Genetic characteristics and phylogenetic analysis of Brazilian clinical strains of Pseudomonas aeruginosa harboring CRISPR/Cas systems

Luz, Ana Carolina de Oliveira; Silva, Wilson José da; Nascimento, José Bandeira do; Silva, Julia Mariana Assis da; Balbino, Valdir de Queiroz; Leal-Balbino, Tereza Cristina

doi:10.1007/s00294-021-01173-4

Cited by 6 publications

(5 citation statements)

References 38 publications

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“…Dual inhibition of type I-E and I-F CRISPR-Cas systems may be beneficial for phage survival, given that these two CRISPR types are the most common, often co-existing in the sequenced genomes of P. aeruginosa ( 13 , 45 ). For example, phylogenetic studies of CRISPR-Cas systems in P. aeruginosa revealed that 12 out of 672 genomes contained both type I-E and I-F CRISPR-Cas systems ( 13 ).…”

Section: Discussionmentioning

confidence: 99%

The structure of AcrIE4-F7 reveals a common strategy for dual CRISPR inhibition by targeting PAM recognition sites

Hong

Lee

Park

et al. 2022

Nucleic Acids Research

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Bacteria and archaea use the CRISPR-Cas system to fend off invasions of bacteriophages and foreign plasmids. In response, bacteriophages encode anti-CRISPR (Acr) proteins that potently inhibit host Cas proteins to suppress CRISPR-mediated immunity. AcrIE4-F7, which was isolated from Pseudomonas citronellolis, is a fused form of AcrIE4 and AcrIF7 that inhibits both type I-E and type I-F CRISPR-Cas systems. Here, we determined the structure of AcrIE4-F7 and identified its Cas target proteins. The N-terminal AcrIE4 domain adopts a novel α-helical fold that targets the PAM interaction site of the type I-E Cas8e subunit. The C-terminal AcrIF7 domain exhibits an αβ fold like native AcrIF7, which disables target DNA recognition by the PAM interaction site in the type I-F Cas8f subunit. The two Acr domains are connected by a flexible linker that allows prompt docking onto their cognate Cas8 targets. Conserved negative charges in each Acr domain are required for interaction with their Cas8 targets. Our results illustrate a common mechanism by which AcrIE4-F7 inhibits divergent CRISPR-Cas types.

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Section: Discussionmentioning

confidence: 99%

The structure of AcrIE4-F7 reveals a common strategy for dual CRISPR inhibition by targeting PAM recognition sites

Hong

Lee

Park

et al. 2022

Nucleic Acids Research

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“…The possession of three CRISPR/Cas systems simultaneously (I-F + I-E + III-U), as well as the combination of I-E and I-F CRISPR/Cas types, were specific characteristics of the ST654 isolates in our P. aeruginosa collection. The simultaneous presence of I-E and I-F CRISPR/Cas types was previously documented in several works on single isolates belonging to the STs 252, 387 and 3137 [ 12 , 16 , 17 , 50 ]. To the best of our knowledge, this is the first reported case of carrying three different CRISPR/Cas systems simultaneously in the genomes of clinical P. aeruginosa isolates.…”

Section: Discussionmentioning

confidence: 83%

“…In a later work, the same research group characterized 13 Brazilian isolates harboring CRISPR/Cas systems, their phage protein and anti-CRISPR protein contents, and their genetic relationships with other publicly available genomes. This study revealed that similar CRISPR/Cas types and spacer contents were present in the strains with the same ST, and that I-F/I-E strains and lineages were not closely related [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia

et al. 2021

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Pseudomonas aeruginosa is a member of the ESKAPE opportunistic pathogen group, which includes six species of the most dangerous microbes. This pathogen is characterized by the rapid acquisition of antimicrobial resistance, thus causing major healthcare concerns. This study presents a comprehensive analysis of clinical P. aeruginosa isolates based on whole-genome sequencing data. The isolate collection studied was characterized by a variety of clonal lineages with a domination of high-risk epidemic clones and different CRISPR/Cas element patterns. This is the first report on the coexistence of two and even three different types of CRISPR/Cas systems simultaneously in Russian clinical strains of P. aeruginosa. The data include molecular typing and genotypic antibiotic resistance determination, as well as the phylogenetic analysis of the full-length cas gene and anti-CRISPR genes sequences, predicted prophage sequences, and conducted a detailed CRISPR array analysis. The differences between the isolates carrying different types and quantities of CRISPR/Cas systems were investigated. The pattern of virulence factors in P. aeruginosa isolates lacking putative CRISPR/Cas systems significantly differed from that of samples with single or multiple putative CRISPR/Cas systems. We found significant correlations between the numbers of prophage sequences, antibiotic resistance genes, and virulence genes in P. aeruginosa isolates with different patterns of CRISPR/Cas-elements. We believe that the data presented will contribute to further investigations in the field of bacterial pathoadaptability, including antimicrobial resistance and the role of CRISPR/Cas systems in the plasticity of the P. aeruginosa genome.

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“…Another important point is about CRISPR-Cas, that a recent study reported several types of CRISPR-Cas systems in Brazilian isolates of clinical P. aeruginosa , including I–F, I-E and/or I–C types ( de Oliveira Luz et al., 2021 ). Moreover, other recent study comprising 300 P aeruginosa strains from environmental and clinical niches shows that very few genomes of clinical origin carry exclusively the CAS-Type I-E system (25/300), and even fewer within genomes of environmental origin (7/300) ( Wheatley and MacLean, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

Genome sequence of Pseudomonas aeruginosa PA1-Petro—A role model of environmental adaptation and a potential biotechnological tool

Oliveira

Dias²,

Neves

2022

Heliyon

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Genetic characteristics and phylogenetic analysis of Brazilian clinical strains of Pseudomonas aeruginosa harboring CRISPR/Cas systems

Cited by 6 publications

References 38 publications

The structure of AcrIE4-F7 reveals a common strategy for dual CRISPR inhibition by targeting PAM recognition sites

The structure of AcrIE4-F7 reveals a common strategy for dual CRISPR inhibition by targeting PAM recognition sites

CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia

Genome sequence of Pseudomonas aeruginosa PA1-Petro—A role model of environmental adaptation and a potential biotechnological tool

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