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

Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types
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).
0305-1048
10868-10878
Payne, Leighton J.
349440d6-7c74-48d0-8ddd-62a26f7d5cb8
Todeschini, Thomas, Christopher
882a8867-6cc5-4f5c-a8e3-16d92c7010b4
Wu, Yi
9ee1023a-7e89-4260-9030-5c8b9fb2e1d8
Perry, Benjamin J.
73bee187-7555-42ba-b1eb-d333c31ba6be
Ronson, Clive W.
19660242-82fb-4112-b0b0-812604ace34c
Fineran, Peter C.
c70efeb2-7afa-4c74-a20a-541122d4a0cf
Luzia De Nobrega, Franklin
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Jackson, Simon A.
c6a25fbe-5b3a-4779-8db3-3fa22a7ddeea
Payne, Leighton J.
349440d6-7c74-48d0-8ddd-62a26f7d5cb8
Todeschini, Thomas, Christopher
882a8867-6cc5-4f5c-a8e3-16d92c7010b4
Wu, Yi
9ee1023a-7e89-4260-9030-5c8b9fb2e1d8
Perry, Benjamin J.
73bee187-7555-42ba-b1eb-d333c31ba6be
Ronson, Clive W.
19660242-82fb-4112-b0b0-812604ace34c
Fineran, Peter C.
c70efeb2-7afa-4c74-a20a-541122d4a0cf
Luzia De Nobrega, Franklin
6532795d-88a4-4f05-9b26-6af5b8f21a0d
Jackson, Simon A.
c6a25fbe-5b3a-4779-8db3-3fa22a7ddeea

Payne, Leighton J., Todeschini, Thomas, Christopher, Wu, Yi, Perry, Benjamin J., Ronson, Clive W., Fineran, Peter C., Luzia De Nobrega, Franklin and Jackson, Simon A. (2021) Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Research, 49, 10868-10878. (doi:10.1093/nar/gkab883).

Record type: Article

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).

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Accepted/In Press date: 17 September 2021
Published date: 4 October 2021

Identifiers

Local EPrints ID: 456197
URI: http://eprints.soton.ac.uk/id/eprint/456197
ISSN: 0305-1048
PURE UUID: 970b2fef-1e59-4d6d-8423-c23f69c1093a
ORCID for Thomas, Christopher Todeschini: ORCID iD orcid.org/0009-0000-1648-8029
ORCID for Franklin Luzia De Nobrega: ORCID iD orcid.org/0000-0002-8238-1083

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Date deposited: 26 Apr 2022 16:46
Last modified: 18 Jun 2024 02:00

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Contributors

Author: Leighton J. Payne
Author: Yi Wu
Author: Benjamin J. Perry
Author: Clive W. Ronson
Author: Peter C. Fineran
Author: Simon A. Jackson

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