: 26470017 PMCID: PMC4607164 DOI: 10.1371/journal.pone.0140680] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 09/29/2015] [Indexed: 11/30/2022] Open
Abstract
RNA editing in plant mitochondria and plastids alters specific nucleotides from cytidine (C) to uridine (U) mostly in mRNAs. A number of PLS-class PPR proteins have been characterized as RNA recognition factors for specific RNA editing sites, all containing a C-terminal extension, the E domain, and some an additional DYW domain, named after the characteristic C-terminal amino acid triplet of this domain. Presently the recognition factors for more than 300 mitochondrial editing sites are still unidentified. In order to characterize these missing factors, the recently proposed computational prediction tool could be of use to assign target RNA editing sites to PPR proteins of yet unknown function. Using this target prediction approach we identified the nuclear gene MEF35 (Mitochondrial Editing Factor 35) to be required for RNA editing at three sites in mitochondria of Arabidopsis thaliana. The MEF35 protein contains eleven PPR repeats and E and DYW extensions at the C-terminus. Two T-DNA insertion mutants, one inserted just upstream and the other inside the reading frame encoding the DYW domain, show loss of editing at a site in each of the mRNAs for protein 16 in the large ribosomal subunit (site rpl16-209), for cytochrome b (cob-286) and for subunit 4 of complex I (nad4-1373), respectively. Editing is restored upon introduction of the wild type MEF35 gene in the reading frame mutant. The MEF35 protein interacts in Y2H assays with the mitochondrial MORF1 and MORF8 proteins, mutation of the latter also influences editing at two of the three MEF35 target sites. Homozygous mutant plants develop indistinguishably from wild type plants, although the RPL16 and COB/CYTB proteins are essential and the amino acids encoded after the editing events are conserved in most plant species. These results demonstrate the feasibility of the computational target prediction to screen for target RNA editing sites of E domain containing PLS-class PPR proteins.
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Affiliation(s)
- Nadja Brehme
- Molekulare Botanik, Universität Ulm, Ulm, Germany
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Glass F, Härtel B, Zehrmann A, Verbitskiy D, Takenaka M. MEF13 Requires MORF3 and MORF8 for RNA Editing at Eight Targets in Mitochondrial mRNAs in Arabidopsis thaliana. MOLECULAR PLANT 2015; 8:1466-77. [PMID: 26048647 DOI: 10.1016/j.molp.2015.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/07/2015] [Accepted: 05/17/2015] [Indexed: 05/02/2023]
Abstract
RNA editing sites in plant mitochondria and plastids are addressed by pentatricopeptide repeat (PPR) proteins with E or E and DYW domains, which recognize a specific nucleotide motif upstream of the edited nucleotide. In addition, some sites require MORF proteins for efficient RNA editing. Here, we assign the novel E domain-containing PPR protein, MEF13, as being required for editing at eight sites in Arabidopsis thaliana. A SNP in ecotype C24 altering the editing level at only one of the eight target sites was located by genomic mapping. An EMS mutant allele of the gene for MEF13 was identified in a SNaPshot screen of a mutated plant population. At all eight target sites of MEF13, editing levels are reduced in both morf3 and morf8 mutants, but at only one site in morf1 mutants, suggesting that specific MEF13-MORF interactions are required. Yeast two-hybrid analyses detect solid connections of MEF13 with MORF1 and weak contact with MORF3 proteins. Yeast three-hybrid (Y3H) analysis shows that the presence of MORF8 enhances the connection between MEF13 and MORF3, suggesting that a MORF3-MORF8 heteromer may form stably or transiently to establish interaction with MEF13.
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Affiliation(s)
| | | | - Anja Zehrmann
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
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Zhong Y, Cheng CZ, Jiang NH, Jiang B, Zhang YY, Wu B, Hu ML, Zeng JW, Yan HX, Yi GJ, Zhong GY. Comparative Transcriptome and iTRAQ Proteome Analyses of Citrus Root Responses to Candidatus Liberibacter asiaticus Infection. PLoS One 2015; 10:e0126973. [PMID: 26046530 PMCID: PMC4457719 DOI: 10.1371/journal.pone.0126973] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 04/09/2015] [Indexed: 11/23/2022] Open
Abstract
Root samples of 'Sanhu' red tangerine trees infected with and without Candidatus Liberibacter asiaticus (CLas) were collected at 50 days post inoculation and subjected to RNA-sequencing and isobaric tags for relative and absolute quantification (iTRAQ) to profile the differentially expressed genes (DEGs) and proteins (DEPs), respectively. Quantitative real-time PCR was subsequently used to confirm the expression of 16 selected DEGs. Results showed that a total of 3956 genes and 78 proteins were differentially regulated by HLB-infection. Among the most highly up-regulated DEPs were sperm specific protein 411, copper ion binding protein, germin-like proteins, subtilisin-like proteins and serine carboxypeptidase-like 40 proteins whose transcript levels were concomitantly up-regulated as shown by RNA-seq data. Comparison between our results and those of the previously reported showed that known HLB-modulated biological pathways including cell-wall modification, protease-involved protein degradation, carbohydrate metabolism, hormone synthesis and signaling, transcription activities, and stress responses were similarly regulated by HLB infection but different or root-specific changes did exist. The root unique changes included the down-regulation in genes of ubiquitin-dependent protein degradation pathway, secondary metabolism, cytochrome P450s, UDP-glucosyl transferases and pentatricopeptide repeat containing proteins. Notably, nutrient absorption was impaired by HLB-infection as the expression of the genes involved in Fe, Zn, N and P adsorption and transportation were significantly changed. HLB-infection induced some cellular defense responses but simultaneously reduced the biosynthesis of the three major classes of secondary metabolites, many of which are known to have anti-pathogen activities. Genes involved in callose deposition were up-regulated whereas those involved in callose degradation were also up-regulated, indicating that the sieve tube elements in roots were hanging on the balance of life and death at this stage. In addition, signs of carbohydrate starvation were already eminent in roots at this stage. Other interesting genes and pathways that were changed by HLB-infection were also discussed based on our findings.
