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Analysis of Germin-like Protein Genes (OsGLPs) Family in Rice Using Various In silico Approaches
Current Bioinformatics ( IF 2.4 ) Pub Date : 2019-12-31 , DOI: 10.2174/1574893614666190722165130
Muhammad Ilyas 1 , Muhammad Irfan 1 , Tariq Mahmood 2 , Hazrat Hussain 3 , Latif-ur-Rehman 3 , Ijaz Naeem 3 , Khaliq-ur-Rahman 4
Affiliation  

Background: Germin-like Proteins (GLPs) play an important role in various stresses. Rice contains 43 GLPs, among which many remain functionally unexplored. The computational analysis will provide significant insight into their function.

Objective: To find various structural properties, functional importance, phylogeny and expression pattern of all OsGLPs using various bioinformatics tools.

Methods: Physiochemical properties, sub-cellular localization, domain composition, Nglycosylation and Phosphorylation sites, and 3D structural models of the OsGLPs were predicted using various bioinformatics tools. Functional analysis was carried out with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Blast2GO servers. The expression profile of the OsGLPs was predicted by retrieving the data for expression values from tissuespecific and hormonal stressed array libraries of RiceXPro. Their phylogenetic relationship was computed using Molecular and Evolutionary Genetic Analysis (MEGA6) tool.

Results: Most of the OsGLPs are stable in the cellular environment with a prominent expression in the extracellular region (57%) and plasma membrane (33%). Besides, 3 basic cupin domains, 7 more were reported, among which NTTNKVGSNVTLINV, FLLAALLALASWQAI, and MASSSF were common to 99% of the sequences, related to bacterial pathogenicity, peroxidase activity, and peptide signal activity, respectively. Structurally, OsGLPs are similar but functionally they are diverse with novel enzymatic activities of oxalate decarboxylase, lyase, peroxidase, and oxidoreductase. Expression analysis revealed prominent activities in the root, endosperm, and leaves. OsGLPs were strongly expressed by abscisic acid, auxin, gibberellin, cytokinin, and brassinosteroid. Phylogenetically they showed polyphyletic origin with a narrow genetic background of 0.05%. OsGLPs of chromosome 3, 8, and 12 are functionally more important due to their defensive role against various stresses through co-expression strategy.

Conclusion: The analysis will help to utilize OsGLPs in future food programs.



中文翻译:

利用多种计算机模拟方法分析水稻中的胚芽样蛋白基因(OsGLPs)家族

背景:胚芽蛋白样蛋白(GLP)在各种压力下均起重要作用。水稻含有43种GLP,其中许多仍未开发。计算分析将为他们的功能提供重要的见识。

目的:利用各种生物信息学工具,发现所有OsGLP的各种结构特性,功能重要性,系统发育和表达模式。

方法:使用多种生物信息学工具预测了OsGLP的理化特性,亚细胞定位,结构域组成,N糖基化和磷酸化位点以及3D结构模型。使用检索工具检索相互作用的基因/蛋白质(STRING)和Blast2GO服务器进行功能分析。通过从RiceXPro的组织特异性和激素应激阵列文库中检索表达值的数据,可以预测OsGLP的表达谱。使用分子和进化遗传分析(MEGA6)工具计算了它们的系统发生关系。

结果:大多数OsGLP在细胞环境中稳定,并在细胞外区域(57%)和质膜(33%)中有突出的表达。此外,报道了3个基本的铜蛋白结构域,另外7个,其中NTTNKVGSNVTLINV,FLLAALLALASWQAI和MASSSF是99%序列共有的,分别与细菌致病性,过氧化物酶活性和肽信号活性有关。在结构上,OsGLP相似,但在功能上它们具有草酸脱羧酶,裂解酶,过氧化物酶和氧化还原酶的新型酶促活性。表达分析显示在根,胚乳和叶子中有突出的活性。脱落酸,生长素,赤霉素,细胞分裂素和油菜素固醇强烈表达OsGLP。从系统发育上看,他们显示出多系起源,遗传背景狭窄,仅为0.05%。

结论:该分析将有助于在未来的食品计划中利用OsGLP。

更新日期:2019-12-31
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