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Genome-wide identification, classification and expression analysis of GHMP genes family in Arabidopsis thaliana

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Abstract

The GHMP genes family, a unique class of ATP-dependent enzymes, consists of galactokinases, homoserine kinases, mevalonate kinases and phosphomevalonate kinase etc. It was implicated in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. Previous studies mainly focused on the structure, catalytic mechanism or function in abiotic stress signaling. In this study, we integrated the research progress on GHMP genes and identified 12 members (five previously discovered and seven newly identified here) of this family in Arabidopsis thaliana. The gene ontology, phylogenetic relationship, motifs, cis-acting element, expression profiles, structures and protein–protein interaction network of GHMP family were analyzed. The neighbor-joining tree and cluster of gene structures indicated that the 12 members were divided into two classes. The three motifs in the GHMP family were highly conserved among the GHMP family by Multiple EM for Motif Elicitation, providing further proof on their phylogenetic relationship. Additionally, prediction on cis-acting elements indicated that these genes were likely to be involved in multiple responses stimulated by various hormones and abiotic stress. It is roughly consistent with the data of microarray. The identification and bioinformatic analysis of GHMP family in Arabidopsis thaliana could provide reference data for further study on their biological functions, especially in the responsiveness to hormones and stress signaling.

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Acknowledgments

This research was supported by Grants from the National Natural Science Foundation of China (31071076, 61472127, 30871325 and 61272395), the Program for New Century Excellent Talents in University (NCET-10-0363 to X. Guo), the Excellent Youth Foundation of Hunan Province (11JJ1005), the Ph.D. Programs Foundation of Ministry of Education of China (20130161110005), Changsha Science and Technology Funds (K1406036-21 to X. Guo), International S&T Cooperation Program of Hunan Province (2014WK3012 to J. Ye, 2015WK to X. Guo), the interdisciplinary research project of Hunan University (2015 to X. Guo), the National Key Technology R&D Program (2012BAH09B02), and the SIT Project of Hunan University, 2013 and 2014.

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    1. College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, People’s Republic of China

      Wenjun Xiao, Hongping Chang, Ping Zhou, Congying Yuan, Cheng Zhang, Runyu Yao, Xiutao Lu, Zhuang He, Rong Hu & Xinhong Guo

    2. Key Laboratory for Embedded and Network Computing of Hunan Province, The College of Information Science and Engineering, Hunan University, Changsha, 410082, People’s Republic of China

      Lijun Cai

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    1. Wenjun Xiao
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    Handling editor: Martin Lysak.

    W. Xiao and H. Chang contributed equally to this work.

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    606_2015_1219_MOESM1_ESM.jpg

    Supplementary material 1 (JPEG 4394 kb) Supplemental Fig. S1 Protein-coding sequences alignment of 12 GHMP genes in Arabidopsis thaliana. The conservative amino acids were highlighted in blue, while the more conservative in red

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    Xiao, W., Chang, H., Zhou, P. et al. Genome-wide identification, classification and expression analysis of GHMP genes family in Arabidopsis thaliana . Plant Syst Evol 301, 2125–2140 (2015). https://doi.org/10.1007/s00606-015-1219-9

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