彩色棉多药和有毒化合物输出蛋白MATE家族基因的鉴定及表达分析

doi:10.3724/SP.J.1006.2018.01380

Abstract

Abstract:

MATE (multidrug and toxic compound extrusion) is a transport proteins family that can transport toxins, glucosamine, antibiotics and drugs. In this study, the MATE family genes were identified from genome database of Gossypium hirsutum L. through bioinformatics analysis and phylogenetic relationship, chromosome distribution, gene structure and expression patterns of this family were comprehensively compared. A total of 91 GhMATE genes were found in the cotton genome and named as GhMATE1-GhMATE91. MATE genes of cotton were classified into seven groups namely A, B, C, D, E, F, and G with a classification is consistent with Arabidopsis. Multiple sequence alignment and conserved domain prediction indicated that 84 of the 91 GhMATE proteins contained 12 typical transmembrane domains. The chromosome mapping analysis showed that GhMATE genes were distributed with different densities over 25 chromosomes and clustered into five clusters. The qPCR showed that the GhMATE genes expressed in all tissues of cotton with different expression patterns. GhMATE13 and GhMATE23 were preferentially expressed in brown cotton fibers than in white cotton fibre, suggesting that they may play an important role in brown color formation of cotton fibre. This study provides valuable informations for dissecting functions and molecular mechanisms of MATEs in cotton.

Key words: Gossypium hirsutum L., naturally colored cotton, MATE family, bioinformatics, qRT-PCR (quantitative real-time PCR)

Zuo-Min WANG,Jin LIU,Shi-Chao SUN,Xin-Yu ZHANG,Fei XUE,Yan-Jun LI,Jie SUN. Identification and Expression Analysis of Multidrug and Toxic Compound Extrusion Protein Family Genes in Colored Cotton[J].Acta Agronomica Sinica, 2018, 44(9): 1380-1392.

Figures/Tables 7

Table 1

Table 2

Identification of MATE protein family members in Gossypium hirsutum L."

