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Thielen M, Gärtner B, Knoop V, Schallenberg-Rüdinger M, Lesch E. Conquering new grounds: plant organellar C-to-U RNA editing factors can be functional in the plant cytosol. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:895-915. [PMID: 38753873 DOI: 10.1111/tpj.16804] [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: 02/21/2024] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024]
Abstract
Plant mitochondrial and chloroplast transcripts are subject to numerous events of specific cytidine-to-uridine (C-to-U) RNA editing to correct genetic information. Key protein factors for this process are specific RNA-binding pentatricopeptide repeat (PPR) proteins, which are encoded in the nucleus and post-translationally imported into the two endosymbiotic organelles. Despite hundreds of C-to-U editing sites in the plant organelles, no comparable editing has been found for nucleo-cytosolic mRNAs raising the question why plant RNA editing is restricted to chloroplasts and mitochondria. Here, we addressed this issue in the model moss Physcomitrium patens, where all PPR-type RNA editing factors comprise specific RNA-binding and cytidine deamination functionalities in single proteins. To explore whether organelle-type RNA editing can principally also take place in the plant cytosol, we expressed PPR56, PPR65 and PPR78, three editing factors recently shown to also function in a bacterial setup, together with cytosolic co-transcribed native targets in Physcomitrium. While we obtained unsatisfying results upon their constitutive expression, we found strong cytosolic RNA editing under hormone-inducible expression. Moreover, RNA-Seq analyses revealed varying numbers of up to more than 900 off-targets in other cytosolic transcripts. We conclude that PPR-mediated C-to-U RNA editing is not per se incompatible with the plant cytosol but that its limited target specificity has restricted its occurrence to the much less complex transcriptomes of mitochondria and chloroplast in the course of evolution.
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Affiliation(s)
- Mirjam Thielen
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Béla Gärtner
- 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
| | - Mareike Schallenberg-Rüdinger
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Elena Lesch
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
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Azad MTA, Sugi T, Qulsum U, Kato K. Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite. Microorganisms 2024; 12:137. [PMID: 38257964 PMCID: PMC10819399 DOI: 10.3390/microorganisms12010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Transcriptional variation has been studied but post-transcriptional modification due to RNA editing has not been investigated in Plasmodium. We investigated developmental stage-specific RNA editing in selected genes in Plasmodium falciparum 3D7. We detected extensive amination- and deamination-type RNA editing at 8, 16, 24, 32, 40, and 46 h in tightly synchronized Plasmodium. Most of the editing events were observed in 8 and 16 h ring-stage parasites. Extensive A-to-G deamination-type editing was detected more during the 16 h ring stage (25%) than the 8 h ring stage (20%). Extensive U-to-C amination-type editing was detected more during the 16 h ring stage (31%) than the 8 h ring stage (22%). In 28S, rRNA editing converted the loop structure to the stem structure. The hemoglobin binding activity of PF3D7_0216900 was also altered due to RNA editing. Among the expressed 28S rRNA genes, PF3D7_0532000 and PF3D7_0726000 expression was higher. Increased amounts of the transcripts of these two genes were found, particularly PF3D7_0726000 in the ring stage and PF3D7_0532000 in the trophozoite and schizont stages. Adenosine deaminase (ADA) expression did not correlate with the editing level. This first experimental report of RNA editing will help to identify the editing machinery that might be useful for antimalarial drug discovery and malaria control.
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Affiliation(s)
- Md Thoufic Anam Azad
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Tatsuki Sugi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Nishi10-Kita 20, Sapporo 001-0020, Japan
| | - Umme Qulsum
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
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Milarska SE, Androsiuk P, Paukszto Ł, Jastrzębski JP, Maździarz M, Larson KW, Giełwanowska I. Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis. Sci Rep 2023; 13:18774. [PMID: 37907682 PMCID: PMC10618263 DOI: 10.1038/s41598-023-46017-y] [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: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.
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Affiliation(s)
- Sylwia E Milarska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Keith W Larson
- Climate Impacts Research Centre, Umeå University, 90187, Umeå, Sweden
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Xie Y, Chan PL, Kwan HS, Chang J. The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of Coprinopsis cinerea. J Fungi (Basel) 2023; 9:915. [PMID: 37755023 PMCID: PMC10532568 DOI: 10.3390/jof9090915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/17/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Coprinopsis cinerea is one of the model species used in fungal developmental studies. This mushroom-forming Basidiomycetes fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in C. cinerea development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in C. cinerea during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in C. cinerea. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that C. cinerea applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation.
