Reannotation of the ribonucleotide reductase in a cyanophage reveals life history strategies within the virioplankton

Harrison, Amelia O.; Rm, Moore; Polson, Shawn W.; Wommack, K. Eric

doi:10.1101/467415

Cited by 1 publication

(3 citation statements)

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“…The majority of RNRs were O 2 -independent class II enzymes (62%) and were further sub-classified as follows according to clades defined in (Sakowski et al, 2014): class II RTPR (46%), class II “Other” (18%). The remaining RNRs were O 2 -dependent class I enzymes in the “Other” clade (28%) and the recently defined Cyano SP clade (10%) (Harrison et al, 2018; Supplementary Table S2). Recent work has shown that the Cyano II clade defined by Sakowski et al (2014) is not a class II RNR, but is instead a class I RNR (Harrison et al, 2018).…”

Section: Resultsmentioning

confidence: 99%

“…The remaining RNRs were O 2 -dependent class I enzymes in the “Other” clade (28%) and the recently defined Cyano SP clade (10%) (Harrison et al, 2018; Supplementary Table S2). Recent work has shown that the Cyano II clade defined by Sakowski et al (2014) is not a class II RNR, but is instead a class I RNR (Harrison et al, 2018). As a consequence, the clade was renamed from Cyano II to Cyano SP.…”

Section: Resultsmentioning

confidence: 99%

“…These contigs were then categorized by the presence of the following genes involved in DNA replication: helicase (UvrD-like, DnaB-like, Gp4-like, RecB-like, SNF2-like) and ribonucleotide reductase (Class I Other, Class II Other, and Class II RTPR), as previously defined (Sakowski et al, 2014; Supplementary Table S2). The Class I Cyano SP ribonucleotide reductase has been recently defined (Harrison et al, 2018) based on Class II Cyano sequences from a previous study (Sakowski et al, 2014; Supplementary Table S2). Contigs from the PacBio-Illumina hybrid assembly with full-length PolA sequences were annotated and sorted into groups based on PolA phylogeny and replication organization.…”

Section: Methodsmentioning

confidence: 99%

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Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton

et al. 2018

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Shotgun metagenomics, which allows for broad sampling of viral diversity, has uncovered genes that are widely distributed among virioplankton populations and show linkages to important biological features of unknown viruses. Over 25% of known dsDNA phage carry the DNA polymerase I (polA) gene, making it one of the most widely distributed phage genes. Because of its pivotal role in DNA replication, this enzyme is linked to phage lifecycle characteristics. Previous research has suggested that a single amino acid substitution might be predictive of viral lifestyle. In this study Chesapeake Bay virioplankton were sampled by shotgun metagenomic sequencing (using long and short read technologies). More polA sequences were predicted from this single viral metagenome (virome) than from 86 globally distributed virome libraries (ca. 2,100, and 1,200, respectively). The PolA peptides predicted from the Chesapeake Bay virome clustered with 69% of PolA peptides from global viromes; thus, remarkably the Chesapeake Bay virome captured the majority of known PolA peptide diversity in viruses. This deeply sequenced virome also expanded the diversity of PolA sequences, increasing the number of PolA clusters by 44%. Contigs containing polA sequences were also used to examine relationships between phylogenetic clades of PolA and other genes within unknown viral populations. Phylogenic analysis revealed five distinct groups of phages distinguished by the amino acids at their 762 (Escherichia coli IAI39 numbering) positions and replication genes. DNA polymerase I sequences from Tyr762 and Phe762 groups were most often neighbored by ring-shaped superfamily IV helicases and ribonucleotide reductases (RNRs). The Leu762 groups had non-ring shaped helicases from superfamily II and were further distinguished by an additional helicase gene from superfamily I and the lack of any identifiable RNR genes. Moreover, we found that the inclusion of ribonucleotide reductase associated with PolA helped to further differentiate phage diversity, chiefly within lytic podovirus populations. Altogether, these data show that DNA Polymerase I is a useful marker for observing the diversity and composition of the virioplankton and may be a driving factor in the divergence of phage replication components.

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