Research Progress of RNA Editing

doi:10.13560/j.cnki.biotech.bull.1985.2021-1326

Abstract

Abstract:

RNA editing is a post-transcriptional process on the target transcripts by base insertion,deletion,or replacement. This important epigenetic phenomenon is also considered as a correction mechanism for genetic restoration at the RNA level. Here,we reviewed the RNA editing systems based on PPR gene family in plants and CRISPR/Cas editing system in animal, introduced the important role of RNA editing in the plant growth and development, and prospected future application of RNA editing. In addition we also summarized the recent research on RNA editing database,which support the follow-up research of RNA editing.

Key words: RNA editing, organelles, PPR protein, RNA editosomes, CRISPR/Cas

ZHU Lin, XIAN Feng-jun, ZHANG Qian-nan, HU Jun. Research Progress of RNA Editing[J]. Biotechnology Bulletin, 2022, 38(1): 1-14.

Figures/Tables 2

References 122

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序号 No.	蛋白 Protein	靶标基因 Target genes	研究对象 Object	定位 Location	类别 Class	氨基酸变化 Changes of amino acid	基因表达受阻后表型 Phenotype after blocked gene expression	文献 Reference
1	PPS1	nad3-155,nad3-172,nad3-173, nad3-190,nad3-191	Rice	Mitochondria	DYW	Pro-Leu	生长缓慢、矮化和发育迟缓、花药短小、花粉不育、柱头发芽率和结实率低电子传递链复合体丰度及活性降低,线粒体嵴坍塌,导致其形态结构异常	[42]
2	PPR756	atp6-368.ccmC-236.nad7-83	Rice	Mitochondria	E	Pro-Leu,Pro-Leu,Ser-Leu	营养生长时期发育迟缓,生殖生长时期花粉干瘪,产生雄性不育现象	[43]
3	OGR1	cox2-167.cox3-572.ccmC-458 nad2-1457.nad4-401 nad4-416 nad4-433	Rice	Mitochondria	DYW	Ser-Leu.Ser-Phe.Ser-Leu. Ser-Leu.Ser-Phe.Pro-Leu Leu-Phe	生长迟缓、分蘖少、种子萌发延迟、胚乳不透明、矮化、部分不育	[44]
4	PGL1	ndhD-878.ccmFc-543	Rice	Chloroplast/Mitochondria	DYW	Ser-Leu.Val-Val	叶色淡绿,叶绿素含量显著降低,类囊体结构排列松散	[45]
5	PPR16	rpoB-545	Rice	Chloroplast	DYW	Ser-Leu	早期叶片黄化,后期返绿,叶绿素合成变慢	[46]
6	ATP4	rps8-182	Rice/Maize	Chloroplast	P	Ser-Leu	低温白化,生长发育缺陷,雄性不育	[47]
7	SMK1	nad7-836	Rice/Maize	Mitochondria	E	Pro-Leu	种子的胚和胚乳发育异常,苗期致死	[48]
8	EMP5	rpl16-458	Maize	Mitochondria	DYW	Pro-Leu	生长迟缓,种子发育不良	[49]]
9	Emp7	ccmFN-1553	Maize	Mitochondria	E	Ser-Phe	胚和胚乳的发育受阻,胚胎致死	[50]
10	Emp9	ccmB-43.rps4-335	Maize	Mitochondria	E+	Pro-Ser.Pro-Leu	果皮塌陷,胚和胚乳发育受阻,胚胎致死	[51]
11	PPR2263	nad5-1550.cob-908	Maize	Mitochondria	DYW	Thr-Ile.Pro-Leu	籽粒和幼苗生长缺陷,叶片窄短,开花晚,线粒体结构受损	[52]
12	AEF1/ MPR25	atpF-92.nad5-1580	Arabidopsis/Rice	Plastid/Mitochondria	E	Pro-Leu.Ser-Leu	苗期生长缓慢,光合作用速率降低,叶色黄绿	[53-54]
