水稻泛素结合酶基因家族的生物信息学与表达分析

doi:10.16819/j.1001-7216.2016.5177

摘要/Abstract

摘要：

泛素/蛋白酶体系统在植物的生长发育、形态建成和抗病反应等过程中起着重要的作用。近年的研究表明,某些病原菌能够模拟寄主植物泛素/蛋白酶体系统组分,从而达到利用该系统为病原菌服务的目的。泛素结合酶是泛素化反应过程中的第二个酶,对植物泛素/蛋白酶体系统的正常运行不可或缺。已有的研究表明,水稻基因组数据库中存在48个预测的泛素结合酶基因。为了初步揭示这些泛素结合酶基因在植物抗病防御反应中的功能,研究其与植物抗病性的关系。本研究通过生物信息学、RNA-seq和qRT-PCR的方法,分析了水稻泛素结合酶基因家族的特征及其表达模式。系统进化树分析表明,48个水稻泛素结合酶基因可分为3个大组,总共7个亚组。蛋白结构域分析表明,水稻泛素结合酶基因主要由一个泛素结合酶催化结构域组成。电子表达谱分析表明,大多数水稻泛素结合酶基因能被稻瘟病菌诱导表达。启动子区顺式作用元件分析表明,4个抗病相关顺式作用元件和1个过敏性反应相关顺式作用元件在48个水稻泛素结合酶基因的启动子区有很高的分布。稻瘟病菌接种亲和性和非亲和性水稻单基因系的RNA-seq结果表明,处理36 h读取到的水稻泛素结合酶基因为44个,其中高表达基因数量超过读取到的泛素结合酶基因总数的50%。qRT-PCR分析结果表明稻瘟病菌的侵染在亲和和非亲和组合中都能诱导部分水稻泛素结合酶基因的表达。在非亲和组合中水稻泛素结合酶基因的表达倾向于受到抑制。

关键词: 水稻, 泛素结合酶, 泛素/蛋白酶体系统, 生物信息学, 稻瘟病菌, RNA-seq, qRT-PCR

Abstract:

The ubiquitin / proteasome system plays an important role in plant growth and development, morphogenesis and disease resistance. Recent studies have shown that some pathogens can mimic the host plant ubiquitin / proteasome system components to achieve their own purposes. Ubiquitin-conjugating enzyme is the second enzyme in the ubiquitination process and is indispensable for the plant ubiquitin/proteasome system. Previous studies showed that there are 48 predicted ubiquitin-conjugating enzyme genes in rice genome. In order to preliminarily elucidate the functions of rice ubiquitin-conjugating enzyme genes in plant disease resistance, bioinformatic, RNA-seq and qRT-PCR methods were used to analyze characteristics and expression patterns of rice ubiquitin-conjugating enzyme gene family. Phylogenetic tree analyses indicate that the 48 rice ubiquitin-conjugating enzyme genes can be divided into 3 groups, 7 sub-groups in total. Protein domain analysis showed that ubiquitin-conjugating enzyme genes mainly consist of a big ubiquitin-conjugating enzyme catalytic domain. Expression analysis in silico suggested that most of the rice ubiquitin-conjugating enzymes can be induced by blast fungus infection. Plant cis-acting elements analysis indicated that four pathogen resistance cis-acting elements and one hypersensitivity reaction cis-acting element have high distribution in the promoter region of the 48 rice ubiquitin-conjugating enzyme genes. RNA-seq data from compatible and incompatible monogenic rice after rice blast fungus infection showed that 44 rice ubiquitin-conjugating enzyme genes were expressed at 36 hours after treatment, among which more than 50% were highly expressed genes. qRT-PCR analysis showed that expression of some ubiquitin-conjugating enzyme genes can be induced by the inoculation of rice blast fungus both in compatible and incompatible monogenic rice. However, in incompatible rice the expression of rice ubiquitin-conjugating enzyme genes tends to be inhibited after rice blast fungus inoculation.

Key words: rice, ubiquitin-conjugating enzyme, ubiquitin/proteasome system, bioinformatics, Magnaporthe oryzae, RNA-seq, qRT-PCR

中图分类号:

Q755
S511.01

刘鑫, 张恒, 阚虎飞, 周立帅, 黄昊, 宋林林, 翟焕趁, 张君, 鲁国东. 水稻泛素结合酶基因家族的生物信息学与表达分析[J]. 中国水稻科学, 2016, 30(3): 223-231.

Xin LIU, Heng ZHANG, Hu-fei KAN, Li-shuai ZHOU, Hao HUANG, Lin-lin SONG, Huan-chen ZHAI, Jun ZHANG, Guo-dong LU. Bioinformatic and Expression Analysis of Rice Ubiquitin-conjugating Enzyme Gene Family[J]. Chinese Journal OF Rice Science, 2016, 30(3): 223-231.

