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Bioinformatics identification of the methylerythritol phosphate pathway associated genes in Arabidopsis thaliana with ceh1 mutant

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Abstract

The methylerythritol phosphate (MEP) pathway for the production of isoprenoids is recently discovered. The current study aimed to identify MEP pathway disorder-related molecular mechanisms and potential genes in Arabidopsis thaliana. Microarray data (GSE61675) obtained from ceh1 mutant plants and corresponding parental lines were retrieved from Gene Expression Omnibus (GEO) database and were applied for differentially expressed genes (DEGs) screening. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed. Protein-protein interaction (PPI) network was then constructed and displayed by Cytoscape software. Total 762 DEGs including 620 up-regulated and 142 down-regulated genes were screened. In addition, a great many of DEGs were mainly involved in biosynthesis and metabolism-related pathways, such as stilbenoid, diarylheptanoid, and gingerol biosynthesis, and biosynthesis of terpenoids and steroids. Moreover, a PPI network contained 90 down-regulated genes and 497 up-regulated genes were obtained. Up-regulated DEGs including glutaredoxin (GRX480, cytochrome BC1 synthase (BCS1, syntaxin of plants 121 (SYP121) and A. thaliana MAP kinase 11 (ATMPK11) with higher degree in this network were hub nodes. Pathways including stilbenoid, diarylheptanoid, and gingerol biosynthesis obtained in our study were consistent with previous studies. Importantly, GRX480, BCS1 and ATMPK11 could have close interactions with the MEP pathway and may play important roles in the biosynthesis of isoprenoids.

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Abbreviations

DAVID:

database for annotation, visualization, and integrated discovery

DEGs:

differentially expressed genes

GEO:

Gene Expression Omnibus

HPL:

hydroperoxide lyase

IspH/HDR:

hydroxymethylbutenyl diphosphate reductase

JA:

jasmonic acid

KEGG:

Kyoto Encyclopedia of Genes and Genomes

MAP kinases:

mitogen-activated protein kinases

MEcPP:

methylerythritol cyclodiphosphate

MEP:

methylerythritol phosphate

MVA:

mevalonic acid

NCBI:

National Center for Biotechnology Information

PPI:

protein-protein interaction

STRING:

Search Tool for the Retrieval of Interacting Genes

SA:

salicylic acid

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Authors and Affiliations

  1. College of Plant Sciences, Jilin University, Changchun, China

    C. Lang & J. Xi

  2. College of Biology and Food Engineering, Jilin Institute of Chemical Technology, Jilin, China

    C. Lang

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  1. C. Lang
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  2. J. Xi
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Correspondence to J. Xi.

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Lang, C., Xi, J. Bioinformatics identification of the methylerythritol phosphate pathway associated genes in Arabidopsis thaliana with ceh1 mutant. Russ J Plant Physiol 63, 293–299 (2016). https://doi.org/10.1134/S1021443716020096

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  • DOI: https://doi.org/10.1134/S1021443716020096

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