13	SLO1	nad4-449.nad9-328	Arabidopsis	Mitochondria	E	Pro-Leu.Arg-Trp	生长缓慢,发育延迟	[55]
14	SLO2	nad4L-110,nad1-2,nad1-40, nad7-739,mttB-144,mttB-145,mttB-666	Arabidopsis	Mitochondria	E+	Ser-Leu,Thr-Met,Leu-Leu,Leu-Phe,Phe-Phe,Pro-Ser,Ser-Leu	叶片出芽迟缓,根生长受限,开花晚电子传递链复合体I、III和IV丰度和活性降低,碳能量失衡	[56]
15	MEF9	nad7-200	Arabidopsis	Mitochondria	E	Ser-Phe	生长稍慢,抽薹和花座延迟	[57]
16	MEF10	nad2-842	Arabidopsis	Mitochondria	DYW	Ser-Phe	生长延迟,没有明显的表型差异	[58]
17	LOI1 （MEF11）	cox3-422,ccb203-344,nad4-124	Arabidopsis	Mitochondria	DYW	Pro-Leu,Pro-Leu,Leu-Leu	对类异戊二烯合成的特异性抑制剂具有抗性,影响异戊二烯生物合成	[59]
18	MEF13	nad7-213,ccmFc-50,ccmFc-415,cox3-314,nad2-59,nad4-158,nad5-1665,nad5-1916	Arabidopsis	Mitochondria	E	Asp-Asp,Pro-Leu,Leu-Phe,Ser-Phe,Ser-Phe,Pro-Leu,Leu-Leu,Ser-Phe	生长发育缓慢,莲座叶叶茎缩短	[60]
19	SLG1	nad3-250	Arabidopsis	Mitochondria	E+	Pro-Ser	生长缓慢和发育迟缓,对ABA的响应增强,H2O2积累增加,耐旱性增强	[61]
20	AHG11	nad4-376	Arabidopsis	Mitochondria	E+	Cys-Arg	影响ABA信号传递及细胞响应	[62]
21	OTP87	nad7-24,atp1-1178	Arabidopsis	Mitochondria	E	Ile- Ile,Ser-Leu	生长缓慢,发育迟缓,株型较小	[63]
22	RARE1	accD-794	Arabidopsis	Chloroplast	DYW	Ser-Leu	纯合突变体生长旺盛,发育迅速	[64]
23	CLB19	rpoA-200,clpP-559	Arabidopsis	Chloroplast	E+	Ser-Phe,His-Tyr	叶色淡黄,叶绿体发育受损,发育迟缓,幼苗早死	[65]
24	VAC1	accD-794,ndhF-290	Arabidopsis	Chloroplast	DYW	Ser-Leu	纯合突变体白化致死,杂合突变体叶色呈浅黄绿,叶绿体发育受损	[66]
25	QED1	accD-794,matK-640,ndhB-872,rpoB-2432	Arabidopsis	Chloroplast	DYW	Ser-Leu,His-Tyr,Ser-Leu,Ser-Leu	生长缓慢,生长5周后叶片出现黄色区域	[67]
26	YS1	rpoB-338	Arabidopsis	Chloroplast	DYW	Ser-Phe	光合能力下降,光合色素复合物减少,叶绿体结构异常	[68]
27	LPA66	psbF-77	Arabidopsis	Chloroplast	DYW	Ser-Phe	生长缓慢,叶色淡绿,光系统Ⅱ功能受损	[69]
28	AtECB2	accD-794	Arabidopsis	Chloroplast	DYW	Leu-Ser	白化致死,叶绿体缺乏有组织的类囊体膜,光合蛋白水平下降	[70]
29	PpPPR45	rps14-2	Physcomitrella patens	Chloroplast	DYW	Met-Thr	生长迟缓,颜色淡绿,光合活性降低	[71]
30	PpPPR56	nad3-230,nad4-272	Physcomitrella patens	Mitochondria	DYW	Ser-Leu	生长发育轻微阻滞	[72]
31	PpPPR65	ccmFc-103,ccmFc-122	Physcomitrella patens	Mitochondria	DYW	Pro-Ser,Ser-Phe	生长发育严重阻滞	[73]
32	PpPPR71	ccmFc-122	Physcomitrella patens	Mitochondria	DYW	Ser-Phe	生长发育明显阻滞	[74]
33	PpPPR77	cox2-370,cox3-733	Physcomitrella patens	Mitochondria	DYW	Arg-Trp	生长发育严重阻滞	[72]
34	PpPPR78	cox1-755,rps14-137	Physcomitrella patens	Mitochondria	DYW	Ser-Leu	生长发育轻微阻滞	[75]
35	PpPPR79	nad5-598	Physcomitrella patens	Mitochondria	DYW	Arg-Cys	生长发育严重阻滞	[75]
36	PpPPR91	nad5-244	Physcomitrella patens	Mitochondria	DYW	Arg-Trp	生长发育严重阻滞	[71]
37	PpPPR98	atp9-92	Physcomitrella patens	Mitochondria	DYW	Ser-Leu	生长发育无明显差异,转录水平较野生型低35%	[73]

