Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types.

Adenosine Triphosphatases / genetics Antibiosis / genetics Archaea / classification Archaeal Proteins / genetics Bacteria / classification Bacterial Proteins / genetics Bacteriophages / genetics CRISPR-Cas Systems DNA Helicases / genetics DNA Modification Methylases / genetics Markov Chains Phylogeny Software Terminology as Topic

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
08 11 2021
Historique:
accepted: 17 09 2021
revised: 13 09 2021
received: 05 08 2021
pubmed: 5 10 2021
medline: 24 12 2021
entrez: 4 10 2021
Statut: ppublish

Résumé

To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).

Identifiants

DOI: 10.1093/nar/gkab883 PMID: 34606606 PMC: PMC8565338
pubmed: 34606606
pii: 6381132
doi: 10.1093/nar/gkab883
pmc: PMC8565338
doi:

Substances chimiques

Archaeal Proteins 0
Bacterial Proteins 0
DNA Modification Methylases EC 2.1.1.-
Adenosine Triphosphatases EC 3.6.1.-
DNA Helicases EC 3.6.4.-

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

10868-10878

Informations de copyright

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Leighton J Payne (LJ)

Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
ORCID: 0000-0003-2305-6827

Thomas C Todeschini (TC)

School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.

Yi Wu (Y)

School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.

Benjamin J Perry (BJ)

Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.

Clive W Ronson (CW)

Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
Genetics Otago, University of Otago, Dunedin, New Zealand.
ORCID: 0000-0002-2217-9676

Peter C Fineran (PC)

Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
Genetics Otago, University of Otago, Dunedin, New Zealand.
Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
ORCID: 0000-0002-4639-6704

Franklin L Nobrega (FL)

School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.
ORCID: 0000-0002-8238-1083

Simon A Jackson (SA)

Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
Genetics Otago, University of Otago, Dunedin, New Zealand.
Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
ORCID: 0000-0002-4512-3093

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Classifications MeSH

questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Hydrolases › Acid anhydride hydrolases › Adenosine triphosphatases › Identification and classification of antiviral...
questionsmedicales.fr › Phénomènes biologiques › Antibiose › Identification and classification of antiviral...
questionsmedicales.fr › Archéobactéries › Identification and classification of antiviral...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines d'archée › Identification and classification of antiviral...
questionsmedicales.fr › Bactéries › Identification and classification of antiviral...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines bactériennes › Identification and classification of antiviral...
questionsmedicales.fr › Virus › Bactériophages › Identification and classification of antiviral...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Épigenèse génétique › Extinction de l'expression des gènes › Systèmes CRISPR-Cas › Identification and classification of antiviral...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Isomerases › Helicase › Identification and classification of antiviral...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Transferases › One-carbon group transferases › Methyltransferases › DNA modification methylases › Identification and classification of antiviral...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Statistiques comme sujet › Processus stochastiques › Chaines de Markov › Identification and classification of antiviral...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Identification and classification of antiviral...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Identification and classification of antiviral...
questionsmedicales.fr › Sciences de l'information › Langage › Linguistique › Terminologie comme sujet › Identification and classification of antiviral...