Two Blast-independent tools, CyPerl and CyExcel, for harvesting hundreds of novel cyclotides and analogues from plant genomes and protein databases
Two Blast-independent tools, CyPerl and CyExcel, for harvesting hundreds of novel cyclotides and analogues from plant genomes and protein databases
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DOI：
10.1007/s00425-014-2229-5
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发表时间：
2014-12
期刊：
影响因子：
4.3
通讯作者：
Jun Zhang;Zhengshuang Hua;Zebo Huang;Qizhu Chen;Qingyun Long;D. Craik;A. Baker;Wensheng Shu;B. Liao
中科院分区：
文献类型：
--
作者：
Jun Zhang;Zhengshuang Hua;Zebo Huang;Qizhu Chen;Qingyun Long;D. Craik;A. Baker;Wensheng Shu;B. Liao
主要结论两种高通量工具从植物中获得了数百种新的环肽及其类似物，环肽是基因编码的主链环化多肽，具有多种与植物防御相关的生物活性。然而，基因组规模或数据库规模的评价环肽一直罕见的。在这里，一个新的时间效率的Perl程序，CyPerl，开发用于搜索cyclotides从预测的ORF的34个可用的植物基因组和现有的植物蛋白质序列从Genbank数据库。通过去除重复序列、评估其半胱氨酸分布区域（CDR）并在用户友好的Excel（Microsoft Office）模板CyExcel中与CyBase收集的环肽进行比较来进一步分析CyPerl分离的序列。经过基因组筛选，用CyPerl和CyExcel软件从10个科30种植物基因组中鉴定出186个ORF，其中含有145个独特的环肽类似物，菜豆和玉米是含环肽类似物最丰富的两种植物。经过蛋白质数据库筛选，从7个植物科中鉴定出266种独特的环肽及其类似物。通过与288个独特的CyBase列出的环肽合并，从13个植物科中获得510个独特的环肽和类似物。在这项研究中，总共鉴定了7个新的植物家族含有环肽类似物和202个新的环肽类似物。本研究建立了两个独立于Blast的工具，用于从植物基因组和蛋白质数据库中筛选环肽类化合物，也显著拓宽了环肽类化合物及其类似物的植物分布和序列多样性。
Main conclusionTwo high-throughput tools harvest hundreds of novel cyclotides and analogues in plants.Cyclotides are gene-encoded backbone-cyclized polypeptides displaying a diverse range of bioactivities associated with plant defense. However, genome-scale or database-scale evaluations of cyclotides have been rare so far. Here, a novel time-efficient Perl program, CyPerl, was developed for searching cyclotides from predicted ORFs of 34 available plant genomes and existing plant protein sequences from Genbank databases. CyPerl-isolated sequences were further analyzed by removing repeats, evaluating their cysteine-distributed regions (CDRs) and comparing with CyBase-collected cyclotides in a user-friendly Excel (Microsoft Office) template, CyExcel. After genome-screening, 186 ORFs containing 145 unique cyclotide analogues were identified by CyPerl and CyExcel from 30 plant genomes tested from 10 plant families.Phaseolus vulgarisandZea mayswere the richest two species containing cyclotide analogues in the plants tested. After screening protein databases, 266 unique cyclotides and analogues were identified from seven plant families. By merging with 288 unique CyBase-listed cyclotides, 510 unique cyclotides and analogues were obtained from 13 plant families. In total, seven novel plant families containing cyclotide analogues and 202 novel cyclotide analogues were identified in this study. This study has established two Blast-independent tools for screening cyclotides from plant genomes and protein databases, and has also significantly widened the plant distribution and sequence diversity of cyclotides and their analogues.