| Orginal Article |
|
|
|
|
| Functions of RNA Editing Factors and Its Mechanisms in Plant Organelles |
WANG Ke-ru,ZHU Hong-liang( ) |
| College of Food Science and Nutrutuinal Engineering, China Agricultural University, Beijing 100083, China |
|
|
|
Abstract In flowering plants, cytosine C at hundreds of sites is usually converted into uracil U by deamination in mitochondrials and chloroplasts, which is a regulation mechanism of genetic information at the transcriptional level. RNA editing requires protein-protein or protein-RNA interaction to assemble into a complex"editosome" for recognition at special sites in plant organelles. Reachers have found that plant RNA editing is regulated by editosome pentapeptide repeat PPR proteins, and nor-PPR protein including that RNA editing factor interacting proteins/multiple organellar RNA editing factor (RIP/MORF), organelle RNA recognition motif(ORRM) proteins, organelle zinc-finger (OZ) proteins and others. These explain that plant RNA editing not only has a high diversity in PPR specific factors, but also nor-PPR protein components. The absence of RNA editing will cause adverse effects such as stunted growth, development of plants and fruit ripening. The most recent progress in the field and discuss the editosomes for the evolution of RNA editing and for futue findings were systematically summarized.
|
|
Received: 15 July 2019
Published: 18 April 2020
|
|
|
|
Corresponding Authors:
Hong-liang ZHU
E-mail: hlzhu@cau.edu.cn
|
|
|
| [1] |
Shi X, Germain A, Hanson M , et al. RNA recognition motif-containing protein ORRM4 broadly affects mitochondrial RNA editing and impacts plant development and flowering. Plant Physiology, 2015,170(1):294.
|
|
|
| [2] |
Takenaka M, Zehrmann A, Verbitskiy D , et al. RNA editing in plants and its evolution. Annual Review of Genetics, 2013,47(1):335-352.
|
|
|
| [3] |
Blanc V, Litvak S, Araya A . RNA editing in wheat mitochondria proceeds by a deamination mechanism. FEBS Letters, 1995,373(1):56-60.
|
|
|
| [4] |
Daniil V , Merwe J A V D, Anja Z, et al. Multiple specificity recognition motifs enhance plant mitochondrial RNA editing in vitro. Journal of Biological Chemistry, 2008,283(36):24374-24381.
|
|
|
| [5] |
Chen L T, Liu Y G . Male sterility and fertility restoration in crops. Annual Review of Plant Biology, 2014,65(1):579-606.
|
|
|
| [6] |
Emi K, Masao T, Toshiharu S . A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature, 2005,433(7023):326-330.
|
|
|
| [7] |
Qi W W, Tian Z R, Lu L , et al. Editing of mitochondrial transcripts nad3 and cox2 by Dek10 is essential for mitochondrial function and maize plant development. Genetics, 2017,205(4):1489-1501.
|
|
|
| [8] |
Zhang Z, Cui X, Wang Y , et al. The RNA editing factor WSP1 is essential for chloroplast development in rice. Molecular Plant, 2017,10(1):86-98.
|
|
|
| [9] |
Gualberto J M, Lamattina L, Bonnard G , et al. RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature, 1989,341(6243):660-662.
|
|
|
| [10] |
Yang Y, Zhu G, Li R , et al. The RNA editing factor SlORRM4 is required for normal fruit ripening in tomato. Plant Physiology, 2017,175(4) : 1265-2017.
|
|
|
| [11] |
Tao S, Xiaowen S, Giulia F , et al. A zinc finger motif-containing protein is essential for chloroplast RNA editing. PLoS Genetics, 2015,11(3):e1005028.
|
|
|
| [12] |
Ping Y, Quanxiu L, Chuangye Y , et al. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature, 2013,504(7478):168.
|
|
|
| [13] |
Takenaka M, Zehrmann A, Brennicke A , et al. Improved computational target site prediction for pentatricopeptide repeat RNA editing factors. PLoS One, 2013,8(6):e65343.
|
|
|
| [14] |
Sun T, Bentolila S, Hanson M R . The unexpected diversity of plant organelle RNA editosomes. Trends Plant Sci, 2016,21(11):962-973.
|
|
|
| [15] |
Li M, Xia L, Zhang Y , et al. Plant editosome database: a curated database of RNA editosome in plants. Nucleic Acids Research, 2019,47(1):962-973.
|
|
|
| [16] |
Small I D, Peeters N . The PPR motif-a TPR-related motif prevalent in plant organellar proteins. Trends in Biochemical Sciences, 2000,25(2):45-47.
|
|
|
| [17] |
Hayes M L, Hanson M R . Assay of editing of exogenous RNAs in chloroplast extracts of Arabidopsis, maize, pea, and tobacco. Methods Enzymol, 2007,424(424):459-482.
|
|
|
| [18] |
Hegeman C E, Hayes M L, Hanson M R . Substrate and cofactor requirements for RNA editing of chloroplast transcripts in Arabidopsis in vitro. The Plant Journal, 2005,42(1):124-132.
|
|
|
| [19] |
Hayes M L, Giang K, Berhane B , et al. Identification of two pentatricopeptide repeat genes required for rna editing and zinc binding by c-terminal cytidine deaminase-like domains. The Journal of biological chemistry, 2013,288(51):36519-36529.
|
|
|
| [20] |
Hayes M L, Dang K N, Diaz M F , et al. A conserved glutamate residue in the C-terminal deaminase domain of pentatricopeptide repeat proteins is required for RNA editing activity. The Journal of biological chemistry, 2015,290(16):10136-10142.