基因 Gene	序列号 Sequence number	染色体 Chr.	编码序列 Coding sequence (bp)	蛋白残基数 Protein length (aa)	分子量 Molecular weight (kD)	等电点 pI	亚细胞定位预测 Subcellular location prediction
GhMATE1	GhA01G0453	1	1455	484	48.1	7.72	细胞膜Cell membrane
GhMATE2	GhA01G0959	1	1455	484	49.3	8.62	细胞膜Cell membrane
GhMATE3	GhA03G0955	3	1383	460	46.4	5.21	叶绿体Chloroplast
GhMATE4	GhA03G1185	3	1554	517	48.1	9.05	细胞质Cytoplasm
GhMATE5	GhA03G1186	3	1545	514	48.2	6.48	细胞膜Cell membrane
GhMATE6	GhA03G1321	3	1470	489	47.1	7.58	液泡膜Tonoplast
GhMATE7	GhA03G1323	3	1467	488	47.2	7.58	细胞膜Cell membrane
GhMATE8	GhA04G0255	4	1275	424	45.3	8.62	细胞膜Cell membrane
GhMATE9	GhA04G0282	4	1416	471	47.0	7.96	细胞膜Cell membrane
GhMATE10	GhA05G1449	5	1575	524	48.0	5.85	细胞质Cytoplasm
GhMATE11	GhA05G1901	5	1476	491	47.5	8.36	叶绿体Chloroplast
GhMATE12	GhA06G0259	6	1479	492	48.5	8.36	细胞质Cytoplasm
GhMATE13	GhA09G0073	9	1470	489	48.1	8.86	液泡膜Tonoplast
GhMATE14	GhA08G2343	8	1497	498	53.7	5.60	细胞膜Cell membrane
GhMATE15	GhA09G0412	9	1521	506	49.9	5.49	细胞膜Cell membrane
GhMATE16	GhA10G0781	10	1458	485	49.3	5.55	细胞膜Cell membrane
GhMATE17	GhA11G0039	11	1404	467	45.6	8.52	细胞膜Cell membrane
GhMATE18	GhA11G0040	11	1533	510	48.5	8.65	细胞膜Cell membrane
GhMATE19	GhA11G1853	11	1473	490	49.5	8.34	细胞膜Cell membrane
GhMATE20	GhA11G2034	11	1452	483	48.7	8.58	细胞膜Cell membrane
GhMATE21	GhA11G3233	11	1473	490	48.2	8.22	液泡膜Tonoplast
GhMATE22	GhA11G3238	11	1419	472	48.8	8.43	细胞膜Cell membrane
GhMATE23	GhA12G0812	12	1503	500	53.8	6.99	液泡膜Tonoplast
GhMATE24	GhA12G0971	12	1368	455	36.6	6.21	细胞膜Cell membrane
GhMATE25	GhA12G2733	12	1431	476	42.8	8.28	细胞膜Cell membrane
GhMATE26	GhA13G0797	13	1518	505	48.7	8.17	细胞膜Cell membrane
GhMATE27	GhA13G1248	13	1455	484	48.0	6.18	细胞膜Cell membrane
GhMATE28	GhD01G0136	1	1586	528	49.5	5.08	细胞膜Cell membrane
GhMATE29	GhD01G1006	1	1452	483	49.5	8.89	细胞膜Cell membrane
GhMATE30	GhD02G1336	2	1518	505	50.8	5.59	叶绿体Chloroplast
GhMATE31	GhD02G1620	2	1563	520	48.1	9.00	细胞质Cytoplasm
GhMATE32	GhD02G1621	2	1545	514	48.4	7.66	细胞膜Cell membrane
GhMATE33	GhD02G1761	2	1449	482	47.2	8.38	细胞膜Cell membrane
GhMATE34	GhD02G1762	2	1470	489	47.0	7.96	细胞膜Cell membrane
GhMATE35	GhD05G1622	5	1557	518	47.4	5.98	细胞质Cytoplasm
GhMATE36	GhD05G2137	5	1476	491	47.8	8.34	叶绿体Chloroplast
GhMATE37	GhD05G3073	5	1488	495	45.9	7.05	细胞膜Cell membrane
GhMATE38	GhD05G3385	5	1416	471	44.2	8.28	细胞膜Cell membrane
GhMATE39	GhD06G0281	6	1479	492	52.6	5.17	细胞膜Cell membrane
基因 Gene	序列号 Sequence number	染色体 Chr.	编码序列 Coding sequence (bp)	蛋白残基数 Protein length (aa)	分子量 Molecular weight (kD)	等电点 pI	亚细胞定位预测 Subcellular location prediction
GhMATE40	GhD08G2334	8	1476	491	43.8	8.39	细胞膜Cell membrane
GhMATE41	GhD09G0426	9	1476	491	49.9	5.75	细胞膜Cell membrane
GhMATE42	GhD10G0979	10	1479	492	48.5	8.82	细胞膜Cell membrane
GhMATE43	GhD11G0038	11	1533	510	48.5	8.65	细胞膜Cell membrane
GhMATE44	GhD11G2135	11	1473	490	49.6	8.68	细胞质Cytoplasm
