Noncanonical DNA polymerization by aminoadenine-based siphoviruses

Abstract

Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous to the Klenow fragment of bacterial DNA polymerase I that includes 3′-exonuclease but lacks 5′-exonuclease, were found to preferentially select for aminoadenine instead of adenine in deoxynucleoside triphosphate incorporation templated by thymine. Polymerase genes occur in synteny with genes for a biosynthesis enzyme that produces aminoadenine deoxynucleotides in a wide array of Siphoviridae bacteriophages. Congruent phylogenetic clustering of the polymerases and biosynthesis enzymes suggests that aminoadenine has propagated in DNA alongside adenine since archaic stages of evolution.

Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8

“…ZTGC-DNA phages usually encode PolA and PrimPol, families that were shown to be implicated in plasmidic or viral DNA replication ( 16 , 17 ). Although the sole polymerase of S-2L (a PrimPol) is unspecific towards Z ( 7 ), other phages do rely on highly Z-specific PolA enzymes called DpoZ ( 5 ).…”

“…Phylogenetically speaking, DpoZ are split into two distinct subfamilies: ϕVC8-like and Wayne-like ( 5 ). Both harbour 5′-3′ polymerase and 3′-5′ exonuclease domains and display a strong exonuclease activity.…”

“…Both harbour 5′-3′ polymerase and 3′-5′ exonuclease domains and display a strong exonuclease activity. ϕVC8-like DpoZ were studied in detail for phages ϕVC8 and SH-Ab 15497, showing catalytic efficiencies greater by 1–2 orders of magnitude with dZTP than with dATP ( 5 ). This would make them useful tools for controlling the replication of synthetic ZTGC-DNA organisms that could be generated with a set of 3 genes implicated in 2-aminoadenine metabolism ( 9 ).…”

“…Importantly, phages S-2L (with PrimPol) and ϕVC8-like (with DpoZ) harbour in their genomes a well-conserved gene for a nucleotide phosphohydrolase (DatZ) ( 5–7 ). In S-2L, we showed that DatZ removes the triphosphate tail of dATP (and of no other dNTP), rendering it unusable as a substrate for a PrimPol DNA polymerase.…”

A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution

“…Three recent studies found that several bacteriophages can replace adenine with noncanonical nucleobases aminoadenine, which is preferably used by phage DNA polymerase. 39 , 40 , 41 The ecological significance of these dU-containing marine bacteriophages remains to be determined given they have likely been underestimated in ocean surveys due to an inability of conventional metagenomic sequence libraries to detect dU-DNA. However, it is clear that phages represent a rich source of novel, non-canonical base modifications that together expand the genetic blueprint of life on Earth.…”