bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2022.05.06.490884

Understanding the role of c-di-AMP signaling in determining antibiotic tolerance in Mycobacterium smegmatis: generation of resistant mutants and regrowth of persisters

Pal, A. K.·Ghosh, A.
View original source ↗Export metadata ↓

Abstract

In this study, we probe the role of secondary messenger c-di-AMP in drug tolerance, which includes both persister and resistant mutant characterization of Mycobacterium smegmatis. Specifically, with the use of c-di-AMP null and overproducing mutants, we showed how c-di-AMP plays a significant role in resistance mutagenesis against antibiotics with different mechanisms of action. We elucidated the specific molecular mechanism linking the elevated intracellular c-di-AMP level and high mutant generation and highlighted the significance of non-homology-based DNA repair. Further investigation enabled us to identify the unique mutational landscape of target and non-target mutation categories linked to intracellular c-di-AMP levels. Overall fitness cost of unique target mutations was estimated in different strain backgrounds, and then we showed the critical role of c-di-AMP in driving epistatic interactions between resistance genes, resulting in the evolution of multi-drug tolerance. Finally, we identified the role of c-di-AMP in persister cells regrowth and mutant enrichment upon cessation of antibiotic treatment.

Source connections

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Pal, A. K., Ghosh, A.. 2022-05-06. Understanding the role of c-di-AMP signaling in determining antibiotic tolerance in Mycobacterium smegmatis: generation of resistant mutants and regrowth of persisters. https://doi.org/10.1101/2022.05.06.490884

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Polyphyletic origins and lineage-specific expansion of chemosensory systems in phylum Actinomycetota

Phylum Actinomycetota (syn. Actinobacteriota or Actinobacteria), one of the largest well-studied bacterial phyla, is renowned for complex morphology, non-motility, ecological versatility, and secondary metabolite production. Chemosensory systems (CSS) are among the most sophisticated prokaryotic signal transduction architectures, yet their evolutionary distribution in this phylum remains poorly understood. Here, a comparative genomic analysis of 693 high-quality genomes spanning the phylum resolves the diversity, distribution, and evolutionary trajectories of CSS. Despite extensive genomic complexity and ecological versatility, only 6.9% of genomes encode complete CSS clusters, confined to a subset of lineages within a few classes, indicating lineage-specific retention or loss. In contrast, two-component systems (TCS) are ubiquitously abundant, with hybrid kinases enriched in CSS-deficient classes, suggesting functional compensation for the absence of dedicated chemosensory pathways. Basal lineages retain simplified CSS (F1 or F5), whereas Actinomycetes show lineage-specific expansion into multiple classes (F5, F8, F9, and ACF), often co-occurring, indicative of enhanced sensory complexity. The phylogeny of CheA homologs shows a polyphyletic distribution, supporting a mosaic evolutionary history shaped by multiple independent acquisitions, diversification, and gene loss. Collectively, our findings show that, unlike motile bacteria, members of Actinomycetota rely predominantly on TCS-driven regulatory networks, with CSS retained only in select lineages where ecological demands require enhanced environmental sensing. This work provides a phylum-wide evolutionary framework for the emergence, diversification, and functional specialization of CSS in non-motile bacteria.

microbiology↗
bioRxiv2026

Integrating Microbial Ecology and Sustainability: Linking Agricultural Waste Gas Streams to Microbial Community Shifts in a Photobioreactor

Photobioreactors (PBRs) coupled to animal housing offer potential for mitigating gaseous emissions such as CO2 and NH3 while simultaneously producing biomass. Here, we present a time-resolved characterization of microbial community dynamics, with a focus on the genetic potential for carbon and nitrogen metabolism. Using a cone-shaped, helical PBR cultivating Arthrospira platensis (Spirulina) and supplied with exhaust air from a chicken house, we characterized microbial communities over continuous exhaust-air exposure and periodic biomass harvesting. Microbiome and gene-centric profiling revealed temporal variation in community composition and in the representation of genes associated with carbon and nitrogen metabolism. Cycle-based dissolved inorganic nitrogen balances showed that the decrease in dissolved inorganic nitrogen was only partially recovered in harvested biomass, while ammonia-oxidizing microorganisms were associated with structured, low-light niches. These observations indicate ammonia-oxidizing potential but do not establish a quantitatively relevant nitrification flux. Structured carrier matrices provided attached-growth niches harboring microbial populations underrepresented in the circulating suspension, while pre-colonized carriers facilitated biomass development during re-inoculation. Overall, our results show that coupling PBRs to agricultural exhaust streams can support biomass production while sustaining spatially structured microbial communities with taxonomic and functional potential. These findings may inform their further development for emission mitigation and circular biomass production.

microbiology↗
bioRxiv2026

Engineered DNA materials shape microbial physiology and ecological selection

Extracellular DNA (eDNA) is both a structural component of microbial biofilms and a potential reservoir of genetic information, yet its role as an ecological material remains largely unexplored. Here we establish engineered extracellular materials as determinants of microbial physiology and community assembly across increasing biological complexity. A three-dimensional DNA hydrogel altered bacterial stress-associated responses, elicited species-dependent phenotypes and transcriptional changes in a defined consortium, and shaped community succession in wastewater-derived microbiomes. Distinct responses to surface-bound oligonucleotides reveal that DNA presentation matters beyond its mere presence. Strikingly, metagenomic sequencing identified rare, hydrogel-specific candidate junctions linking material-derived DNA to microbial genomic sequences, suggesting a previously unexplored interface between extracellular DNA materials and microbial genetic information. These findings reveal a dual role for engineered DNA: its material organization shapes microbial physiology and ecological selection, while its encoded sequences may engage with microbial genomic processes.

microbiology↗