Epigenetic silencing and host genome evolution determine fate of viral insertions in Acanthamoeba DOI Open Access

Cédric Blais,

Morgan Colp,

Luke A. Sarre

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 3, 2024

ABSTRACT Acanthamoeba is a cosmopolitan freshwater amoebae known for its association with Nucleocytoplasmic Large DNA Viruses (NCLDVs). Previous studies have shown that spp. undergo lateral gene transfer (LGT) NCLDVs. Here we leveraged chromosome-scale assemblies of two strains castellanii , Neff and C3, to investigate the occurrence genomic context viral LGT in . We show ‘footprints’ C3 genomes are largely non-overlapping genes found disproportionately large sub-telomeric insertions. Multiple partial copies these insertions throughout genome, but they not expressed do encode functions their own mobility. Viral regions hyper-methylated highly condensed, suggesting expression recently acquired suppressed heterochromatic regions. propose three-step model origin fate sequences : (i) integration from giant viruses, (ii) epigenetic suppression DNAs, which allows them persist (iii) deterioration by point mutation intra- inter-chromosomal recombination. integrations transient may long-lasting effects on fitness host amoeba. Our work strengthens growing body showing widespread protists extends relevance silencing mechanisms evolution Amoebozoa highlight importance genome dynamics understanding endogenized elements.

Language: Английский

The polinton-like supergroup of viruses: evolution, molecular biology, and taxonomy DOI
Eugene V. Koonin, Matthias Fischer, Jens H. Kuhn

et al.

Microbiology and Molecular Biology Reviews, Journal Year: 2024, Volume and Issue: 88(3)

Published: July 18, 2024

SUMMARYPolintons are 15-20 kb-long self-synthesizing transposons that widespread in eukaryotic, and particular protist, genomes. Apart from a transposase protein-primed DNA polymerase, polintons encode homologs of major minor jelly-roll capsid proteins, DNA-packaging ATPases, proteases involved maturation diverse eukaryotic viruses kingdom

Language: Английский

Citations

6
Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins DOI Creative Commons
Mart Krupovìč, Jens H. Kuhn, Matthias Fischer

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(23)

Published: May 28, 2024

The phylum Preplasmiviricota (kingdom Bamfordvirae , realm Varidnaviria ) is a broad assemblage of diverse viruses with comparatively short double-stranded DNA genomes (<50 kbp) that produce icosahedral capsids built from double jelly-roll major capsid proteins. Preplasmiviricots infect hosts all cellular domains, testifying to their ancient origin, and, in particular, are associated six the seven supergroups eukaryotes. comprise four groups viruses, namely, polintons, polinton-like (PLVs), virophages, and adenovirids. We used protein structure modeling analysis show protein-primed polymerases (pPolBs) cytoplasmic linear plasmids encompass an N-terminal domain homologous terminal proteins (TPs) prokaryotic PRD1-like tectivirids eukaryotic adenovirids involved replication initiation, followed by viral ovarian tumor–like cysteine deubiquitinylase (vOTU) domain. vOTU likely responsible for cleavage TP large pPolB polypeptide inactivated adenovirids, which separate protein. Many PLVs transpovirons encode distinct derivative retains TP, vOTU, polymerization palm domains but lacks exonuclease instead contains superfamily 1 helicase Analysis presence/absence inactivation replacement other preplasmiviricots enabled us outline complete scenario origin evolution.

Language: Английский

Citations

4
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals DOI Creative Commons

Danae Stephens,

Zahra Faghihi,

Mohammad Moniruzzaman

et al.

Virus Evolution, Journal Year: 2024, Volume and Issue: 10(1)

Published: Jan. 1, 2024

Abstract Stony corals (Order: Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene contributing ongoing decline reef health and coverage. While viruses established modulators of microbial dynamics, their interactions within holobiont impact on physiology remain unclear. To address this key knowledge gap, we investigated diverse stony genomes for ‘endogenous’ viruses. Our study uncovered a remarkable number integrated viral elements recognized ‘Polintoviruses’ (Class Polintoviricetes) thirty Scleractinia genomes; with several species harboring hundreds thousands polintoviruses. We reveal massive paralogous expansion polintoviruses genomes, alongside presence closely related Polinton-like (PLVs), group that exist free virions. These results suggest multiple integrations PLV-relatives, along expansions, shaped genomes. Re-analysis existing gene expression data reveals all polintovirus structural non-structural hallmark genes expressed, providing support virion production from results, revealing significant diversity across order, open new research avenue into possible roles disease, genomic plasticity, environmental adaptation organisms

Language: Английский

Citations

3
Transposon-mediated genic rearrangements underlie variation in small RNA pathways DOI Creative Commons
Gaotian Zhang,

Marie-Anne Félix,

Erik C. Andersen

et al.