序号 No.	蛋白 Protein	靶标基因 Target genes	研究对象 Object	定位 Location	类别 Class	氨基酸变化 Changes of amino acid	基因表达受阻后表型 Phenotype after blocked gene expression	文献 Reference
1	PPS1	nad3-155,nad3-172,nad3-173, nad3-190,nad3-191	Rice	Mitochondria	DYW	Pro-Leu	生长缓慢、矮化和发育迟缓、花药短小、花粉不育、柱头发芽率和结实率低电子传递链复合体丰度及活性降低,线粒体嵴坍塌,导致其形态结构异常	[42]
2	PPR756	atp6-368.ccmC-236.nad7-83	Rice	Mitochondria	E	Pro-Leu,Pro-Leu,Ser-Leu	营养生长时期发育迟缓,生殖生长时期花粉干瘪,产生雄性不育现象	[43]
3	OGR1	cox2-167.cox3-572.ccmC-458 nad2-1457.nad4-401 nad4-416 nad4-433	Rice	Mitochondria	DYW	Ser-Leu.Ser-Phe.Ser-Leu. Ser-Leu.Ser-Phe.Pro-Leu Leu-Phe	生长迟缓、分蘖少、种子萌发延迟、胚乳不透明、矮化、部分不育	[44]
4	PGL1	ndhD-878.ccmFc-543	Rice	Chloroplast/Mitochondria	DYW	Ser-Leu.Val-Val	叶色淡绿,叶绿素含量显著降低,类囊体结构排列松散	[45]
5	PPR16	rpoB-545	Rice	Chloroplast	DYW	Ser-Leu	早期叶片黄化,后期返绿,叶绿素合成变慢	[46]
6	ATP4	rps8-182	Rice/Maize	Chloroplast	P	Ser-Leu	低温白化,生长发育缺陷,雄性不育	[47]
7	SMK1	nad7-836	Rice/Maize	Mitochondria	E	Pro-Leu	种子的胚和胚乳发育异常,苗期致死	[48]
8	EMP5	rpl16-458	Maize	Mitochondria	DYW	Pro-Leu	生长迟缓,种子发育不良	[49]]
9	Emp7	ccmFN-1553	Maize	Mitochondria	E	Ser-Phe	胚和胚乳的发育受阻,胚胎致死	[50]
10	Emp9	ccmB-43.rps4-335	Maize	Mitochondria	E+	Pro-Ser.Pro-Leu	果皮塌陷,胚和胚乳发育受阻,胚胎致死	[51]
11	PPR2263	nad5-1550.cob-908	Maize	Mitochondria	DYW	Thr-Ile.Pro-Leu	籽粒和幼苗生长缺陷,叶片窄短,开花晚,线粒体结构受损	[52]
12	AEF1/ MPR25	atpF-92.nad5-1580	Arabidopsis/Rice	Plastid/Mitochondria	E	Pro-Leu.Ser-Leu	苗期生长缓慢,光合作用速率降低,叶色黄绿	[53-54]
13	SLO1	nad4-449.nad9-328	Arabidopsis	Mitochondria	E	Pro-Leu.Arg-Trp	生长缓慢,发育延迟	[55]
14	SLO2	nad4L-110,nad1-2,nad1-40, nad7-739,mttB-144,mttB-145,mttB-666	Arabidopsis	Mitochondria	E+	Ser-Leu,Thr-Met,Leu-Leu,Leu-Phe,Phe-Phe,Pro-Ser,Ser-Leu	叶片出芽迟缓,根生长受限,开花晚电子传递链复合体I、III和IV丰度和活性降低,碳能量失衡	[56]
15	MEF9	nad7-200	Arabidopsis	Mitochondria	E	Ser-Phe	生长稍慢,抽薹和花座延迟	[57]
16	MEF10	nad2-842	Arabidopsis	Mitochondria	DYW	Ser-Phe	生长延迟,没有明显的表型差异	[58]
17	LOI1 （MEF11）	cox3-422,ccb203-344,nad4-124	Arabidopsis	Mitochondria	DYW	Pro-Leu,Pro-Leu,Leu-Leu	对类异戊二烯合成的特异性抑制剂具有抗性,影响异戊二烯生物合成	[59]
