Bioinformatics Prediction and Evolution Analysis of Arabinogalactan Proteins in the Plant Kingdom.
Bioinformatics Prediction and Evolution Analysis of Arabinogalactan Proteins in the Plant Kingdom.
复制标题
植物界阿拉伯半乳聚糖蛋白的生物信息学预测与进化分析
DOI：
10.3389/fpls.2017.00066
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发表时间：
2017
影响因子：
5.6
通讯作者：
Ma H
中科院分区：
文献类型：
--
作者：
Ma Y;Yan C;Li H;Wu W;Liu Y;Wang Y;Chen Q;Ma H
阿拉伯半乳聚糖蛋白（AGPs）是一类细胞外糖蛋白，与植物的生长和发育有关。随着许多植物物种基因组测序数量的快速增长，现在可以预测AGPs家族成员，以便于进行功能研究。在先前鉴定拟南芥AGPs的基础上，本研究提出了一种系统筛选“经典”和“嵌合”家族成员的综合策略。编写了一个名为Finding - AGP的Python脚本，用于在给定阈值下查找类似AGP的序列并筛选AGP候选物。以信号肽的存在作为必要条件，对经典AGPs、富含赖氨酸的经典AGPs、AGP - 伸展蛋白杂合体和非经典AGPs进行了初步筛选，并且主要针对类成束蛋白、类植物花青素和类木质素AGPs进行了BLAST搜索。然后采用糖模块指数和部分PAST（脯氨酸、丙氨酸、丝氨酸和苏氨酸）百分比来识别AGP候选物。该综合策略成功地在47种植物物种中发现了AGP基因家族，主要结果总结如下：（i）AGPs在被子植物中含量丰富，并且在莱茵衣藻中发现了许多具有丝氨酸 - 脯氨酸重复序列的“古老”AGPs；（ii）经典AGPs、AG - 肽和富含赖氨酸的经典AGPs分别首先出现在小立碗藓、江南卷柏和欧洲云杉中；（iii）引入了9个嵌合AGPs亚家族，作为新鉴定的类似于类成束蛋白、类植物花青素和类木质素AGPs的嵌合亚家族；（iv）富含赖氨酸结构域的长度和氨基酸组成差异很大，表明在进化过程中存在插入/缺失模型。我们的研究结果不仅提供了一种识别AGP基因家族的有力手段，而且还可能解释了AGPs在维持植物细胞壁以及将细胞外信号转导到细胞质中的作用。
Arabinogalactan proteins (AGPs) are a family of extracellular glycoproteins implicated in plant growth and development. With a rapid growth in the number of genomes sequenced in many plant species, the family members of AGPs can now be predicted to facilitate functional investigation. Building upon previous advances in identifying Arabidopsis AGPs, an integrated strategy of systematical AGP screening for “classical” and “chimeric” family members is proposed in this study. A Python script named Finding-AGP is compiled to find AGP-like sequences and filter AGP candidates under the given thresholds. The primary screening of classical AGPs, Lys-rich classical AGPs, AGP-extensin hybrids, and non-classical AGPs was performed using the existence of signal peptides as a necessary requirement, and BLAST searches were conducted mainly for fasciclin-like, phytocyanin-like and xylogen-like AGPs. Then glycomodule index and partial PAST (Pro, Ala, Ser, and Thr) percentage are adopted to identify AGP candidates. The integrated strategy successfully discovered AGP gene families in 47 plant species and the main results are summarized as follows: (i) AGPs are abundant in angiosperms and many “ancient” AGPs with Ser-Pro repeats are found in Chlamydomonas reinhardtii; (ii) Classical AGPs, AG-peptides, and Lys-rich classical AGPs first emerged in Physcomitrella patens, Selaginella moellendorffii, and Picea abies, respectively; (iii) Nine subfamilies of chimeric AGPs are introduced as newly identified chimeric subfamilies similar to fasciclin-like, phytocyanin-like, and xylogen-like AGPs; (iv) The length and amino acid composition of Lys-rich domains are largely variable, indicating an insertion/deletion model during evolution. Our findings provide not only a powerful means to identify AGP gene families but also probable explanations of AGPs in maintaining the plant cell wall and transducing extracellular signals into the cytoplasm.