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

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 ∼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’.

Phylogenomic Network and Comparative Genomics Reveal a Diverged Member of the ϕKZ-Related Group, Marine Vibrio Phage ϕJM-2012

“…First, the presence of unidirectional promoters that showed a consensus sequence similar to that of EL and their preponderance in most of the HPRs may reflect the fact that JM-2012 retained this particular feature of the KZ-related hyperplastic portion (27), despite the extensive disruption of its genomic architecture. Second, relative to the other regions, the higher correlation of putative promoters and the transcriptional orientations of the predicted gene sequences in the HPRs suggest that the HPR-related genes may be functional (77). Thus, these variable regions could have specific niche-defining roles in the adaptation of JM-2012 to its particular host and environment (78).…”

“…Notably, the orientations of ORF55 and ORF56 were reversed compared to those in the other KZ tail fiber orthologs or paralogs (which undergo sense-positioned transcription). Given the absence of predicted reverse promoters in JM-2012, it can be inferred that these structural genes have nonessential functions (27,77). In contrast, ORF27 and ORF139, which harbor new relevant genes, appear to be functional.…”

Illuminating structural proteins in viral “dark matter” with metaproteomics

“…Computationally, artificial neural networks have been used to predict viral capsid and tail proteins from metagenomic data, which has been validated through in vivo expression and visualization of four putative viral structural genes (17). Experimentally, divergent structural proteins from cultivated viral isolates have been annotated using mass spectrometry (MS)-based proteomics (13,(18)(19)(20). Metaproteomics has now emerged as a powerful tool to investigate microbial communities (21,22), and here we apply this approach to marine viral communities to identify virionassociated proteins and facilitate annotation of the structural components of viral dark matter, generating new insights regarding the structural proteins in natural viral communities.…”

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

“…In contrast, S-EIV1 codes from both strands, and similar to Roseophage SIO1 (Rohwer et al, 2000) does not encode RNA polymerase, implying that host transcription machinery is used during infection; this has also been suggested for the siphovirus P-SS2 that infects Prochlorococcus sp. (MIT9313) (Sullivan et al, 2009).…”

“…( Chen and Lu, 2002;Mann et al, 2005;Millard et al, 2009;Sullivan et al, 2010;Huang et al, 2012;Sabehi et al, 2012) and Prochlorococcus spp. (Sullivan et al, 2005(Sullivan et al, , 2009Sullivan et al, 2010;Labrie et al, 2013), as well as one from a myovirus that infects both genera (Weigele et al, 2007). Most cyanophage isolates are myoviruses with genome size ranges from 161 to 252 kb, and share core genes involved in virion structure, DNA replication and host-derived genes with T4-like phage (Mann et al, 2005;Millard et al, 2009;Sullivan et al, 2010) A number of sequenced marine cyanophages are also podoviruses, having genomes between 42 kb and 47 kb, and sharing similar genome architecture, as well as core genes with T7-like phages, including genes involved in virion structure, DNA replication and that are host-derived (Chen and Lu, 2002;Sullivan et al, 2005;Labrie et al, 2013).…”