Multi-omics analysis identifies a role for <i>Streptococcus suis</i> MnmE in growth regulation and environmental adaptation

ABSTRACT Streptococcus suis is a major bacterial pathogen of pigs and a significant zoonotic threat to human health. A critical unresolved question is whether the bacterium can rapidly respond to adverse environmental conditions by regulating the expression of mRNA rich in specific codons, thereby facilitating colonization and infection. MnmE, a highly conserved multi-domain GTPase, plays a key role in tRNA U 34 modification, which is essential for maintaining translational fidelity across both bacterial and eukaryotic organisms. Compared with wild-type S. suis , a Δ mnmE mutant displayed growth defects, altered morphology, reduced virulence, impaired environmental tolerance, reduced capsular polysaccharide production, and defective carbohydrate utilization. Omics analyses confirmed perturbations in carbohydrate metabolism, transcription/translation, and ion transport, consistent with phenotypic changes. Notably, mRNA enriched in U 34 codons did not solely determine protein expression upon loss of U 34 tRNA modification enzymes, instead revealing a translational bias toward A-ending codons within synonymous codons. Furthermore, we demonstrated that MnmE is required for intracellular metal ion homeostasis by influencing the expression of proteins related to metal ion transport, which in turn affects intracellular reactive oxygen species levels and the ability to survive. These findings highlight that MnmE is indispensable for S. suis physiology and pathogenicity. IMPORTANCE Streptococcus suis is a major swine and zoonotic pathogen. While bacterial tRNA modifications are known to fine-tune translation, their role in coordinating pathogenesis and stress adaptation remains poorly characterized. Here, we demonstrate that the tRNA-modifying GTPase MnmE is essential for S. suis virulence and environmental resilience. Through integrated multi-omics and phenotypic analyses, we show that MnmE deletion cripples carbohydrate metabolism, disrupts metal homeostasis, and attenuates virulence by globally dysregulating stress-response networks and virulence effectors. Crucially, we reveal that U 34 codon enrichment in mRNAs does not predict translational outcomes when MnmE is absent, uncovering new complexity in post-transcriptional regulation. This work advances our understanding of tRNA modification as a node linking translational fidelity to metabolic adaptation and pathogenicity, extending beyond model microorganisms.