杜仲ABC转运蛋白基因家族成员鉴定与分析

doi:10.3969/j.issn.1004-1524.2021.09.02

浙江农业学报 ›› 2021, Vol. 33 ›› Issue (9): 1581-1591.DOI: 10.3969/j.issn.1004-1524.2021.09.02

杜仲ABC转运蛋白基因家族成员鉴定与分析

蔡方阳¹(), 赵懿琛¹^,^*(), 李义², 赵德刚¹^,³

1.贵州大学生命科学学院/茶学院/山地植物资源保护与种质创新省部共建教育部重点实验室,贵州贵阳 550025
2.美国康涅狄格大学转基因植物研究中心,斯托斯康涅狄格州 06269
3.贵州省农业科学院农业农村部植物新品种测试贵阳分中心,贵州贵阳 550006

收稿日期:2020-11-09 出版日期:2021-09-25 发布日期:2021-10-09
作者简介:* 赵懿琛,E-mail: yczhao@gzu.edu.cn
蔡方阳(1997—),女,贵州安顺人,硕士研究生,研究方向为植物基因工程。E-mail: caifangyang1997@163.com
通讯作者: 赵懿琛
基金资助:
国家自然科学基金(31660076);贵州省教育厅青年科技人才成长项目(黔教科KY〔2016〕126);贵州省生物学一流学科建设项目(GYNY〔2017〕009)

Identification and analysis of ABC transporters family from Eucommia ulmoides

CAI Fangyang¹(), ZHAO Yichen¹^,^*(), LI Yi², ZHAO Degang¹^,³

1. College of Life Sciences/College of Tea Sciences/Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region of Ministry of Education, Guizhou University, Guiyang 550025, China
2. Transgenic Plant Facility Department of Plant Science, University of Connecticut, Storrs, CT 06269, USA
3. Guiyang Branch Center for Testing of New Plant Varieties of Ministry of Agriculture and Rural Affairs, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China

Received:2020-11-09 Online:2021-09-25 Published:2021-10-09
Contact: ZHAO Yichen

摘要/Abstract

摘要：

ABC转运蛋白(ATP—binding cassette transpoter)是一类庞大而古老的跨膜运输蛋白家族,在生物体内参与多种物质的转运积累、有害物质解毒、气孔调节、植物防御等生理活动。杜仲(Eucommia ulmoides Oliv)作为重要的中药材,其药用成分主要为次生代谢产物,次生代谢物转运与积累过程需要ABC转运蛋白的参与。利用生物信息学手段对杜仲ABC转运蛋白基因家族进行鉴定,并分析该家族蛋白质性质和结构、跨膜结构、亚细胞定位、系统进化关系。研究表明,EuABC家族生物信息学预测有76个成员,含有1~7个保守基序;编码蛋白多为稳定蛋白,主要分布于细胞质膜上,二级结构以α-螺旋和无规卷曲为主要构成元件;进化树分析表明,杜仲ABC转运蛋白家族可分为8个亚家族(A~G;I),每组成员数量分别为3、19、14、1、1、1、29、8。研究结果可为进一步研究杜仲次生代谢物质转运与积累奠定基础,也为其他植物ABC转运蛋白家族的研究提供了参考依据。

关键词: 杜仲, ABC转运蛋白, 基因家族, 跨膜结构, 亚细胞定位, 进化树

Abstract:

