Biology subjects

Mugunthan, S.

Publications and source records attributed to Mugunthan, S..

3 recordsLinked to original sources

bioRxiv2025

From short-lived to persistent: The significance of extracellular RNA in disinfected drinking water microbiomes

To assure the safe distribution of drinking water, it is critical to identify adaptations that allow microorganisms to thrive in an oligotrophic system under disinfectant stress. Microbial adaptive responses are determined using RNA-based differential transcriptomics which cannot be performed in environmental settings due to lack of a baseline. This study introduces the concept of using extracellular RNA (eRNA) as a reference to determine important adaptive features in disinfected drinking water microbiome. Using this method, we determined energy efficiency, dynamic membrane composition, oxidative stress response, and proper protein folding to be extremely important for survival in drinking water systems. Additionally, multiple antibiotic resistance genes are expressed and upregulated in intracellular RNA fraction, indicating selection pressure. Non-coding RNA and transfer-messenger RNA found in eRNA suggest important regulatory functions. This study advances our understanding of eRNA in drinking water microbiomes and provides a framework for exploration in other environmental systems.

ecology↗

bioRxiv2019

Isolation of a putative S-layer protein from anammox biofilm extracellular matrix using ionic liquid extraction

Anaerobic ammonium oxidation (anammox) performing bacteria self-assemble into compact biofilms by expressing extracellular polymeric substances (EPS). Anammox EPS are poorly characterized, largely due to their low solubility in typical aqueous solvents. Pronase digestion achieved 19.5 {+/-} 0.9 and 41.4 {+/-} 1.4% (w/w) more solubilization of Candidatus Brocadia sinica-enriched anammox granules than DNase and amylase respectively. Nuclear magnetic resonance profiling of the granules confirmed that proteins were dominant. We applied ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate and N,N- dimethylacetamide (EMIM-Ac/DMAc) mixture to extract the major structural proteins. Further treatment by anion exchange chromatography isolated homologous S/T-rich proteins BROSI_A1236 and UZ01_01563, which were major components of the extracted proteins and sequentially highly similar to putative anammox surface-layer (S-layer) protein KUSTD1514. EMIM-Ac/DMAc extraction enriched for these putative S-layer proteins against all other major proteins, along with six monosaccharides (i.e. arabinose, xylose, rhamnose, fucose, galactose and mannose). The sugars, however, contributed <0.5% (w/w) of total granular biomass, and were likely co-enriched as glycoprotein appendages. This study demonstrates that S-layer proteins are major constituents of anammox biofilms and can be isolated from the matrix using an ionic liquid-based solvent.

bioengineering↗

bioRxiv2019

The biofilm matrix scaffold of Pseudomonas species consists of non-canonically base paired extracellular DNA and RNA

While extracellular DNA (eDNA) is recognized as a critical biofilm matrix component, it is not understood how it contributes to biofilm function. Here we isolate eDNA from Pseudomonas biofilms using ionic liquids, and discover that its key biophysical signatures, i.e. fluid viscoelasticity, nucleic acid conformation, and temperature and pH dependencies of gel to solution transitions, are maintained. Solid-state analysis of isolated eDNA, as a proxy for eDNA structure in biofilms, revealed non-canonical Hoogsteen base pairs, triads or tetrads involving guanine and thymine or uracil. These were less abundant in chromosomal DNA and undetected as eDNA underwent gel-sol transition. Purine-rich RNA was present in the eDNA network, which potentially enables eDNA to be the main cross-linking exopolymer in the matrix through non-canonical nucleobase interactions. Our study suggests that Pseudomonas assemble extracellular DNA and RNA into a network with viscoelastic properties, which underpin their persistence and spreading, and may aid the development of more effective controls for biofilm-associated infections.

biochemistry↗