Analysis of the Streptococcus mutans proteome during acid and oxidative stress reveals modules of co-expression and an expanded role for the TreR transcriptional regulator

Streptococcus mutans promotes a tooth-damaging dysbiosis in the oral microbiota because it can form biofilms and survive acid stress better than most of its ecological competitors, which are typically health-associated. Many of these commensals produce hydrogen peroxide, therefore S. mutans must manage both oxidative stress and acid stress with coordinated and complex physiological responses. In this study, the proteome of S. mutans was examined during regulated growth in acid and oxidative stresses, as well as in deletion mutants with impaired oxidative stress phenotypes, {Delta}nox and {Delta}treR. 607 proteins exhibited significantly different abundance levels across the conditions tested, and correlation network analysis identified modules of co-expressed proteins that were responsive to the deletion of nox and/or treR, as well as acid and oxidative stress. The data provided evidence explaining the ROS-sensitive and mutacin-deficient phenotypes exhibited by the {Delta}treR strain. SMU.1069-1070, a poorly understood LytTR system, had elevated abundance in the {Delta}treR strain. S. mutans LytTR systems regulate mutacin production and competence, which may explain how TreR affects mutacin production. Furthermore, the gene cluster that produces mutanobactin, a lipopeptide important in ROS tolerance, displayed reduced abundance in the {Delta}treR strain. The role of Nox as a keystone in the oxidative stress response was also emphasized. Crucially, this dataset provides oral health researchers with a proteome atlas that will enable a more complete understanding of the S. mutans stress responses that are required for pathogenesis, and facilitate the development of new and improved therapeutic approaches for dental caries. ImportanceDental caries is the most common chronic infectious disease worldwide, and disproportionally affects marginalized socioeconomic groups. Streptococcus mutans is a considered a primary etiologic agent of caries, with its pathogenicity dependent on coordinated physiologic stress responses that mitigate the damage caused by the oxidative and acid stress common within dental plaque. In this study, the proteome of S. mutans was examined during growth in acidic and oxidative stresses, as well in nox and treR deletion mutants. 607 proteins were differentially expressed across the strains/growth conditions, and modules of co-expressed proteins were identified, which enabled mapping the acid and oxidative stress responses across S. mutans metabolism. The presence of TreR was linked to mutacin production via LytTR system signaling and to oxidative stress via mutanobactin production. The data provided by this study will guide future research elucidating S. mutans pathogenesis and developing improved preventative and treatment modalities for dental caries.