ATP-binding cassette (ABC) transpoter is ancient and huge family of transmembrane transport proteins, which are involved in the transport and accumulation of a variety of substances, detoxification of harmful substances, stomatal regulation, plant defense and other physiological activities in organisms. Eucommia ulmoides Oliv, as an important Chinese medicinal material, is mainly composed of secondary metabolites, and the transport and accumulation of secondary metabolites require the participation of ABC transporters. In this study, ABC transporter gene family in E. ulmoides was identified, then its molecular characteristics were analyzed from the aspects of gene identification, protein properties, protein structure, transmembrane structure, subcellular localization and phylogenetic relationship by bioinformatics method. The results predicted by bioinformatics showed that EuABC transporter protein family had 76 members, including 1-7 conserved motifs; most of the encoded proteins were stable proteins, which were mainly distributed on the plasma membrane, and the main component of secondary structure was α-helix and random coil, mainly distributed in the plasma membrane. Analysis of evolutionary tree showed that EuABC transporter family could be divided into eight subfamilies (A-G and I), and the number of members in each group was 3, 19, 14, 1, 1, 1, 29 and 8, respectively. The research results provided a favorable foundation for further study on the transport and accumulation of secondary metabolites in E. ulmoides, and also provided a reference for study of ABC transporter families of other plant.

Key words: Eucommia ulmoides Oliv, ATP-binding cassette transporters, gene family, transmembrane structure, subcellular localization, phylogenetic tree

中图分类号:

蔡方阳, 赵懿琛, 李义, 赵德刚. 杜仲ABC转运蛋白基因家族成员鉴定与分析[J]. 浙江农业学报, 2021, 33(9): 1581-1591.

CAI Fangyang, ZHAO Yichen, LI Yi, ZHAO Degang. Identification and analysis of ABC transporters family from Eucommia ulmoides[J]. Acta Agriculturae Zhejiangensis, 2021, 33(9): 1581-1591.

