甜菜应答盐胁迫PUB基因的生物信息学分析

doi:10.11924/j.issn.1000-6850.casb2021-0536

中国农学通报 ›› 2021, Vol. 37 ›› Issue (33): 120-127.doi: 10.11924/j.issn.1000-6850.casb2021-0536

所属专题：生物技术

甜菜应答盐胁迫PUB基因的生物信息学分析

王爽¹^,²(), 李海英¹^,²()

¹黑龙江大学农业微生物技术教育部工程研究中心,哈尔滨 150500
²黑龙江大学生命科学学院/黑龙江省普通高校分子生物学重点实验室,哈尔滨 150080

收稿日期:2021-05-19 修回日期:2021-07-13 出版日期:2021-11-25 发布日期:2022-01-06
通讯作者: 李海英
作者简介:王爽,女,1998年出生,黑龙江大庆人,硕士研究生,研究方向：植物分子生物学。通信地址：150080 黑龙江省哈尔滨市学府路74号黑龙江大学生命科学学院320室,Tel：18846434098,E-mail： suangsuang0923@163.com。
基金资助:
国家自然科学基金“转录因子BvGT-1调控乙二醛酶I基因参与甜菜单体附加系耐盐的分子机制”(32072122);2021年黑龙江大学校级研究生创新科研项目(YLSCX2021-207HLJU)

PUB Gene in Sugar Beet Response to Salt Stress: Bioinformatics Analysis

Wang Shuang¹^,²(), Li Haiying¹^,²()

¹Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500
²Key Laboratory of Microbiology, College of Heilongjiang Province/School of Life Sciences, Heilongjiang University, Harbin 150080

Received:2021-05-19 Revised:2021-07-13 Online:2021-11-25 Published:2022-01-06
Contact: Li Haiying

摘要/Abstract

摘要：

旨在为研究甜菜U-box型E3泛素连接酶提供理论基础。以甜菜T710-Mu品系为试验材料,前期通过转录组数据获得在盐胁迫下差异表达的甜菜PUB基因(plant U-box gene),利用生物信息学的方法对这些PUB基因进行分析,主要包括理化性质分析、染色体定位分析、基因序列分析、结构域分析、家族分类分析以及互作蛋白预测。结果显示甜菜PUB基因在甜菜9条染色体上均有定位,并且包含PUB蛋白具有的多个保守结构域,如U-box,Pkinase、Pkinase-Tyr、Usp、Arm以及KAP结构域,以拟南芥U-box家族分类为依据发现甜菜U-box多位于ClassⅡ、ClassⅢ、ClassⅣ中,甜菜PUB蛋白可作为E3泛素连接酶与多种功能蛋白相互作用,实现泛素化修饰。植物PUB蛋白具有E3泛素连接酶活性,在植物生长发育过程以及抵抗环境压力中起到重要作用。

关键词: 甜菜, 盐胁迫, U-box, E3泛素连接酶, 生物信息学

Abstract:

The aim was to provide a theoretical basis for studying sugar beet U-box E3 ubiquitin ligases from the perspective of bioinformatics. The beet T710-Mu strain was used as the experimental material. The BvPUB gene (plant U-box gene) that was differentially expressed under salt stress was obtained from transcriptome data at the early stage, and bioinformatics methods was used to analyze these PUB genes. They mainly included physical and chemical properties analysis, chromosome localization analysis, gene sequence analysis, domain analysis, family classification analysis and interaction protein prediction. The results showed that the BvPUB genes was localized on all 9 chromosomes, and contained multiple conserved domains of PUB protein, such as U-box, Pkinase, Pkinase-Tyr, Usp, ARM and KAP domains, which could be divided into ClassⅡ, ClassⅢ, ClassⅣ according to structural characteristics of the Arabidopsis U-box family. Sugar beet PUB proteins could act as E3 ubiquitin ligases to interact with a variety of functional proteins to achieve ubiquitination modification. Plant PUB protein had E3 ubiquitin ligase activity, which played an important role in plant growth and development and resistance to environmental stress.

Key words: sugar beet, salt stress, U-box, ubiquitin ligase, bioinformatics

中图分类号:

S566.3

王爽, 李海英. 甜菜应答盐胁迫PUB基因的生物信息学分析[J]. 中国农学通报, 2021, 37(33): 120-127.

