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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志  2020, Vol. 40 Issue (3): 125-131    DOI: 10.13523/j.cb.1907029
综述     
植物细胞器RNA编辑因子的功能及其作用机制 *
王柯茹,朱鸿亮()
中国农业大学食品科学与营养工程学院 北京 100083
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
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摘要:

在植物线粒体和叶绿体转录本上,数百个胞嘧啶(C)位点经脱氨基反应变为尿嘧啶(U),这是一种在转录本水平上对遗传信息进行修饰或调控的机制.在植物细胞器中,RNA编辑过程需要不同家族的RNA编辑因子相互作用组装成复杂的编辑复合体,特异地识别编辑位点进行编辑.最初的研究发现,植物RNA编辑受到高特异性五环肽重复(pentatricopeptide repeat, PPR)蛋白的调控,目前在植物中发现400多种PPR家族蛋白,编辑作用复杂.之后对RNA编辑因子互作蛋白/多细胞器RNA编辑因子(RNA editing factor interacting proteins /multiple organellar RNA editing factors,RIP/MORF),细胞器RNA识别基序(organelle RNA recognition motif,ORRM),细胞器锌指蛋白(organelle zinc-finger,OZ)等的研究表明,这些非PPR蛋白组分可以与PPR蛋白形成编辑复合体,共同参与编辑,且RNA编辑复合体具有多样性.RNA编辑因子的缺失会引起植物的生长发育受阻,果实成熟延迟等,对RNA编辑因子的研究显得尤为重要.对植物中RNA编辑因子的功能及其作用机制研究进展进行综述,旨在为后续RNA编辑的研究提供一定的参考.

关键词: RNA编辑细胞器PPR蛋白非PPR蛋白    
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.

Key words: RNA editing    Organelles    PPR protein    Nor-PPR protein
收稿日期: 2019-07-15 出版日期: 2020-04-18
ZTFLH:  Q819  
基金资助: * 国家自然科学基金(31972472,31672208)
通讯作者: 朱鸿亮     E-mail: hlzhu@cau.edu.cn
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引用本文:

王柯茹,朱鸿亮. 植物细胞器RNA编辑因子的功能及其作用机制 *[J]. 中国生物工程杂志, 2020, 40(3): 125-131.

WANG Ke-ru,ZHU Hong-liang. Functions of RNA Editing Factors and Its Mechanisms in Plant Organelles. China Biotechnology, 2020, 40(3): 125-131.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.1907029        https://manu60.magtech.com.cn/biotech/CN/Y2020/V40/I3/125

蛋白质家族 蛋白质成员 亚细胞定位 编辑位点
MORF MORF1[26] 线粒体 atp4, atp9, ccmFN2, ccmB, ccmC, ccmFC, cox2, cox3,matR,nad1,nad2,nad4,nad5,nad6,nad7,mttB,rpl5,rps3,rps4
MORF2[26] 叶绿体 ndhB, ndhD, psbE, psbF, atpF, clpP, accD, matK, ndhF, ndhG, petL, rpoB, rps14, rpoA, psbZ, rps12, rpl23
MORF3[26] 线粒体 atp4, ccmFN2, ccmB, ccmFN1, ccmFC, cox3, cob, nad1, nad2, nad3, nad4L, nad5, nad7, mttB, rpl5, rps3, rps4
MORF4[26] 线粒体 ccmFC,
MORF6 线粒体 nad4
MORF8[27] 线粒体
叶绿体
rps12, petL, ndhD, ndhB, rpoC1, accD, rpoB, ndhF, ccmFN2, ccmB, ccmC, ccmFN1, cob, cox2, matR, nad2, nad3, nad4L, nad5, nad6, nad7, orf25, mttB, rpl2, rpl5, rpl16,rps3,rps4
MORF9 叶绿体 ndhB, ndhD, psbF, atpF, clpP, accD, matK, ndhF, ndhG, petL, rpoB, rps14, rpoA, psbZ, rps12, rpl23
ORRM ORRM1[28] 叶绿体 accD, clpP, matK, ndhB, ndhD, ndhG, rpoA, rpoB, rps12, rps14, atpA, ndhA, petB, rpl2, rpl20, rpoC2, rps8, ycf3
ORRM2[29] 线粒体 rpl16, ccmFC, rps12, cob, nad7, nad5, rps3, nad2, nad4, rps4, nad9, pseudo-rps14, ccmC, rps7, ccmB, nad6, orf114, rpl5, mttB, nad3
ORRM3[2] 线粒体 mttB, ccmB, rps12, nad4, nad5, atp1, cob, nad9, ccmC, cox2, rps3, nad7, nad1, orf240A, orf114, nad6, rps4, nad2, ccmFC, rpl16, pseudo-rps14, rps7, rpl5, nad3
ORRM4[1] 线粒体 ccmFN1, cox3, mttB, nad9, orf114, orf240A, rpl16, rpl5, rps12, pseudo-rps14, rps4, rps7, atp4, atp8, ccmB, ccmC, ccmFC ccmFN2, cob, cox2, matR, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, rpl2, rps3, sdh4
ORRM5[30] 线粒体 atp8, rps3, ccmFN2, rps4, nad4, ccmB, atp1, nad7, nad5, nad3
ORRM6[31] 叶绿体 psbF, accD
OZ OZ1[11] 叶绿体 ndhD, petL, ndhG, psbZ, rps12, psbF, rpl23, ndhB, rpoA, ndhF, rpoB, rpoC1, clpP, matK, accD
PPO PPO1[32] 叶绿体 ndhB, ndhD, rpl23, rpoC1, ndhF, ndhG, petL
表1  拟南芥中非PPR蛋白家族成员
图1  不同RNA编辑因子形成编辑复合体参与细胞器RNA编辑,RNA的特定位点发生C变U的编辑
[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.
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