Pastor Chui: Information Processing Differences Between Archaea and Eukarya 3

“DNA Helicase activity “DNA helicases are essential enzymes functioning in DNA replication by separating double-stranded DNA into single strands so that each strand can be copied. One of the important components of eukaryotic DNA helicase function is the MCM2-7 heterohexamer, which is made of six different proteins, each belonging to a distinct protein family (Bochman and Schwacha 2009). MCM stands for mini chromosome maintenance complex, which has a role in both the initiation and the elongation phases of DNA replication in the replication fork. Note that like the individual components of Orc1-6, each member of the MCM2-7 is essential for yeast DNA replication. Deletion of MCMs 2, 3, 5, 6, 7 cause lethality in yeast (http://www.yeastgenome.org) (fig. 2). “Most importantly, archaea lack proteins homologous to those eukaryotic proteins required to activate the licensed eukaryotic origins of replication, including cyclin-dependent kinase CDK and Dbf4 and Dbf4-dependent kinase DDK, all essential for the viability of yeast (Bochman and Schwacha 2009; Tye 2000) (fig. 2). Therefore, the archaeal helicases alone are not enough to open up the double-stranded DNA in eukarya. Even if they could license the eukaryotic origins of replication, the licensed origins could not be activated and no DNA replication would occur and no eukaryote could survive or propagate. Thus, this lack of genes to activate the licensed origins of replication constitutes an unbridgeable chasm between archaea and eukarya. Alternatively, archaea helicases are able to open up the double-stranded DNA in eukarya but the necessary cell-cycle dependent regulation of DNA replication cannot occur, resulting in eukaryotic cell death. “Primase “DNA replication starts with the synthesis of an RNA primer by DNA primase in all domains of life because DNA polymerases are incapable of de novo DNA synthesis. DNA primase is a type of RNA polymerase that creates an RNA primer that DNA polymerase uses to replicate single stranded DNA. The RNA primer is later removed by exo- and/or endonucleases. “The single subunit protein DnaG serves as the primase in bacteria, while eukaryotic primase is composed of two subunits PriS and PriL in a complex with the eukaryotic-specific DNA polymerase α and its accessory B subunit. Homologues of PriS and PriL have been identified in archaea, but not DNA polymerase α. However, the Pol α is required in eukarya to synthesize a short DNA fragment (10~30 nucleotides) after the RNA primer and only after Pol α has done its job, other eukaryotic polymerases can then function and finish the process of DNA replication. Therefore, the lack of Pol α in archaea is a dramatic barrier for any archaeal cell to be able to evolve into a eukaryote. “With the knowledge of DNA replication in archaea and bacteria, it defies evolution that eukarya use a special eukaryote-specific polymerase, Pol α, in their DNA replication. While the two principle enzymes for synthesizing DNA during eukaryotic DNA replication are Pol δ and Pol ε, neither Pol δ nor Pol ε is capable of performing its task until Pol α has synthesized a short DNA fragment after the RNA primer synthesized by the primase. The fact that no homolog of Pol α has been identified in bacteria or archaea along with other missing eukaryotic-like enzymes, prompted Leipe and colleagues to propose that the foundational process of DNA replication had at least two independent origins (Leipe, Aravind, and Koonin 1999). “B.1 RNA polymerase “Without any phosphorylation of CTD, Pol II is inactive in initiating transcription, although the formation of the initiation complex can only occur when CTD is not phosphorylated. Different combinations of the post-translational modification, known as the CTD code, are crucial for the differential binding of hundreds of diverse factors, directly or indirectly (Egloff et al. 2012; Heidemann et al. 2013). These factors, a few listed in Fig. 5C, are required for eukaryotic transcription initiation, elongation, termination, and RNA processing (Egloff et al. 2012; Hsin and Manley 2012). “It is clear that without the CTD of Rpb1, no Pol II transcription would be possible, which includes all eukaryotic protein-coding genes, long noncoding RNAs, and many small nuclear RNAs. Thus, no eukaryote would survive without this CTD. Indeed, it has been found that deletion of the CTD is lethal in yeast, flies, and mice. Thus, the simple fact that eukaryotic transcription requires the CTD renders the archaeal transcription machinery unsuitable for transcribing eukaryotic genomes. Thus, the necessity of the CTD alone in eukarya creates an unbridgeable chasm between archaea and eukarya....