Evolution of replication machines

Abstract

The machines that decode and regulate genetic information require the translation, transcription and replication pathways essential to all living cells. Thus, it might be expected that all cells share the same basic machinery for these pathways that were inherited from the primordial ancestor cell from which they evolved. A clear example of this is found in the translation machinery that converts RNA sequence to protein. The translation process requires numerous structural and catalytic RNAs and proteins, the central factors of which are homologous in all three domains of life, bacteria, archaea and eukarya. Likewise, the central actor in transcription, RNA polymerase, shows homology among the catalytic subunits in bacteria, archaea and eukarya. In contrast, while some “gears” of the genome replication machinery are homologous in all domains of life, most components of the replication machine appear to be unrelated between bacteria and those of archaea and eukarya. This review will compare and contrast the central proteins of the “replisome” machines that duplicate DNA in bacteria, archaea and eukarya, with an eye to understanding the issues surrounding the evolution of the DNA replication apparatus.

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction

“…DNA replication is hypothesized to have existed in DNA viruses even before the emergence of the Last Universal Common Ancestor ( 42 ). Hence, it is possible that the proposed scheme may have appeared early in evolution and may be common for all dPols ( 43 , 44 ).…”

CMG–Pol epsilon dynamics suggests a mechanism for the establishment of leading-strand synthesis in the eukaryotic replisome

“…These two functions must be tightly coordinated to prevent the rise of genome instability, which is a major cause of cancer. DNA unwinding by a replicative helicase involves single-strand translocation of a hexameric motor, whereas DNA synthesis requires template priming by a primase and extension by dedicated replicative DNA polymerases (2). In eukaryotes, the helicase function is performed by the Cdc45-MCM-GINS (CMG) complex (3,4) and the primase function is played by Pol alpha (5), whereas DNA synthesis is catalyzed by two specialized DNA polymerases, Pol epsilon and delta.…”

Tree of motility – A proposed history of motility systems in the tree of life

“…Nonetheless, taking into account that the evolution of life has been ongoing for ~4 billion years, it appears that novel motility mechanisms only sporadically evolve. It is also noteworthy that different modes of motility have evolved, considering that other vital processes, such as the mechanisms for ATP synthesis (Gogarten & Taiz, 1992) and protein synthesis (Yao & O'Donnell, 2016), have retained core machineries. This is probably because motility is established by the interaction of the organism with its environment.…”