图/表 7

参考文献 37

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蛋白编号 Protein No.	蛋白ID Protein ID	氨基酸数量 Number of amino acid/aa	分子量 Molecular weight/ku	等电点 Isoelectric point	不稳定系数 Instability index	脂肪系数 Aliphatic index	亲水性平均值 Average of hydropathicity
EuABC1	Gglean009277	605	68.30	7.47	35.56	95.17	-0.207
EuABC2	Gglean010379	229	25.89	9.63	38.64	113.62	-0.103
EuABC3	Gglean022807	262	28.73	5.48	33.72	114.16	0.022
EuABC4	Gglean008919	582	65.86	6.96	34.82	101.00	0.157
EuABC5	Gglean015764	571	62.40	7.62	40.25	93.78	0.135
EuABC6	Gglean009228	644	71.97	9.07	35.95	101.09	0.101
EuABC7	Gglean017382	592	65.92	9.03	47.87	67.82	-0.429
EuABC8	Gglean027789	537	59.82	8.63	33.01	103.58	-0.072
EuABC9	Gglean016985	191	20.90	5.72	26.92	107.28	0.073
EuABC10	Gglean017749	248	27.51	8.25	38.94	90.36	-0.400
EuABC11	Gglean016195	1 406	158.50	9.05	40.90	101.03	-0.019
EuABC12	Gglean025992	871	94.10	8.76	35.98	99.89	0.189
EuABC13	Gglean019731	639	71.64	8.69	43.98	104.60	0.168
EuABC14	Gglean012088	1 424	158.58	6.33	37.34	102.25	0.118
EuABC15	Gglean026080	598	66.40	9.43	50.74	111.32	0.354
EuABC16	Gglean015867	1 040	115.44	8.64	37.85	85.97	-0.162
EuABC17	Gglean022907	303	33.09	9.46	39.50	89.41	-0.194
EuABC18	Gglean021671	1 476	162.58	8.82	40.81	88.56	-0.09
EuABC19	Gglean008060	1 222	134.49	9.49	35.29	95.43	-0.038
EuABC20	Gglean015762	636	69.64	7.61	41.43	94.75	0.105
EuABC21	Gglean006939	962	108.21	9.32	48.82	97.69	-0.042
EuABC22	Gglean029793	221	24.67	9.09	42.55	86.88	-0.465
EuABC23	Gglean004114	660	72.14	9.46	39.41	94.24	0.130
EuABC24	Gglean011164	815	90.84	6.55	41.71	89.95	-0.025
EuABC25	Gglean027773	791	86.14	8.97	39.76	97.43	0.154
EuABC26	Gglean010916	482	54.49	6.94	50.71	79.59	-0.476
EuABC27	Gglean016106	1 156	125.74	8.99	36.68	99.04	0.102
EuABC28	Gglean008223	264	28.65	6.62	29.97	90.83	-0.074
EuABC29	Gglean029210	121	13.32	9.10	36.70	91.74	-0.215
EuABC30	Gglean012281	1 019	111.45	8.04	37.74	100.52	0.127
EuABC31	Gglean022250	740	81.66	9.02	38.11	96.20	0.004
EuABC32	Gglean014318	303	33.17	9.25	44.62	97.62	0.014
EuABC33	Gglean006319	253	27.85	9.52	39.74	87.08	-0.067
EuABC34	Gglean028668	1 020	114.01	7.53	35.58	102.68	0.112
EuABC35	Gglean025928	636	71.37	8.96	36.98	92.08	0.067
EuABC36	Gglean015760	669	73.38	6.21	43.61	89.96	0.060
EuABC37	Gglean003711	1 278	141.77	8.50	35.65	108.30	0.145
EuABC38	Gglean003513	1 307	146.52	6.27	33.94	100.86	0.093
EuABC39	Gglean006940	386	43.50	5.98	41.12	97.72	-0.216
EuABC40	Gglean025990	1 337	143.65	7.90	42.14	94.12	0.058
EuABC41	Gglean005248	1 489	168.03	8.64	37.32	103.08	0.147
EuABC42	Gglean001213	588	66.04	8.94	37.19	103.42	0.203
EuABC43	Gglean030784	667	73.81	9.13	44.60	95.83	0.062
EuABC44	Gglean030795	1 172	127.87	8.79	33.33	98.26	0.067
EuABC45	Gglean019352	602	67.50	6.38	39.08	84.78	-0.406
EuABC46	Gglean015332	1 183	129.41	8.48	39.71	98.10	0.053
EuABC47	Gglean007362	255	29.22	9.09	55.45	72.55	-0.951
EuABC48	Gglean000593	1 249	136.00	8.54	37.57	101.29	0.142
EuABC49	Gglean017080	573	63.20	9.33	45.86	95.08	0.014
EuABC50	Gglean012210	738	81.77	6.66	46.77	85.85	-0.069
EuABC51	Gglean004160	623	68.80	9.27	27.79	95.09	0.022
EuABC52	Gglean001110	2 196	243.19	6.26	40.52	87.40	-0.083
EuABC53	Gglean027992	1 424	158.47	6.06	36.92	102.87	0.125
EuABC54	Gglean012778	1 217	137.09	6.65	35.18	100.16	0.054
EuABC55	Gglean023010	1 340	145.75	8.52	30.30	96.85	0.056
EuABC56	Gglean025245	335	36.37	9.16	39.01	102.45	-0.017
EuABC57	Gglean008160	1 484	165.94	8.38	40.42	105.71	0.184
EuABC58	Gglean027383	1 394	157.13	8.95	31.75	104.31	0.098
EuABC59	Gglean019062	1 409	155.20	6.81	42.98	96.48	0.044
EuABC60	Gglean023655	652	73.63	9.04	46.13	97.90	-0.019
EuABC61	Gglean027129	649	73.21	8.46	51.14	101.74	0.134
EuABC62	Gglean028669	1 477	164.75	7.82	37.55	106.87	0.148
EuABC63	Gglean021945	1 376	157.11	9.12	36.66	97.82	0.092
EuABC64	Gglean011177	870	97.58	8.58	34.06	91.62	-0.001
EuABC65	Gglean012022	1 136	122.57	7.59	35.70	103.77	0.145
EuABC66	Gglean019405	756	83.60	9.23	43.27	94.42	0.093
EuABC67	Gglean024474	189	20.90	4.90	38.51	103.23	0.229
EuABC68	Gglean000632	1 265	143.18	7.52	34.65	96.79	0.034
EuABC69	Gglean003223	323	34.74	7.69	54.85	94.18	-0.085
EuABC70	Gglean029351	812	91.80	8.87	39.14	90.85	-0.077
EuABC71	Gglean012021	380	41.44	7.08	29.45	101.08	0.002
EuABC72	Gglean026837	636	71.11	9.14	45.30	93.96	0.069
EuABC73	Gglean006318	627	69.61	9.20	40.48	98.23	0.129
EuABC74	Gglean026344	1 216	136.79	5.66	33.89	98.18	0.140
EuABC75	Gglean030665	500	54.31	8.84	42.27	95.80	0.057
EuABC76	Gglean004525	824	92.05	9.10	40.70	109.37	0.174

