TY - JOUR
T1 - The Caulobacter crescentus phage phiCbK
T2 - Genomics of a canonical phage
AU - Gill, Jason J.
AU - Berry, Joel D.
AU - Russell, William K.
AU - Lessor, Lauren
AU - Escobar-Garcia, Diego A.
AU - Hernandez, Daniel
AU - Kane, Ashley
AU - Keene, Jennifer
AU - Maddox, Matthew
AU - Martin, Rebecca
AU - Mohan, Sheba
AU - Thorn, Ashlyn M.
AU - Russell, David H.
AU - Young, Ry
N1 - Funding Information:
The authors would like to thank students in the Texas A&M University Bacteriophage Genomics class of 2010 for the initial isolation of phages: Rachel Gubbels, Alex Klattenhoff, Kristen Thomas and Joshua Tsau for phages Colossus, Rogue and Swift; Justin Kaspar, Bryan Johnson, David Migl and Misty Reynolds for Karma and Storm; Jared Fradette, Andrew Hawrylak, Ashlyn Thorn and TJ Tidwell for Magneto. The authors would like to thank Roger Hendrix of the University of Pittsburgh for the direct phage concentration protocol, and Elizabeth Wright of Emory University for her insights into the structure of phiCbK and its head filament. This work was supported by NSF Award No. 0949351 and by support to the Center for Phage Technology from the Texas A&M University IUMRI program. Proteomic studies were supported by the NSF Major Research Instrumentation Program Grant DBI-0821700.
PY - 2012/10/10
Y1 - 2012/10/10
N2 - 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.
AB - 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.
KW - Bacteriophage
KW - Caulobacter crescentus
KW - Genomics
KW - phiCbK
UR - http://www.scopus.com/inward/record.url?scp=84867218839&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84867218839&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-13-542
DO - 10.1186/1471-2164-13-542
M3 - Article
C2 - 23050599
AN - SCOPUS:84867218839
VL - 13
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
IS - 1
M1 - 542
ER -