The protein structurome of Orthornavirae and its dark matter DOI Creative Commons
Pascal Mutz, Antônio Pedro Camargo, Harutyun Sahakyan

et al.

mBio, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 23, 2024

ABSTRACT Metatranscriptomics is uncovering more and diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in realm Riboviria. Thorough protein annotation comparison are essential to get insights into functions proteins virus evolution. In addition sequence- hmm profile‑based methods, structure adds a powerful tool uncover relationships. We constructed an “structurome” consisting already annotated as well unannotated (“dark matter”) domains encoded genomes. used modeling similarity searches illuminate remaining dark matter hundreds thousands orthornavirus The vast majority showed either “generic” folds, such single α-helices, or no high confidence predictions. Nevertheless, variety lineage-specific globular that were new orthornaviruses general particular identified within proteomic orthornaviruses, including several predicted nucleic acid-binding nucleases. addition, we case exaptation cellular nucleoside monophosphate kinase RNA-binding families. Notwithstanding continuing discovery numerous it appears all conserved large groups have been identified. rest proteome seems be dominated by poorly structured intrinsically disordered ones likely mediate specific virus-host interactions. IMPORTANCE Advanced methods for prediction, AlphaFold2, greatly expand our capability identify infer their evolutionary This particularly pertinent known evolve rapidly result often cannot adequately characterized analysis sequences. performed exhaustive prediction comparative uncharacterized results show consists mostly all-α-helical readily assigned function various interactions between host proteins. great although unexpected represented individual

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
Recent Advances in the Structure and Assembly of Non-enveloped Spherical Viruses DOI
Sangita Venkataraman,

H.S. Savithri,

M.R.N. Murthy

et al.

Virology, Journal Year: 2025, Volume and Issue: 606, P. 110454 - 110454

Published: Feb. 20, 2025

Language: Английский

Citations

0
DNA polymerase swapping in Caudoviricetes bacteriophages DOI Creative Commons
Natalya Yutin, Igor Tolstoy, Pascal Mutz

et al.

Virology Journal, Journal Year: 2024, Volume and Issue: 21(1)

Published: Aug. 26, 2024

Abstract Background Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show broad range of variation their repertoires replication proteins. Some duplodnaviruses encode (nearly) complete systems whereas others lack (almost) all genes required for replication, relying on host machinery. polymerases (DNAPs) comprise centerpiece apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), protein structures and sequences within each family being, generally, highly conserved. More than half DNAP A, B C. We showed previously that multiple pairs closely viruses order Crassvirales different families. Methods Groups phages which swapping likely occurred were identified as subtrees defined depth comprehensive evolutionary tree tailed bacteriophages included swaps validated by constrained analysis was performed phylogenetic large terminase subunits, phage encoding swapped aligned using Mauve. discovered unusual predicted AlphaFold2. Results four additional groups class Caudoviricetes apparently occasions, replacements occurring both between A B, C, distinct subfamilies same family. always occurs “in situ”, without changes organization surrounding genes. In several cases, is only region substantial divergence genomes, others, swap involved neighboring other proteins genome replication. addition, we two undetected, divergent encoded some along main implicated Conclusions Replacement one many independent occasions during evolution phages, resulting very DNAPs. driven selection avoidance antiphage mechanisms targeting remain to be identified, and/or against replicon incompatibility.

Language: Английский

Citations

1
The protein structurome of Orthornavirae and its dark matter DOI Creative Commons
Pascal Mutz, Antônio Pedro Camargo, Harutyun Sahakyan

et al.

mBio, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 23, 2024

ABSTRACT Metatranscriptomics is uncovering more and diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in realm Riboviria. Thorough protein annotation comparison are essential to get insights into functions proteins virus evolution. In addition sequence- hmm profile‑based methods, structure adds a powerful tool uncover relationships. We constructed an “structurome” consisting already annotated as well unannotated (“dark matter”) domains encoded genomes. used modeling similarity searches illuminate remaining dark matter hundreds thousands orthornavirus The vast majority showed either “generic” folds, such single α-helices, or no high confidence predictions. Nevertheless, variety lineage-specific globular that were new orthornaviruses general particular identified within proteomic orthornaviruses, including several predicted nucleic acid-binding nucleases. addition, we case exaptation cellular nucleoside monophosphate kinase RNA-binding families. Notwithstanding continuing discovery numerous it appears all conserved large groups have been identified. rest proteome seems be dominated by poorly structured intrinsically disordered ones likely mediate specific virus-host interactions. IMPORTANCE Advanced methods for prediction, AlphaFold2, greatly expand our capability identify infer their evolutionary This particularly pertinent known evolve rapidly result often cannot adequately characterized analysis sequences. performed exhaustive prediction comparative uncharacterized results show consists mostly all-α-helical readily assigned function various interactions between host proteins. great although unexpected represented individual

Language: Английский

Citations

1