Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity
Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity
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DOI：
10.1038/s41598-020-68407-2
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发表时间：
2020-07-09
影响因子：
4.6
通讯作者：
Verchot, Jeanmarie
中科院分区：
文献类型：
--
作者：
Herath, Venura;Gayral, Mathieu;Verchot, Jeanmarie
内质网（ER）免疫球蛋白结合蛋白（BiP）是参与正常蛋白质成熟和通过未折叠蛋白质反应（UPR）重折叠畸形蛋白质的分子伴侣。植物BiPs是一个多基因家族，参与植物的发育、免疫和对环境胁迫的应答。本研究通过系统发育、氨基酸序列、三维蛋白质建模和基因结构分析，在马铃薯基因组中鉴定了三个BiP同源物。这些分析表明，StBiP 1和StBiP 2与AtBiP 2分组，而StBiP 3与AtBiP 3分组。虽然蛋白质序列和折叠结构是高度相似的，这些StBiPs是可区分的，它们的表达模式在不同的组织和响应环境应激源，如热处理，化学品，或病毒诱导剂的UPR。从头算启动子分析显示，马铃薯和拟南芥BiP 1和BiP 2启动子高度富集与发育过程相关的顺式调控元件（克雷斯），而BiP 3启动子富集与应激相关的克雷斯。这些克雷斯的频率和线性分布产生了两个系统发育分支，进一步解决了通过基因同源性和外显子/内含子相位分析确定的组。这些数据揭示了BiP启动子的CRE结构可能在发育和应激相关线索下定义其时空表达模式。
The endoplasmic reticulum (ER) immunoglobulin binding proteins (BiPs) are molecular chaperones involved in normal protein maturation and refolding malformed proteins through the unfolded protein response (UPR). Plant BiPs belong to a multi-gene family contributing to development, immunity, and responses to environmental stresses. This study identified three BiP homologs in the Solanum tuberosum (potato) genome using phylogenetic, amino acid sequence, 3-D protein modeling, and gene structure analysis. These analyses revealed that StBiP1 and StBiP2 grouped with AtBiP2, whereas StBiP3 grouped with AtBiP3. While the protein sequences and folding structures are highly similar, these StBiPs are distinguishable by their expression patterns in different tissues and in response to environmental stressors such as treatment with heat, chemicals, or virus elicitors of UPR. Ab initio promoter analysis revealed that potato and Arabidopsis BiP1 and BiP2 promoters were highly enriched with cis-regulatory elements (CREs) linked to developmental processes, whereas BiP3 promoters were enriched with stress related CREs. The frequency and linear distribution of these CREs produced two phylogenetic branches that further resolve the groups identified through gene phylogeny and exon/intron phase analysis. These data reveal that the CRE architecture of BiP promoters potentially define their spatio-temporal expression patterns under developmental and stress related cues.