A metabolome genome-wide association study implicates histidine N-pi-methyltransferase as a key enzyme in N-methylhistidine biosynthesis in Arabidopsis thaliana

Kai Uchida; June-Sik Kim; Muneo Sato; Hiromitsu Tabeta; Keiichi Mochida; Masami Yokota Hirai

doi:10.3389/fpls.2023.1201129

A metabolome genome-wide association study implicates histidine N-pi-methyltransferase as a key enzyme in N-methylhistidine biosynthesis in Arabidopsis thaliana

Front Plant Sci. 2023 Jun 8:14:1201129. doi: 10.3389/fpls.2023.1201129. eCollection 2023.

Authors

Kai Uchida¹, June-Sik Kim^{1

2}, Muneo Sato¹, Hiromitsu Tabeta¹, Keiichi Mochida^{1

3

4

5}, Masami Yokota Hirai^{1

6}

Affiliations

¹ RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
² Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan.
³ Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan.
⁴ School of Information and Data Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan.
⁵ RIKEN Baton Zone Program, Yokohama, Kanagawa, Japan.
⁶ Department of Applied Biosciences, Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Japan.

Abstract

A genome-wide association study (GWAS), which uses information on single nucleotide polymorphisms (SNPs) from many accessions, has become a powerful approach to gene identification. A metabolome GWAS (mGWAS), which relies on phenotypic information based on metabolite accumulation, can identify genes that contribute to primary and secondary metabolite contents. In this study, we carried out a mGWAS using seed metabolomic data from Arabidopsis thaliana accessions obtained by liquid chromatography-mass spectrometry to identify SNPs highly associated with the contents of metabolites such as glucosinolates. These SNPs were present in genes known to be involved in glucosinolate biosynthesis, thus confirming the effectiveness of our analysis. We subsequently focused on SNPs detected in an unknown methyltransferase gene associated with N-methylhistidine content. Knockout and overexpression of A. thaliana lines of this gene had significantly decreased and increased N-methylhistidine contents, respectively. We confirmed that the overexpressing line exclusively accumulated histidine methylated at the pi position, not at the tau position. Our findings suggest that the identified methyltransferase gene encodes a key enzyme for N-methylhistidine biosynthesis in A. thaliana.

Keywords: GWAS; LC-MS/MS; N-methylhistidine; metabolomic analysis; methyltransferase.