Systematic annotation of hyper-variability hotspots in phage genomes and plasmids

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 16, 2024

Abstract Bacterial and bacteriophage genomes contain genomic regions of hyper-variability (diversity hotspots) caused by insertions mobile genetic elements (MGEs), non-homologous recombination events non-horizontal hypermutation. Accessory genes encoded in the diversity hotspots are involved anti-MGE defence counter-defence, virulence antimicrobial resistance (AMR), thus playing key roles interactions amongst phages, MGEs, bacteria eukaryotic hosts. To date majority research has been focused on either individual or relatively limited sets a small set genomes, typically from single species. A global understanding hotspot dynamics still lacking. address this gap, we developed iLund4u, an algorithm for systematic annotation across millions sequences. Using proteome composition approach, iLund4u detects communities, annotates accessory proteins identifies hotspots. By analysing 873K phage 696K plasmid sequences identified 13.7K 171K diverse protein families there as cargo. Furthermore, allows search functions versus precomputed database. In mode all that encode homologues query protein. searching communities similar proteomes. Detailed documentation, user guide source code available at home page: art-egorov.github.io/ilund4u.

Язык: Английский

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Vaccine development using artificial intelligence and machine learning: A review

International Journal of Biological Macromolecules, Год журнала: 2024, Номер unknown, С. 136643 - 136643

Опубликована: Окт. 1, 2024

Язык: Английский

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Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Дек. 17, 2024

Abstract The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, leaving only three protein-coding genes highly fragmented mitoribosomal rRNAs, raising challenging questions about mitoribosome composition, assembly structure. Our study reveals how Toxoplasma gondii assembles over 40 mt-rRNA fragments using exclusively nuclear-encoded proteins lineage-specific families RNA-binding proteins. Among these are four from the Apetala2/Ethylene Response Factor (AP2/ERF) family, originally known as transcription factors in plants Apicomplexa, now repurposed essential components. Cryo-EM analysis structure demonstrates AP2 function RNA binders to maintain integrity. is also decorated with members belonging RAP (RNA-binding domain abundant Apicomplexa) HPR (heptatricopeptide repeat) families, highlighting unique adaptations parasites. Solving molecular puzzle apicomplexan could inform development therapeutic strategies targeting organellar translation.

Язык: Английский

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AlphaFold2‐guided description of CoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily

Proteins Structure Function and Bioinformatics, Год журнала: 2024, Номер 92(6), С. 776 - 794

Опубликована: Янв. 22, 2024

Abstract Three‐dimensional (3D) structure information, now available at the proteome scale, may facilitate detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with identification a novel family domains related to ferredoxin‐like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) use AlphaFold2 3D models. Domains were initially identified relation intracellular biomineralization calcium carbonates Cyanobacteria. They are part large heavy‐metal‐associated (HMA) superfamily, departing from latter specific structural features. In particular, most them share conserved basic amino acids (hence their name CoBaHMA for Co nserved Ba sic residues HMA ), forming positively charged surface, which is likely interact anionic partners. found diverse modular organizations bacteria, existing form monodomain proteins or as larger proteins, some membrane involved transport lipid metabolism. This suggests that exert regulatory function, involving interactions lipids. hypothesis might have particular resonance context compartmentalization observed cyanobacterial carbonates.

Язык: Английский

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Expanding the phage galaxy: Isolation and characterization of five novel Streptomyces siphoviruses Ankus, Byblos, DekoNeimoidia, Mandalore, and Naboo

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 17, 2024

Key features of the actinobacterial genus Streptomyces are multicellular, filamentous growth and production a broad portfolio bioactive molecules. These characteristics appear to play an important role in phage-host interactions modulated by phages during infection. To accelerate research such investigation novel immune systems multicellular bacteria, phage isolation, sequencing, characterization needed. This is prerequisite for establishing systematic collections that appropriately cover diversity comparative analyses. As part public outreach programme within priority SPP 2330, involving local schools, we describe isolation five siphoviruses infecting S. griseus , venezuelae olivaceus . All isolates virulent members two existing genera and, additionally, establish new Stanwilliamsviridae family. In addition extensive set tRNAs proteins involved replication, about 80% genes encode hypothetical proteins, underlining yet underexplored genomic dark matter still found bacteriophages actinobacteria. Taken together, Ankus, Byblos, DekoNeimoidia, Mandalore, Naboo expand contribute ongoing field interactions.

Язык: Английский

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