BEREN: A bioinformatic tool for recovering Giant viruses, Polinton-like Viruses, and Virophages in metagenomic data DOI Creative Commons
Benjamin Minch, Mohammad Moniruzzaman

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

Опубликована: Окт. 9, 2024

Abstract Viruses in the kingdom Bamfordvirae , specifically giant viruses (NCLDVs) phylum Nucleocytoviricota and smaller members Preplasmiviricota phylum, are widespread important groups of that infect eukaryotes. While this such as viruses, polinton-like virophages have gained large interest from researchers recent years, there is still a lack streamlined tools for recovery their genomes metagenomic datasets. Here, we present BEREN, comprehensive bioinformatic tool to unlock diversity these metagenomes through five modules NCLDV genome, contig, marker gene recovery, metabolic protein annotation, genome identification annotation. BEREN’s performance was benchmarked against other mainstream virus using mock metagenome, demonstrating superior rates contigs genomes. Applied real-world dataset Baltic Sea, BEREN identified diverse members, giving insight into viral interactions functions region. Overall, offers user-friendly, transparent solution studying ecological functional roles eukaryotic facilitating broader access analysis.

Язык: Английский

Nucleocytoviricota Viral Factories Are Transient Organelles Made by Phase Separation DOI
Sofia Rigou, Alain Schmitt, Audrey Lartigue

и другие.

Опубликована: Сен. 30, 2024

Phase separation is a common mechanism utilized by viruses to achieve replication, host manipulation and virion morphogenesis. The newly defined phylum _Nucleocytoviricota_ encompass ubiquitous diverse including _Poxviridae,_ the climate-modulating _Emiliania huxleyi_ virus previously termed Nucleocytoplasmic large DNA (NCLDV). Cytoplasmic members of this form viral factories but their nature remains unknow. Here we show that these are formed phase separation. We demonstrate mimivirus multilayered using at least two scaffold proteins. also generate pipeline bioinformatically identify putative proteins in all other despite major primary sequence variability. Such predictions were based on conserved molecular grammar governed electrostatic interactions. Scaffold candidates validated for family _Marseilleviridae_ highlighted role H5 as protein poxviruses. Finally, provide repertoire client nucleus-like factory important sub-compartmentalization functions central dogma. Overall, reveal new acquisition nuclear-like entirely re-classified biomolecular condensates.

Язык: Английский

Процитировано

3
Nucleocytoviricota viral factories are transient organelles made by phase separation DOI Creative Commons
Sofia Rigou, Alain Schmitt, Audrey Lartigue

и другие.

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

Опубликована: Сен. 2, 2024

Phase separation is a common mechanism utilized by viruses to achieve replication, host manipulation and virion morphogenesis. The newly defined phylum Nucleocytoviricota encompass ubiquitous diverse including Poxviridae, the climate-modulating Emiliania huxleyi virus previously termed Nucleocytoplasmic large DNA (NCLDV). Cytoplasmic members of this form viral factories but their nature remains unknow. Here we show that these are formed phase separation. We demonstrate mimivirus multilayered using at least two scaffold proteins. also generate pipeline bioinformatically identify putative proteins in all other despite major primary sequence variability. Such predictions were based on conserved molecular grammar governed electrostatic interactions. Scaffold candidates validated for family Marseilleviridae highlighted role H5 as protein poxviruses. Finally, provide repertoire client nucleus-like factory important sub-compartmentalization functions central dogma. Overall, reveal new acquisition nuclear-like entirely re-classified biomolecular condensates.

Язык: Английский

Процитировано

2
BEREN: A bioinformatic tool for recovering Giant viruses, Polinton-like Viruses, and Virophages in metagenomic data DOI Creative Commons
Benjamin Minch, Mohammad Moniruzzaman

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

Опубликована: Окт. 9, 2024

Abstract Viruses in the kingdom Bamfordvirae , specifically giant viruses (NCLDVs) phylum Nucleocytoviricota and smaller members Preplasmiviricota phylum, are widespread important groups of that infect eukaryotes. While this such as viruses, polinton-like virophages have gained large interest from researchers recent years, there is still a lack streamlined tools for recovery their genomes metagenomic datasets. Here, we present BEREN, comprehensive bioinformatic tool to unlock diversity these metagenomes through five modules NCLDV genome, contig, marker gene recovery, metabolic protein annotation, genome identification annotation. BEREN’s performance was benchmarked against other mainstream virus using mock metagenome, demonstrating superior rates contigs genomes. Applied real-world dataset Baltic Sea, BEREN identified diverse members, giving insight into viral interactions functions region. Overall, offers user-friendly, transparent solution studying ecological functional roles eukaryotic facilitating broader access analysis.

Язык: Английский

Процитировано

1