PADLOC: a web server for the identification of antiviral defence systems in microbial genomes

Abstract

Most bacteria and archaea possess multiple antiviral defence systems that protect against infection by phages, archaeal viruses and mobile genetic elements. Our understanding of the diversity of defence systems has increased greatly in the last few years, and many more systems likely await discovery. To identify defence-related genes, we recently developed the Prokaryotic Antiviral Defence LOCator (PADLOC) bioinformatics tool. To increase the accessibility of PADLOC, we describe here the PADLOC web server (freely available at https://padloc.otago.ac.nz), allowing users to analyse whole genomes, metagenomic contigs, plasmids, phages and archaeal viruses. The web server includes a more than 5-fold increase in defence system types detected (since the first release) and expanded functionality enabling detection of CRISPR arrays and retron ncRNAs. Here, we provide user information such as input options, description of the multiple outputs, limitations and considerations for interpretation of the results, and guidance for subsequent analyses. The PADLOC web server also houses a precomputed database of the defence systems in > 230,000 RefSeq genomes. These data reveal two taxa, Campylobacterota and Spriochaetota, with unusual defence system diversity and abundance. Overall, the PADLOC web server provides a convenient and accessible resource for the detection of antiviral defence systems.

In depth characterization of an archaeal virus-host system reveals numerous virus exclusion mechanisms

“…Only one gene, predicted to be potentially involved in virus defence (ACAM34UNSW_01791), an Argonaut related nuclease (PADLOC [43]) that is still present in ACAM34_UNSW, is slightly upregulated (log2=0.9) in ACAM34_UNSW, but not in ACAM34_DSMZ (Hlac_2785) at any time point. We suggest that ACAM34UNSW_01791 is activated in ACAM34_UNSW due to the lack of other defence mechanisms, however, its activity does not seem to interrupt the lytic cycle of HRTV-DL1.…”

“…Within the 30 most downregulated genes at T2 we find genes encoding for ribosomal proteins, for proteins involved in amino acid metabolism, proteins involved in energy production and conversion and proteins involved in oxidative stress response (Supplementary table 9), being a typical signature for a virus driven takeover of the host cell metabolism [51,52]. Only one gene, predicted to be potentially involved in virus defence (ACAM34UNSW_01791), an Argonaut related nuclease (PADLOC [53]) that is still present in ACAM34_UNSW, is slightly upregulated (log2=0.9) in ACAM34_UNSW, but not in ACAM34_DSMZ (Hlac_2785) at any time point. We suggest that ACAM34UNSW_01791 is activated in ACAM34_UNSW due to the lack of other defence mechanisms, however, its activity does not seem to interrupt the lytic cycle of HRTV-DL1.…”

Phage genome cleavage enables resuscitation from Cas13-induced bacterial dormancy

“…To better understand the context in which type VI CRISPR systems function, we sequenced the genomes of 62 diverse isolates of L. seeligeri , and evaluated their anti-phage defense system content. We searched for components of CRISPR, restriction-modification (RM), BREX, Abi, DISARM, CBASS, Pycsar, and Deity systems 25 . Of these defenses, CRISPR and RM systems were by far the most well- represented in L. seeligeri genomes (Fig S1A).…”

A Glimpse at the Anti-Phage Defenses Landscape in the Foodborne Pathogen Salmonella enterica subsp. enterica serovar Typhimurium

“…Typhimurium was investigated for its anti-phage defense systems content. The anti-phage systems detection was based on the PADLOC webserver [ 28 , 29 ], which uses the hidden Markov model’s (HMM) protein similarities prediction [ 28 ]. The webserver is designed to detect and classify a large range of anti-phage defense systems [ 29 ].…”