To acquire or resist: the complex biological effects of CRISPR–Cas systems

Bondy‐Denomy, Joseph; Davidson, Alan R.

doi:10.1016/j.tim.2014.01.007

Cited by 97 publications

(74 citation statements)

References 82 publications

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“…xsiRNA: extremophilic short interfering RNA; xRISC: extremophilic RNA induced silencing complexes their invading phages and plasmids (Horvath et al 2008). Also, the prophages account on their genetic variation across closely related strains and contribute in evolution of adaptive immune systems, which was agreed to earlier works (Marraffini and Sontheimer 2009;Bondy-Denomy and Davidson 2014). Structural parameters or sequence motifs in the repeats are very essential for the enzymes or structural proteins involved in adaptation, crRNA biogenesis and interference (Alkhnbashi et al 2014).…”

Section: Discussionsupporting

confidence: 57%

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: 57%

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

Chellapandi

Ranjani

2015

Syst Synth Biol

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“…CRISPR-Cas systems recently have been the subject of intense research in genome editing applications (12), but the evolutionary roles of most endogenous microbial systems remain unknown (27). Even less is known concerning evolutionary outcomes of housing active CRISPR-Cas systems beyond the prevention of foreign DNA uptake (7), spacer acquisition events (4), and mutation caused by chromosomal self-targeting (28)(29)(30)(31)(32).…”

Section: Significancementioning

confidence: 99%

CRISPR-based screening of genomic island excision events in bacteria

Selle

Klaenhammer

Barrangou

2015

Proc. Natl. Acad. Sci. U.S.A.

112

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Genomic analysis of Streptococcus thermophilus revealed that mobile genetic elements (MGEs) likely contributed to gene acquisition and loss during evolutionary adaptation to milk. Clustered regularly interspaced short palindromic repeats-CRISPR-associated genes (CRISPR-Cas), the adaptive immune system in bacteria, limits genetic diversity by targeting MGEs including bacteriophages, transposons, and plasmids. CRISPR-Cas systems are widespread in streptococci, suggesting that the interplay between CRISPRCas systems and MGEs is one of the driving forces governing genome homeostasis in this genus. To investigate the genetic outcomes resulting from CRISPR-Cas targeting of integrated MGEs, in silico prediction revealed four genomic islands without essential genes in lengths from 8 to 102 kbp, totaling 7% of the genome. In this study, the endogenous CRISPR3 type II system was programmed to target the four islands independently through plasmid-based expression of engineered CRISPR arrays. Targeting lacZ within the largest 102-kbp genomic island was lethal to wild-type cells and resulted in a reduction of up to 2.5-log in the surviving population. Genotyping of Lac − survivors revealed variable deletion events between the flanking insertion-sequence elements, all resulting in elimination of the Lac-encoding island. Chimeric insertion sequence footprints were observed at the deletion junctions after targeting all of the four genomic islands, suggesting a common mechanism of deletion via recombination between flanking insertion sequences. These results established that self-targeting CRISPR-Cas systems may direct significant evolution of bacterial genomes on a population level, influencing genome homeostasis and remodeling.CRISPR | lactic acid bacteria | transposons | IS-elements | Cas9

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“…We sought to survey and investigate one type II system in L. gasseri for its potential activity, based on key characteristics alluding to its functionality. The system exhibited maintenance of CRISPR arrays, diversity of spacer content, spacers targeting invasive genetic elements and intra-species/system synteny of Cas operons (Bondy-Denomy & Davidson, 2014). In this study, the distribution of a type II CRISPR-Cas system amongst L. gasseri strains was determined, and its functionality in vivo was demonstrated in L. gasseri JV-V03 and NCK 1342.…”

Section: Introductionmentioning

confidence: 93%

“…Despite the high prevalence of CRISPR-Cas in bacteria, relatively few systems have been experimentally characterized for their functional activity and ecological role as adaptive immune systems targeting invasive genetic elements in vivo (Bondy-Denomy & Davidson, 2014). Intensive study of Streptococcus thermophilus has provided valuable insights into how CRISPR-Cas systems shape the dynamic interplay between phages and their bacterial hosts (Barrangou et al, 2007;Levin et al, 2013;Paez-Espino et al, 2013;Sun et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Occurrence and activity of a type II CRISPR-Cas system in Lactobacillus gasseri

et al. 2015

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Bacteria encode clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated genes (cas), which collectively form an RNA-guided adaptive immune system against invasive genetic elements. In silico surveys have revealed that lactic acid bacteria harbour a prolific and diverse set of CRISPR-Cas systems. Thus, the natural evolutionary role of CRISPR-Cas systems may be investigated in these ecologically, industrially, scientifically and medically important microbes. In this study, 17 Lactobacillus gasseri strains were investigated and 6 harboured a type II-A CRISPR-Cas system, with considerable diversity in array size and spacer content. Several of the spacers showed similarity to phage and plasmid sequences, which are typical targets of CRISPR-Cas immune systems. Aligning the protospacers facilitated inference of the protospacer adjacent motif sequence, determined to be 59-NTAA-39 flanking the 39 end of the protospacer. The system in L. gasseri JV-V03 and NCK 1342 interfered with transforming plasmids containing sequences matching the most recently acquired CRISPR spacers in each strain. We report the distribution and function of a native type II-A CRISPR-Cas system in the commensal species L. gasseri. Collectively, these results open avenues for applications for bacteriophage protection and genome modification in L. gasseri, and contribute to the fundamental understanding of CRISPR-Cas systems in bacteria.

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To acquire or resist: the complex biological effects of CRISPR–Cas systems

Cited by 97 publications

References 82 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-based screening of genomic island excision events in bacteria

Occurrence and activity of a type II CRISPR-Cas system in Lactobacillus gasseri

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