蛋白编号 Protein No.	蛋白ID Protein ID	氨基酸数量 Number of amino acid/aa	分子量 Molecular weight/ku	等电点 Isoelectric point	不稳定系数 Instability index	脂肪系数 Aliphatic index	亲水性平均值 Average of hydropathicity
EuABC1	Gglean009277	605	68.30	7.47	35.56	95.17	-0.207
EuABC2	Gglean010379	229	25.89	9.63	38.64	113.62	-0.103
EuABC3	Gglean022807	262	28.73	5.48	33.72	114.16	0.022
EuABC4	Gglean008919	582	65.86	6.96	34.82	101.00	0.157
EuABC5	Gglean015764	571	62.40	7.62	40.25	93.78	0.135
EuABC6	Gglean009228	644	71.97	9.07	35.95	101.09	0.101
EuABC7	Gglean017382	592	65.92	9.03	47.87	67.82	-0.429
EuABC8	Gglean027789	537	59.82	8.63	33.01	103.58	-0.072
EuABC9	Gglean016985	191	20.90	5.72	26.92	107.28	0.073
EuABC10	Gglean017749	248	27.51	8.25	38.94	90.36	-0.400
EuABC11	Gglean016195	1 406	158.50	9.05	40.90	101.03	-0.019
EuABC12	Gglean025992	871	94.10	8.76	35.98	99.89	0.189
EuABC13	Gglean019731	639	71.64	8.69	43.98	104.60	0.168
EuABC14	Gglean012088	1 424	158.58	6.33	37.34	102.25	0.118
EuABC15	Gglean026080	598	66.40	9.43	50.74	111.32	0.354
EuABC16	Gglean015867	1 040	115.44	8.64	37.85	85.97	-0.162
EuABC17	Gglean022907	303	33.09	9.46	39.50	89.41	-0.194
EuABC18	Gglean021671	1 476	162.58	8.82	40.81	88.56	-0.09
EuABC19	Gglean008060	1 222	134.49	9.49	35.29	95.43	-0.038
EuABC20	Gglean015762	636	69.64	7.61	41.43	94.75	0.105
EuABC21	Gglean006939	962	108.21	9.32	48.82	97.69	-0.042
EuABC22	Gglean029793	221	24.67	9.09	42.55	86.88	-0.465
EuABC23	Gglean004114	660	72.14	9.46	39.41	94.24	0.130
EuABC24	Gglean011164	815	90.84	6.55	41.71	89.95	-0.025
EuABC25	Gglean027773	791	86.14	8.97	39.76	97.43	0.154
EuABC26	Gglean010916	482	54.49	6.94	50.71	79.59	-0.476
EuABC27	Gglean016106	1 156	125.74	8.99	36.68	99.04	0.102
EuABC28	Gglean008223	264	28.65	6.62	29.97	90.83	-0.074
EuABC29	Gglean029210	121	13.32	9.10	36.70	91.74	-0.215
EuABC30	Gglean012281	1 019	111.45	8.04	37.74	100.52	0.127
EuABC31	Gglean022250	740	81.66	9.02	38.11	96.20	0.004
EuABC32	Gglean014318	303	33.17	9.25	44.62	97.62	0.014
EuABC33	Gglean006319	253	27.85	9.52	39.74	87.08	-0.067
EuABC34	Gglean028668	1 020	114.01	7.53	35.58	102.68	0.112
EuABC35	Gglean025928	636	71.37	8.96	36.98	92.08	0.067
EuABC36	Gglean015760	669	73.38	6.21	43.61	89.96	0.060
EuABC37	Gglean003711	1 278	141.77	8.50	35.65	108.30	0.145
EuABC38	Gglean003513	1 307	146.52	6.27	33.94	100.86	0.093
EuABC39	Gglean006940	386	43.50	5.98	41.12	97.72	-0.216
EuABC40	Gglean025990	1 337	143.65	7.90	42.14	94.12	0.058
EuABC41	Gglean005248	1 489	168.03	8.64	37.32	103.08	0.147
EuABC42	Gglean001213	588	66.04	8.94	37.19	103.42	0.203
EuABC43	Gglean030784	667	73.81	9.13	44.60	95.83	0.062
EuABC44	Gglean030795	1 172	127.87	8.79	33.33	98.26	0.067
EuABC45	Gglean019352	602	67.50	6.38	39.08	84.78	-0.406
EuABC46	Gglean015332	1 183	129.41	8.48	39.71	98.10	0.053
EuABC47	Gglean007362	255	29.22	9.09	55.45	72.55	-0.951
EuABC48	Gglean000593	1 249	136.00	8.54	37.57	101.29	0.142
EuABC49	Gglean017080	573	63.20	9.33	45.86	95.08	0.014
EuABC50	Gglean012210	738	81.77	6.66	46.77	85.85	-0.069
EuABC51	Gglean004160	623	68.80	9.27	27.79	95.09	0.022
EuABC52	Gglean001110	2 196	243.19	6.26	40.52	87.40	-0.083
EuABC53	Gglean027992	1 424	158.47	6.06	36.92	102.87	0.125
EuABC54	Gglean012778	1 217	137.09	6.65	35.18	100.16	0.054
EuABC55	Gglean023010	1 340	145.75	8.52	30.30	96.85	0.056
EuABC56	Gglean025245	335	36.37	9.16	39.01	102.45	-0.017
EuABC57	Gglean008160	1 484	165.94	8.38	40.42	105.71	0.184
EuABC58	Gglean027383	1 394	157.13	8.95	31.75	104.31	0.098
EuABC59	Gglean019062	1 409	155.20	6.81	42.98	96.48	0.044
EuABC60	Gglean023655	652	73.63	9.04	46.13	97.90	-0.019
EuABC61	Gglean027129	649	73.21	8.46	51.14	101.74	0.134
EuABC62	Gglean028669	1 477	164.75	7.82	37.55	106.87	0.148
EuABC63	Gglean021945	1 376	157.11	9.12	36.66	97.82	0.092
EuABC64	Gglean011177	870	97.58	8.58	34.06	91.62	-0.001
EuABC65	Gglean012022	1 136	122.57	7.59	35.70	103.77	0.145
EuABC66	Gglean019405	756	83.60	9.23	43.27	94.42	0.093
EuABC67	Gglean024474	189	20.90	4.90	38.51	103.23	0.229
EuABC68	Gglean000632	1 265	143.18	7.52	34.65	96.79	0.034
EuABC69	Gglean003223	323	34.74	7.69	54.85	94.18	-0.085
EuABC70	Gglean029351	812	91.80	8.87	39.14	90.85	-0.077
EuABC71	Gglean012021	380	41.44	7.08	29.45	101.08	0.002
EuABC72	Gglean026837	636	71.11	9.14	45.30	93.96	0.069
EuABC73	Gglean006318	627	69.61	9.20	40.48	98.23	0.129
EuABC74	Gglean026344	1 216	136.79	5.66	33.89	98.18	0.140
EuABC75	Gglean030665	500	54.31	8.84	42.27	95.80	0.057
EuABC76	Gglean004525	824	92.05	9.10	40.70	109.37	0.174