|
|
|
| [21] |
Mizuki T, Daniil V ,erwe J A V D, et al. In vitro RNA editing in plant mitochondria does not require added energy. Febs Letters, 2007,581(14):2743-2747.
|
|
|
| [22] |
Emi K, Masao T, Toshiharu S . A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature, 2005,433(7023):326-330.
|
|
|
| [23] |
Liu Y, Xiu Z, Robert M , et al. Empty pericarp5 encodes a pentatricopeptide repeat protein that is required for mitochondrial RNA editing and seed development in maize. Plant Cell, 2013,25(3):868-883.
|
|
|
| [24] |
Rtel B H, Takenaka M, Zehrmann A , et al. MEF10 is required for RNA editing at nad2-842 in mitochondria of Arabidopsis thaliana and interacts with MORF8. Plant Molecular Biology, 2013,81(4/5):337-346.
|
|
|
| [25] |
Barkan A, Small I . Pentatricopeptide repeat proteins in plants. Annual Review of Plant Biology, 2014,65(1):415-442.
|
|
|
| [26] |
Har Tel B, Takenaka M, Verbitskiy D , et al. Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants. Proceedings of the National Academy of Sciences of the United States of America, 2012,109(13):5104-5109.
|
|
|
| [27] |
Stephane B, Heller W P, Tao S , et al. RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proceedings of the National Academy of Sciences of the United States of America, 2012,109(22):8372-8373.
|
|
|
| [28] |
Sun T, Germain A, Giloteaux L , et al. An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize. Proceedings of the National Academy of Sciences of the United States of America, 2013,110(12):E1169-E1178.
|
|
|
| [29] |
Shi X, Hanson M R, Bentolila S . Two RNA recognition motif-containing proteins are plant mitochondrial editing factors. Nucleic Acids Res, 2015,43(7):3814-3825.
|
|
|
| [30] |
Shi X, Castandet B, Germain A , et al. ORRM5, an RNA recognition motif-containing protein, has a unique effect on mitochondrial RNA editing. Journal of Experimental Botany, 2017,68(11):2833-2847.
|
|
|
| [31] |
Hackett J B, Shi X, Kobylarz A T , et al. An organelle RNA recognition motif protein is required for photosystem II subunit psbF transcript editing. Plant Physiol, 2017,173(4):2278-2293.
|
|
|
| [32] |
Zhang F, Tang W, Hedtke B , et al. Tetrapyrrole biosynthetic enzyme protoporphyrinogen IX oxidase 1 is required for plastid RNA editing. Proceedings of the National Academy of Sciences of the United States of America, 2014,111(5):2023-2028.
|
|
|
| [33] |
Stéphane B, Julyun O, Hanson M R , et al. Comprehensive high-resolution analysis of the role of an Arabidopsis gene family in RNA editing. PLoS Genetics, 2013,9(6):e1003584.
|
|
|
| [34] |
Bayer-Császár E, Haag S, J?rg A , et al. The conserved domain in MORF proteins has distinct affinities to the PPR and E elements in PPR RNA editing factors. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2017,1860(8):S2009003094.
|
|
|
| [35] |
Yu Q, Huang C, Yang Z , et al. MORF2 tightly associates with MORF9 to regulate chloroplast RNA editing in Arabidopsis. Plant Science 2019,278(278):64-69.
|
|
|
| [36] |
Hackett J B, Lu Y . Whole-transcriptome RNA-seq, gene set enrichment pathway analysis, and exon coverage analysis of two plastid RNA editing mutants. Plant Signal Behav, 2017,12(5):e1312242.
|
|
|
| [37] |
Cao Z L, Yu Q B, Sun Y , et al. A point mutation in the pentatricopeptide repeat motif of the AtECB2 protein causes delayed chloroplast development. J Integr Plant Biol, 2011,53(4):258-269.
|
|
|
| [38] |
Robbins J C, Heller W P, Hanson M R . A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript. RNA, 2009,15(6):1142-1153.
|
|
|
| [39] |
Yu Q B, Jiang Y, Chong K , et al. AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana. Plant J, 2009,59(6):1011-1023.
|
|
|
| [40] |
Boussardon C, Salone V, Avon A , et al. Two interacting proteins are necessary for the editing of the NdhD-1 site in Arabidopsis plastids. Plant Cell, 2012,24(9):3684-3694.
|
|
|
| [41] |
Huang C, Yu Q B, Li Z R , et al. Porphobilinogen deaminase HEMC interacts with the PPR-protein AtECB2 for chloroplast RNA editing. Plant J, 2017,92(4):546-556.
|
|
|
| [42] |
Zehrmann A, Hartel B, Glass F , et al. Selective homo- and heteromer interactions between the multiple organellar RNA editing factor (MORF) proteins in Arabidopsis thaliana. J Biol Chem, 2015,290(10):6445-6456.
|
|
|
| [43] |
Zhang F, Tang W, Hedtke B , et al. Tetrapyrrole biosynthetic enzyme protoporphyrinogen IX oxidase 1 is required for plastid RNA editing. Proceedings of the National Academy of Sciences of the United States of America, 2014,111(5):2023-2028.
|
|
|
| [44] |
Tillich M, Hardel S L, Kupsch C , et al. Chloroplast ribonucleoprotein CP31A is required for editing and stability of specific chloroplast mRNAs. Proceedings of the National Academy of Sciences of the United States of America, 2009,106(14):6002-6007.
|
|
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
