Residue profile in predivergence sequences as a guide to the origin of DNA replication

Abstract

DNA dependent RNA polymerase core subunits abb' conserved residues at frequencies most closely matched with codons at stage 10.4-11.1 in code evolution. An excess of acidic residues (stage 2 additions) lowered this estimate, but not by more than 2.3 stages. With 1 tryptophan (stage 14 addition) in 529 conserved residues, abb' significantly under-represented this amino acid, consistent with a cut-off in its residue profile before completion of the genetic code. Residue profiles in FEN-1 homologs and DNA topoisomerase I-5' placed their origin at stage 11-13. Prokaryote septation protein, FtsZ, arose earlier, between stage 8-11. Proteolipid in an ATP-driven proton pump served as a marker for cell membrane formation. It indicated this event took place near stage 7. Cell division, DNA replication and transcription were inferred to have originated in a protocell antecedent of the last common ancestor. Late-forming residue profiles characterized RNA dependent RNA replicase, DNA polymerase, reverse transcriptase and ribonucleotide reductase. This suggests some early processes, including RNA replication and deoxynucleotide synthesis, once depended on catalysts not found in extant residue sequences. Early formation of topoisomerase I, and enzymes that synthesize and trim RNA-DNA hybrids was viewed as evidence for a mixed duplex, with linear RNA and DNA strands, in the transition from an RNA to DNA genome.