Abstract
P-SSP7 is a T7-like phage that infects the cyanobacterium Prochlorococcus MED4. MED4 is a member of the high-light-adapted Prochlorococcus ecotypes that are abundant in the surface oceans and contribute significantly to primary production. P-SSP7 has become a model system for the investigation of T7-like phages that infect Prochlorococcus. It was classified as T7-like based on genome content and organization. However, because its genome assembled as a circular molecule, it was thought to be circularly permuted and to lack the direct terminal repeats found in other T7-like phages. Here we sequenced the ends of the P-SSP7 genome and found that the genome map is linear and contains a 206 bp repeat at both genome ends. Furthermore, we found that a 728 bp region of the genome originally placed downstream of the last ORF is actually located upstream of the first ORF on the genome map. These findings suggest that P-SSP7 is likely to use the direct terminal repeats for genome replication and packaging in a similar manner to other T7-like phages. Moreover, these results highlight the importance of experimentally verifying the ends of phage genomes, and will facilitate the use of P-SSP7 as a model for the correct assembly and end determination of the many T7-like phages isolated from the marine environment that are currently being sequenced.
Highlights
T7-like podoviruses that infect cyanobacteria are often isolated on high-light-adapted Prochlorococcus ecotypes [1], abundant unicellular cyanobacteria that contribute significantly to primary production in the oceans [2]
In order to assess whether the P-SSP7 phage genome has discrete termini, we used high molecular weight DNA extracted from phage particles to sequence its ends
The sequence at the left end of the genome map was determined using a series of three primers, the first of which extends outwards from ORF1 (Fig. 1A)
Summary
T7-like podoviruses that infect cyanobacteria are often isolated on high-light-adapted Prochlorococcus ecotypes [1], abundant unicellular cyanobacteria that contribute significantly to primary production in the oceans [2]. In addition to a common set of T7-like core genes this phage encodes psbA, a host-like photosynthesis gene often found in cyanophages [7,8,9,10]. This gene is expressed during infection and is thought to be involved in the energy production needed for maximal phage replication [11]. It is one of a few marine phages for which structural analyses of the phage particle have been carried out [12]
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