Long stretches of short tandem repeats are present in the largest replicons of the <i>Archaea Haloferax mediterranei</i> and <i>Haloferax volcanii</i> and could be involved in replicon partitioning

Mojica, Francisco J. M.; Ferrer, Consuelo; Juez, G.; Rodrı́guez-Valera, Francisco

doi:10.1111/j.1365-2958.1995.mmi_17010085.x

Cited by 274 publications

(180 citation statements)

References 20 publications

(42 reference statements)

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“…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).…”

Section: Brief History Of Crispr Researchmentioning

confidence: 64%

“…Early in 1995 Mojica et al suggested that the repeats were involved in replicon partitioning, based on their observations that an increased copy number of the repeats in Haloferax volcanii resulted in altered replicon segregation 7 . This effect, however, was not reproduced in similar experiments carried out in M. tuberculosis 14 .…”

Section: Brief History Of Crispr Researchmentioning

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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Section: Brief History Of Crispr Researchmentioning

confidence: 64%

Section: Brief History Of Crispr Researchmentioning

confidence: 99%

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

2008

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“…volcanii (Mojica et al 1995;. It suggests the functional integrity of TRs and CRISPRs may contribute a significant role in the molecular process of their genomes as such.…”

Section: Discussionmentioning

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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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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“…In 1995, Mojica and colleagues noticed long segments of short repeats in Archaea Haloferax mediterranei and Haloferax volcanii [103]. And five years later, after a computational analysis of known microbial genomes, the group characterized the clustered repeated short elements they had seen, calling them Short Regularly Spaced Repeats (SRSRs) [104].…”

Section: Discovery Of Crispr-casmentioning

confidence: 99%

Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

Cooper

Overstreet

2014

Physics of Life Reviews

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Recent evidence supports that prokaryotes exhibit adaptive immunity in the form of CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) and Cas (CRISPR associated proteins). The CRISPR-Cas system confers resistance to exogenous genetic elements such as phages and plasmids by allowing for the recognition and silencing of these genetic elements. Moreover, CRISPR-Cas serves as a memory of past exposures. This suggests that the evolution of the immune system has counterparts among the prokaryotes, not exclusively among eukaryotes. Mathematical models have been proposed which simulate the evolutionary patterns of CRISPR, however large gaps in our understanding of CRISPR-Cas function and evolution still exist. The CRISPR-Cas system is analogous to small RNAs involved in resistance mechanisms throughout the tree of life, and a deeper understanding of the evolution of small RNA pathways is necessary before the relationship between these convergent systems is to be determined. Presented in this review are novel RNAi therapies based on CRISPR-Cas analogs and the potential for future therapies based on CRISPR-Cas system components.

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Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning

Cited by 274 publications

References 20 publications

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

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

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

Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

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