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作物学报 ›› 2019, Vol. 45 ›› Issue (3): 365-380.doi: 10.3724/SP.J.1006.2019.84099

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

甘蓝型油菜NRT1.5和NRT1.8家族基因的生物信息学分析及其对氮-镉胁迫的响应

梁桂红1,2,华营鹏1,2,周婷1,2,廖琼1,2,宋海星1,2,张振华1,2,*()   

  1. 1湖南农业大学资源环境学院, 湖南长沙 410128
    2南方粮油作物协同创新中心, 湖南长沙 410128
  • 收稿日期:2018-07-18 接受日期:2018-10-08 出版日期:2019-03-12 网络出版日期:2018-11-02
  • 通讯作者: 张振华
  • 作者简介:E-mail: ghliang1119@163.com
  • 基金资助:
    本研究由国家重点研发计划项目(2017YFD0200100);本研究由国家重点研发计划项目(2017YFD0200103);国家现代农业(油菜)产业技术体系建设专项资助

Bioinformatics analysis and response to nitrate-cadmium stress of NRT1.5 and NRT1.8 family genes in Brassica napus

Gui-Hong LIANG1,2,Ying-Peng HUA1,2,Ting ZHOU1,2,Qiong LIAO1,2,Hai-Xing SONG1,2,Zhen-Hua ZHANG1,2,*()   

  1. 1 College of Resource and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
    2 Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, Hunan, China
  • Received:2018-07-18 Accepted:2018-10-08 Published:2019-03-12 Published online:2018-11-02
  • Contact: Zhen-Hua ZHANG
  • Supported by:
    This study was supported by the National Key R&D Program of China(2017YFD0200100);This study was supported by the National Key R&D Program of China(2017YFD0200103);the China Agriculture Research System

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摘要：

植物对硝酸盐的吸收和转运需要硝酸盐转运体(nitrate transporters, NRTs)的协助。在拟南芥中, 硝酸盐的长途转运及其在根部和地上部的分配, 主要受NRT1家族的两个成员NRT1.5和NRT1.8的协同调控, 且两者的表达均受到硝酸盐的强烈诱导。本文以AtNRT1.5和AtNRT1.8基因序列为基础序列, 采用生物信息学方法鉴定了白菜、甘蓝和甘蓝型油菜中NRT1.5和NRT1.8同源基因, 并对基因结构和分子特性、基因拷贝数变异、基因染色体分布、系统进化树、蛋白保守序列比对和跨膜结构域、基因响应低氮和镉胁迫的转录组测序以及基因共表达网络进行了分析。结果表明, 白菜、甘蓝及甘蓝型油菜中NRT1.5和NRT1.8蛋白均含有保守的跨膜结构域和保守基序(F-Y-L-A-L-N-L- G-S-L), 属于MFS (major facilitator superfamily)超家族的小肽转运体PTR (peptide transporter)家族。转录组测序结果表明, 甘蓝型油菜低氮处理72 h, 根部NRT1.5基因的表达丰度上调而抑制NRT1.8的表达; 镉处理条件下, 乙烯/茉莉酸-硝酸盐转运体介导的信号途径能够促进NRT1.8表达上调而抑制NRT1.5的表达, 从而使更多的硝酸盐从地上部运输到根部, 提高植物抗镉胁迫的能力。本研究为进一步了解甘蓝型油菜NRT1.5和NRT1.8家族基因的生物学功能及其对氮-镉胁迫的响应奠定基础, 同时为NRT1.5和NRT1.8家族基因在其他物种中的生物信息学研究提供参考。

关键词: 甘蓝型油菜, 生物信息学, NRT1.5, NRT1.8, 硝酸盐, 镉

Abstract:

The absorption and transportation of nitrate in plants require the assistance of nitrate transporters (NRTs). The expression of two members of the NRT1 family, including NRT1.5 and NRT1.8 genes was strongly induced by nitrate, and regulated the long-distance transport and distribution of nitrate between roots and shoots in Arabidopsis. NRT1.5 and NRT1.8 homologous genes in B. rapa, B. oleracea, and B. napus were identified by bioinformatics with the basic sequences of AtNRT1.5 and AtNRT1.8 and analyzed in gene structures and proteins molecular characterization, gene copy number variations, chromosome locations, evolutionary relationship tree, proteins conservative sequence alignment and the transmembrane domains. NRT1.5 and NRT1.8 responsive to the low concentration nitrate and cadmium stress were also determined by transcriptome analysis and co-expression network analysis, showing that NRT1.5 and NRT1.8 proteins belong to major facilitator superfamily (MFS) and peptide transporter (PTR) with the conservative transmembrane domains and motifs (F-Y-L-A-L-N-L-G-S-L) in B. rapa, B. oleracea, and B. napus. High-throughput transcriptome analysis showed that the expression of NRT1.5 gene was up-regulated and the NRT1.8 was down-regulated by low concentration nitrate treatment for 72 h in roots, which caused more nitrate transferred from roots to shoots. On the contrary, the ethylene/jasmonic acid-NRT signaling module could promote NRT1.8 up-regulation and inhibit the expression of NRT1.5 by cadmium treatment. So that more nitrate transported from shoots to roots and improved the ability of plants to resist cadmium stress. This study is valuable for the research of biological functions of NRT1.5 and NRT1.8 family genes in B. napus and the responses to nitrate-cadmium stress. Our results also provide references for the bioinformatic study of NRT1.5 and NRT1.8 family genes in other plant species.

