Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are diverse immune systems found in many prokaryotic genomes that target invading foreign DNA such as bacteriophages and plasmids. There are multiple types of CRISPR with arguably the most enigmatic being Type IV. During an investiga...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-08-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2020.01937/full |
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| author | Enas Newire Alp Aydin Samina Juma Virve I. Enne Adam P. Roberts Adam P. Roberts |
| author_facet | Enas Newire Alp Aydin Samina Juma Virve I. Enne Adam P. Roberts Adam P. Roberts |
| author_sort | Enas Newire |
| collection | DOAJ |
| description | Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are diverse immune systems found in many prokaryotic genomes that target invading foreign DNA such as bacteriophages and plasmids. There are multiple types of CRISPR with arguably the most enigmatic being Type IV. During an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a Type IV-A3 CRISPR-Cas system was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002–2003) and a single K. pneumoniae isolate from the United Kingdom (isolated in 2017). Sequence analysis of all other genomes available in GenBank revealed that this CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on a bacterial chromosome. This system is exclusively located on IncHI1B/IncFIB plasmids and is associated with multiple putative transposable elements. Expression of the cas loci was confirmed in the available clinical isolates by RT-PCR. In all cases, the CRISPR-Cas system has a single CRISPR array (CRISPR1) upstream of the cas loci which has several, conserved, spacers which, amongst things, match regions within conjugal transfer genes of IncFIIK/IncFIB(K) plasmids. Our results reveal a Type IV-A3 CRISPR-Cas system exclusively located on IncHI1B/IncFIB plasmids in Enterobacteriaceae that is likely to be able to target IncFIIK/IncFIB(K) plasmids presumably facilitating intracellular, inter-plasmid competition. |
| first_indexed | 2024-04-11T17:35:07Z |
| format | Article |
| id | doaj.art-ec7b7956cd4a4b168f3b5889bf8e041d |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-11T17:35:07Z |
| publishDate | 2020-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-ec7b7956cd4a4b168f3b5889bf8e041d2022-12-22T04:11:44ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-08-011110.3389/fmicb.2020.01937555928Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in EnterobacteriaceaeEnas Newire0Alp Aydin1Samina Juma2Virve I. Enne3Adam P. Roberts4Adam P. Roberts5UCL Eastman Dental Institute, University College London, London, United KingdomCentre for Clinical Microbiology, Royal Free Hospital, University College London, London, United KingdomCentre for Clinical Microbiology, Royal Free Hospital, University College London, London, United KingdomCentre for Clinical Microbiology, Royal Free Hospital, University College London, London, United KingdomDepartment of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United KingdomCentre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United KingdomClustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are diverse immune systems found in many prokaryotic genomes that target invading foreign DNA such as bacteriophages and plasmids. There are multiple types of CRISPR with arguably the most enigmatic being Type IV. During an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a Type IV-A3 CRISPR-Cas system was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002–2003) and a single K. pneumoniae isolate from the United Kingdom (isolated in 2017). Sequence analysis of all other genomes available in GenBank revealed that this CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on a bacterial chromosome. This system is exclusively located on IncHI1B/IncFIB plasmids and is associated with multiple putative transposable elements. Expression of the cas loci was confirmed in the available clinical isolates by RT-PCR. In all cases, the CRISPR-Cas system has a single CRISPR array (CRISPR1) upstream of the cas loci which has several, conserved, spacers which, amongst things, match regions within conjugal transfer genes of IncFIIK/IncFIB(K) plasmids. Our results reveal a Type IV-A3 CRISPR-Cas system exclusively located on IncHI1B/IncFIB plasmids in Enterobacteriaceae that is likely to be able to target IncFIIK/IncFIB(K) plasmids presumably facilitating intracellular, inter-plasmid competition.https://www.frontiersin.org/article/10.3389/fmicb.2020.01937/fullType IVIncFIIKIncFIB(K)inter-plasmid competitionmobile genetic element |
| spellingShingle | Enas Newire Alp Aydin Samina Juma Virve I. Enne Adam P. Roberts Adam P. Roberts Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae Frontiers in Microbiology Type IV IncFIIK IncFIB(K) inter-plasmid competition mobile genetic element |
| title | Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae |
| title_full | Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae |
| title_fullStr | Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae |
| title_full_unstemmed | Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae |
| title_short | Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae |
| title_sort | identification of a type iv a crispr cas system located exclusively on inchi1b incfib plasmids in enterobacteriaceae |
| topic | Type IV IncFIIK IncFIB(K) inter-plasmid competition mobile genetic element |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2020.01937/full |
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