Comparative analysis of CRISPR loci in different Listeria monocytogenes lineages

Di, Huiling; Ye, Lei; He, Yan; Meng, Hecheng; Yamasak, Shinji; Shi, Lei

doi:10.1016/j.bbrc.2014.10.018

Cited by 33 publications

(32 citation statements)

References 32 publications

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“…Many L. monocytogenes isolates have type II-A CRISPR-Cas systems (Sesto et al, 2014) and their CRISPR spacers possess identity to many virulent, temperate, and integrated phages (Di et al, 2014; Sesto et al, 2014). However, there is no experimental evidence of canonical CRISPR-Cas function.…”

Section: Resultsmentioning

confidence: 99%

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

Rauch

Silvis

Hultquist

et al. 2017

Cell

420

505

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SUMMARY Bacterial CRISPR-Cas systems utilize sequence-specific RNA-guided nucleases to defend against bacteriophage infection. As a counter-measure, numerous phages are known that produce proteins to block the function of Class 1 CRISPR-Cas systems. However, currently no proteins are known to inhibit the widely used Class 2 CRISPR-Cas9 system. To find these inhibitors, we searched cas9-containing bacterial genomes for the co-existence of a CRISPR spacer and its target, a potential indicator for CRISPR inhibition. This analysis led to the discovery of four unique type II-A CRISPR-Cas9 inhibitor proteins encoded by Listeria monocytogenes prophages. More than half of L. monocytogenes strains with cas9 contain at least one prophage-encoded inhibitor, suggesting widespread CRISPR-Cas9 inactivation. Two of these inhibitors also blocked the widely used Streptococcus pyogenes Cas9 when assayed in Escherichia coli and human cells. These natural Cas9-specific “anti-CRISPRs” present tools that can be used to regulate the genome engineering activities of CRISPR-Cas9.

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Section: Resultsmentioning

confidence: 99%

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

Rauch

Silvis

Hultquist

et al. 2017

Cell

420

505

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“…Foremost among these are the CRISPR sequences together with adjacent Cas genes and the restriction modification (RM) systems, which are widely distributed among prokaryotes (33). CRISPR/Cas genes comprise the adaptive immune system in many bacterial species including L. monocytogenes and have a role in defense of the bacterial cell against invading bacteriophages or plasmid-derived elements (34). Immunity against foreign invasion in bacteria is achieved first by integration of a small piece of viral or plasmid DNA (known as a spacer sequence) into the CRISPR locus.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomic Analysis of Two Serotype 1/2b Listeria monocytogenes Isolates from Analogous Environmental Niches Demonstrates the Influence of Hypervariable Hotspots in Defining Pathogenesis

et al. 2016

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The vast majority of clinical human listeriosis cases are caused by serotype 1/2a, 1/2b, 1/2c, and 4b isolates of Listeria monocytogenes. The ability of L. monocytogenes to establish a systemic listeriosis infection within a host organism relies on a combination of genes that are involved in cell recognition, internalization, evasion of host defenses, and in vitro survival and growth. Recently, whole genome sequencing and comparative genomic analysis have proven to be powerful tools for the identification of these virulence-associated genes in L. monocytogenes. In this study, two serotype 1/2b strains of L. monocytogenes with analogous isolation sources, but differing infection abilities, were subjected to comparative genomic analysis. The results from this comparison highlight the importance of accessory genes (genes that are not part of the conserved core genome) in L. monocytogenes pathogenesis. In addition, a number of factors, which may account for the perceived inability of one of the strains to establish a systemic infection within its host, have been identified. These factors include the notable absence of the Listeria pathogenicity island 3 and the stress survival islet, of which the latter has been demonstrated to enhance the survival ability of L. monocytogenes during its passage through the host intestinal tract, leading to a higher infection rate. The findings from this research demonstrate the influence of hypervariable hotspots in defining the physiological characteristics of a L. monocytogenes strain and indicate that the emergence of a non-pathogenic isolate of L. monocytogenes may result from a cumulative loss of functionality rather than by a single isolated genetic event.

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“…The average length of spacers were 31 bp, ranging from 28 to 34. Diversity in the length and sequence of spacers affects the activity of CRISPR systems in bacteria . In Di et al studies, CRISPR loci containing a more number of the spacers with length of 30 bp were more active than loci containing a less number with length of 36 bp, which indicates the effect of the number and length of the spacer on activity of CRISPR loci .…”

Section: Discussionmentioning

confidence: 98%

“…sequence of spacers affects the activity of CRISPR systems in bacteria [10,30]. In Di et al studies, CRISPR loci containing a more number of the spacers with length of 30 bp were more active than loci containing a less number with length of 36 bp, which indicates the effect of the number and length of the spacer on activity of CRISPR loci [30]. In our study, all strains possess spacers with an average length of 31 bp; therefore, CRISPR loci in our selected strains are likely more active than previously studied strains with shorter spacers.…”

Section: Discussionmentioning

confidence: 99%

Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli

Rahmatabadi

Nezafat

Negahdaripour

et al. 2016

J. Basic Microbiol.

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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) system is a novel type of innate defense system in prokaryotes for destruction of exogenous elements. To gain further insight into behavior and organization of the system, the extensive analysis of the available sequenced genomes is necessary. The dynamic nature of CRISPR loci is possibly valuable for typing and relative analyses of strains and microbial population. There are a few orderly bioinformatics investigations about the structure of CRISPR sequences in the Escherichia coli strains. In this study, 57 CRISPR loci were selected from 32 Escherichia coli strains to investigate their structural characteristics and potential functions using bioinformatics tools. Our results showed that most strains contained several loci that mainly included conserved direct repeats, while the spacers were highly variable. Moreover, RNA analysis of the sequences indicated that all loci could form stable RNA secondary structures and showed homology mostly with phages compared to plasmids. Only three strains included cas genes around their loci.

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Comparative analysis of CRISPR loci in different Listeria monocytogenes lineages

Cited by 33 publications

References 32 publications

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins

Comparative Genomic Analysis of Two Serotype 1/2b Listeria monocytogenes Isolates from Analogous Environmental Niches Demonstrates the Influence of Hypervariable Hotspots in Defining Pathogenesis

Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli

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