蛋白名称 Protein name	α螺旋比例 Alpha helix/%	延伸链比例 Extended strand/%	β折叠比例 β-sheet	无规卷曲比例 Random coil/%	亚家族 Subfamily
EuABC24	38.40	18.77	6.01	36.81	A
EuABC52	41.94	14.34	5.42	38.30	A
EuABC64	41.72	18.16	4.48	35.63	A
EuABC25	50.95	14.92	5.31	28.82	B
EuABC51	54.57	14.61	4.82	26.00	B
EuABC67	33.33	26.98	7.94	31.75	B
EuABC8	58.78	15.27	4.96	20.99	C
EuABC11	54.91	14.65	5.12	25.32	C
EuABC29	30.58	22.31	10.74	36.36	C
EuABC26	36.72	17.63	3.94	41.70	D
EuABC1	40.99	17.36	7.93	33.72	E
EuABC45	50.50	15.78	6.98	26.74	F
EuABC6	47.05	14.91	4.81	33.23	G
EuABC10	44.35	14.92	4.44	36.29	G
EuABC17	33.00	20.79	7.92	38.28	G
EuABC2	46.29	12.23	6.11	35.37	I
EuABC7	35.64	14.36	5.57	44.43	I
EuABC21	57.48	10.91	3.85	27.75	I