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Affiliation(s)
- Yichun Xie
- State Key Laboratory of Agrobiotechnology, Food Research Center, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China;
| | - Po-Lam Chan
- Food Research Center, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hoi-Shan Kwan
- Food Research Center, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jinhui Chang
- Department of Food Science and Nutrition, and Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong SAR, China
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Pecori R, Chillón I, Lo Giudice C, Arnold A, Wüst S, Binder M, Marcia M, Picardi E, Papavasiliou FN. ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts. Front Cell Dev Biol 2023; 10:1080626. [PMID: 36684421 PMCID: PMC9852825 DOI: 10.3389/fcell.2022.1080626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Despite hundreds of RNA modifications described to date, only RNA editing results in a change in the nucleotide sequence of RNA molecules compared to the genome. In mammals, two kinds of RNA editing have been described so far, adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. Recent improvements in RNA sequencing technologies have led to the discovery of a continuously growing number of editing sites. These methods are powerful but not error-free, making routine validation of newly-described editing sites necessary. During one of these validations on DDX58 mRNA, along with A-to-I RNA editing sites, we encountered putative U-to-C editing. These U-to-C edits were present in several cell lines and appeared regulated in response to specific environmental stimuli. The same findings were also observed for the human long intergenic non-coding RNA p21 (hLincRNA-p21). A more in-depth analysis revealed that putative U-to-C edits result from A-to-I editing on overlapping antisense RNAs that are transcribed from the same loci. Such editing events, occurring on overlapping genes transcribed in opposite directions, have recently been demonstrated to be immunogenic and have been linked with autoimmune and immune-related diseases. Our findings, also confirmed by deep transcriptome data, demonstrate that such loci can be recognized simply through the presence of A-to-I and U-to-C mismatches within the same locus, reflective A-to-I editing both in the sense-oriented transcript and in the cis-natural antisense transcript (cis-NAT), implying that such clusters could be a mark of functionally relevant ADAR1 editing events.
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Affiliation(s)
- Riccardo Pecori
- Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, Germany,Helmholtz Institute for Translational Oncology (HI-TRON), Mainz, Germany,*Correspondence: Riccardo Pecori, ; Fotini Nina Papavasiliou,
| | - Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Claudio Lo Giudice
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, Italy
| | - Annette Arnold
- Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, Germany
| | - Sandra Wüst
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response,” German Cancer Research Centre (DKFZ), Research Program Infection, Inflammation and Cancer, Division Virus Associated Carcinogenesis (F170), Heidelberg, Germany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response,” German Cancer Research Centre (DKFZ), Research Program Infection, Inflammation and Cancer, Division Virus Associated Carcinogenesis (F170), Heidelberg, Germany
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Ernesto Picardi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, Italy
| | - Fotini Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Centre (DKFZ), Research Program Immunology and Cancer, Heidelberg, Germany,*Correspondence: Riccardo Pecori, ; Fotini Nina Papavasiliou,
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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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C-to-U RNA Editing: A Site Directed RNA Editing Tool for Restoration of Genetic Code. Genes (Basel) 2022; 13:genes13091636. [PMID: 36140804 PMCID: PMC9498875 DOI: 10.3390/genes13091636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
The restoration of genetic code by editing mutated genes is a potential method for the treatment of genetic diseases/disorders. Genetic disorders are caused by the point mutations of thymine (T) to cytidine (C) or guanosine (G) to adenine (A), for which gene editing (editing of mutated genes) is a promising therapeutic technique. In C-to-Uridine (U) RNA editing, it converts the base C-to-U in RNA molecules and leads to nonsynonymous changes when occurring in coding regions; however, for G-to-A mutations, A-to-I editing occurs. Editing of C-to-U is not as physiologically common as that of A-to-I editing. Although hundreds to thousands of coding sites have been found to be C-to-U edited or editable in humans, the biological significance of this phenomenon remains elusive. In this review, we have tried to provide detailed information on physiological and artificial approaches for C-to-U RNA editing.
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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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The U-to-C RNA editing affects the mRNA stability of nuclear genes in Arabidopsis thaliana. Biochem Biophys Res Commun 2021; 571:110-117. [PMID: 34325125 DOI: 10.1016/j.bbrc.2021.06.098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/24/2022]
Abstract
Cytidine-to-uridine (C-to-U) RNA editing has been generally observed in land plants; however, reverse (U-to-C) RNA editing is a rare phenomenon. In this study, we investigated the U-to-C RNA editing-related genes in Arabidopsis tissues and the effects on mRNA stability, with a special focus on PPR proteins. A previous study showed the extensive occurrence of U-to-C RNA editing in 12-day and 20-dayold Arabidopsis seedlings. Here, we have demonstrated the effects of this "reverse" RNA editing on the mRNA stability for all seven edited genes. We also identified U-to-C RNA editing in the nuclear PPR gene (AT2G19280) in 12-day-old seedlings of Arabidopsis thaliana. The U-to-C RNA editing sites were found in the untranslated region (3' UTR) of the mature mRNA and may affect its secondary structure. We also examined the correlation between U-to-C RNA editing-related genes and their mRNA abundance. Furthermore, we investigated the effects of U-to-C RNA editing in Arabidopsis using the transcription inhibitor actinomycin D (Act D). The addition of Act D to the seedlings of transgenic Arabidopsis generated by Agrobacterium-mediated transformation showed that single nucleotide base conversion adversely affected the mRNA secondary structure and stability.
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