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Xing J, Zhang Y, Song W, Ali NA, Su K, Sun X, Sun Y, Jiang Y, Zhao X. Comprehensive identification, characterization, and expression analysis of the MORF gene family in Brassica napus. BMC PLANT BIOLOGY 2024; 24:475. [PMID: 38816808 PMCID: PMC11138011 DOI: 10.1186/s12870-024-05177-3] [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: 12/07/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND RNA editing in chloroplast and mitochondrion transcripts of plants is an important type of post-transcriptional RNA modification in which members of the multiple organellar RNA editing factor gene family (MORF) play a crucial role. However, a systematic identification and characterization of MORF members in Brassica napus is still lacking. RESULTS In this study, a total of 43 MORF genes were identified from the genome of the Brassica napus cultivar "Zhongshuang 11". The Brassica napus MORF (BnMORF) family members were divided into three groups through phylogenetic analysis. BnMORF genes distributed on 14 chromosomes and expanded due to segmental duplication and whole genome duplication repetitions. The majority of BnMORF proteins were predicted to be localized to mitochondria and chloroplasts. The promoter cis-regulatory element analysis, spatial-temporal expression profiling, and co-expression network of BnMORF genes indicated the involvement of BnMORF genes in stress and phytohormone responses, as well as growth and development. CONCLUSION This study provides a comprehensive analysis of BnMORF genes and lays a foundation for further exploring their physiological functions in Brassica napus.
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Affiliation(s)
- Jiani Xing
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yayi Zhang
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Wenjian Song
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Nadia Ahmed Ali
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Kexing Su
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xingxing Sun
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yujia Sun
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yizhou Jiang
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaobo Zhao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Rural Affairs, Key Laboratory of Nuclear Agricultural Sciences of Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Espindula E, Passaglia LMP. Maize-Azospirillum brasilense interaction: accessing maize's miRNA expression under the effect of an inhibitor of indole-3-acetic acid production by the plant. Braz J Microbiol 2024; 55:101-109. [PMID: 38214876 PMCID: PMC10920601 DOI: 10.1007/s42770-023-01236-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
MicroRNA (miRNA) is a class of non-coding RNAs. They play essential roles in plants' physiology, as in the regulation of plant development, response to biotic and abiotic stresses, and symbiotic processes. This work aimed to better understand the importance of maize's miRNA during Azospirillum-plant interaction when the plant indole-3-acetic acid (IAA) production was inhibited with yucasin, an inhibitor of the TAM/YUC pathway. Twelve cDNA libraries from a previous Dual RNA-Seq experiment were used to analyze gene expression using a combined analysis approach. miRNA coding genes (miR) and their predicted mRNA targets were identified among the differentially expressed genes. Statistical differences among the groups indicate that Azospirillum brasilense, yucasin, IAA concentration, or all together could influence the expression of several maize's miRNAs. The miRNA's probable targets were identified, and some of them were observed to be differentially expressed. Dcl4, myb122, myb22, and morf3 mRNAs were probably regulated by their respective miRNAs. Other probable targets were observed responding to the IAA level, the bacterium, or all of them. A. brasilense was able to influence the expression of some maize's miRNA, for example, miR159f, miR164a, miR169j, miR396c, and miR399c. The results allow us to conclude that the bacterium can influence directly or indirectly the expression of some of the identified mRNA targets, probably due to an IAA-independent pathway, and that they are somehow involved in the previously observed physiological effects.
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Affiliation(s)
- Eliandro Espindula
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil.
