Abstract
Using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plastid and certain DNA viruses, including the recently reported Sputnik virus. Using contextual information from domain architectures and gene-neighborhoods we present evidence that they are likely to possess both primase and DNA polymerase activity, comparable to the previously reported prim-pol proteins. These newly identified polymerases help in defining the minimal functional core of superfamily A DNA polymerases and related RNA polymerases. Thus, they provide a framework to understand the emergence of both DNA and RNA polymerization activity in this class of enzymes. They also provide evidence that enigmatic DNA viruses, such as Sputnik, might have emerged from mobile elements coding these polymerases.This article was reviewed by Eugene Koonin and Mark Ragan.
Highlights
Advances in structural biology have reinforced the conclusions from earlier protein sequence studies that the catalytic domains of all known nucleic acid polymerases belong to four basic folds [1,2,3,4]
More recently we showed that archaeo-eukaryotic type primases contain a derived version of this fold, which is further related to DNA-binding domains of certain viral replication initiation proteins and the catalytic domain of rolling circle replicator tyrosine recombinases [5]
Identification of a novel family of nucleic acid polymerases D5-like proteins of the AAA+ superfamily prototyped by the poxviral D5 ATPase are the most prevalent DNA helicase encoded by genomes of medium to large DNA viruses, certain self-replicating plasmids and transposons [5]
Summary
Advances in structural biology have reinforced the conclusions from earlier protein sequence studies that the catalytic domains of all known nucleic acid polymerases belong to four basic folds [1,2,3,4]. Networks representing this contextual information suggest that different families of DNA polymerases, primases, helicases and associated replication proteins frequently displace each other in different genomes or mobile elements, thereby reinforcing their functional equivalence (Fig. 1A).
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