Department of Environmental and Plant Biology, Molecular and Cellular Biology Program, Ohio University, Athens, OH, USA.
Russ College of Engineering and Technology, Center for Intelligent, Distributed and Dependable Systems, Ohio University, Athens, OH, USA.
Methods Mol Biol. 2020;2149:463-481. doi: 10.1007/978-1-0716-0621-6_26.
Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall proteins that function in diverse aspects of plant growth and development. This superfamily consists of three members: arabinogalactan-proteins (AGPs), extensins (EXTs), and proline-rich proteins (PRPs). Hybrid and chimeric HRGPs also exist. A bioinformatic software program, BIO OHIO 2.0, was developed to expedite the genome-wide identification and classification of AGPs, EXTs, and PRPs based on characteristic HRGP motifs and biased amino acid compositions. This chapter explains the principles of identifying HRGPs and provides a stepwise tutorial for using the BIO OHIO 2.0 program with genomic/proteomic data. Here, as an example, the genome/proteome of the common bean (Phaseolus vulgaris) is analyzed using the BIO OHIO 2.0 program to identify and characterize its set of HRGPs.
羟脯氨酸丰富的糖蛋白（HRGPs）是植物细胞壁蛋白的一个超家族，在植物生长和发育的多个方面发挥作用。该超家族由三个成员组成：阿拉伯半乳聚糖蛋白（AGPs）、伸展蛋白（EXTs）和富含脯氨酸的蛋白（PRPs）。还存在杂交和嵌合 HRGPs。开发了一种生物信息学软件程序 BIO OHIO 2.0，以根据特征 HRGP 基序和偏性氨基酸组成加速 AGPs、EXTs 和 PRPs 的全基因组鉴定和分类。本章解释了鉴定 HRGPs 的原理，并提供了使用 BIO OHIO 2.0 程序与基因组/蛋白质组数据的分步教程。在这里，作为一个例子，使用 BIO OHIO 2.0 程序分析普通菜豆（Phaseolus vulgaris）的基因组/蛋白质组，以鉴定和表征其一组 HRGPs。
