番茄20S蛋白酶体基因家族鉴定及生物信息学分析

doi:10.16420/j.issn.0513-353x.2023-0833

摘要/Abstract

摘要：

20S蛋白酶体能够通过自身或泛素—蛋白酶体系统特异性降解细胞质和细胞核中的蛋白质，维持细胞蛋白质稳态。本研究中鉴定出21个番茄（Solanum lycopersicum L.）20S蛋白酶体基因家族成员，并对其进行生物信息分析。结果表明，番茄20S蛋白酶体大多数基因含有相似的启动子和内含子，其中，编码α亚基的基因保守性较好，而编码β亚基的基因保守性较差；亚细胞定位发现，绝大多数基因在细胞质中发挥功能；染色体定位和基因复制分析发现，21个20S蛋白酶体基因不均匀地分布在12条染色体上，存在2对片段复制基因对；进化分析表明，编码α亚基和编码β亚基的基因被划分在不同的类群或亚群；多物种共线性分析发现，番茄与辣椒（Capsicum annuum L.）和马铃薯（Solanum tuberosum L.）之间的同源基因对较多，而与拟南芥[Arabidopsis thaliana（L.）Heynh.]、水稻（Oryza sativa L.）和玉米（Zea mays L.）同源的基因对较少。SlPRA1-01、SlPRA10-04、SlPRA11-05和SlPRA16-09这4个基因在3个物种中均形成基因对；启动子和组织特异性表达分析结果显示，20S蛋白酶体基因家族在番茄逆境胁迫和生长发育中发挥着重要作用。

关键词: 番茄, 20S蛋白酶体, 泛素—蛋白酶体系统, 生物信息分析

Abstract:

20S proteasome is able to maintain cellular protein homeostasis by specifically degrading proteins in the cytoplasm and nucleus either by itself or by the ubiquitin-proteasome system. In this study，21 members of the 20S proteasome gene family of tomato（Solanum lycopersicum L.）were identified and bioinformatically analyzed. The results showed that most of the genes of the tomato 20S proteasome contain similar promoters and introns，with the genes encoding the α-subunit being better conserved and those encoding the β-subunit being poorly conserved；Subcellular localisation reveals that the majority of genes function in the cytoplasm；Chromosomal localisation and gene duplication analyses revealed that the 21 20S proteasome genes were unevenly distributed across 12 chromosomes，with the presence of two fragment duplication gene pairs；Evolutionary analyses showed that genes encoding the α-subunit and β-subunit were classified in different taxa or subgroups；Multi-species colinearity analysis revealed more homologous gene pairs between chili（Capsicum annuum L.），potato（Solanum tuberosum L.），and tomato. However fewer homologous gene pairs between Arabidopsis，rice（Oryza sativa L.），maize（Zea mays L.），and tomato. SlPRA1-01，SlPRA10-04，SlPRA11-05，and SlPRA16-09 formed gene pairs in three species. Promoter and tissue-specific expression analyses revealed that the 20S proteasome gene family exhibited important role in tomato adversity stress and growth and development.

Key words: tomato, 20S proteasome, ubiquitin-proteasome system, bioinformatics analysis

闫超凡, 孙雪梅, 钟启文, 邵登魁, 邓昌蓉, 文军琴. 番茄20S蛋白酶体基因家族鉴定及生物信息学分析[J]. 园艺学报, 2024, 51(2): 266-280.

YAN Chaofan, SUN Xuemei, ZHONG Qiwen, SHAO Dengkui, DENG Changrong, WEN Junqin. Identification and Bioinformatics Analysis of 20S Proteasome Gene Family in Tomato[J]. Acta Horticulturae Sinica, 2024, 51(2): 266-280.

