The Caulobacter crescentus phage phiCbK: genomics of a canonical phage
| Autor: | Diego A Escobar-Garcia, Jason J. Gill, Daniel Hernandez, Rebecca Martin, Jennifer L. Keene, David H. Russell, Ry Young, Ashley Kane, Matthew Maddox, Ashlyn M Thorn, Sheba Mohan, Lauren Lessor, Joel Berry, William K. Russell |
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| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
DNA Replication
lcsh:QH426-470 phiCbK viruses lcsh:Biotechnology Molecular Sequence Data Genomics Genome Viral Biology Siphoviridae Proteomics Genome Bacteriophage 03 medical and health sciences chemistry.chemical_compound lcsh:TP248.13-248.65 DNA Packaging Caulobacter crescentus Genetics Amino Acid Sequence Phylogeny 030304 developmental biology Viral Structural Proteins 0303 health sciences Endodeoxyribonucleases Base Sequence 030306 microbiology DNA replication biology.organism_classification lcsh:Genetics chemistry Protein Biosynthesis Proteome DNA Viral DNA Biotechnology Research Article |
| Zdroj: | BMC Genomics, Vol 13, Iss 1, p 542 (2012) BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | Background The bacterium Caulobacter crescentus is a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool in C. crescentus biology, and has been studied in its own right as a model for viral morphogenesis. Although a system of some interest, to date little genomic information is available on phiCbK or its relatives. Results Five novel phiCbK-like C. crescentus bacteriophages, CcrMagneto, CcrSwift, CcrKarma, CcrRogue and CcrColossus, were isolated from the environment. The genomes of phage phiCbK and these five environmental phage isolates were obtained by 454 pyrosequencing. The phiCbK-like phage genomes range in size from 205 kb encoding 318 proteins (phiCbK) to 280 kb encoding 448 proteins (CcrColossus), and were found to contain nonpermuted terminal redundancies of 10 to 17 kb. A novel method of terminal ligation was developed to map genomic termini, which confirmed termini predicted by coverage analysis. This suggests that sequence coverage discontinuities may be useable as predictors of genomic termini in phage genomes. Genomic modules encoding virion morphogenesis, lysis and DNA replication proteins were identified. The phiCbK-like phages were also found to encode a number of intriguing proteins; all contain a clearly T7-like DNA polymerase, and five of the six encode a possible homolog of the C. crescentus cell cycle regulator GcrA, which may allow the phage to alter the host cell’s replicative state. The structural proteome of phage phiCbK was determined, identifying the portal, major and minor capsid proteins, the tail tape measure and possible tail fiber proteins. All six phage genomes are clearly related; phiCbK, CcrMagneto, CcrSwift, CcrKarma and CcrRogue form a group related at the DNA level, while CcrColossus is more diverged but retains significant similarity at the protein level. Conclusions Due to their lack of any apparent relationship to other described phages, this group is proposed as the founding cohort of a new phage type, the phiCbK-like phages. This work will serve as a foundation for future studies on morphogenesis, infection and phage-host interactions in C. crescentus. |
| Databáze: | OpenAIRE |
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