Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery

Abstract

The elaborate eukaryotic DNA replication machinery evolved from the archaeal ancestors that themselves show considerable complexity. Here we discuss the comparative genomic and phylogenetic analysis of the core replication enzymes, the DNA polymerases, in archaea and their relationships with the eukaryotic polymerases. In archaea, there are three groups of family B DNA polymerases, historically known as PolB1, PolB2 and PolB3. All three groups appear to descend from the last common ancestors of the extant archaea but their subsequent evolutionary trajectories seem to have been widely different. Although PolB3 is present in all archaea, with the exception of Thaumarchaeota, and appears to be directly involved in lagging strand replication, the evolution of this gene does not follow the archaeal phylogeny, conceivably due to multiple horizontal transfers and/or dramatic differences in evolutionary rates. In contrast, PolB1 is missing in Euryarchaeota but otherwise seems to have evolved vertically. The third archaeal group of family B polymerases, PolB2, includes primarily proteins in which the catalytic centers of the polymerase and exonuclease domains are disrupted and accordingly the enzymes appear to be inactivated. The members of the PolB2 group are scattered across archaea and might be involved in repair or regulation of replication along with inactivated members of the RadA family ATPases and an additional, uncharacterized protein that are encoded within the same predicted operon. In addition to the family B polymerases, all archaea, with the exception of the Crenarchaeota, encode enzymes of a distinct family D the origin of which is unclear. We examine multiple considerations that appear compatible with the possibility that family D polymerases are highly derived homologs of family B. The eukaryotic DNA polymerases show a highly complex relationship with their archaeal ancestors including contributions of proteins and domains from both the family B and the family D archaeal polymerases.

Keywords: DNA polymerases; DNA replication; archaea; enzyme inactivation; mobile genetic elements.

Figure 1

Phylogenetic analysis of the polymerase B family in archaea. The MUSCLE program (Edgar, 2004) was used for construction of sequence alignments. The tree was reconstructed using the FastTree program (Price et al., 2010) (179 sequences and 209 aligned positions). The complete tree is available in the Supplementary Figure S3. The sequences are denoted by their GI numbers, species names, refseq genome UID number and the arCOG number to which the respective protein currently assigned. Several branches are collapsed and shown as triangles denoted by the respective lineage taxonomy name. Color code: Euryarchaeota, dark blue, with the exception of Halobacteria that are shown in orange; Crenarchaeota, light blue; deeply branched archaeal lineages (Thaumarchaeota, Korarchaeota, Nanoarchaeota), purple; Nanoarchaea, red. The conserved neighborhoods (if any) are shown on the right side of the tree for the respective branches. Homologous genes are shown by arrows of the same color; genes are shown approximately to scale. Color code: polymerase genes are shown by red outline, inteins are shown by yellow triangles, uncharacterized genes are rendered in gray. The arCOG numbers are provided underneath the respective gene arrows for all non-polymerase genes. Abbreviations: arORC2—ORC/CDC6 AAA+ ATPases, arORC2 subfamily (Makarova and Koonin, 2013), HTH—helix-turn-helix; P.AW—the conserved motif for the respective uncharacterized protein.

Figure 2

Phyletic patterns for the major groups of archaeal DNAPs. Phyletic patterns for the indicated protein families (filled circles show presence and empty circles show absence) are superimposed over the phylogenetic tree of archaea. The number of paralogs are indicated by a number, if more than one paralog of the respective family is encoded in the genome. The tree topology is based on the phylogeny of concatenated ribosomal proteins.

Figure 3

Genome maps of archaeal PolB-encoding mobile genetic elements. (A) Casposons of families 1 and 2. NitAR1-C1 is present in the genome of Candidatus Nitrosopumilus koreensis AR1 (NC_018655; nucleotide coordinates: 655308 to 663492), whereas MetMaz-C1 is from Methanosarcina mazei Go1 (NC_003901; nucleotide coordinates: 3946601 to 3956653). (B) Tyrosine recombinases-encoding elements. IgnAgg-E3 is found in the genome of Ignisphaera aggregans DSM 17230 (NC_014471; nucleotide coordinates: 1844012 to 1868704) and ArcSul-E1 is from Archaeoglobus sulfaticallidus PM70-1 (NC_021169; nucleotide coordinates: 873590 to 894826). Predicted protein-coding genes are indicated with arrows, indicating the direction of transcription. Genes for PolBs are shown in red, cas1 genes are in cyan, and genes for tyrosine recombinases are colored blue. Abbreviations: TIR, terminal inverted repeats; att, attachment site; ZBD, Zinc-binding domain-containing protein; HNH, HNH family endonuclease; (w)HTH, (winged) helix-turn-helix proteins; RBD, RNA-binding domain.

Figure 4

Reconstruction of the complements of replicative DNAPs in the last archaeal and eukaryotic ancestors and a hypothetical scenario of their evolutionary relationships. (A) Polymerase B and D family genes projected to archaeal (LACA) and eukaryotic (LECA) last common ancestors and their domain organization. Homologous domains are shown by shapes of the same color. Inactivated domains are crossed. For eukaryotic polymerase families, human and yeast gene names are provided. (B) The unrooted phylogenetic tree of active polymerases of B family. The MUSCLE program (Edgar, 2004) was used for construction of multiple sequence alignments. The tree was reconstructed using the FastTree program (Price et al., 2010) (141 sequences and 264 aligned positions). The complete tree is available in the Supplementary Figure S4. The tree is rendered as a scheme, with all major groups collapsed. (C) The inferred evolutionary relationships between archaeal and eukaryotic replicative DNAPs. Details on the involvement of PolD in the evolution of eukaryotic DNAPs are discussed in the text. The question mark denotes an uncertainty in evolutionary scenario.