GhMATE45	GhD11G2314	11	1452	483	48.7	8.57	细胞膜Cell membrane
GhMATE46	GhD11G2334	11	1464	487	43.8	8.39	液泡膜Tonoplast
GhMATE47	GhD12G0830	12	1521	506	53.9	6.99	细胞膜Cell membrane
GhMATE48	GhD12G1083	12	1530	509	48.6	5.47	细胞膜Cell membrane
GhMATE49	GhD13G1038	13	1377	548	41.9	7.61	细胞膜Cell membrane
GhMATE50	GhD13G2211	13	1434	477	47.2	9.22	细胞膜Cell membrane
GhMATE51	GhD07G0751	7	1314	434	47.8	7.49	细胞膜Cell membrane
GhMATE52	GhD01G0461	1	1455	484	53.0	5.83	细胞膜Cell membrane
GhMATE53	GhA01G0098	1	1125	374	40.6	8.94	细胞膜Cell membrane
GhMATE54	GhA12G0513	12	1416	471	51.8	7.83	液泡膜Tonoplast
GhMATE55	GhA07G0673	7	1314	437	47.4	5.33	细胞膜Cell membrane
GhMATE56	GhA05G2769	5	1452	483	52.7	6.59	细胞膜Cell membrane
GhMATE57	GhD03G1484	3	1563	520	56.6	8.46	液泡膜Tonoplast
GhMATE58	GhA08G1613	8	1608	535	58.3	8.08	细胞膜Cell membrane
GhMATE59	GhA12G2353	12	1644	547	59.7	6.69	细胞膜Cell membrane
GhMATE60	GhA13G1249	13	1293	430	46.8	9.08	细胞膜Cell membrane
GhMATE61	GhD07G0089	7	1512	503	55.1	6.59	细胞膜Cell membrane
GhMATE62	GhA06G0589	6	1575	524	56.8	8.62	细胞膜Cell membrane
GhMATE63	GhD09G1100	9	1506	507	54.0	5.89	细胞质Cytoplasm
GhMATE64	GhA10G2322	10	1401	466	50.7	8.19	细胞膜Cell membrane
GhMATE65	GhD09G2422	9	1311	436	47.4	7.05	细胞膜Cell membrane
GhMATE66	GhA03G0114	3	1500	499	54.3	9.02	细胞膜Cell membrane
GhMATE67	GhD02G0545	2	1482	493	53.2	7.94	叶绿体Chloroplast
GhMATE68	GhA10G1472	10	1398	465	50.1	7.48	细胞膜Cell membrane
GhMATE69	GhA03G2015	3	1563	520	56.5	8.21	细胞膜Cell membrane
GhMATE70	GhA03G1320	3	1341	446	49.1	8.04	细胞膜Cell membrane
GhMATE71	GhD05G2075	5	1662	553	60.3	7.47	细胞质Cytoplasm
GhMATE72	GhD11G0087	11	1602	533	58.1	8.54	细胞膜Cell membrane
GhMATE73	GhA09G0385	9	1581	526	57.8	8.70	细胞膜Cell membrane
GhMATE74	GhA08G2165	8	1530	509	55.5	8.36	细胞膜Cell membrane
GhMATE75	GhD06G0667	6	1575	524	57.0	8.58	细胞膜Cell membrane
GhMATE76	GhA09G1094	9	1509	502	54.1	5.67	细胞膜Cell membrane
GhMATE77	GhD05G0259	5	1617	538	58.4	7.51	细胞膜Cell membrane
GhMATE78	GhD10G1146	10	1404	466	50.7	8.19	液泡膜Tonoplast
GhMATE79	GhA02G0487	2	1524	507	54.8	7.48	细胞膜Cell membrane
GhMATE80	GhA05G2384	5	1386	467	50.3	6.51	叶绿体Chloroplast
GhMATE81	GhD12G2539	12	1119	392	42.6	5.48	细胞膜Cell membrane
GhMATE82	GhD06G2314	6	1611	536	58.4	6.46	细胞膜Cell membrane
GhMATE83	GhD12G2490	12	1632	543	59.2	8.90	细胞膜Cell membrane
基因 Gene	序列号 Sequence number	染色体 Chr.	编码序列 Coding sequence (bp)	蛋白残基数 Protein length (aa)	分子量 Molecular weight (kD)	等电点 pI	亚细胞定位预测 Subcellular location prediction
GhMATE84	GhA11G0083	11	1602	533	58.1	8.34	细胞膜Cell membrane
GhMATE85	GhD09G0403	9	1611	536	58.8	8.15	细胞膜Cell membrane
GhMATE86	GhA09G2299	9	1404	467	50.7	7.09	细胞质Cytoplasm
GhMATE87	GhA05G0185	5	1614	537	58.3	7.50	细胞膜Cell membrane
GhMATE88	GhD03G1526	3	1500	499	54.0	8.85	叶绿体Chloroplast
GhMATE89	GhD11G3461	11	1569	522	56.1	5.02	细胞膜Cell membrane
GhMATE90	GhA03G0113	3	1500	424	45.7	8.40	细胞质Cytoplasm
GhMATE91	GhD10G1714	10	1530	509	54.9	6.98	细胞膜Cell membrane

