Harvard Forest soil enrichment for viruses and small bacteria
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PROVIDER: PRJNA916515 | ENA |
REPOSITORIES: ENA
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Project description:Giant viruses are extraordinary members of the virosphere due to their structural complexity and high diversity in gene content. Haptophytes are ecologically important primary producers in the ocean, and all known viruses that infect haptophytes are giant viruses. Our in-depth electron microscopic, phylogenomic and virion proteomic analyses of two haptophyte-infecting giant viruses, Haptolina ericina virus RF02 (HeV RF02) and Prymnesium kappa virus RF02 (PkV RF02), unravel their large capacity for host manipulation and arsenals that functions during the infection cycle from virus entry to release. The virus infection induces significant morphological changes of host cell that are manipulated to build a virus proliferation factory. Both viruses’ genomes encode a putative nucleoprotein (dinoflagellate/viral nucleoprotein; DVNP), which was also found in the virion proteome of PkV RF02. Phylogenetic analysis suggests that DVNPs are widespread in marine giant metaviromes. Furthermore, the analysis shows that the dinoflagellate homologues were possibly acquired from viruses of the order Imitervirales.
2025-02-21 | PXD060762 | Pride
Project description:Whole-genome sequencing analysis of amphora-shaped giant viruses.
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Project description:Viruses with large DNA genomes often carry auxiliary metabolic genes that reprogram host physiology, yet their contributions to host redox and membrane homeostasis remain poorly understood. Here we report the discovery and functional reconstitution of viral homologs of vitamin K epoxide reductase (VKOR) encoded by giant viruses. Using phylogenetic and genomic context analysis, we find that viral VKOR genes are frequently located adjacent to -carboxylase-like epoxidase and fatty acid desaturase domains, consistent with a putative modular redox pathway for membrane lipid modification. To investigate their function, we expressed viral VKORs in an Escherichia coli strain lacking disulfide bond–forming enzymes and examined both their membrane topology and activity. Remarkably, a minimal set of residue substitutions enabled proper membrane insertion and restored bacterial motility, demonstrating that viral VKORs are catalytically competent electron shuttles. Structural modeling supports their integration into the endoplasmic reticulum–like environment in the host. Finally, we show that VKORs and gamma-carboxylase-like epoxidase-desaturases from Fadolivirus and Yasminevirus giant viruses are expressed during infection of Vermamoeba vermiformis, where they may couple vitamin K epoxidation to desaturation-driven lipid remodeling. These findings expand the known functional repertoire of giant viruses and uncover a previously unrecognized viral strategy for manipulating host redox metabolism and membrane composition.
2026-08-10 | GSE341297 | GEO
Project description:Stain diversity of giant viruses infecting chlorarachniophyte algae in the subtropical Pacific
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Project description:In contrast to living organisms, viruses lack the machinery necessary for protein synthesis, instead co-opting host factors to translate viral transcripts. Giant DNA viruses, which encode putative orthologs of translation factors, challenge this dogma and blur the line between cellular and acellular biology. Here, we discover a complete mRNA cap-binding complex in mimivirus that we name viral IF4F. This complex associates with host ribosomes to orchestrate the temporally regulated synthesis of structural proteins critical for assembly of viral progeny. The m7G cap-binding subunit of viral IF4F has evolved specificity for viral cap structures through additional interactions with methylated adenosines in mRNAs. Viral IF4F further facilitates dynamic gene expression required to evade host abiotic stresses that normally restrict viral replication. Our study thereby extends a paradigm of eukaryotic translation regulation to include viruses and illuminates a series of evolutionary innovations to a core process of life.
2025-12-04 | GSE290007 | GEO
Project description:5-methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. However, in many eukaryotes 5mC has gained complex roles in gene regulation beyond parasite control. Animals are a paradigmatic case for 5mC evolution, as they show widespread variability across lineages, ranging from gene regulation and transposable element control to loss of this base modification. Here we show that the protist animal relative Amoebidium appalachense displays both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, large hypermethylated regions of the Amoebidium genome derive from viral insertions, including hundreds of endogenised giant viruses contributing 14% of the encoded genes. Using a combination of inhibitors and functional genomic assays, we demonstrate that 5mC silences these giant virus insertions. Moreover, alternative Amoebidium isolates show polymorphic giant virus insertions, highlighting a dynamic process of infection, endogenisation and purging. Therefore we propose that 5mC is critical for the controlled co-existence of newly acquired viral DNA into eukaryotic genomes, making Amoebidium a unique model to understand the hybrid origins of eukaryotic genomes.
2024-07-15 | GSE249241 | GEO