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

Abstract

c Bacteria of the genus Pseudoalteromonas are ubiquitous in the world's oceans. Marine bacteria have been posited to be associated with a major ancient branch of podoviruses related to T7. Yet, although Pseudoalteromonas phages belonging to the Corticoviridae and the Siphoviridae and prophages belonging to the Myoviridae have been reported, no Pseudoalteromonas podovirus was previously known. Here, a new lytic Pseudoalteromonas marina phage, RIO-1, belonging to the Podoviridae was isolated and characterized with respect to morphology, genomic sequence, and biological properties. Its major encoded proteins were distantly similar to those of T7. The most similar previously sequenced viruses were Pseudomonas phage PA11 and Salinivibrio phage CW02. Whereas many elements of the morphology and gene organization of RIO-1 are similar to those of podoviruses broadly related to T7, RIO-1 conspicuously lacked an RNA polymerase gene. Since definitions of a T7 supergroup have included similarity in the DNA polymerase gene, a detailed phylogenetic analysis was conducted, and two major DNA polymerase clades in Autographivirinae and several structural variants of the polA family represented in podoviruses were found. RIO-1 carries an operon similar to that in a few other podoviruses predicted to specify activities related to ␥-glutamyl amide linkages and/or unusual peptide bonds. Most growth properties of RIO-1 were typical of T7-like phages, except for a long latent period.V iral particles outnumber bacteria in the world's oceans by a factor of about 10:1 and are thought to enforce diversity at the base of the microbiological community by restraining overgrowth of any particularly successful microbial species and returning their biomolecules as nutrients into the water through lysis (1, 2). This role rests critically on a network of specific host-virus interactions. Estimates of viral diversity by metagenomics tend to indicate extraordinarily high numbers of viral species (3-5), yet the total number of sequenced marine bacteriophages as of the last published count (6) was only 17. Current marine phage sequencing initiatives are expected to raise this to only a few hundred.Two of the earliest marine phages genomically characterized were the podoviruses roseophage SIO1 (7) and vibriophage VpV262 (8). These exemplify a group of podoviruses that are vaguely similar to enterobacterial phage T7 but lack the singlechain RNA polymerase and have two converging transcription units rather than one unidirectional transcription unit. It was postulated that this description represented an ancestral phage type present in ancient oceans and widespread descendants would be found in oceanic bacterial species.Pseudoalteromonas is a genus of gammaproteobacteria with many species, all found in marine environments. The genus contains specialists for various marine habitats ranging from sea ice (9) to deep-sea sediments (10). Its species are divided into pigmented and nonpigmented species; the former are known for habitation of marine biofilms and p...

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

“…Similar genes have been found in other podoviruses (Hardies et al, 2013). Collectively these genes encode proteins that perform functions necessary to synthesize three unusual linkages in peptidoglycan peptide side chains (Iyer et al, 2002; Hardies et al, 2013), including a gamma-glutamyl amidoligase (PSAHP1_00043), a second uncharacterized amidoligase (PSAHP1_00046), and an ATP grasp enzyme (PSAHP1_00047). Beyond synthesis, there are also peptidoglycan degradation genes encoded in the PSA-HP1 genome, including gamma-glutamyl cyclotransferase (PSAHP1_00040) and glutamine amidotransferase (PSAHP1_00042).…”

Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

“…The genes provided by the phage might induce a change in the structures responsible for phage recognition and act as a serotype conversion mechanism to avoid superinfection by other phages (87). Similar mechanisms have been described for other marine and nonmarine podoviruses (88)(89)(90).…”

“…The only two proteins identified as part of the TSS VIII in PMPs are CsgF and CsgG, which implies that if no other proteins in the operon are functional, it would code for only an extracellular chaperone and a pore-forming complex, respectively. The CsgG pore is too small to allow for virion exit (the CsgG pore has 40-Å inner diameter, while the HTVC008M capsid diameter is 550 Å) (10,86), and the only report of functional amyloids in viruses was in eukaryotic viruses, where they have the role of inhibiting programmed cell death of their eukaryotic host by sequestering effector proteins (89), which does not require the presence of the curli transporter. The simplest explanation would be that the pore structure might enhance the uptake of larger molecules.…”

Nutrients and Other Environmental Factors Influence Virus Abundances across Oxic and Hypoxic Marine Environments

“…For example, in the microalgae Phaeocystis globosa and Heterosigma akashiwo , lysis of infected cells occurred over a narrow temperature range and the different viruses were inactivated above temperatures ranging from 20 to 35 °C [13,14]. A similar pattern of inactivation at 40 °C was shown for a phage of the marine prokaryote Pseudoalteromonas marina [15]. Inactivation temperatures for marine viruses, however, are usually above 20 °C, which is higher than that which many virus–host systems are likely to encounter in temperate and Arctic waters, but can play a role in microenvironments in temperate waters.…”