Did DNA replication evolve twice independently?

“In contrast, the core components of transcription and translation are highly conserved in all domains of life (Edgell and Doolittle 1997; Leipe et al. 1999), and they contain few inteins.”

“Several authors suggested that the last universal ancestor of the three domains of life, LUCA, had an RNA or RNA/DNA genome, and that most proteins involved in DNA metabolism only appeared after the divergence of the major cellular lineages (34,35).”

“, the universality of the translation machinery in all domains of life suggests that proteins most likely evolved in the RNA world before DNA (e.g.,”

“Several genes encoding eukaryotic-like DNA replication proteins are present in archaeal genomes (4, 7, 12, 24).”

“Recent sequence analyses of the complete genomes from several organisms in Archaea, the third domain of life, confirmed that the proteins relating to the genetic information system, including DNA replication, are structurally more similar to eukaryotic proteins than those from Bacteria (reviewed in Edgell & Doolittle…”

“Viruses may have predated cells (Forterre et al., 2004; Koonin et al., 2015; Leipe et al., 1999), and thereby provided a large pool of genetic diversity that homologous recombination could plumb for genes and ultimately splice them together into a genome that encodes sufficient chemistry to enable…”

“proteins are known to be involved in DNA metabolism (46).”

“observations that DNA originated late on, only after the main phyletic lines of divergence were established (Mushegian and Koonin 1996; Aravind et al. 1999; Freeland et al. 1999; Leipe et al. 1999; Poole and Logan 2005; Forterre 2005, 2006; Di Giulio 2006a; Glansdorff et al. 2008).”

“In a comparison of sequences of proteins involved in DNA replication, it was proposed that the LUCA had a genetic system that contained both RNA and DNA, but the latter was, at that time, produced by reverse transcription (83).”

“We can thus suppose, from the principle of actualism, that many cellular lineages also disappeared both during the evolution from the first cells to LUCA or from LUCA to the modern cellular world.”

“SfAV encodes a DNA polymerase (ORF 1) of the B family, which, like the principal replication enzymes in prokaryotes and eukaryotes, contains a nucleotide-polymerizing domain (II-VI-III-I-V) fused to an N-terminal 3 to 5 exonuclease domain (67).”

“…RNA polymerase and 50-30 flap exonuclease (FEN-1), exhibit significant sequence homology among bacteria, archaea and eukaryote sources, as required of pre-divergence proteins (Gropp et al., 1986; Sweetser et al., 1987; Langer et al., 1995; Edgell and Doolittle, 1997; Leipe et al., 1999; Section 4).”

“To explain this observation, Koonin and colleagues have suggested that LUCA had an RNA genome, but used DNA as a replication intermediate (much like a retrovirus) (Leipe et al., 1999).”

“sist of organisms with genomes of RNA, or RNA-DNA hybrid, or DNA with an RNA replication intermediate.(30,45,47) The 858 M.”

“Given that certain reconstructions of LUCA posit a notable role for RNA-based genetic material [23], it is possible that this ancestral enzyme might have had a prominent role in LUCA as an enzyme that repaired RNA through its polymerase or nucleotidyltransferase activity.”

“The enzyme gradually converted RNA genomes into DNA genomes (Brosius, 1999d; Leipe et al., 1999).”

“It is likewise accepted that there are numerous similarities between archaea and eukaryotes [18] – eukaryote-like histones have been found in both euryarchaea and crenarchaea [19]; archaea and eukaryotes make use of small RNAs (known as small nucleolar or snoRNAs in eukaryotes) to guide ribose methylation and pseudour…”

“While most information transfer processes, such as transcription and translation, are performed by enzymes that share homology in cells from all domains of life, comparative genomics reveals the surprising finding that the core enzymes of DNA replication: polymerases, helicase, primase, and ssDNA binding proteins, sha…”

“Pour expliquer la présence, dans la liste des protéines universelles, des ARN polymérases impliquées dans la transcription de l’ADN et de quelques protéines 3R, Koonin et ses collaborateurs ont proposé un Luca dont le génome était composé d’ARN, mais qui contenait déjà de l’ADN répliqué par rétrotranscription [10] : c…”

“Eukaryotic and archaeal primases have a similar structural organization, which indicates a common evolutionary ancestor [29].”

“In addition, after the total genome sequences of several archaeal organisms were determined, it was confirmed that several genes encoding proteins sharing sequence similarities with eukaryotic DNA replication proteins are present in all archaeal genomes (5, 10, 15, 32).”

“Thus, under the symbiogenetic scenario for the origin of eukaryotes, there are two basic cell types, archaeal and bacterial, which differ in many fundamental features, above all, the structure and biogenesis of the cell membranes and the organization and origin of the DNA replication machinery.(61,62) These major diff…”

“Moreover, the idea of a common origin for all living beings faces substantial difficulties, including the lack of homology in the core DNA replication system components and the distinct enzymes required for lipid membrane biosynthesis in archaea and bacteria (Leipe et al., 1999; Pereto et al., 2004).”

“(i) did not have a typical, large DNA genome (Forterre 2006; Leipe et al. 1999) and/or.”

