Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types.
Nucleic Acids Res
; 49(19): 10868-10878, 2021 11 08.
Article
em En
| MEDLINE
| ID: mdl-34606606
ABSTRACT
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).
Texto completo:
1
Temas:
ECOS
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Financiamentos_gastos
Bases de dados:
MEDLINE
Assunto principal:
Bactérias
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Proteínas de Bactérias
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Bacteriófagos
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Software
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Archaea
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Proteínas Arqueais
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Antibiose
Tipo de estudo:
Diagnostic_studies
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Health_economic_evaluation
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Prognostic_studies
Idioma:
En
Revista:
Nucleic Acids Res
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
Nova Zelândia