图/表 6

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基因 Gene	表达诱导因素 Expression inducing factors
基因 Gene	稻瘟病菌侵染 Blast fungus infection	盐胁迫 Salinity stress	脱落酸 Abscisic acid	赤霉素 Gibberellin	细胞分裂素 Cytokinin	寡聚糖几丁质 Chitin oligosaccharide
OsUBC1	+	+	+	+	+	+
OsUBC2	+	+	+	+	+	+
OsUBC3	+	+	n	n	+	n
OsUBC4	+	+	+	+	+	+
OsUBC5	+	+	+	+	+	+
OsUBC6	+	+	+	+	+	+
OsUBC7	+	+	n	n	+	n
OsUBC8	+	+	+	+	+	+
OsUBC9	n	n	+	+	+	+
OsUBC10	+	+	+	+	+	+
OsUBC11	+	+	+	+	+	+
OsUBC12	+	+	n	n	+	n
OsUBC13	+	+	n	n	+	n
OsUBC14	n	n	+	+	n	+
OsUBC15	n	n	n	n	n	n
OsUBC16	+	+	+	+	+	+
OsUBC17	+	+	+	+	+	+
OsUBC18	+	+	+	+	+	+
OsUBC19	+	+	+	+	+	+
OsUBC20	N	N	N	N	N	N
OsUBC21	N	N	N	N	N	N
OsUBC22	N	N	N	N	N	N
OsUBC23	N	N	N	N	N	N
OsUBC24	+	+	+	+	+	+
OsUBC25	N	N	N	N	N	N
OsUBC26	+	+	+	+	+	+
OsUBC27	+	+	+	+	+	+
OsUBC28	+	+	+	+	+	+
OsUBC29	+	+	+	+	+	+
OsUBC30	+	+	+	+	+	+
OsUBC31	+	+	n	n	+	n
OsUBC32	+	+	+	+	+	+
OsUBC33	+	+	+	+	+	+
OsUBC34	+	+	+	+	+	+
OsUBC35	N	N	N	N	N	N
OsUBC36	N	N	N	N	N	N
OsUBC37	+	+	n	n	+	+
OsUBC38	+	+	+	+	+	+
OsUBC39	N	N	N	N	N	N
OsUBC40	+	+	+	+	+	+
OsUBC41	+	+	n	n	+	N
OsUBC42	+	+	+	+	+	+
OsUBC43	+	+	+	+	+	+
OsUBC44	+	+	+	+	+	+
OsUBC45	+	+	+	+	+	+
OsUBC46	+	+	+	+	+	+
OsUBC47	+	+	n	n	+	N
OsUBC48	+	+	+	+	+	+

基因 Gene	表达诱导因素 Expression inducing factors
基因 Gene	稻瘟病菌侵染 Blast fungus infection	盐胁迫 Salinity stress	脱落酸 Abscisic acid	赤霉素 Gibberellin	细胞分裂素 Cytokinin	寡聚糖几丁质 Chitin oligosaccharide
OsUBC1	+	+	+	+	+	+
OsUBC2	+	+	+	+	+	+
OsUBC3	+	+	n	n	+	n
OsUBC4	+	+	+	+	+	+
OsUBC5	+	+	+	+	+	+
OsUBC6	+	+	+	+	+	+
OsUBC7	+	+	n	n	+	n
OsUBC8	+	+	+	+	+	+
OsUBC9	n	n	+	+	+	+
OsUBC10	+	+	+	+	+	+
OsUBC11	+	+	+	+	+	+
OsUBC12	+	+	n	n	+	n
OsUBC13	+	+	n	n	+	n
OsUBC14	n	n	+	+	n	+
OsUBC15	n	n	n	n	n	n
OsUBC16	+	+	+	+	+	+
OsUBC17	+	+	+	+	+	+
OsUBC18	+	+	+	+	+	+
OsUBC19	+	+	+	+	+	+
OsUBC20	N	N	N	N	N	N
OsUBC21	N	N	N	N	N	N
OsUBC22	N	N	N	N	N	N
OsUBC23	N	N	N	N	N	N
OsUBC24	+	+	+	+	+	+
OsUBC25	N	N	N	N	N	N
OsUBC26	+	+	+	+	+	+
OsUBC27	+	+	+	+	+	+
OsUBC28	+	+	+	+	+	+
OsUBC29	+	+	+	+	+	+
OsUBC30	+	+	+	+	+	+
OsUBC31	+	+	n	n	+	n
OsUBC32	+	+	+	+	+	+
OsUBC33	+	+	+	+	+	+
OsUBC34	+	+	+	+	+	+
OsUBC35	N	N	N	N	N	N
OsUBC36	N	N	N	N	N	N
OsUBC37	+	+	n	n	+	+
OsUBC38	+	+	+	+	+	+
OsUBC39	N	N	N	N	N	N
OsUBC40	+	+	+	+	+	+
OsUBC41	+	+	n	n	+	N
OsUBC42	+	+	+	+	+	+
OsUBC43	+	+	+	+	+	+
OsUBC44	+	+	+	+	+	+
OsUBC45	+	+	+	+	+	+
OsUBC46	+	+	+	+	+	+
OsUBC47	+	+	n	n	+	N
OsUBC48	+	+	+	+	+	+