Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium
CRISPR-Cas systems constitute adaptive immune systems for antiviral defense in bacteria. We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR...
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| Veröffentlicht in: | PloS one 2015-07, Vol.10 (7), p.e0133661-e0133661 |
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| creator | Briner, Alexandra E Lugli, Gabriele Andrea Milani, Christian Duranti, Sabrina Turroni, Francesca Gueimonde, Miguel Margolles, Abelardo van Sinderen, Douwe Ventura, Marco Barrangou, Rodolphe |
| description | CRISPR-Cas systems constitute adaptive immune systems for antiviral defense in bacteria. We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR spacer content. We identified the elements necessary for the successful targeting and inference of foreign DNA in select Type II CRISPR-Cas systems, including the tracrRNA and target PAM sequence. Bifidobacterium species have a very high frequency of CRISPR-Cas occurrence (77%, 37 of 48). We found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages. A large number of CRISPR spacers in bifidobacteria show perfect homology to prophage sequences harbored in the chromosomes of other species of Bifidobacterium, including some spacers that self-target the chromosome. A correlation was observed between strains that lacked CRISPR-Cas systems and the number of times prophages in that chromosome were targeted by other CRISPR spacers. The presence of prophage-targeting CRISPR spacers and prophage content may shed light on evolutionary processes and strain divergence. Finally, elements of Type II CRISPR-Cas systems, including the tracrRNA and crRNAs, set the stage for the development of genome editing and genetic engineering tools. |
| doi_str_mv | 10.1371/journal.pone.0133661 |
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We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR spacer content. We identified the elements necessary for the successful targeting and inference of foreign DNA in select Type II CRISPR-Cas systems, including the tracrRNA and target PAM sequence. Bifidobacterium species have a very high frequency of CRISPR-Cas occurrence (77%, 37 of 48). We found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages. A large number of CRISPR spacers in bifidobacteria show perfect homology to prophage sequences harbored in the chromosomes of other species of Bifidobacterium, including some spacers that self-target the chromosome. A correlation was observed between strains that lacked CRISPR-Cas systems and the number of times prophages in that chromosome were targeted by other CRISPR spacers. The presence of prophage-targeting CRISPR spacers and prophage content may shed light on evolutionary processes and strain divergence. Finally, elements of Type II CRISPR-Cas systems, including the tracrRNA and crRNAs, set the stage for the development of genome editing and genetic engineering tools.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0133661</identifier><identifier>PMID: 26230606</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adaptation ; Bifidobacterium - genetics ; Bifidobacterium bifidum ; Chromosomes, Bacterial - genetics ; Clustered Regularly Interspaced Short Palindromic Repeats - genetics ; CRISPR ; CRISPR-Cas Systems - genetics ; Deoxyribonucleic acid ; Divergence ; DNA ; DNA - genetics ; Evolution ; Evolution, Molecular ; Food ; Genes ; Genetic engineering ; Genetic Variation - genetics ; Genome editing ; Genome, Bacterial - genetics ; Genomes ; Genomics ; Laboratories ; Life sciences ; Nutrition ; Phylogenetics ; Prophages - genetics ; Proteins ; Studies</subject><ispartof>PloS one, 2015-07, Vol.10 (7), p.e0133661-e0133661</ispartof><rights>2015 Briner et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Briner et al 2015 Briner et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-c7a8774a1a3e3e08c5f0d43b03970dcccde0968aa52bdfc21456120f1286973f3</citedby><cites>FETCH-LOGICAL-c526t-c7a8774a1a3e3e08c5f0d43b03970dcccde0968aa52bdfc21456120f1286973f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521832/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521832/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26230606$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Briner, Alexandra E</creatorcontrib><creatorcontrib>Lugli, Gabriele Andrea</creatorcontrib><creatorcontrib>Milani, Christian</creatorcontrib><creatorcontrib>Duranti, Sabrina</creatorcontrib><creatorcontrib>Turroni, Francesca</creatorcontrib><creatorcontrib>Gueimonde, Miguel</creatorcontrib><creatorcontrib>Margolles, Abelardo</creatorcontrib><creatorcontrib>van Sinderen, Douwe</creatorcontrib><creatorcontrib>Ventura, Marco</creatorcontrib><creatorcontrib>Barrangou, Rodolphe</creatorcontrib><title>Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>CRISPR-Cas systems constitute adaptive immune systems for antiviral defense in bacteria. We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR spacer content. We identified the elements necessary for the successful targeting and inference of foreign DNA in select Type II CRISPR-Cas systems, including the tracrRNA and target PAM sequence. Bifidobacterium species have a very high frequency of CRISPR-Cas occurrence (77%, 37 of 48). We found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages. A large number of CRISPR spacers in bifidobacteria show perfect homology to prophage sequences harbored in the chromosomes of other species of Bifidobacterium, including some spacers that self-target the chromosome. A correlation was observed between strains that lacked CRISPR-Cas systems and the number of times prophages in that chromosome were targeted by other CRISPR spacers. The presence of prophage-targeting CRISPR spacers and prophage content may shed light on evolutionary processes and strain divergence. Finally, elements of Type II CRISPR-Cas systems, including the tracrRNA and crRNAs, set the stage for the development of genome editing and genetic engineering tools.</description><subject>Adaptation</subject><subject>Bifidobacterium - genetics</subject><subject>Bifidobacterium bifidum</subject><subject>Chromosomes, Bacterial - genetics</subject><subject>Clustered Regularly Interspaced Short Palindromic Repeats - genetics</subject><subject>CRISPR</subject><subject>CRISPR-Cas Systems - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>Divergence</subject><subject>DNA</subject><subject>DNA - genetics</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Food</subject><subject>Genes</subject><subject>Genetic engineering</subject><subject>Genetic Variation - genetics</subject><subject>Genome editing</subject><subject>Genome, Bacterial - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Laboratories</subject><subject>Life sciences</subject><subject>Nutrition</subject><subject>Phylogenetics</subject><subject>Prophages - 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We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR spacer content. We identified the elements necessary for the successful targeting and inference of foreign DNA in select Type II CRISPR-Cas systems, including the tracrRNA and target PAM sequence. Bifidobacterium species have a very high frequency of CRISPR-Cas occurrence (77%, 37 of 48). We found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages. A large number of CRISPR spacers in bifidobacteria show perfect homology to prophage sequences harbored in the chromosomes of other species of Bifidobacterium, including some spacers that self-target the chromosome. A correlation was observed between strains that lacked CRISPR-Cas systems and the number of times prophages in that chromosome were targeted by other CRISPR spacers. The presence of prophage-targeting CRISPR spacers and prophage content may shed light on evolutionary processes and strain divergence. Finally, elements of Type II CRISPR-Cas systems, including the tracrRNA and crRNAs, set the stage for the development of genome editing and genetic engineering tools.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26230606</pmid><doi>10.1371/journal.pone.0133661</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Adaptation Bifidobacterium - genetics Bifidobacterium bifidum Chromosomes, Bacterial - genetics Clustered Regularly Interspaced Short Palindromic Repeats - genetics CRISPR CRISPR-Cas Systems - genetics Deoxyribonucleic acid Divergence DNA DNA - genetics Evolution Evolution, Molecular Food Genes Genetic engineering Genetic Variation - genetics Genome editing Genome, Bacterial - genetics Genomes Genomics Laboratories Life sciences Nutrition Phylogenetics Prophages - genetics Proteins Studies |
| title | Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium |
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