Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types
| Autor: | Yi Wu, Simon A. Jackson, Thomas C Todeschini, Peter C. Fineran, Franklin L. Nobrega, Benjamin J. Perry, Clive W. Ronson, Leighton J Payne |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
AcademicSubjects/SCI00010
Archaeal Proteins Computational biology Viral infection Genome Bacterial Proteins Terminology as Topic Antibiosis Genetics CRISPR Bacteriophages DNA Modification Methylases Phylogeny Synteny Adenosine Triphosphatases biology Bacteria DNA Helicases Computational Biology biology.organism_classification Archaea Markov Chains Identification (biology) Mobile genetic elements CRISPR-Cas Systems Software |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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). |
| Databáze: | OpenAIRE |
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