Characterization of the Streptococcus mutans SMU.1703c-SMU.1702c Operon Reveals Its Role in Riboflavin Import and Response to Acid Stress

Decoding gene expression dynamics in planktonic and biofilm cells of Streptococcus mutans: regulation and role of mutanofactin genes in biofilm formation

Introduction

Dental caries is the most prevalent chronic infectious disease globally, with Streptococcus mutans recognized as a primary causative agent due to its acidogenicity and robust biofilm-forming ability. In S. mutans biofilm formation, the role of autoinducers has been extensively studied, while the influence of other small molecules remains largely unexplored. Mutanofactins, a class of polyketide/non-ribosomal lipopeptide secondary metabolites, are emerging as potential modulators of S. mutans biofilm development.

Methods

Transcriptomic analysis was conducted to examine gene expression patterns in S. mutans NMT4863 across distinct growth phases and lifestyles, aiming to identify metabolic factors influencing biofilm formation. Transcriptomic profiles were compared between cells in early-, mid-, and late-exponential-, and stationary phase, as well as between planktonic and biofilm cells. Differentially expressed genes were identified, and pathway analyses revealed significant alterations in key metabolic and regulatory pathways. Specifically, the biosynthetic mutanofactin gene cluster was analyzed via quantitative real-time polymerase chain reaction.

Results

Several genes and operons were differentially expressed across the tested growth phases, with 1,095 genes showing differential expression between stationary-phase, planktonic and biofilm cells. Pathway analysis revealed significant changes in ascorbate metabolism, carbohydrate utilization and transport systems, lipoic acid metabolism, bacterial toxin pathways, two-component regulatory systems, and secondary metabolite biosynthesis. Notably, expression of the muf gene cluster, was elevated in early exponential-phase cells relative to stationary-phase cells. Additionally, the mufCDEFGHIJ genes were identified as components of a single transcriptional unit (muf operon). MufC, a transcriptional regulator of the TetR/AcrR-family, acts as a positive regulator of the muf operon in strain NMT4863. Bioinformatic analysis pinpointed a 20-bp regulatory sequence in the muf operon promoter region (5'-AAATGAGCTATAATTCATTT-3'). Interestingly, the muf operon was found to be significantly downregulated in biofilm cells.

Conclusion

This study provides key insights into gene expression dynamics that drive biofilm formation in S. mutans NMT4863, with a particular emphasis on the role of the muf operon. This operon is governed by the TetR/AcrR-family regulator MufC and plays a central role in biofilm development, offering a novel perspective on the molecular basis of S. mutans biofilm formation and resilience.

Riboswitch Distribution in the Human Gut Microbiome Reveals Common Metabolite Pathways

Riboswitches are widely distributed, conserved RNAs which regulate metabolite levels in bacterial cells through direct, noncovalent binding of their cognate metabolite. Various riboswitch families are highly enriched in gut bacteria, suggestive of a symbiotic relationship between the host and bacteria. Previous studies of the distribution of riboswitches have examined bacterial taxa broadly. Thus, the distribution of riboswitches associated with bacteria inhabiting the intestines of healthy individuals is not well understood. To address these questions, we survey the gut microbiome for riboswitches by including an international database of prokaryotic genomes from the gut samples. Using Infernal, a program that uses RNA-specific sequence and structural features, we survey this data set using existing riboswitch models. We identify 22 classes of riboswitches with vitamin cofactors making up the majority of riboswitch-associated pathways. Our finding is reproducible in other representative databases from the oral as well as the marine microbiomes, underscoring the importance of thiamine pyrophosphate, cobalamin, and flavin mononucleotide in gene regulation. Interestingly, riboswitches do not vary significantly across microbiome representatives from around the world despite major taxonomic differences; this suggests an underlying conservation. Further studies elucidating the role of bacterial riboswitches in the host metabolome are needed to illuminate the consequences of our finding.

Deciphering the molecular functionality of Cdc45 in replisomal complex

The members of DHH superfamily have been reported with diverse substrate spectrum and play pivotal roles in replication, repair, and RNA metabolism. This family comprises phosphatases, phosphoesterase and bifunctional enzymes having nanoRNase and phosphatase activities. Cell cycle factor Cdc45, a member of this superfamily, is crucial for movement of the replication fork during DNA replication and an important component of the replisome. The specific protein-protein interactions of Cdc45 with other factors along with helicase moderate the faithful DNA replication process. However, the exact biochemical functions of this factor are still unknown and need further investigation. Here, we studied the biochemical roles of Cdc45 and its molecular interactions within the replisomal complex. The alteration in the level of protein, observed when DNA damage is induced in-vivo, suggests its association with DNA replication stress. We analyzed protein Cdc45, providing new insights about the molecular and biochemical functionality of this replisomal factor.