Wang Shuang, Li Haiying. PUB Gene in Sugar Beet Response to Salt Stress: Bioinformatics Analysis[J]. Chinese Agricultural Science Bulletin, 2021, 37(33): 120-127.

图/表 7

参考文献 20

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基因名称	登录号	染色体	起始位置/bp	终止位置/bp	氨基酸/aa	分子量/Da	等电点
BvPUB 1	LOC104904112	09	36506579	36508444	427	47013.04	7.92
BvPUB 2	LOC104903642	09	27445807	27449366	478	53228.16	8.59
BvPUB 3	LOC104903735	09	27293192	27304359	871	96472.89	6.41
BvPUB 4	LOC104900875	08	5871693	5875241	429	45142.51	5.43
BvPUB 5	LOC104900131	07	41602143	41606809	664	72065.89	5.13
BvPUB 6	LOC104900121	07	41505285	41513838	847	96138.82	8.01
BvPUB 7	LOC104899939	07	39609286	39615718	1034	114154.44	5.60
BvPUB 8	LOC104899785	07	37319509	37331173	723	80364.18	7.62
BvPUB 9	LOC104899783	07	37308789	37314093	773	84983.99	6.00
BvPUB 10	LOC104897603	06	55290621	55296404	784	86546.32	6.27
BvPUB 11	LOC104895519	06	7697736	7703627	820	93366.02	5.49
BvPUB 12	LOC104895449	06	6754220	6755873	421	46801.16	8.38
BvPUB 13	LOC104895410	06	6353253	6354503	417	47028.05	5.77
BvPUB 14	LOC104895041	06	2373895	2380036	750	83938.88	6.30
BvPUB 15	LOC104894904	06	692177	695704	318	34288.42	8.33
BvPUB 16	LOC104894729	05	51156937	51163732	754	82630.32	6.79
BvPUB 17	LOC104894345	05	47547553	47551647	245	27885.88	7.08
BvPUB 18	LOC104894251	05	45927032	45928897	682	76147.85	8.04
BvPUB 19	LOC104894207	05	45232472	45234885	559	61449.08	6.83
BvPUB 20	LOC104890423	04	5916107	5919169	470	52925.55	5.93
BvPUB 21	LOC104888531	03	7700131	7707003	910	103089.72	6.33
BvPUB 22	LOC104887725	02	39375337	39381558	606	67985.93	6.46
BvPUB 23	LOC104887722	02	39331036	39338437	836	91677.65	5.56
BvPUB 24	LOC104887625	02	37796618	37809463	430	47165.85	5.02
BvPUB 25	LOC104887545	02	36697852	36699391	331	35475.45	5.04
BvPUB 26	LOC104887488	02	35479251	35484261	837	92419.89	5.55
BvPUB 27	LOC104887006	02	22863210	22866929	513	55583.91	8.50
BvPUB 28	LOC104886790	02	17465918	17472689	835	93586.21	8.03
BvPUB 29	LOC104886722	02	16130627	16138269	784	87302.72	6.74
BvPUB 30	LOC104886603	02	14016706	14022462	751	84225.56	8.73
BvPUB 31	LOC104885156	02	10061218	10062952	365	39501.73	6.33
BvPUB 32	LOC104883224	02	8988596	8991520	511	56152.97	7.34
BvPUB 33	LOC104906776	02	4541998	4545909	370	40244.60	6.26
BvPUB 34	LOC104902107	01	33582472	33590065	351	37730.19	6.18
BvPUB 35	LOC104901828	01	33089330	33092220	446	48554.13	6.55
BvPUB 36	LOC104901082	01	32336771	32347161	812	89120.42	5.30
BvPUB 37	LOC104895459	01	17548412	17550438	394	43776.40	8.48
BvPUB 38	LOC104887398	01	5029470	5033959	394	45251.58	8.28
BvPUB 39	LOC104887386	01	5016761	5023515	830	93260.11	5.43
BvPUB 40	LOC104887375	01	5010225	5015212	794	90409.55	5.08
BvPUB 41	LOC104887362	01	4993976	4999868	722	81963.68	6.04
BvPUB42	LOC104887351	01	4981053	4987682	792	91252.43	5.28

