Biology subjects

Oka, G. U.

Publications and source records attributed to Oka, G. U..

4 recordsLinked to original sources

bioRxiv2026

ppigFinder: an integrated desktop application for bacterial genome annotation and AlphaFold 3 based protein protein interaction screening

Motivation. AlphaFold-based structure prediction has transformed structural biology by enabling accurate protein modelling and providing a powerful framework for inferring protein-protein interactions (PPIs). However, discovering candidate PPIs directly from genome sequences remains a fragmented and largely trial-and-error process, typically requiring separate tools for open reading frame (ORF) prediction, functional annotation, candidate selection, iterative testing of potential partners, manual preparation of individual structural-prediction jobs, and downstream interpretation of confidence metrics. Results. We present Protein-Protein Interaction Genomic Finder (ppigFinder), a standalone, cross-platform desktop application that integrates these steps into a project-oriented graphical workflow for genome-based PPI discovery from nucleotide sequence data. ppigFinder combines ORF prediction, functional annotation, genomic-neighbourhood inspection, AlphaFold 3 job generation, remote job submission, and structural-confidence analysis within a single environment. As a proof of concept, we performed a VirD4-centered AlphaFold 3 interactome screen in Xanthomonas citri pv. citri strain 306, modelling VirD4 (ORF2601) against all 4,303 predicted chromosomal ORFs. Ranking by the minimum interchain predicted aligned error (PAE_min) placed all 14 XVIPCD-containing effector candidates within the top 1% of predictions, with the six top-ranked models corresponding to XVIP candidates. The screen also recovered an XVIPCD-containing protein absent from the reference genome annotation and identified high-confidence candidates predicted to bind VirD4 at a surface opposite to the XVIPCD-binding site.

bioinformatics↗

bioRxiv2026

To Kill or not to Kill: A Conserved trans-intoxication protection factor Blocks X-T4SS-Mediated Fratricide through Interaction with VirB5

Bacteria can outcompete rivals by using specialized secretion systems to deliver toxic effectors into prey cells. How these systems distinguish prey from kin remains a fundamental unanswered question. In many Xanthomonadales (Lysobacterales) species, the antibacterial type IV secretion system (X-T4SS) mediates cell-cell contact-dependent killing of competing bacteria. Here, we identified XAC2611, a chromosomally encoded, cysteine-rich DUF4189 protein, as essential for preventing X-T4SS-mediated fratricide among sibling cells in Xanthomonas citri. XAC2611 homologs are found within or proximal to the genomic loci coding almost all identified X-T4SS. Live-cell microscopy and biochemical data reveal that XAC2611 is abundantly produced and widely distributed throughout the periplasm of recipient cells and is required to prevent X. citri cells from intoxicating each other in a contact-dependent manner. We also show that XAC2611 homologs from Stenotrophomonas maltophilia protect X. citri cells from attack by S. maltophilia. Protein-protein interaction assays show that XAC2611 interacts directly with the VirB5 subunit. Since VirB5 is predicted to be localized at the tip of the X-T4SS pilus, its interaction with XAC2611 in a neighboring sister cell could block X-T4SS-mediated effector delivery. We therefore name this family of proteins trans-intoxication protection factors (Tpfs).

microbiology↗

bioRxiv2025

A ubiquitin-like protein controls assembly of a bacterial Type VIIb secretion system

Type VII secretion systems (T7SS) are crucial bacterial nanomachines that mediate interbacterial competition and host-pathogen interactions in Gram-positive bacteria. Despite their importance, the structural basis for assembly and substrate transport in T7SSb, a widely distributed T7SS variant, remains poorly understood. Here, we present the cryo-EM structure of the T7SSb core complex from Bacillus subtilis, revealing how a ubiquitin-like protein, YukD, coordinates assembly of the secretion machinery. YukD forms extensive interactions with the central channel component YukB and promotes its association with the pseudokinase YukC, creating a stable building block for channel assembly. Using microscopy and competition assays, we demonstrate that YukD is essential for proper T7SSb complex formation and contact-dependent bacterial killing. Structural modeling suggests this YukD-dependent assembly mechanism is conserved across diverse Gram-positive bacteria. Our findings reveal how bacteria have adapted a ubiquitin-like protein as a structural regulator for assembling a large secretion complex.

microbiology↗

bioRxiv2020

Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction

Establishing new experimental animal models to assess the safety and immune response to the antigen used in the development of COVID-19 vaccine is an imperative issue. Based on the advantages of using zebrafish as a model in research, herein we suggest doing this to test the safety of the putative vaccine candidates and to study immune response against the virus. We produced a recombinant N-terminal fraction of the Spike SARS-CoV-2 protein and injected it into adult female zebrafish. The specimens generated humoral immunity and passed the antibodies to the eggs. However, they presented adverse reactions and inflammatory responses similar to severe cases of human COVID-19. The analysis of the structure and function of zebrafish and human Angiotensin-converting enzyme 2, the main human receptor for virus infection, presented remarkable sequence similarities. Moreover, bioinformatic analysis predicted protein-protein interaction of the Spike SARS-CoV-2 fragment and the Toll-like receptor pathway. It might help in the choice of future therapeutic pharmaceutical drugs to be studied. Based on the in vivo and in silico results presented here, we propose the zebrafish as a model for translational research into the safety of the vaccine and the immune response of the vertebrate organism to the SARS-CoV-2 virus.

immunology↗