Biology subjects

LaBonte, S. A.

Publications and source records attributed to LaBonte, S. A..

4 recordsLinked to original sources

bioRxiv2025

Chloramphenicol-mobilized Bacillus subtilis elevates transient expression of multiple antibiotic resistance genes, including the glycopeptides phleomycin and bleomycin

Antibiotic resistance presents an urgent global crisis, exacerbated by antibiotic overuse. Understanding of the regulation of resistance genes within bacterial populations can inform strategies to prevent the spread of antibiotic resistance and reveal how antibiotics shape microbial communities. We identified upregulation of five antibiotic resistance loci in Bacillus subtilis colonies on solid growth media, following exposure to subinhibitory chloramphenicol concentrations. Notably, four resistance loci, bmrCD, vmlR, tlrB, and ytbDE, are regulated by transcription attenuation. Full expression depends upon antibiotic-induced ribosome stalling on upstream leader peptides, promoting transcription of the downstream gene. Here, we use luciferase reporter constructs fused to the 5 regulatory region of each resistance gene to show differential spatiotemporal patterns of antibiotic resistance gene expression, revealing an intrinsic activation in addition to chloramphenicol induction in mobilized B. subtilis colonies. Because expression is under translational regulation, the data suggest natural translation pausing, in addition to antibiotic exposure, is an endogenous function that regulates these antibiotic resistance genes. While VmlR and TlrB have been previously characterized as conferring resistance to LSAPs (lincosamides, streptogramin A, and pleuromutilin) and tylosin, respectively, antibiotics for BmrCD and YtbDE resistance complexes have not yet been identified. We demonstrate that although these resistance genes do not provide resistance to chloramphenicol, pre-exposure to chloramphenicol improved B. subtilis growth when cells were subsequently exposed to subinhibitory concentrations of respective antibiotics. We discovered that BmrCD confers resistance to the DNA-damaging glycopeptides, phleomycin and bleomycin, revealing that resistance arising from stalled ribosomes extends beyond drugs that target translation.

microbiology↗

bioRxiv2024

MOB rules: Antibiotic Exposure Reprograms Metabolism to Mobilize Bacillus subtilis in Competitive Interactions

Antibiotics have dose-dependent effects on exposed bacteria. The medicinal use of antibiotics relies on their growth-inhibitory activities at sufficient concentrations. At subinhibitory concentrations, exposure effects vary widely among different antibiotics and bacteria. Bacillus subtilis responds to bacteriostatic translation inhibitors by mobilizing a population of cells (MOB-Mobilized Bacillus) to spread across a surface. How B. subtilis regulates the antibiotic-induced mobilization is not known. In this study, we used chloramphenicol to identify regulatory functions that B. subtilis requires to coordinate cell mobilization following subinhibitory exposure. We measured changes in gene expression and metabolism and mapped the results to a network of regulatory proteins that direct the mobile response. Our data reveal that several transcriptional regulators coordinately control the reprogramming of metabolism to support mobilization. The network regulates changes in glycolysis, nucleotide metabolism, and amino acid metabolism that are signature features of the mobilized population. Among the hundreds of genes with changing expression, we identified two, pdhA and pucA, where the magnitudes of their changes in expression, and in the abundance of associated metabolites, reveal hallmark metabolic features of the mobilized population. Using reporters of pdhA and pucA expression, we visualized the separation of major branches of metabolism in different regions of the mobilized population. Our results reveal a regulated response to chloramphenicol exposure that enables a population of bacteria in different metabolic states to mount a coordinated mobile response.

microbiology↗

bioRxiv2022

mucG, mucH,and mucI modulate production of mutanocyclin and reutericyclins in Streptococcus mutans B04Sm5

Streptococcus mutans is considered a primary etiologic agent of dental caries, which is the most common chronic infectious disease worldwide. S. mutans B04Sm5 was recently shown to produce reutericyclins and mutanocyclin through the muc biosynthetic gene cluster, and to utilize reutericyclins to inhibit the growth of neighboring commensal Streptococci. In this study, examination of S. mutans and muc phylogeny suggested evolution of an ancestral S. mutans muc into three lineages within one S. mutans clade, and then horizontal transfer of muc to other S. mutans clades. The roles of the mucG and mucH transcriptional regulators, and the mucI transporter, were also examined. mucH was demonstrated to encode a transcriptional activator of muc. mucH deletion reduced production of mutanocyclin and reutericyclins, and eliminated the impaired growth and inhibition of neighboring Streptococci phenotypes which are associated with reutericyclin production. {Delta}mucG had increased mutanocyclin and reutericyclin production, which impaired growth and increased the ability to inhibit neighboring Streptococci. However, deletion of mucG also caused reduced expression of mucD, mucE, and mucI. Deletion of mucI reduced mutanocyclin and reutericylin production, but enhanced growth, suggesting that mucI may not transport reutericyclin as its homolog does in Limosilactobacillus reuteri. Further research is needed to determine the roles of mucG and mucI, and to identify any co-factors affecting the activity of the mucG and mucH regulators. Overall, this study provided pangenome and phylogenetic analysis that serves as a resource for S. mutans research, and began elucidation of the regulation of reutericyclins and mutanocyclin production in S. mutans. ImportanceS. mutans must be able to outcompete neighboring organisms in its ecological niche in order to cause dental caries. S. mutans B04Sm5 inhibited the growth of neighboring commensal Streptococci through production of reutericyclins via the muc biosynthetic gene cluster. In this study, carriage of muc was examined across S. mutans, which showed that 35 of 244 RefSeq S. mutans genomes encoded muc and provided a valuable update to the S. mutans pangenome and phylogeny. The roles of the mucG and mucH transcriptional regulators, and the mucI transporter, were also examined. All 3 genes impacted production of mutanocyclin and reutericyclins, which affected the growth rates, transcriptomes, and the ability of the S. mutans strains to inhibit the growth of neighboring commensals.

microbiology↗

bioRxiv2018

Bacteria-to-human protein networks reveal origins of endogenous DNA damage

DNA damage provokes mutations and cancer, and results from external carcinogens or endogenous cellular processes. Yet, the intrinsic instigators of DNA damage are poorly understood. Here we identify proteins that promote endogenous DNA damage when overproduced: the DNA-damaging proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six DNA-damage-causing function clusters, demonstrating DDP mechanisms in three: reactive-oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their expression in tumors predicts heavy mutagenesis and poor prognosis. Half of tested human homologs, when overproduced in human cells, promote DNA damage and mutation, with DNA-damaging mechanisms like those in E. coli. Together, our work reveals DDP networks that provoke endogenous DNA damage and may indicate functions of many human known and newly implicated cancer-promoting proteins.

cancer biology↗