The role of CRISPR-Cas systems in virulence of pathogenic bacteria - PubMed (original) (raw)

Review

The role of CRISPR-Cas systems in virulence of pathogenic bacteria

Rogier Louwen et al. Microbiol Mol Biol Rev. 2014 Mar.

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. The discovery that CRISPR spacers are often identical to sequence fragments of mobile genetic elements was a major breakthrough that eventually led to the elucidation of CRISPR-Cas as an adaptive immunity system. Key elements of this unique prokaryotic defense system are small CRISPR RNAs that guide nucleases to complementary target nucleic acids of invading viruses and plasmids, generally followed by the degradation of the invader. In addition, several recent studies have pointed at direct links of CRISPR-Cas to regulation of a range of stress-related phenomena. An interesting example concerns a pathogenic bacterium that possesses a CRISPR-associated ribonucleoprotein complex that may play a dual role in defense and/or virulence. In this review, we describe recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular.

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Figures

FIG 1

FIG 1

Overview of expression of cas genes in human-associated bacteria that occupy different host niches. The heat maps indicate which cas genes are induced (shades of red) or repressed (shades of blue) during bacterial responses to changes in the environment. Details are given in the main text. The overview shows that modulation of cas gene expression occurs in diverse Gram-positive and Gram-negative bacteria that together occupy very diverse niches throughout the human body. For F. novicida, adaptation of gene expression in macrophages depends on Cas9, tracRNA, and possibly also scaRNA, which together inhibit expression of an immunogenic lipoprotein (shown in green) (22). All bacteria depicted in this figure possess Cas9, and scaRNA production has been predicted for F. novicida, C. jejuni, L. monocytogenes, and N. meningitidis (22), suggesting that a role of Cas9 in regulation of bacterial gene expression may be more widespread.

FIG 2

FIG 2

Overview of the three type II CRISPR-Cas subtypes. All three subtypes share a conserved set of cas genes: cas1, cas2, and cas9. Type II-A has an additional csn2 gene, and type II-B has an additional cas4 gene (21). Type II-C does not feature an additional cas gene beyond the three conserved cas genes (122). All subtypes feature a small _trans_-encoded RNA called _trans_-activating CRISPR RNA (tracrRNA); type II-C displays variation in the location of tracrRNA. cas9, cas1, and cas2 are indicated with green arrows, and tracrRNA is shown with yellow boxes. Transcription start sites are shown as black arrows upstream of the repeats (red diamonds) and spacers (purple squares) in type II-A (e.g., in Streptococcus spp.) and -B (e.g., in Legionella pneumophila) CRISPR loci, or within each spacer in the case of the minimal type II-C CRISPR systems of Neisseria meningitidis (upper) and Campylobacter jejuni (lower) (122).

FIG 3

FIG 3

Overview of the most important discoveries in CRISPR-Cas research. The original papers describing the major findings are discussed and cited in the main text.

FIG 4

FIG 4

Heat map showing expression of cas genes in human-associated bacteria that occupy different host niches. The heat map indicates which cas genes are induced (shades of red) or repressed (shades of blue) during bacterial responses to changes in the environment. All gene expression data displayed in this figure have been published, are publicly available in the MicrobesOnline (

http://www.microbesonline.org/

) and NCBI Entrez (

http://www.ncbi.nlm.nih.gov/gene/

) gene expression databases, and are further discussed in this review.

FIG 5

FIG 5

Dual function of type II CRISPR-Cas systems. (A) Genomic locus of type II CRISPR-Cas system. The cas operon consists of at least three genes (cas9, cas1, and cas2). A fourth gene (*) is present in type II-A (csn2) and II-B (cas4) systems but not in type II-C systems (122). Adjacent to the cas operon, the CRISPR locus is present (dark purple diamonds indicate repeats, and bright purple squares indicate the spacers), as well as the _trans_-encoded CRISPR RNA (tracrRNA) gene and possibly the recently proposed scaRNA gene (22). The order and orientation of the CRISPR and the genes vary in different genomes. (B) A role in defense against DNAs of invading genetic elements is well established (11), in which processed crRNA and a short version of the tracrRNA (most likely resulting from processing of a longer tracrRNA transcript or transcription from a second promoter; see panel A) eventually are responsible for interaction with target DNA. Eventually, both DNA strands are cleaved at the active sites of Cas9 (red triangles) (20, 129, 130). (C) A distinct role of Cas9 in virulence has been suggested (30), and a molecular basis for how Cas9 can codetermine virulence has been revealed (22): a long version of the tracrRNA shares significant homology with a target transcript, resulting in silencing and probably degradation of this transcript. Involvement of another small CRISPR-associated RNA (scaRNA) has been proposed; if indeed important, this scaRNA may be involved in stabilizing the interaction of the tracrRNA in the Cas9 complex.

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