Kunin, V., Sorek, R. & Hugenholtz, P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8, R61

DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
Genome biology (Impact Factor: 10.81). 02/2007; 8(4):R61. DOI: 10.1186/gb-2007-8-4-r61
Source: PubMed


Clustered regularly interspaced short palindromic repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in approximately 40% of bacterial and most archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CASs), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes.
Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. Some of the clusters present stable, highly conserved RNA secondary structures, while others lack detectable structures. Stable secondary structures exhibit multiple compensatory base changes in the stem region, indicating evolutionary and functional conservation.
We show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification, including specific relationships between CRISPR and CAS subtypes.

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    • "Although very variable in the actual components, CRISPR-mediated immunity works in general in three steps: 1) Acquisition of new spacers into the array, 2) expression and processing of CRISPR RNA (crRNA), and 3) sequence-specific interference (Makarova, Haft, et al. 2011; Wiedenheft et al. 2012). With the rapid increase in the availability of genome sequences, it is now clear that CRISPR-Cas systems are widespread in both bacteria and archaea (Kunin et al. 2007; Horvath et al. 2008; Makarova, Haft, et al. 2011; Wiedenheft et al. 2012; Barrangou and Marraffini 2014). "
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    ABSTRACT: CRISPR-Cas systems are sequence-specific adaptive defenses against phages and plasmids which are widespread in prokaryotes. Here we have studied whether phylogenetic relatedness or sharing of environmental niches affects the distribution and dissemination of Type II CRISPR-Cas systems, firstly in 132 bacterial genomes from 15 phylogenetic classes, ranging from Proteobacteria to Actinobacteria. There was clustering of distinct Type II CRISPR-Cas systems in phylogenetically distinct genera with varying G+C%, which share environmental niches. The distribution of CRISPR-Cas within a genus was studied using a large collection of genome sequences of the closely related Campylobacter species Campylobacter jejuni (N=3,746) and Campylobacter coli (N=486). The Cas gene cas9 and CRISPR-repeat are almost universally present in C. jejuni genomes (98.0% positive) but relatively rare in C. coli genomes (9.6% positive). C. jejuni and agricultural C. coli isolates share the C. jejuni CRISPR-Cas system, which is closely related to, but distinct from the C. coli CRISPR-Cas system found in C. coli isolates from non-agricultural sources. Analysis of the genomic position of CRISPR-Cas insertion suggest that the C. jejuni-type CRISPR-Cas has been transferred to agricultural C. coli. Conversely, the absence of the C. coli-type CRISPR-Cas in agricultural C. coli isolates may be due to these isolates not sharing the same environmental niche, and may be affected by farm hygiene and biosecurity practices in the agricultural sector. Finally, many CRISPR spacer alleles were linked with specific multilocus sequence types, suggesting that these can assist molecular epidemiology applications for C. jejuni and C. coli. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Genome Biology and Evolution 09/2015; DOI:10.1093/gbe/evv174 · 4.23 Impact Factor
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    • "CRISPR associated genes (cas) are encoding a large and heterogeneous family of proteins that carry functional domains typical of nucleases, helicases, polymerases and polynucleotide-binding proteins (Haft et al., 2005). So far, eight different CRISPR-Cas systems subtypes have been identified, each subtype containing a marker cas gene along with a set of variable subtype-specific cas genes (Kunin et al., 2007). Cyanophage infecting M. aeruginosa has been reported (Yoshida-Takashima et al., 2012; Ou et al., 2013), but few studies focus on the genomic features of defense system for this species. "
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    ABSTRACT: Microcystis aeruginosa is one of the most common and dominant bloom-forming cyanobacteria in freshwater lakes around the world. Microcystis cells can produce toxic secondary metabolites, such as microcystins, which are harmful to human health. Two M. aeruginosa strains were isolated from two highly eutrophic lakes in China and their genomes were sequenced. Comparative genomic analysis was performed with the 12 other available M. aeruginosa genomes and closely related unicellular cyanobacterium. Each genome of M. aeruginosa containing at least one clustered regularly interspaced short palindromic repeat (CRISPR) locus and total 71 loci were identified, suggesting it is ubiquitous in M. aeruginosa genomes. In addition to the previously reported subtype I-D cas gene sets, three CAS subtypes I-A, III-A and III-B were identified and characterized in this study. Seven types of CRISPR direct repeat have close association with CAS subtype, confirming that different and specific secondary structures of CRISPR repeats are important for the recognition, binding and process of corresponding cas gene sets. Homology search of the CRISPR spacer sequences provides a history of not only resistance to bacteriophages and plasmids known to be associated with M. aeruginosa, but also the ability to target much more exogenous genetic material in the natural environment. These adaptive and heritable defense mechanisms play a vital role in keeping genomic stability and self-maintenance by restriction of horizontal gene transfer. Maintaining genomic stability and modulating genomic plasticity are both important evolutionary strategies for M. aeruginosa in adaptation and survival in various habitats.
    Frontiers in Microbiology 05/2015; 6. DOI:10.3389/fmicb.2015.00394 · 3.99 Impact Factor
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    • "The spacer sequences generally originate from phage or plasmid DNA (Gasiunas et al., 2014) and they represent a ―memory of past genetic aggressions‖ (Stern et al., 2010). The repeat sequences within a CRISPR locus are conserved, but in different CRISPR loci can vary in both sequence and length although there are partially conserved sequences such as a GTTTg/c motif at the 5énd and a GAAAC motif at the 3énd (Bhaya et al., 2011; Kunin et al., 2007). In addition, the number of repeat–spacer units in a CRISPR locus varies widely among organisms (Wiedenheft et al., 2012). "
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    ABSTRACT: Approximately all sequenced archaeal and half of eubacterial genomes have some sort of adaptive immune system, which enables them to target and cleave invading foreign genetic elements by an RNAi-like pathway. CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems consist of the CRISPR loci with multiple copies of a short repeat sequence separated by variable sequences with similar size that are derived from invaders and cas genes encode proteins involved in RNA binding, endo-and exo-nucleases, helicases, and polymerases activities. There are three main types (I, II and III) of CRISPR/Cas systems. All systems function in three distinct stages: (1) adaptation, (2) crRNA biogenesis, and (3) interference. This review focuses on the features and mechanisms of the CRISPR-Cas systems and current finding about them.
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