Regulatory sequence-based discovery of anti-defense genes in archaeal viruses.
Archaeal Viruses
/ genetics
Archaea
/ genetics
Promoter Regions, Genetic
/ genetics
Clustered Regularly Interspaced Short Palindromic Repeats
/ genetics
Regulatory Sequences, Nucleic Acid
/ genetics
Viral Proteins
/ genetics
Archaeal Proteins
/ genetics
Metagenome
/ genetics
CRISPR-Associated Proteins
/ genetics
CRISPR-Cas Systems
/ genetics
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
02 May 2024
02 May 2024
Historique:
received:
06
09
2023
accepted:
19
04
2024
medline:
3
5
2024
pubmed:
3
5
2024
entrez:
2
5
2024
Statut:
epublish
Résumé
In silico identification of viral anti-CRISPR proteins (Acrs) has relied largely on the guilt-by-association method using known Acrs or anti-CRISPR associated proteins (Acas) as the bait. However, the low number and limited spread of the characterized archaeal Acrs and Aca hinders our ability to identify Acrs using guilt-by-association. Here, based on the observation that the few characterized archaeal Acrs and Aca are transcribed immediately post viral infection, we hypothesize that these genes, and many other unidentified anti-defense genes (ADG), are under the control of conserved regulatory sequences including a strong promoter, which can be used to predict anti-defense genes in archaeal viruses. Using this consensus sequence based method, we identify 354 potential ADGs in 57 archaeal viruses and 6 metagenome-assembled genomes. Experimental validation identified a CRISPR subtype I-A inhibitor and the first virally encoded inhibitor of an archaeal toxin-antitoxin based immune system. We also identify regulatory proteins potentially akin to Acas that can facilitate further identification of ADGs combined with the guilt-by-association approach. These results demonstrate the potential of regulatory sequence analysis for extensive identification of ADGs in viruses of archaea and bacteria.
Identifiants
pubmed: 38698035
doi: 10.1038/s41467-024-48074-x
pii: 10.1038/s41467-024-48074-x
doi:
Substances chimiques
Viral Proteins
0
Archaeal Proteins
0
CRISPR-Associated Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
3699Subventions
Organisme : Novo Nordisk Fonden (Novo Nordisk Foundation)
ID : NNF21OC0067491
Organisme : Novo Nordisk Fonden (Novo Nordisk Foundation)
ID : NNF17OC0031154
Organisme : Det Frie Forskningsråd (Danish Council for Independent Research)
ID : DFF-0135-00402
Informations de copyright
© 2024. The Author(s).
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