CRISPR-Cas Functional Module Exchange in Escherichia coli

Almendros, Cristóbal; Mojica, Francisco J. M.; Díez-Villaseñor, César; Guzmán, Noemí M.; Garcı́a-Martı́nez, Jesús

doi:10.1128/mbio.00767-13

Cited by 31 publications

(46 citation statements)

References 56 publications

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“…A previous study proposed that terminal repeats act as ‘anchor’ units to preserve CRISPR integrity by preventing homologous recombination with upstream CRISPR repeat sequences (Almendros et al, 2014). Moreover, it is widely understood that terminal spacers correspond to the ‘oldest’ memories of the CRISPR array, since adaptation occurs at the leader end (Barrangou et al, 2007; Sternberg et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations

Hullahalli

Rodrigues

Palmer

2017

eLife

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CRISPR-Cas provides a barrier to horizontal gene transfer in prokaryotes. It was previously observed that functional CRISPR-Cas systems are absent from multidrug-resistant (MDR) Enterococcus faecalis, which only possess an orphan CRISPR locus, termed CRISPR2, lacking cas genes. Here, we investigate how the interplay between CRISPR-Cas genome defense and antibiotic selection for mobile genetic elements shapes in vitro E. faecalis populations. We demonstrate that CRISPR2 can be reactivated for genome defense in MDR strains. Interestingly, we observe that E. faecalis transiently maintains CRISPR targets despite active CRISPR-Cas systems. Subsequently, if selection for the CRISPR target is present, toxic CRISPR spacers are lost over time, while in the absence of selection, CRISPR targets are lost over time. We find that forced maintenance of CRISPR targets induces a fitness cost that can be exploited to alter heterogeneous E. faecalis populations.DOI: http://dx.doi.org/10.7554/eLife.26664.001

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Section: Resultsmentioning

confidence: 99%

Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations

Hullahalli

Rodrigues

Palmer

2017

eLife

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“…Instantaneous array loss vs. gradual decay 225 There are two possible routes to complete CRISPR array loss: (1) an all-at-once loss of 226 the array (e.g. due to recombination between flanking insertion sequences [39,40]) and 227 (2) gradual decay due to spacer loss via homologous recombination [28][29][30]. Limited 228 experimental evidence supports (1) spontaneous loss of the entire CRISPR array [41], as 229 do comparisons between closely related genomes [40].…”

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confidence: 99%

Selective maintenance of multiple CRISPR arrays across prokaryotes

Weissman

Fagan

Johnson

2017

Preprint

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Prokaryotes are under nearly constant attack by viral pathogens. To protect against this threat of infection, bacteria and archaea have evolved a wide array of defense mechanisms, singly and in combination. While immune diversity in a single organism likely reduces the chance of pathogen evolutionary escape, it remains puzzling why many prokaryotes also have multiple, seemingly redundant, copies of the same type of immune system. Here, we focus on the highly flexible CRISPR adaptive immune system, which is present in multiple copies in a surprising 21% of the prokaryotic genomes in RefSeq. We use a comparative genomics approach looking across all prokaryotes to demonstrate that having more than one CRISPR system confers a selective advantage to the organism, on average. We hypothesize that a tradeoff between memory span and learning speed could select for both "long-term memory" and "short-term memory" CRISPR arrays, and we go on to develop a mathematical model to confirm that such a tradeoff could lead to selection for multiple arrays.

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“…However, the CRISPR-Cas I-E system appears to be inactive in E. coli under normal laboratory growth conditions (36). Additionally, the host needs to acquire the appropriate spacers for recognizing foreign DNA (36). The acquisition of these spacers is not likely to take place very quickly, even under the prolonged incubation times used in this study.…”

Section: Discussionmentioning

confidence: 87%

“…The reduction of lysogens observed in our study could be caused by CRISPR defense mechanisms that are not activated when BaeSR is absent. However, the CRISPR-Cas I-E system appears to be inactive in E. coli under normal laboratory growth conditions (36). Additionally, the host needs to acquire the appropriate spacers for recognizing foreign DNA (36).…”

Section: Discussionmentioning

confidence: 99%

BaeSR, Involved in Envelope Stress Response, Protects against Lysogenic Conversion by Shiga Toxin 2-Encoding Phages

et al. 2015

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Infection and lysogenic conversion with Shiga toxin-encoding bacteriophages (Stx phages) drive the emergence of new Shiga toxin-producing Escherichia coli strains. Phage attachment to the bacterial surface is the first stage of phage infection. Envelope perturbation causes activation of envelope stress responses in bacterial cells. Although many external factors are known to activate envelope stress responses, the role of these responses in the phage-bacterium interaction remains unexplored. Here, we investigate the link between three envelope signaling systems in E. coli (RcsBC, CpxAR, and BaeSR) and Stx2 phage infection by determining the success of bacterial lysogenic conversion. For this purpose, E. coli DH5␣ wild-type (WT) and mutant strains lacking RcsBC, CpxAR, or BaeSR signaling systems were incubated with a recombinant Stx2 phage (933W). Notably, the number of lysogens obtained with the BaeSR mutant was 5 log 10 units higher than with the WT, and the same differences were observed when using 7 different Stx2 phages. To assess whether the membrane receptor used by Stx phages, BamA, was involved in the differences observed, bamA gene expression was monitored by reverse transcription-quantitative PCR (RT-qPCR) in all host strains. A 4-fold-higher bamA expression level was observed in the BaeSR mutant than in the WT strain, suggesting that differential expression of the receptor used by Stx phages accounted for the increase in the number of lysogenization events. Establishing the link between the role of stress responses and phage infection has important implications for understanding the factors affecting lysogenic conversion, which drives the emergence of new pathogenic clones.T emperate phages are responsible for the conversion of nonpathogenic strains of bacteria to pathogenic strains by transduction of virulence genes (1). Well-known examples are Shiga toxin (Stx) phages, which carry the genes for Shiga toxin (stx). Stx phages can cause the conversion of Escherichia coli and bacteria of other genera to Shiga toxin-producing E. coli (STEC) and other Shiga-toxigenic pathogens (2). A recent example is the STEC outbreak in Germany in May 2011, where an enteroaggregative E. coli O104:H4 strain incorporated an Stx2 phage (3, 4). Because the lysogeny of E. coli by Stx phages has relevant implications for their pathogenicity, a better understanding of the molecular mechanisms underlying phage-host interaction is a challenge for researchers and could help in designing strategies to avoid lysogenization by Stx phages.The first step in phage infection is attachment to the specific receptor on the bacterial surface. The maintenance, adaptation, and protection of the bacterial envelope are essential for bacteria. Stresses that damage and alter the bacterial envelope can lead to activation of stress responses in bacteria by means of various phosphorelay signaling systems (5). In E. coli, five different envelope stress responses have been identified: BaeSR, CpxAR, RcsBC, Psp, and E (5, 6). Each response triggers a si...

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CRISPR-Cas Functional Module Exchange in Escherichia coli

Cited by 31 publications

References 56 publications

Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations

Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations

Selective maintenance of multiple CRISPR arrays across prokaryotes

BaeSR, Involved in Envelope Stress Response, Protects against Lysogenic Conversion by Shiga Toxin 2-Encoding Phages

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