Deshmukh Rupesh, Rana Nitika, Liu Yang, Zeng Shuai, Agarwal Gaurav, Sonah Humira, Varshney Rajeev, Joshi Trupti, Patil Gunvant B, Nguyen Henry T
Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India.
Department of Biotechnology, Panjab University, Chandigarh, India.
Physiol Plant. 2021 Apr;171(4):756-770. doi: 10.1111/ppl.13287. Epub 2020 Dec 14.
Transporters, a class of membrane proteins that facilitate exchange of solutes including diverse molecules and ions across the cellular membrane, are vital component for the survival of all organisms. Understanding plant transporters is important to get insight of the basic cellular processes, physiology, and molecular mechanisms including nutrient uptake, signaling, response to external stress, and many more. In this regard, extensive analysis of transporters predicted in soybean and other plant species was performed. In addition, an integrated database for soybean transporter protein, SoyTD, was developed that will facilitate the identification, classification, and extensive characterization of transporter proteins by integrating expression, gene ontology, conserved domain and motifs, gene structure organization, and chromosomal distribution features. A comprehensive analysis was performed to identify highly confident transporters by integrating various prediction tools. Initially, 7541 transmembrane (TM) proteins were predicted in the soybean genome; out of these, 3306 non-redundant transporter genes carrying two or more transmembrane domains were selected for further analysis. The identified transporter genes were classified according to a standard transporter classification (TC) system. Comparative analysis of transporter genes among 47 plant genomes provided insights into expansion and duplication of transporter genes in land plants. The whole genome resequencing (WGRS) and tissue-specific transcriptome datasets of soybean were integrated to investigate the natural variants and expression profile associated with transporter(s) of interest. Overall, SoyTD provides a comprehensive interface to study genetic and molecular function of soybean transporters. SoyTD is publicly available at http://artemis.cyverse.org/soykb_dev/SoyTD/.
转运蛋白是一类膜蛋白，可促进包括各种分子和离子在内的溶质跨细胞膜交换，是所有生物体生存的重要组成部分。了解植物转运蛋白对于深入了解基本细胞过程、生理学和分子机制（包括养分吸收、信号传导、对外界胁迫的反应等）至关重要。在这方面，对大豆和其他植物物种中预测的转运蛋白进行了广泛分析。此外，还开发了一个大豆转运蛋白综合数据库SoyTD，通过整合表达、基因本体、保守结构域和基序、基因结构组织以及染色体分布特征，将有助于转运蛋白的鉴定、分类和广泛表征。通过整合各种预测工具进行了全面分析，以鉴定高度可信的转运蛋白。最初，在大豆基因组中预测到7541个跨膜（TM）蛋白；其中，选择了3306个携带两个或更多跨膜结构域的非冗余转运蛋白基因进行进一步分析。根据标准转运蛋白分类（TC）系统对鉴定出的转运蛋白基因进行分类。对47个植物基因组中的转运蛋白基因进行比较分析，为陆地植物中转运蛋白基因的扩增和复制提供了见解。整合了大豆的全基因组重测序（WGRS）和组织特异性转录组数据集，以研究与感兴趣的转运蛋白相关的自然变异和表达谱。总体而言，SoyTD提供了一个全面的界面来研究大豆转运蛋白的遗传和分子功能。SoyTD可在http://artemis.cyverse.org/soykb_dev/SoyTD/上公开获取。
