DNA replication is central to all extant cellular organisms, There are subs
tantial functional similarities between the bacterial and the archaeal/euka
ryotic replication machineries, including but not limited to defined origin
s, replication bidirectionality, RNA primers and leading and lagging strand
synthesis. However, several core components of the bacterial replication m
achinery are unrelated or only distantly related to the functionally equiva
lent components of the archaeal/eukaryotic replication apparatus. This is i
n sharp contrast to the principal proteins involved in transcription and tr
anslation, which are highly conserved in all divisions of life. We performe
d detailed sequence comparisons of the proteins that fulfill indispensable
functions in DNA replication and classified them into four main categories
with respect to the conservation in bacteria and archaea/eukaryotes: (i) no
n-homologous, such as replicative polymerases and primases; (ii) containing
homologous domains but apparently non-orthologous and conceivably independ
ently recruited to function in replication, such as the principal replicati
ve helicases or proofreading exonucleases; (iii) apparently orthologous but
poorly conserved, such as the sliding clamp proteins or DNA ligases; (iv)
orthologous and highly conserved, such as clamp-loader ATPases or 5'-->3' e
xonucleases (FLAP nucleases), The universal conservation of some components
of the DNA replication machinery and enzymes for DNA precursor biosynthesi
s but not the principal DNA polymerases suggests that the last common ances
tor (LCA) of all modern cellular life forms possessed DNA but did not repli
cate it the way extant cells do. We propose that the LCA had a genetic syst
em that contained both RNA and DNA, with the latter being produced by rever
se transcription. Consequently, the modern-type system for double-stranded
DNA replication likely evolved independently in the bacterial and archaeal/
eukaryotic lineages.