Biology subjects

Saraf, N.

Publications and source records attributed to Saraf, N..

3 recordsLinked to original sources

bioRxiv2026

Biosurfactant polysaccharide drives dispersal of exopolysaccharide-coated myxospores in Myxococcus xanthus

Bacterial spores are highly resilient cell forms, yet the organization of their protective surface layers in diderm species remains largely unexplored. For the social predatory soil bacterium Myxococcus xanthus, myxospore formation within multicellular fruiting body structures is a key ecological adaptation to surviving conditions of nutrient deprivation. These myxospores were long thought to be outwardly coated with so-called major spore coat (MASC) polysaccharide. Using polysaccharide-deficient mutant strains, electron microscopy, surface hydrophobicity assays, dye binding, and functional swarm complementation, we show that MASC instead forms a protective sub-surface outer-cortex layer, while the exopolysaccharide (EPS) glycocalyx inherited from vegetative cells constitutes the true outermost myxospore coat. EPS mediates inter-myxospore adhesion and supports collective behaviors, whereas secretion of biosurfactant polysaccharide (BPS) reduces myxospore surface stickiness, preventing excessive aggregation. BPS-deficient myxospores form persistent clumps, while EPS-deficient myxospores fail to aggregate or restore EPS-dependent swarm motility of vegetative cells. These results reveal a mechanistic interplay in which MASC serves as a sub-surface protective layer, EPS defines the exterior interface, and BPS tunes surface accessibility to regulate dispersal. Our findings overturn long-standing assumptions about myxospore architecture and illustrate a polysaccharide-driven strategy for controlling aggregation and readiness for germination. More broadly, these results highlight how social diderm bacteria leverage inherited and dynamically remodeled polysaccharide surfaces to coordinate multicellular development, in contrast to the rigid protein-based spore surfaces of Gram-positive species.

microbiology↗

bioRxiv2024

Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich Cryptococcus neoformans transcriptome

The DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodeling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeast Cryptococcus neoformans. The presence of multiple introns per transcript with intronic features more similar to higher eukaryotes makes it a promising model to study spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered its genome-wide but substrate-specific roles in C. neoformans splicing. The splicing functions of Prp16 are dependent on its helicase motif I and motif II that are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity, were investigated to discover that exonic sequences at the 5 splice site (5SS) and 3 splice site (3SS) with stronger affinity for U5 loop 1 as a common feature in these introns. Furthermore, short (60-100nts) and ultra-short introns (<60nts) prevalent in the C. neoformans transcriptome were more sensitive to Prp16 knockdown than longer introns, indicating Prp16 is required for the efficient splicing of short and ultra-short introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable the efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into the fine-tuning spliceosomal helicase functions with variations in cis-element features.

molecular biology↗

bioRxiv2024

Comparative genomic insight into the myxobacterial carbohydrate-degrading potential and their ecological impact.

Myxobacteria are an intriguing group of social-behavior-depicting microbes with unique physiological characteristics such as fruiting body formation, gliding motility, and predation, encompassing the largest genomes (>9 Mb) within the Eubacteria kingdom. These soil-dwelling organisms are crucial for lignocellulosic biomass degradation, which has both ecological and industrial significance. While previous studies have demonstrated polysaccharide deconstruction abilities in a few myxobacterial species, we aim to elucidate the distribution of their Carbohydrate Active Enzymes (CAZymes) domains per organism, with a focus on proteins involved in the catabolism of critical polysaccharides such as cellulose, lignin, xylan, starch, pectin, fructan, chitin, and dextran, across 61 high-quality sequenced myxobacterial genomes. Our findings reveal that 3.5% of the total genes at the median level have domains related to CAZyme functions across different myxobacterial families. Notably, family Archangiaceae (4.4%) and Myxococcaceae (3.7%) members exhibit the most significant genomic diversity and potential for degrading multiple substrates within lignocellulosic biomass. These plentiful CAZymes probably enable these majorly soil-harboring myxobacteria to break down various carbohydrate substrates into simpler biological molecules, which not only allow these organisms to sustain in poor-nutrient environments but also enable them to be critical players in carbon cycling and organic matter decomposition. We conclude that myxobacteria have an unexplored genomic potential that may play an integral role in the degradation of recalcitrant plant biomass, potentially influencing soil health and composition. This study further suggests the critical ecological importance of these CAZymes in sustaining the balance of terrestrial ecosystems and diverse industrial applications. ImportancePolysaccharides are the most abundant polymers making up the Earths biomass. Polysaccharide degradation is well-known to be carried out by diverse microorganisms; however, there is more to be explored concerning the novel organisms that can degrade these biomolecules efficiently along with understanding the newer mechanisms and reactions carried out in this process. Soil-dwelling myxobacteria, model organisms for our study, are unique and under-studied social-behavior-depicting microbes. In this research, we investigated their genetic potential to encode carbohydrate-active enzymes involved in breaking down various substrates, including lignocellulosic biomass which is predominantly present in their habitat. We further emphasized their potential to be utilized in industrial applications amongst the paper-pulp, food-beverage, textile, and biofuel industries.

microbiology↗