Diversified local CRISPR-Cas immunity to viruses of<i>Sulfolobus islandicus</i>

Pauly, Matthew D.; Bautista, María A.; Black, Jesse A.; Whitaker, Rachel J.

doi:10.1098/rstb.2018.0093

Cited by 27 publications

(47 citation statements)

References 89 publications

(159 reference statements)

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“…We had previously established such profiles of diversity in naturally occurring microbial populations [27,34,45] but had not tested their structure in relation to immunity and infection networks.…”

Section: Resultsmentioning

confidence: 99%

“…We use empirical data from three data sets in which both CRISPR alleles and virus strains have been carefully and manually assembled [27,34]. These represent lytic, chronic and temperate virus lifestyles and two different microorganisms from the two domains of life where CRISPR occurs (archaea and bacteria).…”

Section: Resultsmentioning

confidence: 99%

“…The P. aeruginosa database contained 6,231,702 total bp, with 98 viral genomes ranging from 3,588 bp to 309,208 bp. The SSV BLASTn database contained 34 genomes containing 514,147 total bases with the longest sequence being 18,548 bp and the shortest being 11,323 [27,34]. The SIRV BLASTn database was composed of 10 genomes containing 347,896 total bases with the longest sequence being 32,308 bp and the shortest being 32,308.…”

Section: F Detailed Methods For Empirical Data Collectionmentioning

confidence: 99%

“…The second data set is from S. islandicus strains isolated from several springs in the Mutnovsky Volcano in Kamchatka Russia that also were shown to share populations of hosts. The predominant viral population in these hosts is the chronic Sulfolobus Spindle Shaped Virus (SSV) [34]. The third data set consists of longitudinal sampling of humanadapted P. aeruginosa isolates from sputum samples of Cystic Fibrosis patients collected at a hospital in Copenhagen, Denmark and a global set of temperate mu-like viruses from P. aeruginosa viruses extracted from NCBI to substitute for a lack of sequenced contemporary viruses [27,46].…”

Section: Empirical Datamentioning

confidence: 99%

“…The diversity of CRISPR alleles in natural, experimental and simulated populations has been explored [30][31][32][33][34]. It has been shown, for example, that increased strain diversity of Pseudomonas aeruginosa (with strains being clones with different spacer compositions) promotes the ability of the bacterium to control the DMS3vir virus [32].…”

Section: Introductionmentioning

confidence: 99%

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The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification

Pilosof

Alcalá-Corona

Wang

et al. 2019

Preprint

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As a heritable sequence-specific adaptive immune system, CRISPR-Cas is a powerful force shaping strain diversity in host-virus systems. While the diversity of CRISPR alleles has been explored, the associated structure and dynamics of host-virus interactions has not. We develop theory on the role of CRISPR immunity in mediating the interplay between host-virus interaction structure and eco-evolutionary dynamics in a computational model and three natural systems. We show that the structures of networks describing who infects whom and who is protected from whom are modular and weighted-nested, respectively. The dynamic interplay between these networks influences transitions between dynamical regimes of virus diversification and host control,leading to eventual virus extinction. The three empirical systems exhibit weighted nestedness, a pattern our theory shows is indicative of viral control by hosts. Previously missing from studies of microbial host-pathogen systems, the protection network plays a key role in the coevolutionary dynamics. IntroductionThe structure of complex ecological communities is clearly non-random. It is generally argued that interaction structure affects the stability of communities to perturbations [1-3] and arises from coevolutionary dynamics between interacting partners [4][5][6][7], yet the structure-dynamics nexus remains a long-standing central question in community and network ecology. Host-parasite infection networks, in which interaction structure represents 'who infects whom', have been typically described as modular, nested, or both [8,9]. Modularity concerns patterns of specificity, in which the network is partitioned into modules of hosts and parasites that interact densely with each other but sparsely with those outside the group. Nestedness concerns instead patterns of specialization, and describes a network structure in which specialist hosts are infected by subsets of parasites that in turn also infect the more generalist hosts [8,9].Common to all host-parasite network studies is a dominant focus on patterns of infection. Infection structure should critically depend however on the genetic basis of resistance of hosts to pathogens [10]. The emergence of network structure from immune selection has been shown in pathogens of humans such as Plasmodium falciparum [11, 12]. In particular, strain theory developed for pathogens with multilocus encoding of antigens posits that negative frequency dependent selection, mediated by competition for hosts through cross-immunity, can structure pathogen populations into clusters of strains with limited overlap of antigenic repertoires [11][12][13][14][15]. Parasites with 2 . CC-BY-NC-ND 4.0 International license is made available under a resistance by surface mutation can arise quickly to take over CRISPR or restriction-modification systems in providing immunity. This experimental and theoretical evidence for advantages of surface modification may entail strong fitness costs under natural conditions because mutations in surface receptors such a...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: F Detailed Methods For Empirical Data Collectionmentioning

confidence: 99%

Section: Empirical Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification

Pilosof

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Wang

et al. 2019

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Extreme Environments as a Model System to Study How Virus–Host Interactions Evolve Along the Symbiosis Continuum

DeWerff

Whitaker

2021

Encyclopedia of Virology

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Structure and assembly of archaeal viruses

Baquero

Liu

Wang

et al. 2020

Advances in Virus Research

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Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among bacteriophages or viruses of eukaryotes. However, recent environmental studies have shown that archaeal viruses are widespread also in moderate ecosystems, where they play an important ecological role by influencing the turnover of microbial communities, with a global impact on the carbon and nitrogen cycles. In this review, we summarize recent advances in understanding the molecular details of virion organization and assembly of archaeal viruses. We start by briefly introducing the 20 officially recognized families of archaeal viruses and then outline the similarities and differences of archaeal virus assembly with the morphogenesis pathways used by bacterial and eukaryotic viruses, and discuss the evolutionary implications of these observations. Generally, the assembly of the icosahedral archaeal viruses closely follows the mechanisms employed by evolutionarily related bacterial and eukaryotic viruses with the HK97 fold and double jelly-roll major capsid proteins, emphasizing the overall conservation of these pathways over billions of years of evolution. By contrast, archaea-specific viruses employ unique virion assembly mechanisms. We also highlight some of the molecular adaptations underlying the stability of archaeal viruses in extreme environments. Despite considerable progress during the past few years, the archaeal virosphere continues to represent one of the least studied parts of the global virome, with many molecular features awaiting to be discovered and characterized.

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Diversified local CRISPR-Cas immunity to viruses ofSulfolobus islandicus

Cited by 27 publications

References 89 publications

The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification

The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification

Extreme Environments as a Model System to Study How Virus–Host Interactions Evolve Along the Symbiosis Continuum

Structure and assembly of archaeal viruses

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