The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes

Godde, James S.; Bickerton, Amanda

doi:10.1007/s00239-005-0223-z

Cited by 310 publications

(283 citation statements)

References 16 publications

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“…Cas1, cas3, and cas4 proteins are homologous to a DNA repair protein, a helicase, and recB exonuclease, respectively. The predicted proteins of this study are directly contributed in DNA a repair and recombination mechanism, which was agreed to earlier annotation (Brügger et al 2002;Sasaki et al 2004;Godde and Bickerton 2006;Weinberger et al 2012;Quax et al 2013).…”

Section: Discussionsupporting

confidence: 91%

“…CRISPR loci have shown a distinct genetic and molecular diversity in the strains of a thermophilic archaean, Methanocaldococcus jannaschii (Bult et al 1996) and of thermophilic bacterium, Streptococcus thermophilus (Horvath et al 2008). Some of the CRISPR sequences in Thermoanaerobacter tengcongensis and Thermus thermophilus HB8 chromosomes have shared with their existing megaplasmids (Jansen et al 2002;Godde and Bickerton 2006). Spacer sequences have also shown a variation in five strains of Thermotoga neapolitana by geographic locale (DeBoy et al 2006).…”

Section: Introductionmentioning

confidence: 99%

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Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Chellapandi

Ranjani

2015

Syst Synth Biol

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Clustered regularly interspaced short palindromic repeats (CRISPRs) are direct features of the prokaryotic genomes involved in resistance to their bacterial viruses and phages. Herein, we have identified CRISPR loci together with CRISPR-associated sequences (CAS) genes to reveal their immunity against genome invaders in the thermophilic archaea and bacteria. Genomic survey of this study implied that genomic distribution of CRISPR-CAS systems was varied from strain to strain, which was determined by the degree of invading mobiloms. Direct repeats found to be equal in some extent in many thermopiles, but their spacers were differed in each strain. Phylogenetic analyses of CAS superfamily revealed that genes cmr, csh, csx11, HD domain, devR were belonged to the subtypes of cas gene family. The members in cas gene family of thermophiles were functionally diverged within closely related genomes and may contribute to develop several defense strategies. Nevertheless, genome dynamics, geological variation and host defense mechanism were contributed to share their molecular functions across the thermophiles. A thermophilic archaean, Thermococcus gammotolerans and thermophilic bacteria, Petrotoga mobilis and Thermotoga lettingae have shown superoperons-like appearance to cluster cas genes, which were typically evolved for their defense pathways. A cmr operon was identified with a specific promoter in a thermophilic archaean, Caldivirga maquilingensis. Overall, we concluded that knowledge-based genomic survey and phylogeny-based functional assignment have suggested for designing a reliable genetic regulatory circuit naturally from CRISPR-CAS systems, acquired defense pathways, to thermophiles in future synthetic biology.

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Chellapandi

Ranjani

2015

Syst Synth Biol

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“…As indicated above, the repeats tend to vary between distantly-related species, but exceptions are often noted; for example, the arrays in Escherichia coli and Mycobacterium avium contain very similar repeats, although these two organisms are classified in different phyla 14 . This has been explained by horizontal gene transfer of CRISPR systems between organisms, a hypothesis supported by phylogenetic trees of core CAS genes 16,17,22 . Gene transfer was suggested to be mediated by megaplasmids, based on the identification of 10 such plasmids carrying CRISPR arrays 22,33 .…”

Section: Evolution Of Crispr Systemsmentioning

confidence: 99%

“…This has been explained by horizontal gene transfer of CRISPR systems between organisms, a hypothesis supported by phylogenetic trees of core CAS genes 16,17,22 . Gene transfer was suggested to be mediated by megaplasmids, based on the identification of 10 such plasmids carrying CRISPR arrays 22,33 . Interestingly, a CRISPR array was also found within a Clostridium difficile prophage, and it was suggested that the phage uses the CRISPR to limit dispersal of competing phages 34 .…”

Section: Evolution Of Crispr Systemsmentioning

confidence: 99%

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CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

2008

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Arrays of clustered, regularly spaced short palindromic repeats (CRISPR) are widespread in the genomes of many bacteria and almost all archaea. These arrays are composed of direct repeats sized 24-47 bp separated by similarly sized non-repetitive sequences (spacers). It was recently experimentally shown that CRISPR arrays, along with a group of associated proteins, confer resistance to phage. Following exposure to phage, bacteria integrate new spacer sequences that are derived from the phage genome. Acquisition of these spacers enables the bacterial cell to shutdown the phage attack, presumably by an RNA-interference-like mechanism. This Progress discusses the structure and function of CRISPRs and the implications of this new antiviral mechanism in bacteria.2 Bacteriophages constitute the most populous life-forms on Earth 1 . In sea water, an environment in which phage abundance has been extensively studied, it has been estimated that there are 5-10 phage for every bacterial cell 2 . Despite being outnumbered by phage, bacteria proliferate and avoid extinction by using a battery of innate phageresistance mechanisms such as restriction enzymes and abortive infection 3 . In this Progress article we describe the CRISPR system, a recently discovered defence mechanism, which is remarkable because it confers acquired phage resistance in Bacteria and Archaea. A hallmark of this system are arrays of short direct repeats interspersed by non-repetitive spacer sequences, the so-called Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). Additional components of the system include CRISPRassociated (CAS) genes and a leader sequence (Fig. 1A). Brief history of CRISPR researchThe first report that described a CRISPR array, in 1987, was from Ishino et al. who found 14 repeats of 29bp interspersed by 32-33bp non-repeating spacer sequences 4,5 , adjacent to the isozyme converting alkaline phosphatase (iap) gene in Escherichia coli. In subsequent years similar CRISPR arrays were found in Mycobacterium tuberculosis 6 , Haloferax mediterranei 7 , Methanocaldococcus jannaschii 8 , Thermotoga maritima 9 and other bacteria and archaea. The accumulation of sequenced microbial genomes allowed genome-wide computational searches for CRISPRs (the first such analysis was carried out by Mojica et al. in 2000 10 ), and the most recent computational analyses revealed that CRISPRs are found in ~40% of bacterial and ~90% of archaeal genomes sequenced to date 11, 12 (Box 1).In parallel to the initial appreciation of the abundance of CRISPRs 13 , Jansen et al. identified four CRISPR-associated (CAS) genes that were almost always found adjacent to the repeat arrays 14 . Subsequent studies initiated by Koonin and colleagues 15, 16 and Haft et al. 17 uncovered 25-45 additional CAS genes appearing in close proximity to the arrays. The same set of genes is absent from genomes that lack CRISPRs.Several hypotheses for the function of CRISPRs have been proposed. Early in 1995 Mojica et al. suggested that the repeats were involved i...

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Functions and Applications of RNA-Guided CRISPR-Cas Immune Systems

Barrangou

Horvath

2014

Encyclopedia of Molecular Cell Biology and Molecular Medicine

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The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes

Cited by 310 publications

References 16 publications

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

Functions and Applications of RNA-Guided CRISPR-Cas Immune Systems

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