Proteomic and Metabolomic Analyses Provide Insights into the Mechanism on Arginine Metabolism Regulated by tRNA Modification Enzymes GidA and MnmE of Streptococcus suis.

Ting Gao,Rui Zhou,Wan Liang,Yongxiang Tian,Wei Liu,Rui Guo,Fangyan Yuan,Keli Yang,Geng Zou,Zewen Liu,Danna Zhou

doi:10.3389/fcimb.2020.597408

Abstract

GidA and MnmE, two important tRNA modification enzymes, are contributed to the addition of the carboxymethylaminomethyl (cmnm) group onto wobble uridine of tRNA. GidA-MnmE modification pathway is evolutionarily conserved among Bacteria and Eukarya, which is crucial in efficient and accurate protein translation. However, its function remains poorly elucidated in zoonotic Streptococcus suis (SS). Here, a gidA and mnmE double knock-out (DKO) strain was constructed to systematically decode regulatory characteristics of GidA-MnmE pathway via proteomic. TMT labelled proteomics analysis identified that many proteins associated with cell divison and growth, fatty acid biosynthesis, virulence, especially arginine deiminase system (ADS) responsible for arginine metabolism were down-regulated in DKO mutant compared with the wild-type (WT) SC19. Accordingly, phenotypic experiments showed that the DKO strain displayed decreased in arginine consumption and ammonia production, deficient growth, and attenuated pathogenicity. Moreover, targeted metabolomic analysis identified that arginine was accumulated in DKO mutant as well. Therefore, these data provide molecular mechanisms for GidA-MnmE modification pathway in regulation of arginine metabolism, cell growth and pathogenicity of SS. Through proteomic and metabolomic analysis, we have identified arginine metabolism that is the links between a framework of protein level and the metabolic level of GidA-MnmE modification pathway perturbation.

Highlights

TRNA modifications are widely distributed in Bacteria and Eukarya, some of which are conserved in nature
As GidA and MnmE were important tRNA modification enzyme contributed in efficient and accurate protein translation, we performed proteomics to systematically analyze the function of GidA and MnmE modification pathway in suis serotype 2 (SS2)
According to gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis, the main function of the 441 differentially expressed proteins (DEPs) were involved in catalytic activity, binding, transporter activity, transcription regulator activity, and structural molecule activity

Summary

Introduction

TRNA modifications are widely distributed in Bacteria and Eukarya, some of which are conserved in nature. More than 90 modified nucleosides have been found in tRNA (Hori, 2014), such as base isomerization, thiolation, deamination, methylation of a ribose or base, or complex hypermodifications and so on (Boccaletto et al, 2018). In bacteria, modified nucleosides of different chemical structures, present in different positions, and in different species of the tRNA all prevent frameshifts errors (Urbonavicius et al, 2001; Schweizer et al, 2017). TRNA modifications are essential for the control of bacterial gene expression under stressful and changing environments (Gustilo et al, 2008). Hundreds of tRNA modification enzymes have been identified and there are great diversity of enzymes in wobble position modification (Shippy and Fadl, 2014; Hou et al, 2015)

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