Present address: Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial ‘mobilome’
Article first published online: 14 OCT 2009
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: Environmental Viruses: Shaping the biosphere. Guest Editors: Forest Rohwer, David Prangishvili and Debbie Lindell
Volume 11, Issue 11, pages 2935–2951, November 2009
How to Cite
Sullivan, M. B., Krastins, B., Hughes, J. L., Kelly, L., Chase, M., Sarracino, D. and Chisholm, S. W. (2009), The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial ‘mobilome’. Environmental Microbiology, 11: 2935–2951. doi: 10.1111/j.1462-2920.2009.02081.x
Re-use of this article is permitted in accordance with the Terms and Conditions set out at http://www3.interscience.wiley.com/authorresources/onlineopen.html
- Issue published online: 27 OCT 2009
- Article first published online: 14 OCT 2009
- Received 26 April, 2009; accepted 16 July, 2009.
Prochlorococcus, an abundant phototroph in the oceans, are infected by members of three families of viruses: myo-, podo- and siphoviruses. Genomes of myo- and podoviruses isolated on Prochlorococcus contain DNA replication machinery and virion structural genes homologous to those from coliphages T4 and T7 respectively. They also contain a suite of genes of cyanobacterial origin, most notably photosynthesis genes, which are expressed during infection and appear integral to the evolutionary trajectory of both host and phage. Here we present the first genome of a cyanobacterial siphovirus, P-SS2, which was isolated from Atlantic slope waters using a Prochlorococcus host (MIT9313). The P-SS2 genome is larger than, and considerably divergent from, previously sequenced siphoviruses. It appears most closely related to lambdoid siphoviruses, with which it shares 13 functional homologues. The ∼108 kb P-SS2 genome encodes 131 predicted proteins and notably lacks photosynthesis genes which have consistently been found in other marine cyanophage, but does contain 14 other cyanobacterial homologues. While only six structural proteins were identified from the genome sequence, 35 proteins were detected experimentally; these mapped onto capsid and tail structural modules in the genome. P-SS2 is potentially capable of integration into its host as inferred from bioinformatically identified genetic machinery int, bet, exo and a 53 bp attachment site. The host attachment site appears to be a genomic island that is tied to insertion sequence (IS) activity that could facilitate mobility of a gene involved in the nitrogen-stress response. The homologous region and a secondary IS-element hot-spot in Synechococcus RS9917 are further evidence of IS-mediated genome evolution coincident with a probable relic prophage integration event. This siphovirus genome provides a glimpse into the biology of a deep-photic zone phage as well as the ocean cyanobacterial prophage and IS element ‘mobilome’.