Biology subjects

N, A.

Publications and source records attributed to N, A..

3 recordsLinked to original sources

bioRxiv2026

RiboWin: A computational framework to identify non-canonical open reading frames

Abstract Ribosome profiling is widely used to map translation across the genome, yet current sORF discovery pipelines are constrained by their reliance on annotated protein coding regions and by treating biological replicates primarily as tools for quantification rather than as strict filters for reproducibility. This results in two major issues, the systematic exclusion of pseudogene derived loci from analysis and the generation of extremely large candidate sets in which true translation events are difficult to distinguish from noise. To overcome these limitations, a five-stage framework was developed that expands the search space to include pseudogene loci while enforcing dual biological replicate concordance as a hard binary filter. When applied to four human cell lines with matched replicates and benchmarked against existing tools, the framework produces dramatically smaller and more reliable candidate sets, reducing thousands to millions of predicted sORFs down to a small number of high confidence concordant loci. Across HeLa cell cycle conditions, a limited set of unique concordant sORFs was identified spanning multiple transcript classes including upstream ORFs, retained introns, and nonsense mediated decay transcripts, along with a pseudogene derived candidate. Notably, the pseudogene encoded sORF RPL26P19 was detected consistently in HeLa cells but missed or inconsistently identified by existing tools, while a separate pseudogene sORF from UBE3AP2 was observed specifically in normal primary cell types and absent in HeLa. Both candidates were later found to be supported by entries in OpenProt, even though this was not known during the analysis, which gives added confidence that the results are genuine and not biased by prior expectations. Overall, these findings suggest that pseudogenes are not just inactive remnants in the genome but can act as real, functional sources of translated sORFs in a cell type specific manner. At the same time, it becomes clear that most current tools are not designed to detect these signals effectively. This highlights the need for approaches that both broaden the regions being searched and apply stricter reproducibility checks, so that truly meaningful translation events can be identified more reliably.

bioinformatics↗

bioRxiv2024

Direct contact of the bacterial surface induces phase separation in the host phagosome membrane

Mycobacterium tuberculosis (Mtb) establishes intracellular niches by remodeling host membranes into either spacious or compact phagosomes, yet how direct bacterial contact within these distinct compartments facilitates bacterial egress remains unknown. Using fixed cell imaging, in vitro reconstitution of phagosome-like vesicles, and numerical simulations, we uncover that mycobacterial load and its direct contact determines phagosome fate by driving membrane bending, lipid wrapping and phase separation. Low-to-moderate load induces membrane vesiculation, generating compact phagosome-like structures. High bacterial load drives a scaffold-like architecture that primes compartments for rupture via complete lipid phase separation and changes in the membranes bending and area stretch moduli, rendering it more deformable. Notably, physical contact synergizes with the virulence factor ESAT-6, amplifying its membrane-deforming activity to disrupt phagosomal integrity. We propose that mycobacteria actively switch spacious to compact phagosomal states by modulating host membrane mechanics--a process governed by the membrane-to-contact area ratio and proximity to lipid demixing point. These findings reveal a biophysical switch in pathogen-driven membrane remodeling, with broad implications for understanding how intracellular pathogens manipulate host membranes to survive.

biophysics↗

bioRxiv2021

Geminiviral βC1 orchestrates organellar genomic instability to augment viral infection by hijacking host RecA

Chloroplast is the site for transforming light energy to chemical energy. It also acts as a production unit for a variety of defense-related molecules. These defense moieties are necessary to mount a successful counter defence against pathogens including viruses. Geminiviruses disrupt chloroplast homeostasis as a basic strategy for their successful infection inducing vein-clearing, mosaics and chlorosis in infected plants. Here we show that a geminiviral pathogenicity determinant protein {beta}C1 directly interferes with plastid homeostasis. {beta}C1 was capable of inducing organelle-specific nuclease to degrade plastid genome as well as diverted functions of RecA1 protein, a major player in plastid genome maintenance. {beta}C1 interacted with RecA1 in plants and its homolog in bacteria to reduce the ability of host cells to maintain genomic integrity under stresses. Further, reduction in the coding capacity of plastids severely affected retrograde signalling necessary for viral perception and activation of defense. Induction of chloroplast-specific nuclease by {beta}C1 is similar to phosphate starvation-response in which nucleotides are recycled to augment synthesis of new, potentially viral, DNA. These results indicate the presence of a novel strategy in which a viral protein alters host defence by targeting regulators of chloroplast DNA. We predict that the mechanism identified here might have similarities in other plant-pathogen interactions. One line summary{beta}C1 alters plastid genome metabolism.

plant biology↗