Bioinformatics analysis of the MTP gene family in Amaranthus hypochondriacus L. and expression characteristics under cadmium stress
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摘要:
MTP（Metal tolerance protein）又称CDF（Cation diffusion facilitator），是与金属离子转运相关的一类蛋白。为了研究千穗谷（Amaranthus hypochondriacus L.）MTP基因家族的序列特征和进化关系，预测其不同成员的功能和调控机制，我们以最新的千穗谷基因组为参考，鉴定出9个MTP家族成员，分为Zn-CDF（3个）、Zn/Fe-CDF（4个）、Mn-CDF（4个）3个亚族。所有家族成员均具有MTP转运蛋白的典型结构域Cation_efflux，部分成员还包含1个ZT_dimer结构域。染色体定位显示，9个MTP基因分布在7条染色体上。Cd胁迫下，AhMTP7和AhMTP9在根和叶中的表达均被抑制，AhMTP6在叶中被抑制，在根中却被诱导；其余6个MTP基因均受Cd诱导表达，AhMTP2、AhMTP3仅在叶中被诱导，AhMTP5仅在根中被诱导。顺式作用元件分析结果显示，AhMTP启动子中存在多个逆境响应、生长发育和激素信号的顺式作用元件。miRNA预测分析结果表明，15个miRNA靶向7个AhMTP成员。
Abstract:Metal tolerance protein (MTP), also known as cation diffusion facilitator (CDF), is a metal ion transport-related protein. To study the sequence characteristics and evolutionary relationships of the MTP gene family in Amaranthus hypochondriacus L., and to predict the functions and regulatory mechanisms of its members, we took the latest A. hypochondriacus genome as a reference and identified a total of nine members of the A. hypochondriacus MTP family. According to their sequence characteristics, they were divided into three subgroups: Zn-CDF (3), Zn/Fe-CDF (4), and Mn-CDF (4). All family members contained a cation_efflux domain, a typical feature of MTP transporters, with some also containing a ZT_dimer domain. Chromosome mapping showed that the nine MTP genes were distributed on seven chromosomes. Under cadmium (Cd) stress, the expression levels of AhMTP7 and AhMTP9 were inhibited in both leaves and roots, while the expression level of AhMTP6 was inhibited in leaves but induced in roots. The expression levels of the other six AhMTPs were induced by Cd, with AhMTP2 and AhMTP3 only induced in leaves, and AhMTP5 only induced in roots. Promoter cis-acting element analysis identified several cis-acting elements in the AhMTP promoter for stress response, growth and development, and hormone signaling. MicroRNA (miRNA) prediction analysis showed that 15 miRNAs targeted seven AhMTPs.
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Keywords:
- Amaranthus hypochondriacus /
- MTP /
- Gene expression /
- Metal stress /
- Gene families
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图 1 千穗谷、拟南芥和甜菜的MTP基因家族系统发育树
不同颜色字体代表不同物种。黄色：拟南芥；白色：甜菜；黑色：千穗谷。不同颜色分支代表不同组，红色代表组1，绿色代表组5，黑色代表组6，亮蓝色代表组7，黄色代表组8，紫色代表组9，深蓝色代表组12。
Figure 1. Phylogenetic tree of Amaranthus hypochondriacus, Arabidopsis thaliana, and Beta vulgaris
Different color fonts represent different species. Yellow for Arabidopsis thaliana, white for Beta vulgaris, and black for Amaranthus hypochondriacus; Different color branches represent different groups, red for group 1, green for group 5, black for group 6, bright blue for group 7, yellow for group 8, purple for group 9, and dark blue for group 12.
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图 2 千穗谷MTP基因结构与跨膜结构域分析
A：AhMTPs基因结构分析；B：AhMTPs跨膜结构域分析；C：AhMTPs保守结构域分析。
Figure 2. MTP gene structure and transmembrane domain analysis in Amaranthus hypochondriacus
A: Gene structure analysis of AhMTPs; B: Transmembrane domain analysis of AhMTPs; C: Conservative domain analysis of AhMTPs.
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图 3 千穗谷MTP家族成员染色体定位信息
不同颜色代表染色体上基因密度。蓝色越深代表高密度越高。
Figure 3. Chromosome location information of MTP family members in Amaranthus hypochondriacus
Different colors represent gene density on chromosomes. Deeper blue indicates higher density.
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图 4 千穗谷与其他模式植物MTP家族共线性分析
Figure 4. Collinearity analysis of MTP family between Amaranthus hypochondriacus and other model plants
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图 5 千穗谷MTP启动子顺式作用元件预测
Figure 5. Prediction of cis-acting elements in Amaranthus hypochondriacus MTP promoter
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图 6 不同组织千穗谷MTP基因表达量
A：叶；B：根；C：花；D：未成熟种子；E：干物质混合组织；F：茎。
Figure 6. MTP gene expression levels in Amaranthus hypochondriacus in different tissues
A: Leaf; B: Root; C: Flowers; D: Immature seeds; E: Dry matter mixed tissue; F: Stem.
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图 7 镉胁迫下千穗谷MTP基因在根系和叶片中的表达水平
CK-1：对照1 h；Cd-1：镉处理1 h；CK-6：对照6 h；Cd-6：镉处理6 h。不同小写字母代表不同处理之间差异显著（P ＜ 0.05）。
Figure 7. MTP gene expression levels in roots and leaves of Amaranthus hypochondriacus under Cd stress
CK-1: Control for 1 h; Cd-1: Cadmium treatment for 1 h; CK-6: Control for 6 h; Cd-6: Cadmium treatment for 6 h. Different lowercase letters indicate significant differences between treatments (P < 0.05).
表 1 千穗谷MTP家族成员基本信息
Table 1 Basic information of MTP family members in Amaranthus hypochondriacus
基因
Gene登录号
Accession number蛋白长度
Protein length / aa基因长度
Gene length / bp分子量
Molecular weight / Da等电点
Isoelectric point亚细胞定位
LocalizationAhMTP1 AH022184 376 8344 41127.39 8.75 液泡 AhMTP2 AH001412 830 2493 93971.60 6.94 细胞膜/液泡 AhMTP3 AH022259 451 12747 49774.67 7.80 液泡 AhMTP4 AH023492 396 6491 44899.19 4.87 液泡 AhMTP5 AH010891 417 5541 47165.96 5.67 液泡 AhMTP6 AH020319 224 6107 25139.53 9.54 细胞膜/液泡 AhMTP7 AH016853 205 2747 23800.73 6.83 液泡 AhMTP8 AH019735 155 4707 16885.61 5.78 液泡 AhMTP9 AH006882 279 4895 31121.67 4.81 液泡 
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