Biotechnology Bulletin ›› 2022, Vol. 38 ›› Issue (1): 1-14.doi: 10.13560/j.cnki.biotech.bull.1985.2021-1326
ZHU Lin(), XIAN Feng-jun, ZHANG Qian-nan, HU Jun()
Received:
2021-10-21
Online:
2022-01-26
Published:
2022-02-22
Contact:
HU Jun
E-mail:linzhu@whu.edu.cn;junhu@whu.edu.cn
ZHU Lin, XIAN Feng-jun, ZHANG Qian-nan, HU Jun. Research Progress of RNA Editing[J]. Biotechnology Bulletin, 2022, 38(1): 1-14.
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 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
6 | ATP4 | rps8-182 | Rice/Maize | Chloroplast | P | Ser-Leu | 低温白化,生长发育缺陷,雄性不育 | [ |
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 | [ |
8 | EMP5 | rpl16-458 | Maize | Mitochondria | DYW | Pro-Leu | 生长迟缓,种子发育不良 | [ |
9 | Emp7 | ccmFN-1553 | Maize | Mitochondria | E | Ser-Phe | 胚和胚乳的发育受阻,胚胎致死 | [ |
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 | [ |
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 | [ |
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 | [ |
13 | SLO1 | nad4-449.nad9-328 | Arabidopsis | Mitochondria | E | Pro-Leu.Arg-Trp | 生长缓慢,发育延迟 | [ |
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 | [ |
15 | MEF9 | nad7-200 | Arabidopsis | Mitochondria | E | Ser-Phe | 生长稍慢,抽薹和花座延迟 | [ |
16 | MEF10 | nad2-842 | Arabidopsis | Mitochondria | DYW | Ser-Phe | 生长延迟,没有明显的表型差异 | [ |
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 | [ |
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 | [ |
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 | [ |
20 | AHG11 | nad4-376 | Arabidopsis | Mitochondria | E+ | Cys-Arg | 影响ABA信号传递及细胞响应 | [ |
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 | [ |
22 | RARE1 | accD-794 | Arabidopsis | Chloroplast | DYW | Ser-Leu | 纯合突变体生长旺盛,发育迅速 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
29 | PpPPR45 | rps14-2 | Physcomitrella patens | Chloroplast | DYW | Met-Thr | 生长迟缓,颜色淡绿,光合活性降低 | [ |
30 | PpPPR56 | nad3-230,nad4-272 | Physcomitrella patens | Mitochondria | DYW | Ser-Leu | 生长发育轻微阻滞 | [ |
31 | PpPPR65 | ccmFc-103,ccmFc-122 | Physcomitrella patens | Mitochondria | DYW | Pro-Ser,Ser-Phe | 生长发育严重阻滞 | [ |
32 | PpPPR71 | ccmFc-122 | Physcomitrella patens | Mitochondria | DYW | Ser-Phe | 生长发育明显阻滞 | [ |
33 | PpPPR77 | cox2-370,cox3-733 | Physcomitrella patens | Mitochondria | DYW | Arg-Trp | 生长发育严重阻滞 | [ |
34 | PpPPR78 | cox1-755,rps14-137 | Physcomitrella patens | Mitochondria | DYW | Ser-Leu | 生长发育轻微阻滞 | [ |
35 | PpPPR79 | nad5-598 | Physcomitrella patens | Mitochondria | DYW | Arg-Cys | 生长发育严重阻滞 | [ |
36 | PpPPR91 | nad5-244 | Physcomitrella patens | Mitochondria | DYW | Arg-Trp | 生长发育严重阻滞 | [ |
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% | [ |
Table 1 PPR protein involved in RNA editing and its regulation on model plant growth and development
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 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
6 | ATP4 | rps8-182 | Rice/Maize | Chloroplast | P | Ser-Leu | 低温白化,生长发育缺陷,雄性不育 | [ |
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 | [ |
8 | EMP5 | rpl16-458 | Maize | Mitochondria | DYW | Pro-Leu | 生长迟缓,种子发育不良 | [ |
9 | Emp7 | ccmFN-1553 | Maize | Mitochondria | E | Ser-Phe | 胚和胚乳的发育受阻,胚胎致死 | [ |
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 | [ |
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 | [ |
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 | [ |
13 | SLO1 | nad4-449.nad9-328 | Arabidopsis | Mitochondria | E | Pro-Leu.Arg-Trp | 生长缓慢,发育延迟 | [ |
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 | [ |
15 | MEF9 | nad7-200 | Arabidopsis | Mitochondria | E | Ser-Phe | 生长稍慢,抽薹和花座延迟 | [ |
16 | MEF10 | nad2-842 | Arabidopsis | Mitochondria | DYW | Ser-Phe | 生长延迟,没有明显的表型差异 | [ |
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 | [ |
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 | [ |
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 | [ |
20 | AHG11 | nad4-376 | Arabidopsis | Mitochondria | E+ | Cys-Arg | 影响ABA信号传递及细胞响应 | [ |
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 | [ |
22 | RARE1 | accD-794 | Arabidopsis | Chloroplast | DYW | Ser-Leu | 纯合突变体生长旺盛,发育迅速 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
29 | PpPPR45 | rps14-2 | Physcomitrella patens | Chloroplast | DYW | Met-Thr | 生长迟缓,颜色淡绿,光合活性降低 | [ |
30 | PpPPR56 | nad3-230,nad4-272 | Physcomitrella patens | Mitochondria | DYW | Ser-Leu | 生长发育轻微阻滞 | [ |
31 | PpPPR65 | ccmFc-103,ccmFc-122 | Physcomitrella patens | Mitochondria | DYW | Pro-Ser,Ser-Phe | 生长发育严重阻滞 | [ |
32 | PpPPR71 | ccmFc-122 | Physcomitrella patens | Mitochondria | DYW | Ser-Phe | 生长发育明显阻滞 | [ |
33 | PpPPR77 | cox2-370,cox3-733 | Physcomitrella patens | Mitochondria | DYW | Arg-Trp | 生长发育严重阻滞 | [ |
34 | PpPPR78 | cox1-755,rps14-137 | Physcomitrella patens | Mitochondria | DYW | Ser-Leu | 生长发育轻微阻滞 | [ |
35 | PpPPR79 | nad5-598 | Physcomitrella patens | Mitochondria | DYW | Arg-Cys | 生长发育严重阻滞 | [ |
36 | PpPPR91 | nad5-244 | Physcomitrella patens | Mitochondria | DYW | Arg-Trp | 生长发育严重阻滞 | [ |
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% | [ |
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 | [ |
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 | [ |
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 | [ |
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 | [ |
CloroplastDB | 植物叶绿体基因组 | 叶绿体相关RNA编辑事件 | [ |
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 | [ |
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 | [ |
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 | [ |
Table 2 Partial RNA editing database
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 | [ |
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 | [ |
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 | [ |
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 | [ |
CloroplastDB | 植物叶绿体基因组 | 叶绿体相关RNA编辑事件 | [ |
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 | [ |
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 | [ |
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 | [ |
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