蛋白名称 Protein name	α螺旋比例 Alpha helix/%	延伸链比例 Extended strand/%	β折叠比例 β-sheet	无规卷曲比例 Random coil/%	亚家族 Subfamily
EuABC24	38.40	18.77	6.01	36.81	A
EuABC52	41.94	14.34	5.42	38.30	A
EuABC64	41.72	18.16	4.48	35.63	A
EuABC25	50.95	14.92	5.31	28.82	B
EuABC51	54.57	14.61	4.82	26.00	B
EuABC67	33.33	26.98	7.94	31.75	B
EuABC8	58.78	15.27	4.96	20.99	C
EuABC11	54.91	14.65	5.12	25.32	C
EuABC29	30.58	22.31	10.74	36.36	C
EuABC26	36.72	17.63	3.94	41.70	D
EuABC1	40.99	17.36	7.93	33.72	E
EuABC45	50.50	15.78	6.98	26.74	F
EuABC6	47.05	14.91	4.81	33.23	G
EuABC10	44.35	14.92	4.44	36.29	G
EuABC17	33.00	20.79	7.92	38.28	G
EuABC2	46.29	12.23	6.11	35.37	I
EuABC7	35.64	14.36	5.57	44.43	I
EuABC21	57.48	10.91	3.85	27.75	I

蛋白名称 Protein name	亚细胞定位 Subcellular localization	跨膜数量 Transmemb- rane number	亚家族 Sub- family
EuABC24	细胞质膜Plasma membrane	4	A
EuABC52	细胞质膜Plasma membrane	12	A
EuABC64	细胞质膜Plasma membrane	7	A
EuABC25	细胞质膜Plasma membrane	7	B
EuABC51	叶绿体膜Chloroplast membrane	5	B
EuABC67	高尔基体膜Golgi membrane	1	B
EuABC8	叶绿体膜Chloroplast membrane	0	C
EuABC11	细胞质膜Plasma membrane	8	C
EuABC29	叶绿体膜Chloroplast membrane	0	C
EuABC26	核膜Nucleus membrane	0	D
EuABC1	细胞质Cytoplasm	0	E
EuABC45	核膜Nucleus membrane	0	F
EuABC6	细胞质膜Plasma membrane	6	G
EuABC10	核膜Nucleus membrane	0	G
EuABC17	细胞质Cytoplasm	0	G
EuABC2	叶绿体膜Chloroplast membrane	0	I
EuABC7	细胞质膜Plasma membrane	2	I
EuABC21	叶绿体膜Chloroplast membrane	2	I

杜仲ABC转运蛋白基因家族成员鉴定与分析

Identification and analysis of ABC transporters family from Eucommia ulmoides

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