Science Advances, Journal Year: 2024, Volume and Issue: 10(38)

Published: Sept. 20, 2024

Transposable elements (TEs) can alter host gene structure and expression, whereas organisms develop mechanisms to repress TE activities. In the nematode Caenorhabditis elegans , a small interfering RNA pathway dependent on helicase ERI-6/7 primarily silences retrotransposons recent genes of likely viral origin. By studying expression variation among wild C. strains, we found that structural variants transposon remnants underlie in eri-6/7 targets. We further multiple insertions DNA transposons, Polintons, reshuffled locus induced inversion eri-6 some strains. inverted configuration, function was previously shown be repaired by unusual trans-splicing mediated direct repeats. identified these repeats originated from terminal Polintons . Our findings highlight role host-transposon interactions driving rapid genome diversification natural populations shed light evolutionary novelty splicing mechanisms.

Language: Английский

Citations

2
Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins DOI Open Access
Mart Krupovìč, Jens H. Kuhn, Matthias Fischer

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 18, 2024

Abstract The phylum Preplasmiviricota (kingdom Bamfordvirae , realm Varidnaviria ) is a broad assemblage of diverse viruses with comparatively short double-stranded DNA genomes (<50 kbp) that produce icosahedral capsids built from double jelly-roll major capsid proteins. Preplasmiviricots infect hosts all cellular domains, testifying to their ancient origin and, in particular, are associated six the seven supergroups eukaryotes. comprise four groups viruses, namely, polintons, polinton-like (PLVs), virophages, and adenovirids. We employed protein structure modeling analysis show protein-primed polymerases (pPolBs) cytoplasmic linear plasmids encompass an N-terminal domain homologous terminal proteins (TPs) prokaryotic PRD1-like tectivirids eukaryotic adenovirids involved replication initiation, followed by viral ovarian tumor-like cysteine deubiquitinylase (vOTU) domain. vOTU likely responsible for cleavage TP large pPolB polypeptide inactivated adenovirids, which separate protein. Many PLVs transpovirons encode distinct derivative retains TP, polymerization palm domains but lacks exonuclease instead contains supefamily 1 helicase Analysis presence/absence inactivation replacement other preplasmiviricots enabled us outline complete scenario evolution. Significance Structural using advanced artificial intelligence-based methods such as AlphaFold2 may lead insights into evolutionary relationships among unreachable sequence analysis. applied this approach elucidate viruses: identified previously uncharacterized predicted be essential virus genome replication. these suggests evolution part virosphere.

Language: Английский

Citations

0
Epigenetic silencing and host genome evolution determine fate of viral insertions in Acanthamoeba DOI Open Access

Cédric Blais,

Morgan Colp,

Luke A. Sarre

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 3, 2024

ABSTRACT Acanthamoeba is a cosmopolitan freshwater amoebae known for its association with Nucleocytoplasmic Large DNA Viruses (NCLDVs). Previous studies have shown that spp. undergo lateral gene transfer (LGT) NCLDVs. Here we leveraged chromosome-scale assemblies of two strains castellanii , Neff and C3, to investigate the occurrence genomic context viral LGT in . We show ‘footprints’ C3 genomes are largely non-overlapping genes found disproportionately large sub-telomeric insertions. Multiple partial copies these insertions throughout genome, but they not expressed do encode functions their own mobility. Viral regions hyper-methylated highly condensed, suggesting expression recently acquired suppressed heterochromatic regions. propose three-step model origin fate sequences : (i) integration from giant viruses, (ii) epigenetic suppression DNAs, which allows them persist (iii) deterioration by point mutation intra- inter-chromosomal recombination. integrations transient may long-lasting effects on fitness host amoeba. Our work strengthens growing body showing widespread protists extends relevance silencing mechanisms evolution Amoebozoa highlight importance genome dynamics understanding endogenized elements.

Language: Английский

Citations

0