Key words: Brassica napus, bioinformatics, NRT1.5, NRT1.8, nitrate, cadmium

表1

白菜、甘蓝和甘蓝型油菜NRT1.5和NRT1.8基因的分子特性"

基因名
Gene name		 基因编号
Gene ID		 分区
Block		 亚类
Subgenome		 物理位置
Physical position		 编码区长度
CDS (bp)		 外显子/内含子Exon/intron
NRT1.5
BraA5.NRT1.5 Bra010165 B MF2 15109908-15113350 1815 5/4
BraA9.NRT1.5 Bra023267 B LF 20166714-20170510 1833 5/4
BolC5.NRT1.5a Bol020904 B MF2 13227461-13230901 1812 5/4
BolC5.NRT1.5b Bol022226 B LF 10183303-10186752 1236 5/4
BnaA5.NRT1.5 BnaA05g35790D B MF2 1269482-1274007 1845 6/5
BnaA9.NRT1.5 BnaA09g24330D B LF 17085147-17089456 1863 6/5
BnaC5.NRT1.5a BnaC05g28620D B MF2 26898087-26903213 1845 6/5
BnaC5.NRT1.5b BnaC05g24580D B LF 19037761-19041900 1860 6/5
NRT1.8
BraA1.NRT1.8 Bra013547 U LF 6243271-6245298 1752 4/3
BraA3.NRT1.8 Bra038763 U MF1 24230588-24232594 1752 4/3
BolC1.NRT1.8 Bol028440 U LF 8086050-8088075 1752 4/3
BolC6.NRT1.8 Bol024295 U MF1 42081659-42082729 897 3/2
BnaA1.NRT1.8 BnaA01g11510D U LF 5715790-5718126 1752 4/3
BnaA3.NRT1.8 BnaA03g44820D U MF1 22774854-22776862 1752 4/3
BnaC7.NRT1.8 BnaC07g36810D U MF1 38737319-38739325 1752 4/3
BnaCn.NRT1.8 BnaCnng78690D U LF 80520183-80521816 1167 3/2

表2

白菜、甘蓝和甘蓝型油菜NRT1.5和NRT1.8蛋白的分子特性"

基因名
Gene name		 氨基酸数Amino acids 主要氨基酸 Major amino acids 碱性氨基酸Arg+Lys 酸性氨基酸Asp+Glu 分子量MW(kD) 等电点pI 不稳定系数Instability index 亲水性GRAVY 脂肪指数Aliphatic index
NRT1.5
BraA5.NRT1.5 604 Leu, Ser 58 63 67.64 5.93 34.13 0.096 88.79
BraA9.NRT1.5 610 Leu, Ser 59 62 68.17 6.29 31.20 0.073 89.18
BolC5.NRT1.5a 603 Leu, Ser 58 63 67.45 5.93 33.33 0.094 88.77
BolC5.NRT1.5b 411 Leu, Ser 38 44 45.80 5.63 27.54 -0.006 86.13
BnaA5.NRT1.5 614 Leu, Ser 59 64 68.72 5.93 34.82 0.094 88.62
BnaA9.NRT1.5 620 Leu, Ser 60 64 69.41 6.14 32.08 0.082 89.47
BnaC5.NRT1.5a 614 Leu, Ser 59 64 68.71 5.93 34.68 0.094 88.45
BnaC5.NRT1.5b 619 Leu, Ser 59 62 69.35 6.35 33.07 0.094 89.77
NRT1.8
BraA1.NRT1.8 583 Leu, Ser 48 51 64.72 6.22 27.23 0.209 91.66
BraA3.NRT1.8 583 Leu, Ala 51 51 64.55 7.06 29.40 0.218 94.70
BolC1.NRT1.8 583 Leu, Ser 48 52 64.67 6.05 28.13 0.211 92.16
BolC6.NRT1.8 298 Leu, Ala 26 24 32.84 8.18 18.64 0.088 88.36
BnaA1.NRT1.8 583 Leu, Ser 48 51 64.60 6.22 27.84 0.211 91.17
BnaA3.NRT1.8 583 Leu, Ala 52 51 64.60 7.52 27.69 0.208 94.70
BnaC7.NRT1.8 583 Leu, Ser 53 50 64.67 8.18 27.88 0.207 94.85
BnaCn.NRT1.8 388 Leu, Ser 37 38 43.81 6.60 32.07 0.110 87.96

图1

白菜、甘蓝、甘蓝型油菜及拟南芥NRT1.5和NRT1.8基因的拷贝数变异 柱状图顶部数值为该物种拷贝的基因数目。"

