Efficient identification of NLR by using a genome-wide protein domain and motif survey program, Ex-DOMAIN.

IF 1.4 4区生物学 Q4 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Plant Biotechnology Pub Date : 2018-06-25 DOI:10.5511/plantbiotechnology.18.0418a

M. Narusaka, H. Yunokawa, Y. Narusaka

{"title":"Efficient identification of NLR by using a genome-wide protein domain and motif survey program, Ex-DOMAIN.","authors":"M. Narusaka, H. Yunokawa, Y. Narusaka","doi":"10.5511/plantbiotechnology.18.0418a","DOIUrl":null,"url":null,"abstract":"Genomic and amino acid sequences of organisms are freely available from various public databases. We designed a genome-wide survey program, named \"Ex-DOMAIN\" (exhaustive domain and motif annotator using InterProScan), of protein domains and motifs to aid in the identification and characterization of proteins by using the InterProScan sequence analysis application, which can display information and annotations of targeted proteins and genes, conserved protein domains and motifs, chromosomal locations, and structural diversities of target proteins. In this study, we indicated the disease resistance genes (proteins) that play an important role in defense against pathogens in Arabidopsis thaliana (thale cress) and Cucumis sativus (cucumber), by searches based on the conserved protein domains, NB-ARC (a nucleotide-binding adaptor shared by the apoptotic protease-activating factor-1, plant resistance proteins, and Caenorhabditis elegans death-4 protein) and C-terminal leucine-rich repeat (LRR), in the nucleotide-binding domain and LRR (NLR) proteins. Our findings suggest that this program will enable searches for various protein domains and motifs in all organisms.","PeriodicalId":20411,"journal":{"name":"Plant Biotechnology","volume":"35 2 1","pages":"177-180"},"PeriodicalIF":1.4000,"publicationDate":"2018-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5511/plantbiotechnology.18.0418a","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Biotechnology","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.5511/plantbiotechnology.18.0418a","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}

引用次数: 1

Abstract

Genomic and amino acid sequences of organisms are freely available from various public databases. We designed a genome-wide survey program, named "Ex-DOMAIN" (exhaustive domain and motif annotator using InterProScan), of protein domains and motifs to aid in the identification and characterization of proteins by using the InterProScan sequence analysis application, which can display information and annotations of targeted proteins and genes, conserved protein domains and motifs, chromosomal locations, and structural diversities of target proteins. In this study, we indicated the disease resistance genes (proteins) that play an important role in defense against pathogens in Arabidopsis thaliana (thale cress) and Cucumis sativus (cucumber), by searches based on the conserved protein domains, NB-ARC (a nucleotide-binding adaptor shared by the apoptotic protease-activating factor-1, plant resistance proteins, and Caenorhabditis elegans death-4 protein) and C-terminal leucine-rich repeat (LRR), in the nucleotide-binding domain and LRR (NLR) proteins. Our findings suggest that this program will enable searches for various protein domains and motifs in all organisms.

查看原文本刊更多论文

使用全基因组蛋白质结构域和基序调查程序Ex domain有效鉴定NLR。

生物体的基因组和氨基酸序列可以从各种公共数据库中免费获得。我们设计了一个名为“Ex-DOMAIN”（使用InterProScan的详尽结构域和基序注释器）的全基因组蛋白质结构域和基序调查程序，以通过使用InterProScan-序列分析应用程序帮助识别和表征蛋白质，该程序可以显示靶向蛋白质和基因、保守蛋白质结构域，染色体位置和靶蛋白的结构多样性。在本研究中，我们通过基于保守蛋白结构域的搜索，指出了在拟南芥（thale cress）和黄瓜（Cucumis sativus）中对病原体防御起重要作用的抗病基因（蛋白质），NB-ARC（一种由凋亡蛋白酶激活因子-1、植物抗性蛋白和秀丽隐杆线虫死亡-4蛋白共享的核苷酸结合接头）和核苷酸结合结构域和LRR（NLR）蛋白中的C-末端富含亮氨酸重复序列（LRR）。我们的发现表明，该程序将能够在所有生物体中搜索各种蛋白质结构域和基序。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Plant Biotechnology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-PLANT SCIENCES

CiteScore

2.90

自引率

18.80%

发文量

审稿时长

6-12 weeks

期刊介绍： Plant Biotechnology is an international, open-access, and online journal, published every three months by the Japanese Society for Plant Biotechnology. The journal, first published in 1984 as the predecessor journal, “Plant Tissue Culture Letters” and became its present form in 1997 when the society name was renamed to Japanese Society for Plant Cell and Molecular Biology, publishes findings in the areas from basic- to application research of plant biotechnology. The aim of Plant Biotechnology is to publish original and high-impact papers, in the most rapid turnaround time for reviewing, on the plant biotechnology including tissue culture, production of specialized metabolites, transgenic technology, and genome editing technology, and also on the related research fields including molecular biology, cell biology, genetics, plant breeding, plant physiology and biochemistry, metabolic engineering, synthetic biology, and bioinformatics.