SuCComBase: a manually curated repository of plant sulfur-containing compounds.

Sarahani Harun,Nor Azlan Nor Muhammad,Muhammad-Redha Abdullah-Zawawi,Zeti-Azura Mohamed-Hussein,Mohd Rusman Arief A-Rahman

doi:10.1093/database/baz021

Sarahani Harun, Nor Azlan Nor Muhammad + Show 3 more

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https://doi.org/10.1093/database/baz021

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Abstract

Plants produce a wide range of secondary metabolites that play important roles in plant defense and immunity, their interaction with the environment and symbiotic associations. Sulfur-containing compounds (SCCs) are a group of important secondary metabolites produced in members of the Brassicales order. SCCs constitute various groups of phytochemicals, but not much is known about them. Findings from previous studies on SCCs were scattered in published literatures, hence SuCComBase was developed to store all molecular information related to the biosynthesis of SCCs. Information that includes genes, proteins and compounds that are involved in the SCC biosynthetic pathway was manually identified from databases and published scientific literatures. Sets of co-expression data was analyzed to search for other possible (previously unknown) genes that might be involved in the biosynthesis of SCC. These genes were named as potential SCC-related encoding genes. A total of 147 known and 92 putative Arabidopsis thaliana SCC-related genes from literatures were used to identify other potential SCC-related encoding genes. We identified 778 potential SCC-related encoding genes, 4026 homologs to the SCC-related encoding genes and 116 SCCs as shown on SuCComBase homepage. Data entries are searchable from the Main page, Search, Browse and Datasets tabs. Users can easily download all data stored in SuCComBase. All publications related to SCCs are also indexed in SuCComBase, which is currently the first and only database dedicated to plant SCCs. SuCComBase aims to become a manually curated and au fait knowledge-based repository for plant SCCs.

Highlights

Secondary metabolites are metabolites synthesized by living cells that are not directly involved in cellular metabolism of organisms such as growth, development and reproduction [1, 2]
Gene Ontology Consortium [54] was used to identify gene ontology (GO) in known sulfur-containing compounds (SCCs)-related genes, potential SCC-related genes and putative SCC-related genes to provide a clearer understanding of SCC biosynthesis in A. thaliana
We have identified 92 computationally predicted genes that might be involved in the production of SCCs and classified them as putative SCC-related genes

Summary

Introduction

Secondary metabolites are metabolites synthesized by living cells that are not directly involved in cellular metabolism of organisms such as growth, development and reproduction [1, 2]. Secondary metabolites act as chemical defense against plant pests and pathogens. Many experimental findings revealed various important functions of secondary metabolites indicating their role and importance in defense response against pathogens [1, 3,4,5,6]. Apart from being toxic or repellant to herbivores or pests and microbes, they regulate beneficial interactions such as attracting pollinators or seed dispersal and modulation of abiotic stress responses [7,8,9]. SCCs are very important in plant–pest interaction in various types of plant families comprising species-specific defense chemicals such as camalexin in Brassicaceae, glucosinolates (GSLs) in Brassicales, alline in Alliaceae, thiopene in Asteraceae and defensins in other plant families [13]

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