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PMID: 19840100 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome'.

Environmental microbiology ·Vol. 11 ·No. 11 ·2009-11-00 ·Pages 2935-51

Sullivan MB, Krastins B, Hughes JL, Kelly L, Chase M, Sarracino D, Chisholm SW

Abstract

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 approximately 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'.

MeSH Terms
Atlantic Ocean Bacteriophages/chemistry,genetics DNA, Viral/chemistry,genetics Genome, Viral Interspersed Repetitive Sequences Molecular Sequence Data Phylogeny Prochlorococcus/virology Proteome/analysis,genetics Seawater/microbiology,virology Sequence Analysis, DNA Sequence Homology, Amino Acid Sequence Homology, Nucleic Acid Siphoviridae/chemistry,genetics Synteny Viral Structural Proteins/analysis,genetics
Chemicals
DNA, Viral Proteome Viral Structural Proteins
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Sullivan Matthew B
Department of Civil and Environmental Engineering and Department of Biology, MIT, 48-425, Cambridge, MA 02139, USA. [email protected]
Krastins Bryan
Hughes Jennifer L
Kelly Libusha
Chase Michael
Sarracino David
Chisholm Sallie W
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Article Info
Journal
Environmental microbiology
Abbr.
Environ Microbiol
ISSN
1462-2920
DOI
10.1111/j.1462-2920.2009.02081.x
Email
[email protected]
Published
2009-11-00
Epub
2009-00-14
Pages
2935-51
Language
English
Region
England
NLM ID
100883692
PMCID
PMC2784084
Subset
IM
Databases
RefSeq
NC_013021
External Links
PubMed source DOI: 10.1111/j.1462-2920.2009.02081.x PMC Full Text View journal details
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