The ecology and evolution of microbial CRISPR-Cas adaptive immune systems

Westra, Edze R.; Houte, Stineke van; Gandon, Sylvain; Whitaker, Rachel J.

doi:10.1098/rstb.2019.0101

Cited by 49 publications

(55 citation statements)

References 104 publications

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“…The changes in CRISPR gene content may reflect the co-evolution of bacteria and the phages that attack them, in which phages need to escape the recognition of the CRISPR system while the bacteria need to catch more phage sequences through their CRISPR defense system [60]. Westra et al [61] also suggested that CRISPR loci can evolve very rapidly in natural environments. More research in the CRISPR content change with the bacteria-virus co-evolution theme may lead to more interesting discoveries in the CRISPR research realm.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system

Hwangbo

Chu

2019

PLoS ONE

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Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a promising alternative to petroleum-based plastics. However, PHB production is costly due to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glycerol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain ZD1 have not been elucidated. In this study, we discovered a complete pathway of glycerol conversion to PHB, a novel PHB synthesis gene cluster, a salt-tolerant gene cluster, denitrifying genes, and an assimilatory nitrate reduction gene cluster in the ZD1 genome. Interestingly, the novel PHB synthesis gene cluster was found to be conserved among marine Gammaproteobacteria. Higher levels of PHB accumulation were linked to higher expression levels of the PHB synthesis gene cluster in ZD1 grown with glycerol and nitrate under saline conditions. Additionally, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas type-I-E antiviral system was found in the ZD1 genome along with a long spacer list, in which most of the spacers belong to either double-stranded DNA viruses or unknown phages. The results of the genome analysis revealed strain ZD1 used the novel PHB gene cluster to produce PHB from non-sterile crude glycerol under saline conditions.

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Section: Discussionmentioning

confidence: 99%

Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system

Hwangbo

Chu

2019

PLoS ONE

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“…CRISPR-Cas systems were first recognised for their role as phage defence mechanisms (3,(9)(10)(11), and can provide protection by preventing lysogenic conversion (12,13), which is an important mechanism of HGT (14)(15)(16). Although CRISPR-Cas systems can target parasitic genetic elements such as lytic phage, the xenogenic immunity provided by CRISPR-Cas may constrain HGT more broadly (17)(18)(19)(20). There is growing recognition that CRISPR-Cas systems target other mobile genetic elements (17,21,22), and it is suggested that CRISPR-Cas may play a very general role in preventing HGT by targeting integrative conjugative elements (ICE) and plasmids, or DNA that is acquired by transformation.…”

Section: Introductionmentioning

confidence: 99%

“…Although CRISPR-Cas systems were initially characterized as phage defence mechanisms (9, 10), it is becoming increasingly clear that CRISPR-Cas systems also target mobile genetic elements (19)(20)(21)86).…”

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confidence: 99%

CRISPR-Cas systems restrict horizontal gene transfer inPseudomonas aeruginosa

Wheatley

MacLean

2020

Preprint

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CRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by CRISPR-Cas raises the possibility that these systems may constrain horizontal gene transfer. Here we test this hypothesis in the opportunistic pathogen Pseudomonas aeruginosa, which has emerged an important model system for understanding CRISPR-Cas function. Across the diversity of P. aeruginosa, active CRISPR-Cas systems are associated with smaller genomes and a reduced GC content, suggesting that CRISPR-Cas inhibits the acquisition of foreign DNA. Although phage are the major target of CRISPR-Cas spacers, more than 80% of isolates with an active CRISPR-Cas system have spacers that target integrative conjugative elements (ICE) or the conserved conjugative transfer machinery used by plasmids and ICE. Consistent with these results, genomes containing active CRISPR-Cas systems harbor a lower abundance of both prophage and ICE. Crucially, spacers in genomes with active CRISPR-Cas systems map to ICE and phage that are integrated into the chromosomes of closely related genomes lacking CRISPR-Cas immunity, providing direct evidence that CRISPR-Cas constrains horizontal gene transfer in these lineages. In conclusion, we find that CRISPR-Cas acts as an important constraint to horizontal gene transfer, suggesting that CRISPR-Cas may constrain the ability of this pathogen to adapt to new niches and stressors.

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“…nov., was also identified in C. fetus. The mechanisms behind the selection of each system in different bacterial species [56], as well as the role of Cas system type III-D in C. fetus, remain unclear. https://doi.org/10.1371/journal.pone.0227500.g004…”

Section: Genomic Characterizationmentioning

confidence: 99%

Campylobacter portucalensis sp. nov., a new species of Campylobacter isolated from the preputial mucosa of bulls

et al. 2020

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A new species of the Campylobacter genus is described, isolated from the preputial mucosa of bulls (Bos taurus). The five isolates obtained exhibit characteristics of Campylobacter, being Gram-negative non-motile straight rods, oxidase positive, catalase negative and microaerophilic. Phenotypic characteristics and nucleotide sequence analysis of 16S rRNA and hsp60 genes demonstrated that these isolates belong to a novel species within the genus Campylobacter. Based on hsp60 gene phylogenetic analysis, the most related species are C. ureolyticus, C. blaseri and C. corcagiensis. The whole genome sequence analysis of isolate FMV-PI01 revealed that the average nucleotide identity with other Campylobacter species was less than 75%, which is far below the cutoff for isolates of the same species. However, whole genome sequence analysis identified coding sequences highly homologous with other Campylobacter spp. These included several virulence factor coding genes related with host cell adhesion and invasion, transporters involved in resistance to antimicrobials, and a type IV secretion system (T4SS), containing virB2-virB11/ virD4 genes, highly homologous to the C. fetus subsp. venerealis. The genomic G+C content of isolate FMV-PI01 was 28.3%, which is one of the lowest values reported for species of the genus Campylobacter. For this species the name Campylobacter portucalensis sp. nov. is proposed, with FMV-PI01 (= LMG 31504, = CCUG 73856) as the type strain.

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The ecology and evolution of microbial CRISPR-Cas adaptive immune systems

Abstract: One contribution of 17 to a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.

Cited by 49 publications

References 104 publications

Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system

Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system

CRISPR-Cas systems restrict horizontal gene transfer inPseudomonas aeruginosa

Campylobacter portucalensis sp. nov., a new species of Campylobacter isolated from the preputial mucosa of bulls

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