图/表 9

表1 番茄20S蛋白酶体基因家族

Table 1 20S proteasome gene family of tomato

基因 Gene	基因ID Gene ID	染色体定位 Chromosome location	基因位置/ bp Gene location
基因 Gene	基因ID Gene ID	染色体定位 Chromosome location	起始Start	终止End
SlPRA1-01	Solyc01g111450.3.1	Chr01:97599172..97602337（+）	97 599 172	97 602 337
SlPRA2-01	Solyc01g111460.3.1	Chr01:97605332..97606609（-）	97 605 332	97 606 609
SlPRA3-02	Solyc02g070510.3.1	Chr02:40805105..40810898（+）	40 805 105	40 810 898
SlPRA4-02	Solyc02g081700.1.1	Chr02:46112367..46113113（+）	46 112 367	46 113 113
SlPRA5-02	Solyc02g084920.3.1	Chr02:48607717..48616195（-）	48 607 717	48 616 195
SlPRA6-03	Solyc03g033745.1.1	Chr03:5362233..5373114（-）	5 362 233	5 373 114
SlPRA7-03	Solyc03g063420.2.1	Chr03:36767871..36777655（-）	36 767 871	36 777 655
SlPRA8-04	Solyc04g009410.3.1	Chr04:2830248..2840325（+）	2 830 248	2 840 325
SlPRA9-04	Solyc04g024420.3.1	Chr04:31500067..31505977（+）	31 500 067	31 505 977
SlPRA10-04	Solyc04g080590.3.1	Chr04:64787899..64791729（-）	64 787 899	64 791 729
SlPRA11-05	Solyc05g013820.3.1	Chr05:7123832..7132561（-）	7 123 832	7 132 561
SlPRA12-05	Solyc05g056160.3.1	Chr05:66400334..66404473（-）	66 400 334	66 404 473
SlPRA13-07	Solyc07g016200.3.1	Chr07:6438876..6447830（-）	6 438 876	6 447 830
SlPRA14-07	Solyc07g055080.3.1	Chr07:63355928..63361757（+）	63 355 928	63 361 757
SlPRA15-08	Solyc08g016510.3.1	Chr08:7711628..7717929（-）	7 711 628	7 717 929
SlPRA16-09	Solyc09g082320.3.1	Chr09:68500118..68505978（-）	68 500 118	68 505 978
SlPRA17-10	Solyc10g008010.3.1	Chr10:2165246..2178357（+）	2 165 246	2 178 357
SlPRA18-10	Solyc10g077030.2.1	Chr10:60039871..60049610（-）	60 039 871	60 049 610
SlPRA19-10	Solyc10g081130.2.1	Chr10:62399725..62404172（+）	62 399 725	62 404 172
SlPRA20-11	Solyc11g069150.2.1	Chr11:54042842..54049437（-）	54 042 842	54 049 437
SlPRA21-12	Solyc12g009140.2.1	Chr12:2452941..2457449（-）	2 452 941	2 457 449

表1 番茄20S蛋白酶体基因家族

Table 1 20S proteasome gene family of tomato

基因 Gene	基因ID Gene ID	染色体定位 Chromosome location	基因位置/ bp Gene location
基因 Gene	基因ID Gene ID	染色体定位 Chromosome location	起始Start	终止End
SlPRA1-01	Solyc01g111450.3.1	Chr01:97599172..97602337（+）	97 599 172	97 602 337
SlPRA2-01	Solyc01g111460.3.1	Chr01:97605332..97606609（-）	97 605 332	97 606 609
SlPRA3-02	Solyc02g070510.3.1	Chr02:40805105..40810898（+）	40 805 105	40 810 898
SlPRA4-02	Solyc02g081700.1.1	Chr02:46112367..46113113（+）	46 112 367	46 113 113
SlPRA5-02	Solyc02g084920.3.1	Chr02:48607717..48616195（-）	48 607 717	48 616 195
SlPRA6-03	Solyc03g033745.1.1	Chr03:5362233..5373114（-）	5 362 233	5 373 114
SlPRA7-03	Solyc03g063420.2.1	Chr03:36767871..36777655（-）	36 767 871	36 777 655
SlPRA8-04	Solyc04g009410.3.1	Chr04:2830248..2840325（+）	2 830 248	2 840 325
SlPRA9-04	Solyc04g024420.3.1	Chr04:31500067..31505977（+）	31 500 067	31 505 977
SlPRA10-04	Solyc04g080590.3.1	Chr04:64787899..64791729（-）	64 787 899	64 791 729
SlPRA11-05	Solyc05g013820.3.1	Chr05:7123832..7132561（-）	7 123 832	7 132 561
SlPRA12-05	Solyc05g056160.3.1	Chr05:66400334..66404473（-）	66 400 334	66 404 473
SlPRA13-07	Solyc07g016200.3.1	Chr07:6438876..6447830（-）	6 438 876	6 447 830
SlPRA14-07	Solyc07g055080.3.1	Chr07:63355928..63361757（+）	63 355 928	63 361 757
SlPRA15-08	Solyc08g016510.3.1	Chr08:7711628..7717929（-）	7 711 628	7 717 929
SlPRA16-09	Solyc09g082320.3.1	Chr09:68500118..68505978（-）	68 500 118	68 505 978
SlPRA17-10	Solyc10g008010.3.1	Chr10:2165246..2178357（+）	2 165 246	2 178 357
SlPRA18-10	Solyc10g077030.2.1	Chr10:60039871..60049610（-）	60 039 871	60 049 610
SlPRA19-10	Solyc10g081130.2.1	Chr10:62399725..62404172（+）	62 399 725	62 404 172
SlPRA20-11	Solyc11g069150.2.1	Chr11:54042842..54049437（-）	54 042 842	54 049 437
SlPRA21-12	Solyc12g009140.2.1	Chr12:2452941..2457449（-）	2 452 941	2 457 449