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Affiliation(s)
- Yun Zhong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Chun-zhen Cheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Nong-hui Jiang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Bo Jiang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Yong-yan Zhang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Bo Wu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Min-lun Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Ji-wu Zeng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Hua-xue Yan
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Gan-jun Yi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
| | - Guang-yan Zhong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, P.R.China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, P.R.China
- Key Laboratory of Tropical and Subtropical Fruit Tree Researches, Guangdong Province, Guangzhou, 510640, P.R.China
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Lin D, Jiang Q, Zheng K, Chen S, Zhou H, Gong X, Xu J, Teng S, Dong Y. Mutation of the rice ASL2 gene encoding plastid ribosomal protein L21 causes chloroplast developmental defects and seedling death. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:599-607. [PMID: 25280352 DOI: 10.1111/plb.12271] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/22/2014] [Indexed: 05/19/2023]
Abstract
The plastid ribosome proteins (PRPs) play important roles in plastid protein biosynthesis, chloroplast differentiation and early chloroplast development. However, the specialised functions of individual protein components of the chloroplast ribosome in rice (Oryza sativa) remain unresolved. In this paper, we identified a novel rice PRP mutant named asl2 (Albino seedling lethality 2) exhibiting an albino, seedling death phenotype. In asl2 mutants, the alteration of leaf colour was associated with chlorophyll (Chl) content and abnormal chloroplast development. Through map-based cloning and complementation, the mutated ASL2 gene was isolated and found to encode the chloroplast 50S ribosome protein L21 (RPL21c), a component of the chloroplast ribosome large subunit, which was localised in chloroplasts. ASL2 was expressed at a higher level in the plumule and leaves, implying its tissue-specific expression. Additionally, the expression of ASL2 was regulated by light. The transcript levels of the majority of genes for Chl biosynthesis, photosynthesis and chloroplast development were strongly affected in asl2 mutants. Collectively, the absence of functional ASL2 caused chloroplast developmental defects and seedling death. This report establishes the important role of RPL21c in chloroplast development in rice.
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Affiliation(s)
- D Lin
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
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49
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Scotti N, Sannino L, Idoine A, Hamman P, De Stradis A, Giorio P, Maréchal-Drouard L, Bock R, Cardi T. The HIV-1 Pr55 gag polyprotein binds to plastidial membranes and leads to severe impairment of chloroplast biogenesis and seedling lethality in transplastomic tobacco plants. Transgenic Res 2015; 24:319-31. [PMID: 25348481 DOI: 10.1007/s11248-014-9845-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/21/2014] [Indexed: 11/25/2022]
Abstract
Chloroplast genetic engineering has long been recognised as a powerful technology to produce recombinant proteins. To date, however, little attention has been given to the causes of pleiotropic effects reported, in some cases, as consequence of the expression of foreign proteins in transgenic plastids. In this study, we investigated the phenotypic alterations observed in transplastomic tobacco plants accumulating the Pr55(gag) polyprotein of human immunodeficiency virus (HIV-1). The expression of Pr55(gag) at high levels in the tobacco plastome leads to a lethal phenotype of seedlings grown in soil, severe impairment of plastid development and photosynthetic activity, with chloroplasts largely resembling undeveloped proplastids. These alterations are associated to the binding of Pr55(gag) to thylakoids. During particle assembly in HIV-1 infected human cells, the binding of Pr55(gag) to a specific lipid [phosphatidylinositol-(4-5) bisphosphate] in the plasma membrane is mediated by myristoylation at the amino-terminus and the so-called highly basic region (HBR). Surprisingly, the non-myristoylated Pr55(gag) expressed in tobacco plastids was likely able, through the HBR motif, to bind to nonphosphorous glycerogalactolipids or other classes of lipids present in plastidial membranes. Although secondary consequences of disturbed chloroplast biogenesis on expression of nuclear-encoded plastid proteins cannot be ruled out, results of proteomic analyses suggest that their altered accumulation could be due to retrograde control in which chloroplasts relay their status to the nucleus for fine-tuning of gene expression.
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Affiliation(s)
- N Scotti
- CNR-IBBR, Institute of Biosciences and BioResources, National Research Council of Italy, Via Università 133, 80055, Portici, NA, Italy,
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Yuan L, Xiong LG, Deng TT, Wu Y, Li J, Liu SQ, Huang JA, Liu ZH. Comparative profiling of gene expression in Camellia sinensis L. cultivar AnJiBaiCha leaves during periodic albinism. Gene 2015; 561:23-9. [DOI: 10.1016/j.gene.2015.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/31/2014] [Accepted: 01/05/2015] [Indexed: 10/24/2022]
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