基因名称	登录号	染色体	起始位置/bp	终止位置/bp	氨基酸/aa	分子量/Da	等电点
BvPUB 1	LOC104904112	09	36506579	36508444	427	47013.04	7.92
BvPUB 2	LOC104903642	09	27445807	27449366	478	53228.16	8.59
BvPUB 3	LOC104903735	09	27293192	27304359	871	96472.89	6.41
BvPUB 4	LOC104900875	08	5871693	5875241	429	45142.51	5.43
BvPUB 5	LOC104900131	07	41602143	41606809	664	72065.89	5.13
BvPUB 6	LOC104900121	07	41505285	41513838	847	96138.82	8.01
BvPUB 7	LOC104899939	07	39609286	39615718	1034	114154.44	5.60
BvPUB 8	LOC104899785	07	37319509	37331173	723	80364.18	7.62
BvPUB 9	LOC104899783	07	37308789	37314093	773	84983.99	6.00
BvPUB 10	LOC104897603	06	55290621	55296404	784	86546.32	6.27
BvPUB 11	LOC104895519	06	7697736	7703627	820	93366.02	5.49
BvPUB 12	LOC104895449	06	6754220	6755873	421	46801.16	8.38
BvPUB 13	LOC104895410	06	6353253	6354503	417	47028.05	5.77
BvPUB 14	LOC104895041	06	2373895	2380036	750	83938.88	6.30
BvPUB 15	LOC104894904	06	692177	695704	318	34288.42	8.33
BvPUB 16	LOC104894729	05	51156937	51163732	754	82630.32	6.79
BvPUB 17	LOC104894345	05	47547553	47551647	245	27885.88	7.08
BvPUB 18	LOC104894251	05	45927032	45928897	682	76147.85	8.04
BvPUB 19	LOC104894207	05	45232472	45234885	559	61449.08	6.83
BvPUB 20	LOC104890423	04	5916107	5919169	470	52925.55	5.93
BvPUB 21	LOC104888531	03	7700131	7707003	910	103089.72	6.33
BvPUB 22	LOC104887725	02	39375337	39381558	606	67985.93	6.46
BvPUB 23	LOC104887722	02	39331036	39338437	836	91677.65	5.56
BvPUB 24	LOC104887625	02	37796618	37809463	430	47165.85	5.02
BvPUB 25	LOC104887545	02	36697852	36699391	331	35475.45	5.04
BvPUB 26	LOC104887488	02	35479251	35484261	837	92419.89	5.55
BvPUB 27	LOC104887006	02	22863210	22866929	513	55583.91	8.50
BvPUB 28	LOC104886790	02	17465918	17472689	835	93586.21	8.03
BvPUB 29	LOC104886722	02	16130627	16138269	784	87302.72	6.74
BvPUB 30	LOC104886603	02	14016706	14022462	751	84225.56	8.73
BvPUB 31	LOC104885156	02	10061218	10062952	365	39501.73	6.33
BvPUB 32	LOC104883224	02	8988596	8991520	511	56152.97	7.34
BvPUB 33	LOC104906776	02	4541998	4545909	370	40244.60	6.26
BvPUB 34	LOC104902107	01	33582472	33590065	351	37730.19	6.18
BvPUB 35	LOC104901828	01	33089330	33092220	446	48554.13	6.55
BvPUB 36	LOC104901082	01	32336771	32347161	812	89120.42	5.30
BvPUB 37	LOC104895459	01	17548412	17550438	394	43776.40	8.48
BvPUB 38	LOC104887398	01	5029470	5033959	394	45251.58	8.28
BvPUB 39	LOC104887386	01	5016761	5023515	830	93260.11	5.43
BvPUB 40	LOC104887375	01	5010225	5015212	794	90409.55	5.08
BvPUB 41	LOC104887362	01	4993976	4999868	722	81963.68	6.04
BvPUB42	LOC104887351	01	4981053	4987682	792	91252.43	5.28

甜菜应答盐胁迫PUB基因的生物信息学分析

PUB Gene in Sugar Beet Response to Salt Stress: Bioinformatics Analysis

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