图1 番茄20S蛋白酶体基因家族基因结构和保守基序

Fig. 1 Gene structure and conserved motifs of the tomato 20S proteasome gene family

图2 20S蛋白酶体基因家族的染色体定位及复制关系外侧方框代表染色体骨架，中间和内侧方框表示基因密度，每个基因在染色体骨架上的大致分布用短黑线标出。红色、绿色和浅灰色线分别代表相似性为0.98 ~ 0.99、0.97 ~ 0.98和不足0.95及其他基因的连锁群。

Fig. 2 Chromosomal localization and replication relationships of the 20S proteasome gene family The outer box represents the chromosome skeleton，the middle and inner boxes indicate gene density，and the approximate distribution of each tomato 20S proteasome gene is marked on the chromosome skeleton by a short black line. Coloured lines refer to the linkage groups with more than 0.95 similarity，red lines 0.98-0.99，green lines 0.97-0.98，and light grey lines refer to the linkage groups with less than 0.95 similarity and the linkage groups of other genes.

图3 番茄SlPRA17-10和SlPRA20-11在烟草中的亚细胞定位

Fig. 3 Subcellular localization of tomato SlPRA17-10 and SlPRA20-11 in tobacco

图4 番茄20S蛋白酶体基因家族序列相似性

Fig. 4 Sequence similarity of 20S proteasome gene family in tomato

图5 6个物种20S蛋白酶体基因家族序列的系统进化树 α、β分别代表不同α亚基、β亚基。

Fig. 5 Phylogenetic tree of 20S proteasome gene family sequences from six species α and β represent different α-subunits and β-subunits.

图6 不同物种20S蛋白酶体基因的共线性分析灰色线条表示番茄与其他物种之间的共线性区块，红色线条突出了20S蛋白酶体基因对。

Fig. 6 Covariance analysis of 20S proteasome genes in different species Gray lines indicate blocks of covariance between tomato and other species，and red lines highlight 20S proteasome gene pairs.

图7 番茄20S蛋白酶体基因家族顺式作用元件预测

Fig. 7 Predicted cis-acting elements of the tomato 20S proteasome gene family

图8 番茄20S蛋白酶体基因组织特异性表达 A：不同组织和不同发育阶段的相对表达量（TFGD），B：部分基因表达水平的qPCR分析。0 DPA：花期的花，10 DPA：开花后10 d的果实，20 DPA：开花后20 d的果实，33 DPA：成熟果实。COTYL：子叶；HYPO：下胚轴；MERI：植物分生组织；ML：成熟叶片；RT：根；YFB：嫩花蕾；YL：嫩叶；FL：花；FR：果实。

Fig. 8 Tissue-specific expression of 20S proteasome gene in tomato A shows the relative expression of tomato 20S proteasome genes in different tissues and different developmental stages（TFGD），and figure B shows qPCR analysis of the expression levels of some genes. 0 DPA：Anthesis flowers；10 DPA：10 days post anthesis fruit；20 DPA：20 days post anthesis fruit；33 DPA：Rippening fruit. COTYL：Cotyledons；HYPO：Hypocotyl；MERI：Vegitative meristems；ML：Mature leaves；RT：Root；YFB：Young flower buds，YL：Young flower buds；FL：Flower；FR：Fruit.

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