Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses

Abstract

Virioplankton play a crucial role in aquatic ecosystems as topdown regulators of bacterial populations and agents of horizontal gene transfer and nutrient cycling. However, the biology and ecology of virioplankton populations in the environment remain poorly understood. Ribonucleotide reductases (RNRs) are ancient enzymes that reduce ribonucleotides to deoxyribonucleotides and thus prime DNA synthesis. Composed of three classes according to O 2 reactivity, RNRs can be predictive of the physiological conditions surrounding DNA synthesis. RNRs are universal among cellular life, common within viral genomes and virioplankton shotgun metagenomes (viromes), and estimated to occur within >90% of the dsDNA virioplankton sampled in this study. RNRs occur across diverse viral groups, including all three morphological families of tailed phages, making these genes attractive for studies of viral diversity. Differing patterns in virioplankton diversity were clear from RNRs sampled across a broad oceanic transect. The most abundant RNRs belonged to novel lineages of podoviruses infecting α-proteobacteria, a bacterial class critical to oceanic carbon cycling. RNR class was predictive of phage morphology among cyanophages and RNR distribution frequencies among cyanophages were largely consistent with the predictions of the "kill the winner-cost of resistance" model. RNRs were also identified for the first time to our knowledge within ssDNA viromes. These data indicate that RNR polymorphism provides a means of connecting the biological and ecological features of virioplankton populations. viral ecology | viral evolution | phage replication

Elucidating marine virus ecology through a unified heartbeat

“…Likewise, 7 of 10 predicted ORFs on a 12-kb contig containing a class I other RNR shared homology with genes of podoviruses infecting α-proteobacteria, such as Pelagibacter phages HTVC011P and HTVC019P (24) and Roseobacter phage SIO1 (25). Together with findings that many RTPR sequences were similar to RNRs from eukaryotic green algal species, who normally lack these class II B12-dependent forms and likely derive from lateral gene transfer from cohabitating bacteria, Sakowski et al (13) hypothesize that these class II RTPR sequences are from podoviruses that infect B12-producing algaeassociated α-proteobacteria. The fact that distinct RNRs were observed between reference myoviral and podoviral Pelagiphages suggests that RNRs can provide a cultivation-independent means to assess the abundance, distribution, and ecological strategies of this poorly studied group.…”

“…"Omic" approaches have since provided unprecedented insight into virus diversity and even a glimpse into inferred function (11), but infection lifestyles have remained elusive given most virus-derived sequences have no database matches (12). In PNAS, Sakowski et al (13) address these fundamental issues by using ribonucleotide reductases (RNRs) from virus metagenomes as a unifying molecular marker to not only characterize the diversity of resident viruses in distinct marine environments, but to infer their ecological strategies (e.g., specialists vs. generalists) across environmental gradients.…”

“…Sakowski et al (13) argue that RNRs hold unique promise as universal gene targets to help compare phage functional diversity and to infer comparative ecology, given their distribution over a wide range of viruses, including all three Caudovirales families of tailed phages (Myoviridiae, Podoviridae, and Siphoviridae) and viruses infecting hosts within all three domains of life, and their strong ties to lytic marine phage lifestyles (18). They specifically focused on the catalytic (α) subunit of the RNR holoenzyme in virome libraries spanning a broad longitudinal transect of oceanic environments (Gulf of Maine, Chesapeake Bay, and the Dry Tortugas) to examine the biological and ecological features of lytic phage populations within the Caudovirales.…”

Diversity and Ecology of Viruses in Hyperarid Desert Soils

“…In marine virus ecology, the use of conserved viral marker genes such as DNA polymerases (76), ribonucleotide reductases (77), and T4-related structural proteins (78,79) has provided detailed data on viral biodiversity, on intra-and interviral evolutionary relationships, and on oceanic viral turnover rates. The use of these methods to study virus diversity and biogeography in desert soils is relatively new and most commonly involves the sequencing of whole metaviromes (37)(38)(39).…”

Contribution of Next-Generation Sequencing to Aquatic and Fish Virology

“…Contrary to the 16S ribosomal RNA gene that is commonly used for bacterial taxonomic classification, there is no known sequence shared among all viruses [77,78]. A recent discovery revealed that ribonucleotide reductases (RNRs) can be used as potential viral markers because they are widely distributed among dsDNA viral families [79]. For instance, the predicted nucleic acid distribution among viroplankton indicates that dsDNA viruses can comprise 70% of the total viruses and that 93% of dsDNA viroplankton may contain RNRs [79,80].…”