Systematic analysis of JmjC gene family and stress--response expression of KDM5 subfamily genes in Brassica napus.
Systematic analysis of JmjC gene family and stress--response expression of KDM5 subfamily genes in Brassica napus.
复制标题
甘蓝型油菜JmjC基因家族及KDM5亚家族基因胁迫反应表达的系统分析
作者：
He X;Wang Q;Pan J;Liu B;Ruan Y;Huang Y
Jumonji C （JmjC）蛋白通过去除组蛋白中的赖氨酸甲基化，在植物发育和胁迫反应中发挥关键作用。甘蓝型油菜是由油菜和甘蓝自发杂交而成的，是继大豆之后最重要的油料作物。在芸苔属植物中，JmjC蛋白的结构和功能及其与亲本和模式植物拟南芥的关系尚不清楚。系统地鉴定和分析芸苔属作物中的JmjC家族，可以为今后的功能鉴定和油料作物改良提供依据。基于JmjC保守结构域，从油菜数据库中鉴定出rapa （AA）、B. oleracea （CC）和B. napus的JmjC同源物。采用系统发育分析、染色体定位、HMMER搜索、基因结构显示和Logos分析等方法对JmjC同源物的关系进行了表征。利用同义和非同义核苷酸替换来推断同源物之间的基因重复信息。然后利用qRT-PCR检测非生物胁迫下BnKDM5亚家族基因的表达水平。从甘蓝型油菜基因组中鉴定出65个JmjC基因，从油菜基因组中鉴定出29个JmjC基因，从甘蓝基因组中鉴定出23个JmjC基因。通过系统发育分析，将这些基因划分为7个支系，并对其去甲基化催化活性进行了预测。甘蓝型油菜JmjC基因的平均保留率（来自油菜B. rapa（93.1%）和甘蓝B.甘蓝（82.6%）的甘蓝型油菜JmjC基因）超过全基因组水平。JmjC序列在结构域起源、染色体位置、内含子/外显子数量和催化位点上具有高度的保守性。在同源物中证实了基因重复事件。BrKDM5亚家族的许多基因在干旱和NaCl处理下表达量增加，而在高温胁迫下只有少数基因参与表达。本研究首次对芸苔属植物的JmjC基因进行了全基因组鉴定。在异源四倍体形成过程中，BnJmjC的保守性高于甘蓝型油菜全基因组的平均保留率。此外，许多基因的表达谱表明，BnKDM5亚家族基因参与了对盐、干旱和高温的胁迫反应。
Jumonji C (JmjC) proteins exert critical roles in plant development and stress response through the removal of lysine methylation from histones. Brassica napus, which originated from spontaneous hybridization by Brassica rapa and Brassica oleracea, is the most important oilseed crop after soybean. In JmjC proteins of Brassica species, the structure and function and its relationship with the parents and model plant Arabidopsis thaliana remain uncharacterized. Systematic identification and analysis for JmjC family in Brassica crops can facilitate the future functional characterization and oilseed crops improvement. Basing on the conserved JmjC domain, JmjC homologs from the three Brassica species, B. rapa (AA), B. oleracea (CC) and B. napus, were identified from the Brassica database. Some methods, such as phylogenic analysis, chromosomal mapping, HMMER searching, gene structure display and Logos analysis, were used to characterize relationships of the JmjC homologs. Synonymous and nonsynonymous nucleotide substitutions were used to infer the information of gene duplication among homologs. Then, the expression levels of BnKDM5 subfamily genes were checked under abiotic stress by qRT-PCR. Sixty-five JmjC genes were identified from B. napus genome, 29 from B. rapa, and 23 from B. oleracea. These genes were grouped into seven clades based on the phylogenetic analysis, and their catalytic activities of demethylation were predicted. The average retention rate of B. napus JmjC genes (B. napus JmjC gene from B. rapa (93.1%) and B. oleracea (82.6%)) exceeded whole genome level. JmjC sequences demonstrated high conservation in domain origination, chromosomal location, intron/exon number and catalytic sites. The gene duplication events were confirmed among the homologs. Many of the BrKDM5 subfamily genes showed higher expression under drought and NaCl treatments, but only a few genes were involved in high temperature stress. This study provides the first genome-wide characterization of JmjC genes in Brassica species. The BnJmjC exhibits higher conservation during the formation process of allotetraploid than the average retention rates of the whole B. napus genome. Furthermore, expression profiles of many genes indicated that BnKDM5 subfamily genes are involved in stress response to salt, drought and high temperature.
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影响因子：
64.8
作者：
Crevillen, Pedro;Yang, Hongchun;Cui, Xia;Greeff, Christiaan;Trick, Martin;Qiu, Qi;Cao, Xiaofeng;Dean, Caroline
通讯作者：
Dean, Caroline
影响因子：
64.5
作者：
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通讯作者：
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影响因子：
7.2
作者：
Ding, Yong;Avramova, Zoya;Fromm, Michael
通讯作者：
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DOI：
10.1073/pnas.1217020110
发表时间：
2013-01-29
影响因子：
11.1
作者：
Cui, Xiekui;Jin, Ping;Cao, Xiaofeng
通讯作者：
Cao, Xiaofeng
影响因子：
7.2
作者：
Dutta, Aditya;Choudhary, Pratibha;Raina, Ramesh
通讯作者：
Raina, Ramesh