“This reservation is based on the disturbing absence of homology of the replicative DNA polymerases in bacteria and archaea/eukaryotes ( Leipe et al. 1999 ).”

“Recent research suggests thinking about the early stages of life as a pre-cellular RNA gene pool with RNA viruses, retroviruses and—by reverse transcriptase of singlestranded RNA viral genomes—also double-stranded DNA viruses (Leipe et al. 1999; Martin 2005; Koonin et al. 2006; Brosius 2003; Flavell 1995).”

“This mechanistic framework is shared by all cellular organisms, so it is truly remarkable that the protein machinery that bacteria use to replicate their genomes is not directly related, at the primary sequence level, to the machinery that is present in archaea and eukaryote”

“A common ancestry for archaea and eucarya is supported by the similarities in their DNA replication machineries, which differ from those of bacteria (2, 11 ).”

“The replicational cycle of the LUCA was proposed to be mirrored in today’s retroid viruses, especially caulimoviruses and hepadnaviruses (Leipe et al. 1999).”

“Nonorthologous gene displacement is a common phenomenon in genome evolution that encompasses even central cellular functions, in particular key components of the DNA replication machinery (35).”

“Copyright © 2003 The Protein Society 823 viewed for DNA replication in Edgell and Doolittle 1997; Ishino and Cann 1998; Cann and Ishino 1999; Leipe et al. 1999).”

“S1 B and C and S5), RepB is apparently the prototype of a distinct class of primases (36) with high sequence homology and exclusive leading-strand replication mode.”

“Structure of C-family polymerases Bacterial replicases are large DNA polymerases that constitute a unique family referred to as the C-family [13].”

“Third, the DNA replication machinery of these two superkingdoms is very different; many key proteins comprising this machinery have a superkingdom specific distribution [4].”

“The molecular machinery essential for bacterial replication and genome maintenance is surprisingly dissimilar from analogous proteins in eukaryotes, so much so that it is thought that processes such as replication could have evolved independently.(7) From a therapeutic perspective, this difference makes genome mainten…”

“As a historical note, the homology between bacterial and eurkaryotic DNA clamps was only acknowledged when the structures were solved and the similarity of their complexes was identified [41].”

“…encoding ThyA and ThyX may shed light on the actively debated wider issue regarding the origins of viral and cellular DNA (Hendrix et al. 1999; Leipe et al. 1999; Villarreal and DeFilippis 2000; Bell 2001; Forterre 2002; Bamford 2003; Filee et al. 2003; Forterre 2005; Koonin and Martin 2005;…”

“ment with other observations (7), suggests that the OB-”

“It has been proposed that the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages (37).”

“Biochemical research efforts have suggested that the principle of the DNA replication mechanism seems to be the same in the three biological domains, Bacteria, Eukarya, and Archaea (6, 10, 11, 19), although the protein factors with conserved functions are predicted to have evolved from different origins based on the d…”

“It has been suggested [ 22 ] that DNA replication has evolved at least twice independently and that the last common ancestor of Bacteria and Eukaryota/Archea had a genetic system that contained RNA and DNA, with the latter produced by reverse transcription only.”

“, it possessed a functional ribosome of some kind [8].”

“Early cellular evolution was accompanied by gross genetic rearrangements (1–3), which resulted in apparentmodularity of proteins (4) and in unexpected structural similarities and dissimilarities among cellular forms of life (5,6).”

“Specifically, several genes encoding proteins sharing sequence similarities with eukaryotic DNA replication proteins are present in all archaeal genomes sequenced to date (reviewed in Edgell & Doolittle 1997; Ishino & Cann 1998; Leipe et al. 1999), and some of the gene products have been characterized biochemically (r…”

“Many key replication proteins, such as the replicative helicase, DNA polymerases, primase, and single strand binding protein, are evolutionarily unrelated between bacteria and archaea/eukarya (Forterre et al. 2004; Leipe et al. 1999).”

“Despite controversies regarding the chemical nature of the genome of the LCA,((38)) the similarities of DNA replication among cells and the homology between certain components of the DNA replication machinery((39)) suggest that DNA-based genomes may have evolved prior to the existence of the LCA.”

“For some, these genes would be made out of DNA (Forterre 2002; Dworkin et al. 2003); others favor a mixed RNA-DNA genome and replication system (Leipe et al. 1999).”

“Consequently, it is difficult to place any complete DNA-associated processes in the LUCA (Forterre et al. 2004; Harris et al. 2003; Leipe et al. 1999).”

“Many of the central components of the DNA replication machineries in the bacterial and in the archaeoeukaryotic lineage are either unrelated or only distantly related to each other [Edgell and Doolittle, 1997; Leipe et al., 1999].”

“The RNA-LUCA hypothesis has sometimes been refuted because the set of universal protein includes a few proteins involved in DNA metabolism or in the synthesis of DNA precursors (dNTPs) (Leipe et al. 1999, Becerra et al. 2007a, Cantine and Fournier 2018, Koonin et al. 2020).”

“Our observations are consistent with the discovery of DNA and DNA replication at least twice [66] suggesting that the origin of present living organisms was a community of organisms developing more or less independently from one another (the progenote hypothesis [67,68]), splitting and fusing as time elapsed until the…”