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Dhingra Y, Gupta S, Gupta V, Agarwal M, Katiyar-Agarwal S. The emerging role of epitranscriptome in shaping stress responses in plants. PLANT CELL REPORTS 2023; 42:1531-1555. [PMID: 37481775 DOI: 10.1007/s00299-023-03046-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
KEY MESSAGE RNA modifications and editing changes constitute 'epitranscriptome' and are crucial in regulating the development and stress response in plants. Exploration of the epitranscriptome and associated machinery would facilitate the engineering of stress tolerance in crops. RNA editing and modifications post-transcriptionally decorate almost all classes of cellular RNAs, including tRNAs, rRNAs, snRNAs, lncRNAs and mRNAs, with more than 170 known modifications, among which m6A, Ψ, m5C, 8-OHG and C-to-U editing are the most abundant. Together, these modifications constitute the "epitranscriptome", and contribute to changes in several RNA attributes, thus providing an additional structural and functional diversification to the "cellular messages" and adding another layer of gene regulation in organisms, including plants. Numerous evidences suggest that RNA modifications have a widespread impact on plant development as well as in regulating the response of plants to abiotic and biotic stresses. High-throughput sequencing studies demonstrate that the landscapes of m6A, m5C, Am, Cm, C-to-U, U-to-G, and A-to-I editing are remarkably dynamic during stress conditions in plants. GO analysis of transcripts enriched in Ψ, m6A and m5C modifications have identified bonafide components of stress regulatory pathways. Furthermore, significant alterations in the expression pattern of genes encoding writers, readers, and erasers of certain modifications have been documented when plants are grown in challenging environments. Notably, manipulating the expression levels of a few components of RNA editing machinery markedly influenced the stress tolerance in plants. We provide updated information on the current understanding on the contribution of RNA modifications in shaping the stress responses in plants. Unraveling of the epitranscriptome has opened new avenues for designing crops with enhanced productivity and stress resilience in view of global climate change.
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Affiliation(s)
- Yashika Dhingra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, Switzerland
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007, India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Zhang Q, Chen C, Wang Y, He M, Li Z, Shen L, Li Q, Zhu L, Ren D, Hu J, Gao Z, Zhang G, Qian Q. OsPPR11 encoding P-type PPR protein that affects group II intron splicing and chloroplast development. PLANT CELL REPORTS 2023; 42:355-369. [PMID: 36576552 DOI: 10.1007/s00299-022-02961-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/28/2022] [Indexed: 05/20/2023]
Abstract
OsPPR11 belongs to the P-type PPR protein family and can interact with OsCAF2 to regulate Group II intron splicing and affect chloroplast development in rice. Pentatricopeptide repeat (PPR) proteins participate in chloroplasts or mitochondria group II introns splicing in plants. The PPR protein family contains 491 members in rice, but most of their functions are unknown. In this study, we identified a nuclear gene encoding the P-type PPR protein OsPPR11 in chloroplasts. The qRT-PCR analysis demonstrated that OsPPR11 was expressed in all plant tissues, but leaves had the highest expression. The osppr11 mutants had yellowing leaves and a lethal phenotype that inhibited chloroplast development and photosynthesis-related gene expression and reduced photosynthesis-related protein accumulation in seedlings. Moreover, photosynthetic complex accumulation decreased significantly in osppr11 mutants. The OsPPR11 is required for ndhA, and ycf3-1 introns splicing and interact with CRM family protein OsCAF2, suggesting that these two proteins may form splicing complexes to regulate group II introns splicing. Further analysis revealed that OsCAF2 interacts with OsPPR11 through the N-terminus. These results indicate that OsPPR11 is essential for chloroplast development and function by affecting group II intron splicing in rice.
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Affiliation(s)
- Qiang Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Changzhao Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yaliang Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Mengxing He
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Zhiwen Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310006, People's Republic of China
| | - Lan Shen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Qing Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Li Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Deyong Ren
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Jiang Hu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Zhenyu Gao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Guangheng Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Qian Qian
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China.
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572000, People's Republic of China.
