The ΔyidC2 Mutant of Streptococcus mutans is Tired and Hungry

Objectives: All oral streptococci have two YidC paralogs of the universally conserved YidC/Oxa/Alb family of membrane protein chaperone-insertases, the substrates of which include proteins of respiratory chain complexes in bacteria, mitochondria and chloroplast, respectively. In Streptococcus mutans, deletion of either yidC gene affects stress tolerance, biofilm formation, surface-protein biogenesis, and disease severity in a rat model of dental caries, with loss of yidC2 having a greater effect than yidC1. To better understand the phenotypic differences between the ΔyidC1 and ΔyidC2 mutants of S. mutans, RNA-seq was used to compare the transcriptomes of the mutant and parental strains.
Methods: Total RNA was obtained from mid-exponential phase cells and rRNAs were depleted using the Ambion MicrobExpress kit. Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep kit for Illumina. The libraries were sequenced on an Illumina Nextseq500 at >10X coverage (~23 million reads/sample). Differential expression (DE) analysis was performed using Degust (EdgeR algorithm).
Results: There were 253 genes differentially expressed (137 increased and 116 decreased) in the ΔyidC2 mutant compared to the parental strain (>2-fold change; FDR ≤ 0.05). In contrast, the expression of only 15 genes was altered in the ΔyidC1 mutant (5 increased, 10 decreased; FDR ≤ 0.05). Expression of a large number of energy metabolism genes and non-preferred sugar PTS pathways was increased in the ΔyidC2 mutant (tired and hungry), although expression of the dnaK operon was decreased in both yidC mutants.
Conclusions: The pattern of aberrantly regulated genes in the yidC2 mutant indicates compromised energy levels and induction of compensatory carbohydrate scavenging, consistent with the slow growth phenotype of the yidC2 mutant. The decreased expression of the dnaK operon in yidC mutants may indicate previously unrecognized coordinated regulation of expression of genes involved in protein chaperone activity in S. mutans.