18	MEF13	nad7-213,ccmFc-50,ccmFc-415,cox3-314,nad2-59,nad4-158,nad5-1665,nad5-1916	Arabidopsis	Mitochondria	E	Asp-Asp,Pro-Leu,Leu-Phe,Ser-Phe,Ser-Phe,Pro-Leu,Leu-Leu,Ser-Phe	生长发育缓慢,莲座叶叶茎缩短	[60]
19	SLG1	nad3-250	Arabidopsis	Mitochondria	E+	Pro-Ser	生长缓慢和发育迟缓,对ABA的响应增强,H2O2积累增加,耐旱性增强	[61]
20	AHG11	nad4-376	Arabidopsis	Mitochondria	E+	Cys-Arg	影响ABA信号传递及细胞响应	[62]
21	OTP87	nad7-24,atp1-1178	Arabidopsis	Mitochondria	E	Ile- Ile,Ser-Leu	生长缓慢,发育迟缓,株型较小	[63]
22	RARE1	accD-794	Arabidopsis	Chloroplast	DYW	Ser-Leu	纯合突变体生长旺盛,发育迅速	[64]
23	CLB19	rpoA-200,clpP-559	Arabidopsis	Chloroplast	E+	Ser-Phe,His-Tyr	叶色淡黄,叶绿体发育受损,发育迟缓,幼苗早死	[65]
24	VAC1	accD-794,ndhF-290	Arabidopsis	Chloroplast	DYW	Ser-Leu	纯合突变体白化致死,杂合突变体叶色呈浅黄绿,叶绿体发育受损	[66]
25	QED1	accD-794,matK-640,ndhB-872,rpoB-2432	Arabidopsis	Chloroplast	DYW	Ser-Leu,His-Tyr,Ser-Leu,Ser-Leu	生长缓慢,生长5周后叶片出现黄色区域	[67]
26	YS1	rpoB-338	Arabidopsis	Chloroplast	DYW	Ser-Phe	光合能力下降,光合色素复合物减少,叶绿体结构异常	[68]
27	LPA66	psbF-77	Arabidopsis	Chloroplast	DYW	Ser-Phe	生长缓慢,叶色淡绿,光系统Ⅱ功能受损	[69]
28	AtECB2	accD-794	Arabidopsis	Chloroplast	DYW	Leu-Ser	白化致死,叶绿体缺乏有组织的类囊体膜,光合蛋白水平下降	[70]
29	PpPPR45	rps14-2	Physcomitrella patens	Chloroplast	DYW	Met-Thr	生长迟缓,颜色淡绿,光合活性降低	[71]
30	PpPPR56	nad3-230,nad4-272	Physcomitrella patens	Mitochondria	DYW	Ser-Leu	生长发育轻微阻滞	[72]
31	PpPPR65	ccmFc-103,ccmFc-122	Physcomitrella patens	Mitochondria	DYW	Pro-Ser,Ser-Phe	生长发育严重阻滞	[73]
32	PpPPR71	ccmFc-122	Physcomitrella patens	Mitochondria	DYW	Ser-Phe	生长发育明显阻滞	[74]
33	PpPPR77	cox2-370,cox3-733	Physcomitrella patens	Mitochondria	DYW	Arg-Trp	生长发育严重阻滞	[72]
34	PpPPR78	cox1-755,rps14-137	Physcomitrella patens	Mitochondria	DYW	Ser-Leu	生长发育轻微阻滞	[75]
35	PpPPR79	nad5-598	Physcomitrella patens	Mitochondria	DYW	Arg-Cys	生长发育严重阻滞	[75]
36	PpPPR91	nad5-244	Physcomitrella patens	Mitochondria	DYW	Arg-Trp	生长发育严重阻滞	[71]
37	PpPPR98	atp9-92	Physcomitrella patens	Mitochondria	DYW	Ser-Leu	生长发育无明显差异,转录水平较野生型低35%	[73]