Table 2

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Fig. 5

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基因名称 Gene name	上游引物序列 Forward primer sequence (5′-3′)	下游引物序列 Reverse primer sequence (5′-3′)
GhA11G0040	GCTGCCACGGTTTGGATGAT	GCCTCTTGCTCCCAGTTTGT
GhA08G2343	ATTGCTGGCTTGCTCCATACTT	CCACTTGTTAACTCGCGATTGA
GhA13G0797	TTTATCTCCGTTGTTGGCTTCT	CCTGTACCGCGACAGTGAGC
GhD05G1622	ATTGTATTTGCTCTGCGAGATGTTA	TTGCACCGAGGTCGTACTTGA
GhA12G0971	CATCCAAGGGCAGCCAAATA	CCTCCTCCCACAGCAACACC
GhA03G0955	GGCGGCAATAATAATAATGGT	GGATAAGGGTTAATGCTAGAAGC
GhA03G1186	GGTGTTATAGTATCCCTAATCCTCATC	TTCTTTATCCTTTCCTCCGCAAT
GhA05G1901	CGGTGCAGGAAATGCGAAAG	AGCCCAGATACCAGTGATACCAAA
GhA06G0259	GTTAGGCGTCACCATTCTACTCAA	GTTCCTCCAAAGATCATCCCAC
GhA10G0781	GGCAATCCTACGTGGCTTACAT	TTTGCTTTCTCAGCCTCCTTCT
GhD02G1620	TACGATAGCCCTTATTCTGATCATC	TCTCTTTAGTGTCAACGTCACCTCC
GhD11G2314	GAGGAAATGCAAAGGCAGTGAA	CAATAACCATCGGTTGAGACGT
GhD11G2334	AAGTAGCAAACTCCGTGGCAGAC	TTCCCAATCAGTCCTTGAGGTAAT
GhA03G1321	ATAGCAATGAGAAGGAAGTGGTGGAT	TTGTAACAATGGCGAGCAGAAT
GhD01G1006	TTACTTCCCTTACTTCTTCACTACCA	CCCATTTCTTTATACGCCTTTC
GhD13G2211	AACCGTGATAGGCACCGTCAT	TCCAAAGTCCCTTCCCTCCA
GhA09G0412	TGCTATGAGCGTTCGGGTTTC	CATGCGTTCCGTTGTTTGTTC
GhA04G0282	AATCGTTTCGTTTGGTCTTCGC	ACACCTGCCATCCGCTTCCTCT
GhA12G0812 UBQ7	AGCAGTTTCAGACTTGACTCCAC GAAGGCATTCCACCTGACCAAC	GACTCCAATAATCATACCCCACC CTTGACCTTCTTCTTCTTGTGCTTG

Identification and Expression Analysis of Multidrug and Toxic Compound Extrusion Protein Family Genes in Colored Cotton

