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The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile
Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32–57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infec...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786514/ https://www.ncbi.nlm.nih.gov/pubmed/29403466 http://dx.doi.org/10.3389/fmicb.2018.00026 |
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author | Ramírez-Vargas, Gabriel Goh, Shan Rodríguez, César |
author_facet | Ramírez-Vargas, Gabriel Goh, Shan Rodríguez, César |
author_sort | Ramírez-Vargas, Gabriel |
collection | PubMed |
description | Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32–57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infecting MLST Clade 1 strains of C. difficile. Two subgroups of big phage genomes similar to phiCD5763 were identified in 32 NAP(CR1)/RT012/ST-54 C. difficile isolates from Costa Rica and in whole genome sequences (WGS) of 41 C. difficile isolates of Clades 1, 2, 3, and 4 from Canada, USA, UK, Belgium, Iraq, and China. Through comparative genomics we discovered another putative big phage genome in a non-NAP(CR1) isolate from Costa Rica, phiCD2955, which represents other big phage genomes found in 130 WGS of MLST Clade 1 and 2 isolates from Canada, USA, Hungary, France, Austria, and UK. phiCD2955 (131.6 kb, 172 ORFs) is related to a previously reported C. difficile phage genome, phiCD211/phiCDIF1296T. Detailed genome analyses of phiCD5763, phiCD2955, phiCD211/phiCDIF1296T, and seven other putative C. difficile big phage genome sequences of 131–136 kb reconstructed from publicly available WGS revealed a modular gene organization and high levels of sequence heterogeneity at several hotspots, suggesting that these genomes correspond to biological entities undergoing recombination. Compared to other C. difficile phages, these big phages have unique predicted terminase, capsid, portal, neck and tail proteins, receptor binding proteins (RBPs), recombinases, resolvases, primases, helicases, ligases, and hypothetical proteins. Moreover, their predicted gene load suggests a complex regulation of both phage and host functions. Overall, our results indicate that the prevalence of C. difficile big bacteriophages is more widespread than realized and open new avenues of research aiming to decipher how these viral elements influence the biology of this emerging pathogen. |
format | Online Article Text |
id | pubmed-5786514 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-57865142018-02-05 The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile Ramírez-Vargas, Gabriel Goh, Shan Rodríguez, César Front Microbiol Microbiology Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32–57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infecting MLST Clade 1 strains of C. difficile. Two subgroups of big phage genomes similar to phiCD5763 were identified in 32 NAP(CR1)/RT012/ST-54 C. difficile isolates from Costa Rica and in whole genome sequences (WGS) of 41 C. difficile isolates of Clades 1, 2, 3, and 4 from Canada, USA, UK, Belgium, Iraq, and China. Through comparative genomics we discovered another putative big phage genome in a non-NAP(CR1) isolate from Costa Rica, phiCD2955, which represents other big phage genomes found in 130 WGS of MLST Clade 1 and 2 isolates from Canada, USA, Hungary, France, Austria, and UK. phiCD2955 (131.6 kb, 172 ORFs) is related to a previously reported C. difficile phage genome, phiCD211/phiCDIF1296T. Detailed genome analyses of phiCD5763, phiCD2955, phiCD211/phiCDIF1296T, and seven other putative C. difficile big phage genome sequences of 131–136 kb reconstructed from publicly available WGS revealed a modular gene organization and high levels of sequence heterogeneity at several hotspots, suggesting that these genomes correspond to biological entities undergoing recombination. Compared to other C. difficile phages, these big phages have unique predicted terminase, capsid, portal, neck and tail proteins, receptor binding proteins (RBPs), recombinases, resolvases, primases, helicases, ligases, and hypothetical proteins. Moreover, their predicted gene load suggests a complex regulation of both phage and host functions. Overall, our results indicate that the prevalence of C. difficile big bacteriophages is more widespread than realized and open new avenues of research aiming to decipher how these viral elements influence the biology of this emerging pathogen. Frontiers Media S.A. 2018-01-22 /pmc/articles/PMC5786514/ /pubmed/29403466 http://dx.doi.org/10.3389/fmicb.2018.00026 Text en Copyright © 2018 Ramírez-Vargas, Goh and Rodríguez. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Ramírez-Vargas, Gabriel Goh, Shan Rodríguez, César The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile |
title | The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile |
title_full | The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile |
title_fullStr | The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile |
title_full_unstemmed | The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile |
title_short | The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile |
title_sort | novel phages phicd5763 and phicd2955 represent two groups of big plasmidial siphoviridae phages of clostridium difficile |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786514/ https://www.ncbi.nlm.nih.gov/pubmed/29403466 http://dx.doi.org/10.3389/fmicb.2018.00026 |
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