Diversity of microbial defence systems

Cazares, Adrián; Figueroa, Wendy; Cazares, Daniel

doi:10.1038/s41579-022-00702-3

Cited by 3 publications

(2 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In many cases, this structure-based approach reveals homologs with characterised active sites or functional motifs, which can aid in discrimination between defence system proteins and similar non-orthologous proteins. Users may also find it informative to compare their PADLOC results with DefenseFinder, another tool recently developed for defence system identification ( 82 , 83 ).…”

Section: Resultsmentioning

confidence: 99%

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

Payne

Meaden

Mestre³

et al. 2022

Nucleic Acids Research

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

confidence: 99%

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

Payne

Meaden

Mestre³

et al. 2022

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…retroviruses jump in and out constantly, sometimes leaving bits of themselves behind). Archea and bacteria are constantly exposed to the invasion by elements such as phages or plasmids (12). In response they have evolved an arsenal of defense systems such as antiphage systems (frequently physically clustered in genomic 'defense islands') or defense systems specifically targeting foreign plasmids, that limit the intrusion of foreign elements (13,14).…”

Section: Introductionmentioning

confidence: 99%

‘Cannibalism’ of exogenous DNA sequences: The ancestral form of adaptive immunity which entails recognition of danger

et al. 2022

View full text Add to dashboard Cite

Adaptive immunity is a sophisticated form of immune response capable of retaining the molecular memory of a very great diversity of target antigens (epitopes) as non-self. It is capable of reactivating itself upon a second encounter with an immunoglobulin or T-cell receptor antigen-binding site with a known epitope that had previously primed the host immune system. It has long been considered that adaptive immunity is a highly evolved form of non-self recognition that appeared quite late in speciation and complemented a more generalist response called innate immunity. Innate immunity offers a relatively non-specific defense (although mediated by sensors that could specifically recognize virus or bacteria compounds) and which does not retain a memory of the danger. But this notion of recent acquisition of adaptive immunity is challenged by the fact that another form of specific recognition mechanisms already existed in prokaryotes that may be able to specifically auto-protect against external danger. This recognition mechanism can be considered a primitive form of specific (adaptive) non-self recognition. It is based on the fact that many archaea and bacteria use a genome editing system that confers the ability to appropriate viral DNA sequences allowing prokaryotes to prevent host damage through a mechanism very similar to adaptive immunity. This is indistinctly called, ‘endogenization of foreign DNA’ or ‘viral DNA predation’ or, more pictorially ‘DNA cannibalism’. For several years evidence has been accumulating, highlighting the crucial role of endogenization of foreign DNA in the fundamental processes related to adaptive immunity and leading to a change in the dogma that adaptive immunity appeared late in speciation.

show abstract