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作物学报

作物学报 ›› 2018, Vol. 44 ›› Issue (9): 1380-1392.doi: 10.3724/SP.J.1006.2018.01380

• 研究论文 • 上一篇    下一篇

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

王作敏1(),刘瑾1,孙士超2,张新宇2,薛飞2,李艳军2,*(),孙杰2   

  1. 1 石河子大学生命科学学院, 新疆石河子832003
    2 石河子大学农学院 / 新疆生产建设兵团绿洲生态农业重点实验室, 新疆石河子832003
  • 收稿日期:2017-11-01 接受日期:2018-04-11 出版日期:2018-09-10 网络出版日期:2018-05-10
  • 通讯作者: 李艳军
  • 基金资助:
    本研究由国家自然科学基金项目(U1303281);石河子大学动植物育种重点项目(YZZX201601, gxjs2014-yz08)资助

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

Zuo-Min WANG1(),Jin LIU1,Shi-Chao SUN2,Xin-Yu ZHANG2,Fei XUE2,Yan-Jun LI2,*(),Jie SUN2   

  1. 1 College of Life Sciences, Shihezi University, Shihezi 832003, Xinjiang, China
    2 Agricultural College / Key Laboratory of Oasis Eco-agriculture Xinjiang Production and Construction Group, Shihezi University, Shihezi 832003, Xinjiang, China
  • Received:2017-11-01 Accepted:2018-04-11 Published:2018-09-10 Published online:2018-05-10
  • Contact: Yan-Jun LI
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(U1303281);Key Projects of Plant and Animal Breeding of Shihezi University (YZZX201601, gxjs2014-yz08)

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摘要：

植物多药和有毒化合物输出家族(multidrug and toxic compound extrusion, MATE)是一类可转运阳离子染料、氨基葡糖、多种抗生素与药物等次生代谢产物的转运蛋白家族。本研究利用生物信息学手段从陆地棉基因组数据库中鉴定了MATE家族基因, 并从基因的系统进化关系、染色体分布、基因结构和表达模式等方面对该基因家族特征进行了比较分析。共鉴定出91个陆地棉MATE基因, 命名为GhMATE1~GhMATE91。陆地棉MATE蛋白与拟南芥MATE蛋白均可分为A、B、C、D、E、F和G 7个亚家族, 其中84个GhMATE蛋白具有12个典型的跨膜结构域。染色体定位显示, GhMATE家族成员定位在不同的25条染色体上, 共形成5个基因簇。qRT-PCR分析发现, GhMATE家族基因在棉花各组织中均有表达, 但表达模式各不相同, 其中GhMATE13和GhMATE23在棕色棉纤维中的表达量明显高于在白色棉中, 表明它们可能与棕色棉纤维的颜色形成相关。本研究为进一步解析棉花MATE家族基因的功能和作用机制积累了有价值的资料。

关键词: 陆地棉, 彩色棉, MATE家族, 生物信息学, 实时荧光定量PCR

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)

表1

实验中所用的引物"

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

表2

陆地棉MATE蛋白家族成员的鉴定"

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

图1

陆地棉、拟南芥MATE家族蛋白成员进化分析利用MEGA5.1软件及邻位相连法构建进化树, 设置Bootstrap参数为1000次重复, 有7个进化分支被命名为A~G, 7种不同的颜色代表7个亚家族, N0.代表每个分支陆地棉的成员。"

图2

不同亚家族中GhMATE蛋白的多重序列比对"

图3

陆地棉MATE基因的进化树和基因结构比较蓝色表示UTR (上下游序列), 绿色表示编码区, 灰线表示内含子区。"

图4

陆地棉MATE家族基因染色体定位"

图5

MATE家族基因在棉花不同组织中的qRT-PCR分析 R: 根; S: 茎; L: 叶; F: 花; 6~27 DPA:开花后6、9、12、15、18、21、24、27 d纤维。"

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