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[3]	ZHAO Wen-Qing, XU Wen-Zheng, YANG Liu-Yan, LIU Yu, ZHOU Zhi-Guo, WANG You-Hua. Different response of cotton leaves to heat stress is closely related to the night starch degradation [J]. Acta Agronomica Sinica, 2021, 47(9): 1680-1689.
[4]	HUANG Ning, HUI Qian-Long, FANG Zhen-Ming, LI Shan-Shan, LING Hui, QUE You-Xiong, YUAN Zhao-Nian. Identification, localization and expression analysis of beta-carotene isomerase gene family in sugarcane [J]. Acta Agronomica Sinica, 2021, 47(5): 882-893.
[5]	XU Nai-Yin, ZHAO Su-Qin, ZHANG Fang, FU Xiao-Qiong, YANG Xiao-Ni, QIAO Yin-Tao, SUN Shi-Xian. Retrospective evaluation of cotton varieties nationally registered for the Northwest Inland cotton growing regions based on GYT biplot analysis [J]. Acta Agronomica Sinica, 2021, 47(4): 660-671.
[6]	LI Peng, LIU Che, SONG Hao, YAO Pan-Pan, SU Pei-Lin, WEI Yao-Wei, YANG Yong-Xia, LI Qing-Chang. Identification and analysis of non-specific lipid transfer protein family in tobacco [J]. Acta Agronomica Sinica, 2021, 47(11): 2184-2198.
[7]	HUANG Xiao-Fang,BI Chu-Yun,SHI Yuan-Yuan,HU Yun-Zhuo,ZHOU Li-Xiang,LIANG Cai-Xiao,HUANG Bi-Fang,XU Ming,LIN Shi-Qiang,CHEN Xuan-Yang. Discovery and analysis of NBS-LRR gene family in sweet potato genome [J]. Acta Agronomica Sinica, 2020, 46(8): 1195-1207.
[8]	ZHENG Qing-Lei,YU Chen-Jing,YAO Kun-Cun,HUANG Ning,QUE You-Xiong,LING Hui,XU Li-Ping. Cloning and expression analysis of sugarcane Fe/S precursor protein gene ScPetC [J]. Acta Agronomica Sinica, 2020, 46(6): 844-857.
[9]	YAO Jun-Yue,HUA Ying-Peng,ZHOU Ting,WANG Tao,SONG Hai-Xing,GUAN Chun-Yun,ZHANG Zhen-Hua. Identification and function analysis of AVP1, VHA-a2, and VHA-a3 genes in Brassica napus L. [J]. Acta Agronomica Sinica, 2019, 45(8): 1146-1157.
[10]	SUN Ting-Ting,WANG Wen-Ju,LOU Wen-Yue,LIU Feng,ZHANG Xu,WANG Ling,CHEN Yu-Feng,QUE You-Xiong,XU Li-Ping,LI Da-Mei,SU Ya-Chun. Cloning and expression analysis of sugarcane lipoxygenase gene ScLOX1 [J]. Acta Agronomica Sinica, 2019, 45(7): 1002-1016.
[11]	Gui-Hong LIANG,Ying-Peng HUA,Ting ZHOU,Qiong LIAO,Hai-Xing SONG,Zhen-Hua ZHANG. Bioinformatics analysis and response to nitrate-cadmium stress of NRT1.5 and NRT1.8 family genes in Brassica napus [J]. Acta Agronomica Sinica, 2019, 45(3): 365-380.
[12]	Ling WANG,Feng LIU,Ming-Jian DAI,Ting-Ting SUN,Wei-Hua SU,Chun-Feng WANG,Xu ZHANG,Hua-Ying MAO,Ya-Chun SU,You-Xiong QUE. Cloning and Expression Characteristic Analysis of ScWRKY4 Gene in Sugarcane [J]. Acta Agronomica Sinica, 2018, 44(9): 1367-1379.
[13]	Kun GAO,Ying-Peng HUA,Hai-Xing SONG,Chun-Yun GUAN,Zhen-Hua ZHANG,Ting ZHOU. Identification and Bioinformatics Analysis of the PIN Family Gene in Brassica napus [J]. Acta Agronomica Sinica, 2018, 44(9): 1334-1346.
[14]	Huan TAN,Yu-Hui LIU,Li-Xia LI,Li WANG,Yuan-Ming LI,Jun-Lian ZHANG. Cloning and Functional Analysis of R2R3 MYB Genes Involved in Anthocyanin Biosynthesis in Potato Tuber [J]. Acta Agronomica Sinica, 2018, 44(7): 1021-1031.
[15]	Li-Xia QIN, Jing LI, Huan-Yang ZHANG, Sheng LI, Meng-Jie ZHU, Gai-Li JIAO, Shen-Jie WU. Cloning and Expression Analysis of Galactosyltransferase Gene GhGalT1 Promoter in Cotton [J]. Acta Agronomica Sinica, 2018, 44(02): 218-226.