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5
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Zhang Q, Chen C, Wang Y, He M, Li Z, Shen L, Li Q, Zhu L, Ren D, Hu J, Gao Z, Zhang G, Qian Q. OsPPR11 encoding P-type PPR protein that affects group II intron splicing and chloroplast development. PLANT CELL REPORTS 2023; 42:421-431. [PMID: 36576552 DOI: 10.1007/s00299-022-02968-6] [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: 11/14/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
OsPPR11 belongs to the P-type PPR protein family and can interact with OsCAF2 to regulate Group II intron splicing and affect chloroplast development in rice. Pentatricopeptide repeat (PPR) proteins participate in chloroplasts or mitochondria group II introns splicing in plants. The PPR protein family contains 491 members in rice, but most of their functions are unknown. In this study, we identified a nuclear gene encoding the P-type PPR protein OsPPR11 in chloroplasts. The qRT-PCR analysis demonstrated that OsPPR11 was expressed in all plant tissues, but leaves had the highest expression. The osppr11 mutants had yellowing leaves and a lethal phenotype that inhibited chloroplast development and photosynthesis-related gene expression and reduced photosynthesis-related protein accumulation in seedlings. Moreover, photosynthetic complex accumulation decreased significantly in osppr11 mutants. The OsPPR11 is required for ndhA, and ycf3-1 introns splicing and interact with CRM family protein OsCAF2, suggesting that these two proteins may form splicing complexes to regulate group II introns splicing. Further analysis revealed that OsCAF2 interacts with OsPPR11 through the N-terminus. These results indicate that OsPPR11 is essential for chloroplast development and function by affecting group II intron splicing in rice.
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Affiliation(s)
- Qiang Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Changzhao Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yaliang Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Mengxing He
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Zhiwen Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310006, People's Republic of China
| | - Lan Shen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Qing Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Li Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Deyong Ren
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Jiang Hu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Zhenyu Gao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Guangheng Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Qian Qian
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China.
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572000, People's Republic of China.
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6
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Zhao Y, Gao R, Zhao Z, Hu S, Han R, Jeyaraj A, Arkorful E, Li X, Chen X. Genome-wide identification of RNA editing sites in chloroplast transcripts and multiple organellar RNA editing factors in tea plant (Camellia sinensis L.): Insights into the albinism mechanism of tea leaves. Gene X 2023; 848:146898. [DOI: 10.1016/j.gene.2022.146898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
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7
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Zhang A, Xiong Y, Fang J, Liu K, Peng H, Zhang X. Genome-wide identification and expression analysis of peach multiple organellar RNA editing factors reveals the roles of RNA editing in plant immunity. BMC PLANT BIOLOGY 2022; 22:583. [PMID: 36513981 PMCID: PMC9746024 DOI: 10.1186/s12870-022-03982-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Multiple organellar RNA editing factor (MORF) genes play key roles in chloroplast developmental processes by mediating RNA editing of Cytosine-to-Uracil conversion. However, the function of MORF genes in peach (Prunus persica), a perennial horticultural crop species of Rosaceae, is still not well known, particularly the resistance to biotic and abiotic stresses that threaten peach yield seriously. RESULTS In this study, to reveal the regulatory roles of RNA editing in plant immunity, we implemented genome-wide analysis of peach MORF (PpMORF) genes in response to biotic and abiotic stresses. The chromosomal and subcellular location analysis showed that the identified seven PpMORF genes distributed on three peach chromosomes were mainly localized in the mitochondria and chloroplast. All the PpMORF genes were classified into six groups and one pair of PpMORF genes was tandemly duplicated. Based on the meta-analysis of two types of public RNA-seq data under different treatments (biotic and abiotic stresses), we observed down-regulated expression of PpMORF genes and reduced chloroplast RNA editing, especially the different response of PpMORF2 and PpMORF9 to pathogens infection between resistant and susceptible peach varieties, indicating the roles of MORF genes in stress response by modulating the RNA editing extent in plant immunity. Three upstream transcription factors (MYB3R-1, ZAT10, HSFB3) were identified under both stresses, they may regulate resistance adaption by modulating the PpMORF gene expression. CONCLUSION These results provided the foundation for further analyses of the functions of MORF genes, in particular the roles of RNA editing in plant immunity. In addition, our findings will be conducive to clarifying the resistance mechanisms in peaches and open up avenues for breeding new cultivars with high resistance.
