The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii

Zeng, Haiyan; Zhang, Jumei; Li, Chensi; Xie, Tengfei; Ling, Na; Wu, Qingping; Ye, Yingwang

doi:10.1038/srep40206

Cited by 29 publications

(44 citation statements)

References 39 publications

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“…In this study, we further found that a "complete" cas gene cluster of subtype I-F and CRISPR6 (an additional CRISPR array besides the previous five) were integrated in the conserved region adjacent to CRISPR3 (25). The repeat sequence of CRISPR6 was the same as that of CRISPR3 (25). CRISPR3 and CRISPR6 combined with full cas genes formed the subtype I-F CRISPR-Cas system.…”

Section: Distribution Of Crispr-cas Subtypes Among 240mentioning

confidence: 60%

“…In our earlier study, we found five types of CRISPR arrays in the conserved site of C. sakazakii strains, but only CRISPR1 and CRISPR2 neighbored the cas genes of the subtype I-E CRISPR-Cas system (25). In this study, we further found that a "complete" cas gene cluster of subtype I-F and CRISPR6 (an additional CRISPR array besides the previous five) were integrated in the conserved region adjacent to CRISPR3 (25). The repeat sequence of CRISPR6 was the same as that of CRISPR3 (25).…”

Section: Distribution Of Crispr-cas Subtypes Among 240mentioning

confidence: 88%

“…Ogrodzki et al (24) recently reported the existence of one subtype I-E CRISPR-Cas system and many CRISPR arrays in C. sakazakii sequence type 1 (ST1), ST4, ST8, and ST12 strains, which are associated with outbreaks of neonatal meningitis and necrotizing enterocolitis infections. In a previous study, we further classified all of the CRISPR arrays into five types according to their conserved locations in the genome of C. sakazakii and found that the frequent gain/loss of prophages and spacers in CRISPR loci was a likely driver of the rapid evolution of the species (25). In a recent study, Ogrodzki et al first detected the subtype I-F CRISPR-Cas system in C. dublinensis and C. muytjensii, and interestingly, two C. dublinensis ST80 strains had different types of CRISPR-Cas systems (26).…”

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confidence: 99%

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Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity

Zeng¹,

Zhang²,

Wu³

et al. 2018

Appl Environ Microbiol

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strains harboring the CRISPR-Cas system are important foodborne pathogens causing serious neonatal infections. However, the specific role of the CRISPR-Cas system in bacterial evolution remains relatively unexplored. In this study, we investigated the impact of CRISPR-Cas in evolution and obtained 137 new whole-genome sequences of by next-generation sequencing technology. Among the strains examined (n=240), 90.6% (193/213) of prevalent species ,, and strains had intact CRISPR-Cas systems. Two rare species, (n=2) and (n=6), lacked and preserved the CRISPR-Cas system at a low frequency (1/6), respectively. These results suggest that the presence of one CRISPR-Cas system in is important for the species to maintain genome homeostasis for survival. The ancestral strain was likely to harbored both subtype I-E and I-F CRISPR-Cas systems, during the long evolutionary process, subtype I-E was retained, while subtype I-F selectively degenerated in species and was even lost in the major pathovars. Moreover, significantly higher CRISPR activity was observed in plant-associated species than in the virulence-related species and Similar spacers of CRISPR arrays were rarely found among species, suggesting intensive change through adaptive acquisition and loss. Differentiated CRISPR activity appears to be the product of environmental selective pressure and might contribute to the bidirectional divergence and speciation of This study reports the evolutionary history of under the selective pressure of the CRISPR-Cas system. One CRISPR-Cas system in is important for maintaining genome homeostasis, whereas two types of systems may be redundant and not conducive for acquiring beneficial DNA for environmental adaption and pathogenicity. Differentiated CRISPR activity has contributed to the bidirectional divergence and genetic diversity of This perspective makes a significant contribution to the literature by providing new insights into CRISPR-Cas systems in general, while further expanding the roles of CRISPR beyond conferring adaptive immunity and demonstrating a link to adaptation and species divergence in a genus. Moreover, our study provides new insights into the balance between genome homeostasis and the uptake of beneficial DNA related to CRISPR-based activity in the evolution of .

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Section: Distribution Of Crispr-cas Subtypes Among 240mentioning

confidence: 60%

Section: Distribution Of Crispr-cas Subtypes Among 240mentioning

confidence: 88%

mentioning

confidence: 99%

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Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity

Zeng¹,

Zhang²,

Wu³

et al. 2018

Appl Environ Microbiol

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“…Even CRISPR 462 arrays sharing a single set of cas genes may vary greatly in acquisition rate [57]. 463 Similarly, arrays with slightly different consensus repeat sequences may differ in length, 464 despite sharing a set of cas genes [58], which suggests a functional role for repeat 465 sequence modifications in determining spacer insertion rates. Despite this, we found no 466 clear link between array length and repeat sequence in our data, possibly due to a 467 weakly array-length dependent spacer loss rate.…”

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confidence: 99%

“…Even CRISPR arrays sharing a single set of cas genes may vary 445 greatly in acquisition rate [39], and our data suggests a link between consensus 446 repeat sequence and acquisition rate. Arrays with slightly different consensus 447 repeat sequences may differ in length, despite sharing a set of cas genes [52]. 448 This suggests a functional role for repeat sequence modifications in determining 449 spacer insertion rates.…”

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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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CRISPR‐Cas, Horizontal Gene Transfer, and the Flexible (Pan) Genome

Gophna

2022

Crispr

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The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii

Cited by 29 publications

References 39 publications

Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity

Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity

Selective maintenance of multiple CRISPR arrays across prokaryotes

CRISPR‐Cas, Horizontal Gene Transfer, and the Flexible (Pan) Genome

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