数据库名称 Database	整合范围 Research scope	记录事件 Record contents	文献 Reference
REDIportal	人类	450多万个A-to-I类型的编辑事件	[116]
RADAR	人类、小鼠、苍蝇	人类中1 379 403个、小鼠中8 108个和苍蝇中2 698个A-to-I类型的编辑事件	[117]
PREPACT 3.0	RNA编辑因子	编辑位点识别特异性特征编辑因子信息	[118]
dbRES	植物、后生动物、原生动物、真菌和病毒等96种生物	251个转录本中5 437个RNA编辑位点	[119]
RESOPS	陆地植物细胞器	5 754个RNA编辑位点与蛋白质三维结构的对应关系	[120]
CloroplastDB	植物叶绿体基因组	叶绿体相关RNA编辑事件	[121]
GOBASE	植物细胞器基因组	线粒体及叶绿体内RNA编辑事件类型及位点碱基的变化	[122]
REDIdb 3.0	植物细胞器基因组	281个生物体和85个完整的细胞器基因组中的26 618个事件	[114]
PED	植物RNA编辑因子	1 621种植物和1 673个植物细胞器的203种细胞器基因上20 836个RNA编辑事件	[115]

数据库名称 Database	整合范围 Research scope	记录事件 Record contents	文献 Reference
REDIportal	人类	450多万个A-to-I类型的编辑事件	[116]
RADAR	人类、小鼠、苍蝇	人类中1 379 403个、小鼠中8 108个和苍蝇中2 698个A-to-I类型的编辑事件	[117]
PREPACT 3.0	RNA编辑因子	编辑位点识别特异性特征编辑因子信息	[118]
dbRES	植物、后生动物、原生动物、真菌和病毒等96种生物	251个转录本中5 437个RNA编辑位点	[119]
RESOPS	陆地植物细胞器	5 754个RNA编辑位点与蛋白质三维结构的对应关系	[120]
CloroplastDB	植物叶绿体基因组	叶绿体相关RNA编辑事件	[121]
GOBASE	植物细胞器基因组	线粒体及叶绿体内RNA编辑事件类型及位点碱基的变化	[122]
REDIdb 3.0	植物细胞器基因组	281个生物体和85个完整的细胞器基因组中的26 618个事件	[114]
PED	植物RNA编辑因子	1 621种植物和1 673个植物细胞器的203种细胞器基因上20 836个RNA编辑事件	[115]