Campylobacter jejuni Cas9 Modulates the Transcriptome in Caco-2 Intestinal Epithelial Cells

Saha, Chinmoy; Horst-Kreft, Deborah; Kross, Inez; Spek, Peter J. van der; Louwen, Rogier; Baarlen, Peter van

doi:10.3390/genes11101193

Cited by 13 publications

(8 citation statements)

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“…We have previously shown that ~98 % of all C. jejuni genomes have a CRISPR-Cas system, while this is more limited in C. coli, where only ~10 % of C. coli genomes have a CRISPR-Cas system [34]. Since the diversity in CRISPR spacers is also low in the chromosomal version of CRISPR-Cas of C. jejuni and C. coli and most spacers cannot (yet) be linked to mobile elements or phages [34,[59][60][61], the chromosomal copy of Cas9 may perform additional or alternative functions in C. jejuni, such as control or activity in virulence [62][63][64][65][66]. However, this is not the case for the CampyICE1 CRISPR-Cas9 system, as a majority of spacers can be linked to the three main families of plasmids in C. jejuni and C. coli: pTet, pVir and pCC42.…”

Section: Discussionmentioning

confidence: 99%

“…coli and most spacers cannot (yet) be linked to mobile elements or phages [34, 59–61], the chromosomal copy of Cas9 may perform additional or alternative functions in C. jejuni , such as control or activity in virulence [62–66]. However, this is not the case for the CampyICE1 CRISPR-Cas9 system, as a majority of spacers can be linked to the three main families of plasmids in C.…”

Section: Discussionmentioning

confidence: 99%

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A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

2021

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Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICEs) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanisms such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of the pVir, pTet and PCC42 plasmids and a new 70–129 kb ICE (CampyICE1) in the foodborne bacterial pathogens Campylobacter jejuni and Campylobacter coli . CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni and C. coli . CampyICE1 is conserved in structure and gene order, containing blocks of genes predicted to be involved in recombination, regulation and conjugation. CampyICE1 was detected in 134/5829 (2.3 %) C . jejuni genomes and 92/1347 (6.8 %) C . coli genomes. Similar ICEs were detected in a number of non-jejuni/coli Campylobacter species, although these lacked a CRISPR-Cas system. CampyICE1 carries three separate short CRISPR spacer arrays containing a combination of 108 unique spacers and 16 spacer-variant families. A total of 69 spacers and 10 spacer-variant families (63.7 %) were predicted to target Campylobacter plasmids. The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of the pVir, pTet and pCC42 plasmids (188/214 genomes, 87.9 %), suggesting that the CampyICE1-encoded CRISPR-Cas has contributed to the exclusion of competing plasmids. In conclusion, the characteristics of the CRISPR-Cas9 system on CampyICE1 suggests a history of plasmid warfare in Campylobacter .

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

2021

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show abstract

“…We have previously shown that ~98% of all C. jejuni genomes have a CRISPR-Cas system, while this is more limited in C. coli, where only ~10% of C. coli genomes have a CRISPR-Cas system [34]. Since the diversity in CRISPR spacers is also low in the chromosomal version of CRISPR-Cas of C. jejuni and C. coli and most spacers cannot (yet) be linked to mobile elements or phages [34,[57][58][59], it may represent additional or alternative functions for Cas9 in C. jejuni, such as control or activity in virulence [60][61][62][63][64]. However, this is not the case for the CampyICE1 CRISPR-Cas9 system, as a majority of spacers can be linked to the three main families of plasmids in C. jejuni and C. coli: pTet, pVir and pCC42.…”

Section: Discussionmentioning

confidence: 99%

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

Vliet

Charity

Reuter

2021

Preprint

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Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICE) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanism such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution the pVir, pTet and PCC42 plasmids and a new 70-129 kb ICE (CampyICE1) in the foodborne microbial pathogens Campylobacter jejuni and Campylobacter coli. CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni and C. coli. CampyICE1 is conserved in structure and gene order, containing modules of genes predicted to be involved in recombination, regulation, and conjugation. CampyICE1 was detected in 134/5,829 (2.3%) C. jejuni genomes and 92/1,347 (6.8%) C. coli genomes. Similar ICE were detected in a number of non-jejuni/coli Campylobacter species, although these lacked a CRISPR-Cas system. CampyICE1 carries 3 separate short CRISPR spacer arrays containing a combination of 108 unique spacers and 16 spacer variant families, of which 70 spacers were predicted to target the Campylobacter plasmids pVir, pTet, and pCC42. A further nine spacers were predicted to target other Campylobacter plasmids (63.7%). The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of these plasmids (188/214 genomes, 87.9%), implicating that the CampyICE1-encoded CRISPR-Cas has contributed to the exclusion of competing plasmids. In conclusion, the characteristics of the CRISPR-Cas9 system on CampyICE1 suggests a history of plasmid warfare in Campylobacter.

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“…The S. pyogenes mechanism involves Cas9-mediated down-regulation of the FasA/FasB TCS that downregulates adhesion factors ( Gao et al., 2019 ). Campylobacter jejuni and S. agalactiae Cas9s can increase bacterial cytotoxicity, adhesion, and survival within hosts cells ( Louwen et al., 2013 ; Ma et al., 2018 ; Shabbir et al., 2018 ; Saha et al., 2020a ). In S. agalactiae , hyaluronidase activity essential for blood-brain barrier penetration is regulated via Cas9-mediated cleavage of the master regulator regR transcript ( Figure 1B , ( Ma et al., 2018 )).…”

Section: Physiological Roles Of Crispr-cas Observed In Bacteriamentioning

confidence: 99%

The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies

Newsom

Parameshwaran

Martin

et al. 2021

Front. Cell. Infect. Microbiol.

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Bacterial and archaeal CRISPR-Cas systems offer adaptive immune protection against foreign mobile genetic elements (MGEs). This function is regulated by sequence specific binding of CRISPR RNA (crRNA) to target DNA/RNA, with an additional requirement of a flanking DNA motif called the protospacer adjacent motif (PAM) in certain CRISPR systems. In this review, we discuss how the same fundamental mechanism of RNA-DNA and/or RNA-RNA complementarity is utilized by bacteria to regulate two distinct functions: to ward off intruding genetic materials and to modulate diverse physiological functions. The best documented examples of alternate functions are bacterial virulence, biofilm formation, adherence, programmed cell death, and quorum sensing. While extensive complementarity between the crRNA and the targeted DNA and/or RNA seems to constitute an efficient phage protection system, partial complementarity seems to be the key for several of the characterized alternate functions. Cas proteins are also involved in sequence-specific and non-specific RNA cleavage and control of transcriptional regulator expression, the mechanisms of which are still elusive. Over the past decade, the mechanisms of RNA-guided targeting and auxiliary functions of several Cas proteins have been transformed into powerful gene editing and biotechnological tools. We provide a synopsis of CRISPR technologies in this review. Even with the abundant mechanistic insights and biotechnology tools that are currently available, the discovery of new and diverse CRISPR types holds promise for future technological innovations, which will pave the way for precision genome medicine.

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Campylobacter jejuni Cas9 Modulates the Transcriptome in Caco-2 Intestinal Epithelial Cells

Cited by 13 publications

References 58 publications

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies

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