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Affiliation(s)
- Aidi Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yuhong Xiong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kangchen Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huixiang Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiujun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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Rehman O, Uzair M, Chao H, Khan MR, Chen M. Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:892729. [PMID: 35812946 PMCID: PMC9260663 DOI: 10.3389/fpls.2022.892729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Ribonucleic acid editing (RE) is a post-transcriptional process that altered the genetics of RNA which provide the extra level of gene expression through insertion, deletions, and substitutions. In animals, it converts nucleotide residues C-U. Similarly in plants, the role of RNA editing sites (RES) in rice under alkaline stress is not fully studied. Rice is a staple food for most of the world population. Alkaline stress cause reduction in yield. Here, we explored the effect of alkaline stress on RES in the whole mRNA from rice chloroplast and mitochondria. Ribonucleic acid editing sites in both genomes (3336 RESs) including chloroplast (345 RESs) and mitochondria (2991 RESs) with average RES efficiency ∼55% were predicted. Our findings showed that majority of editing events found in non-synonymous codon changes and change trend in amino acids was hydrophobic. Four types of RNA editing A-G (A-I), C-T (C-U), G-A, and T-C were identified in treated and untreated samples. Overall, RNA editing efficiency was increased in the treated samples. Analysis of Gene Ontology revealed that mapped genes were engaged in many biological functions and molecular processes. We also checked the expression of pentatricopeptide repeat (PPR), organelle zinc-finger (OZI), and multiple organellar RNA editing factors/RNA editing factor interacting proteins genes in control and treatment, results revealed upregulation of PPR and OZ1 genes in treated samples. This induction showed the role of these genes in RNA editing. The current findings report that RNA editing increased under alkaline stress which may contribute in adaptation for rice by changing amino acids in edited genes (88 genes). These findings will provide basis for identification of RES in other crops and also will be useful in alkaline tolerance development in rice.
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Affiliation(s)
- Obaid Rehman
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
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Xiong Y, Fang J, Jiang X, Wang T, Liu K, Peng H, Zhang X, Zhang A. Genome-Wide Analysis of Multiple Organellar RNA Editing Factor (MORF) Family in Kiwifruit ( Actinidia chinensis) Reveals Its Roles in Chloroplast RNA Editing and Pathogens Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020146. [PMID: 35050036 PMCID: PMC8779991 DOI: 10.3390/plants11020146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 05/09/2023]
Abstract
Kiwifruit (Actinidia chinensis) is well known for its high vitamin C content and good taste. Various diseases, especially bacterial canker, are a serious threat to the yield of kiwifruit. Multiple organellar RNA editing factor (MORF) genes are pivotal factors in the RNA editosome that mediates Cytosine-to-Uracil RNA editing, and they are also indispensable for the regulation of chloroplast development, plant growth, and response to stresses. Although the kiwifruit genome has been released, little is known about MORF genes in kiwifruit at the genome-wide level, especially those involved in the response to pathogens stress. In this study, we identified ten MORF genes in the kiwifruit genome. The genomic structures and chromosomal locations analysis indicated that all the MORF genes consisted of three conserved motifs, and they were distributed widely across the seven linkage groups and one contig of the kiwifruit genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the kiwifruit MORF gene family members were classified into six groups (Groups A-F). A synteny analysis indicated that two pairs of MORF genes were tandemly duplicated and five pairs of MORF genes were segmentally duplicated. Moreover, based on analysis of RNA-seq data from five tissues of kiwifruit, we found that both expressions of MORF genes and chloroplast RNA editing exhibited tissue-specific patterns. MORF2 and MORF9 were highly expressed in leaf and shoot, and may be responsible for chloroplast RNA editing, especially the ndhB genes. We also observed different MORF expression and chloroplast RNA editing profiles between resistant and susceptible kiwifruits after pathogen infection, indicating the roles of MORF genes in stress response by modulating the editing extend of mRNA. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes, in particular, for clarifying the resistance mechanisms in kiwifruits and breeding new cultivars with high resistance.
