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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• 作者：Jun Zhang (1) (2)
  Zhengshuang Hua (2)
  Zebo Huang (1)
  QiZhu Chen (1)
  Qingyun Long (1)
  David J. Craik (3)
  Alan J. M. Baker (4)
  Wensheng Shu (2)
  Bin Liao (2)
  
  1. School of Biosciences and Biopharmaceutics ; Guangdong Province Key Laboratory for Biotechnology Drug Candidates ; Guangdong Pharmaceutical University ; Guangzhou ; 510006 ; China
  2. School of Life Sciences ; State Key Laboratory of Biocontrol ; Sun Yat-sen University ; Guangzhou ; 510006 ; China
  3. Institute for Molecular Bioscience ; The University of Queensland ; Brisbane ; QLD ; 4072 ; Australia
  4. School of Botany ; The University of Melbourne ; Victoria ; 3010 ; Australia
  
• 关键词：CyPerl ; CyExcel ; Cyclotides ; Genomes ; Protein databases ; Plant family
• 刊名：Planta
• 出版年：2015
• 出版时间：April 2015
• 年：2015
• 卷：241
• 期：4
• 页码：929-940
• 全文大小：2,552 KB
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• 刊物主题：Plant Sciences; Agriculture; Ecology; Forestry;
• 出版者：Springer Berlin Heidelberg
• ISSN：1432-2048

文摘

Main conclusion Two 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 vulgaris and Zea mays were 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.