Biology subjects

Frye, S. A.

Publications and source records attributed to Frye, S. A..

3 recordsLinked to original sources

bioRxiv2025

Biased enrichment of DNA uptake enhancing sequences in Pasteurellaceae and Neisseriaceae

Some naturally transformable bacteria can selectively take up homologous DNA through short conserved motifs termed DNA Uptake Enhancing Sequences (DUES), comprising DNA Uptake Sequences (DUS) in Neisseriaceae and Uptake Signal Sequences (USS) in Pasteurellaceae. Using 177 complete genomes, this study provides the most extensive comparative analysis of DUES distribution, composition, and functional associations to date. Three novel DUS dialects were identified in Neisseria animalis and Vitreoscilla spp., extending the known diversity of the transformation system. Approximately half of all DUES and more than 90% of inverted repeat DUES occurred within predicted transcriptional terminators, and DUES inside coding-sequences were biased toward reading frames minimizing bioenergetic cost, indicating both structural and metabolic selection pressures. Gene Ontology and KEGG analyses revealed extensive but asymmetric functional enrichment: both families showed bias toward genome maintenance processes, yet Neisseriaceae displayed stronger enrichment for DNA repair, replication, and the UvrABC complex, whereas Pasteurellaceae were more associated with homologous recombination and the RecBCD complex. These patterns indicate that while DUES enrichment is broadly conserved, its functional integration diverges between families, reflecting distinct evolutionary adaptations that couple DNA uptake specificity to genome stability and cellular maintenance.

evolutionary biology↗

bioRxiv2025

Type IV minor pilin ComN predicted the USS-receptor in Pasteurellaceae

The Uptake Signal Sequence (USS) receptor, facilitating acquisition of homologous DNA by natural transformation in Haemophilus influenzae and other Pasteurellaceae, remains unknown. Assuming extracellular USS-binding in accordance with experimental data and existing models of the transformation process, discriminating functional gene ontology assessment, cellular localization predictions and deep-learning structural modeling of protein-DNA complexes, a prepilin peptidase-dependent protein A (PpdA), was identified as the strongest USS receptor candidate in different Pasteurellaceae family members with divergent USS specificities. PpdA was the only orthogroup to be modeled to form specific protein-USS complexes significantly better than complexes with sequence-scrambled versions of USS by AlphaFold3. Further analyses of PpdA complexes, from ten different Pasteurellaceae with divergent USS-type enrichment, using geometric deep learning protein-DNA sequence specificity predictions and coevolution analyses were found to further support this USS receptor candidacy. PpdA was found to share overall structural domains with the non-sequence specific DNA receptor FimT in Legionella pneumophila and a particular {beta}-sheet transversing disulfide-bridge with ComP, the DNA uptake sequence receptor of the Neisseriaceae. In compliance with a previously given gene name, we propose ComN to be used for these PpdA orthologs which structurally and evolutionary were here predicted to be the USS-receptors in Pasteurellaceae.

microbiology↗

bioRxiv2024

The conserved ComP structure with two distinct DNA binding modes - systematic modeling with AlphaFold3, RoseTTAFold2NA, Chai-1 and re-docking in HADDOCK

The competence protein ComP is a Type IV minor pilin and the extracellular DNA binding protein involved in natural transformation in the human pathogens Neisseria gonorrhoeae, Neisseria meningitidis, Eikenella corrodens and related Neisseriaceae bacteria. Details of the DNA binding mode of ComP is enigmatic, and the 3D structure of the DNA :: protein complex remains unresolved. Here we characterize the ComP orthologs in a set of Neisseriaceae family members, model their common structural domains and their interaction with different preferred 12 base pair long DNA binding motifs, DNA Uptake Sequences (DUS) and scrambled versions of these. Through systematic in silico modeling using AlphaFold 3, RoseTTAFold2NA, and Chai-1 and model comparisons, we bring a new understanding of the interactions between DNA and ComP. We report six distinct binding modes of which two, here named Epsilon and Gamma, were robustly modeled across platforms and different ComPs. The characteristics and robustness of the predicted models and DNA binding modes from each tool are assessed and discussed. This work expands the knowledge on the ComP :: DUS interaction and guides further wet- and dry-lab systematic and experimental characterization of these complexes through which molecular and clinical interventions may be developed.

microbiology↗