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Affiliation(s)
- Yuhong Xiong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.X.); (J.F.); (X.J.); (T.W.); (K.L.); (H.P.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.X.); (J.F.); (X.J.); (T.W.); (K.L.); (H.P.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohan Jiang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.X.); (J.F.); (X.J.); (T.W.); (K.L.); (H.P.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tengfei Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.X.); (J.F.); (X.J.); (T.W.); (K.L.); (H.P.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kangchen Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.X.); (J.F.); (X.J.); (T.W.); (K.L.); (H.P.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huixiang Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.X.); (J.F.); (X.J.); (T.W.); (K.L.); (H.P.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiujun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.X.); (J.F.); (X.J.); (T.W.); (K.L.); (H.P.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Correspondence: (X.Z.); (A.Z.)
| | - Aidi Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.X.); (J.F.); (X.J.); (T.W.); (K.L.); (H.P.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- Correspondence: (X.Z.); (A.Z.)
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
Chloroplast biogenesis and development are highly complex processes requiring interactions between plastids and nuclear genomic products. Pentatricopeptide repeat (PPR) proteins play an essential role in the development of chloroplasts; however, it remains unclear how RNA editing factors influence soybean development. In this study, a Glycine max pale green leaf 2 mutant (Gmpgl2) was identified with decreased chlorophyll contents. Genetic mapping revealed that a single-nucleotide deletion at position 1949 bp in the Glyma.05g132700 gene in the Gmpgl2 mutant, resulting in a truncated GmPGL2 protein. The nuclear-encoded GmPGL2 is a PLS-type PPR protein that localizes to the chloroplasts. The C-to-U editing efficiencies of rps16, rps18, ndhB, ndhD, ndhE, and ndhF were reduced in the Gmpgl2 mutant. RNA electrophoresis mobility shift assay (REMSA) analysis further revealed that GmPGL2 binds to the immediate upstream sequences at RNA editing sites of rps16 and ndhB in vitro, respectively. In addition, GmPGL2 was found to interact with GmMORF8, GmMORF9, and GmORRM6. These results suggest that GmPGL2 participates in C-to-U RNA editing via the formation of a complex RNA editosome in soybean chloroplasts.
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Affiliation(s)
- Xingxing Feng
- College of Food and Biological Engineering, Xuzhou University of Technology, Xuzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Yaohua Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Cheng Zhiyuan
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Kuanqiang Tang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Guang Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Hui Yu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Jiantian Leng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Qingyu Wang
- College of Plant Science, Jilin University, Changchun, China
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11
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Zhang Q, Shen L, Ren D, Hu J, Zhu L, Gao Z, Zhang G, Guo L, Zeng D, Qian Q. Characterization of the CRM Gene Family and Elucidating the Function of OsCFM2 in Rice. Biomolecules 2020; 10:biom10020327. [PMID: 32085638 PMCID: PMC7072668 DOI: 10.3390/biom10020327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/25/2022] Open
Abstract
The chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins regulate the expression of chloroplast or mitochondrial genes that influence plant growth and development. Although 14 CRM domain proteins have previously been identified in rice, there are few studies of these gene expression patterns in various tissues and under abiotic stress. In our study, we found that 14 CRM domain-containing proteins have a conservative motif1. Under salt stress, the expression levels of 14 CRM genes were downregulated. However, under drought and cold stress, the expression level of some CRM genes was increased. The analysis of gene expression patterns showed that 14 CRM genes were expressed in all tissues but especially highly expressed in leaves. In addition, we analyzed the functions of OsCFM2 and found that this protein influences chloroplast development by regulating the splicing of a group I and five group II introns. Our study provides information for the function analysis of CRM domain-containing proteins in rice.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Qian Qian
- Correspondence: ; Tel.: +86-571-6337-0483
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