附图1

NRT1.5和NRT1.8基因在白菜、甘蓝、甘蓝型油菜及拟南芥中的染色体定位 图a表示NRT1.5基因在拟南芥、甘蓝型油菜、甘蓝及白菜中的染色体定位;图b表示NRT1.8基因在拟南芥、甘蓝型油菜、甘蓝及白菜中的染色体定位。"

图2

白菜、甘蓝、甘蓝型油菜及拟南芥NRT1.5和NRT1.8的基因结构特征 图a表示拟南芥、白菜、甘蓝及甘蓝型油菜NRT1.5的基因结构特征; 图b表示拟南芥、白菜、甘蓝及甘蓝型油菜NRT1.8的基因结构特征。其中, 黄色部分代表CDS序列, 蓝色部分代表上游基因和下游基因, 黑色细线代表基因的内含子。"

图3

不同物种NRT1.5和NRT1.8蛋白的系统发育关系 图a表示在双子叶和单子叶植物中NRT1.5蛋白的系统发育关系; 图b表示在双子叶和单子叶植物中NRT1.8蛋白的系统发育关系。其中, 绿色部分代表双子叶植物, 包括拟南芥、白菜、甘蓝、甘蓝型油菜和胡杨, 红色部分代表单子叶植物, 包括高粱、水稻、小米、玉米和二穗短柄草。"

图4

白菜、甘蓝及甘蓝型油菜中NRT1.5和NRT1.8蛋白的同义突变频率(Ks)和非同义突变频率(Ka) 图a, b, c分别表示白菜、甘蓝及甘蓝型油菜NRT1.5蛋白的同义突变频率和非同义突变频率; 图d, e, f分别表示白菜、甘蓝及甘蓝型油菜NRT1.8蛋白的同义突变频率和非同义突变频率。"

图5

白菜、甘蓝、甘蓝型油菜及拟南芥NRT1.5和NRT1.8蛋白的保守序列比对 图a表示拟南芥、白菜、甘蓝及甘蓝型油菜NRT1.5蛋白的保守序列比对; 图b表示拟南芥、白菜、甘蓝及甘蓝型油菜NRT1.8蛋白的保守序列比对。其中, 蓝色虚线部分表示PTR家族的保守序列(F-Y-L-A-L-N-L-G-S-L)。"

图6

白菜、甘蓝、甘蓝型油菜及拟南芥NRT1.5和NRT1.8蛋白的保守基序特征 图a, d分别表示NRT1.5和NRT1.8蛋白在拟南芥、白菜、甘蓝及甘蓝型油菜中的系统进化关系; 图b, e分别表示NRT1.5和NRT1.8蛋白在拟南芥、白菜、甘蓝及甘蓝型油菜的保守基序; 图c, f分别表示NRT1.5和NRT1.8蛋白中每个保守基序的序列。"

图7

甘蓝型油菜NRT1.5和NRT1.8蛋白的跨膜结构域 图a~d表示甘蓝型油菜中4个NRT1.5蛋白的跨膜结构域, 其中a表示Bna.A5.NRT1.5, b表示Bna.A9.NRT1.5, c表示Bna.C5.NRT1.5a, d表示Bna.C5.NRT1.5b。图e~h表示甘蓝型油菜中4个NRT1.8蛋白的跨膜结构域, 其中a表示Bna.A1.NRT1.8, f表示Bna.A3.NRT1.8, g表示Bna.C7.NRT1.8, h表示Bna.Cn.NRT1.8。"

图8

甘蓝型油菜NRT1.5和NRT1.8基因对低氮的响应及基因共表达网络分析 图a表示甘蓝型油菜地上部和根部NRT1.5家族基因在低氮处理0 h、3 h、72 h 时的基因表达丰度; 图b表示NRT1.5家族基因在低氮处理时的基因共表达网络分析。图c表示甘蓝型油菜地上部和根部NRT1.8家族基因在低氮处理0 h、3 h、72 h 时的基因表达丰度; 图d表示NRT1.8家族基因在低氮处理时的基因共表达网络分析; FPKM表示每千个碱基转录每百万映射读取的fragments。"

图9

甘蓝型油菜NRT1.5和NRT1.8基因对镉胁迫的响应及基因共表达网络分析 图a和图b分别表示甘蓝型油菜地上部和根部NRT1.5家族基因在镉处理时的基因表达丰度; 图c表示NRT1.5家族基因在镉处理时的基因共表达网络分析。图d和图e分别表示甘蓝型油菜地上部和根部NRT1.8家族基因在镉处理时的基因表达丰度; 图f表示NRT1.8家族基因在镉处理时的基因共表达网络分析。FPKM表示每千个碱基转录每百万映射读取的fragments。图中所示显著性差异是单个基因对照和镉处理两两对比, 未达到显著性差异的图中未标记。误差线代表3个独立生物学重复的标准误, a和b表示差异显著(Ρ < 0.05)。"

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