Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1

Abstract

Marine phages have an astounding global abundance and ecological impact. However, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. To infer potential functional and ecological relevance of sequenced marine Pseudoalteromonas phage H105/1, two strategies were used. First, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. This approach revealed 'ecogenomic' patterns of Pseudoalteromonas phage H105/1, such as its estuarine origin. Second, intrinsic genome signatures (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies) were evaluated on a resolved intragenomic level to shed light on the evolution of phage functional modules. On the basis of differential codon adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas spp., regions of the phage genome with the most 'host'-adapted proteins also have the strongest bacterial tetra signature, whereas the least 'host'-adapted proteins have the strongest phage tetra signature. Such a pattern may reflect the evolutionary history of the respective phage proteins and functional modules. Finally, analysis of the structural proteome identified seven proteins that make up the mature virion, four of which were previously unknown. This integrated approach combines both novel and classical strategies and serves as a model to elucidate ecological inferences and evolutionary relationships from phage genomes that typically abound with unknown gene content.

Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans

“…In bacteria, MazG domain proteins have been shown to function in stress responses or removal of noncanonical nucleotides (47)(48)(49). It has been suggested that phage MazG proteins may contribute to phage propagation by helping sustain the metabolism of starved host bacteria (44,46). However, the functions of the diverse MazG proteins in phages remain to be fully elucidated (45).…”

“…Many marine phages have proteins containing MazG domains, suggesting the importance of this domain in the proliferation of marine phages (44)(45)(46). In bacteria, MazG domain proteins have been shown to function in stress responses or removal of noncanonical nucleotides (47)(48)(49).…”

Morphology, Physiological Characteristics, and Complete Sequence of Marine Bacteriophage ϕRIO-1 Infecting Pseudoalteromonas marina

“…The specific host isolate discussed here was isolated from open seawater and is of the latter variety. Pseudoalteromonas phages isolated thus far include PM2, a phage with a small double-stranded circular DNA genome and lipidcontaining virion which is the type phage for the family Corticoviridae (12), and H105/1, a siphovirus (13). Genomic characterization has also indicated the presence of myoviral prophages (13).…”

“…Pseudoalteromonas phages isolated thus far include PM2, a phage with a small double-stranded circular DNA genome and lipidcontaining virion which is the type phage for the family Corticoviridae (12), and H105/1, a siphovirus (13). Genomic characterization has also indicated the presence of myoviral prophages (13). In this study, we address the apparent absence of podoviruses infecting Pseudoalteromonas by isolating and characterizing RIO-1, a podovirus infecting a specific isolate of Pseudoalteromonas marina.…”

Complete Genome of a Novel Pseudoalteromonas Phage PHq0

“…The interactions between phages and bacteria are complex processes in marine ecosystems, which is a key factor dominating the mortality of microorganisms [4]. For a comprehensive investigation of the impact on the bacterial physiological and biochemical process, we need isolation, propagation, and purification of phage-host systems (PHS).…”