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The Old and New Testaments of gene regulation. Evolution of multi-subunit RNA polymerases and co-evolution of eukaryote complexity with the RNAP II CTD.

Burton ZF - Transcription (2014)

Bottom Line: The Old Testament: at their active site, one class of eukaryotic interfering RNAP and ubiquitous multi-subunit RNAPs each have two-double psi β barrel (DPBB) motifs (a distinct pattern for compact 6-β sheet barrels).Analysis of RNAP core protein motifs, therefore, indicates that RNAP evolution can be traced from the RNA-protein world to LUCA (the last universal common ancestor) branching to LECA (the last eukaryotic common ancestor) and to the present day, spanning about 4 billion years.The New Testament: in the eukaryotic lineage, I posit that splitting RNAP functions into RNAPs I, II and III and innovations developed around the CTD heptad repeat of RNAP II and the extensive CTD interactome helps to describe how greater structural, cell cycle, epigenetic and signaling complexity co-evolved in eukaryotes relative to eubacteria and archaea.

View Article: PubMed Central - PubMed

Affiliation: a Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing, MI USA.

ABSTRACT
I relate a story of genesis told from the point of view of multi-subunit RNA polymerases (RNAPs) including an Old Testament (core RNAP motifs in all cellular life) and a New Testament (the RNAP II heptad repeat carboxy terminal domain (CTD) and CTD interactome in eukarya). The Old Testament: at their active site, one class of eukaryotic interfering RNAP and ubiquitous multi-subunit RNAPs each have two-double psi β barrel (DPBB) motifs (a distinct pattern for compact 6-β sheet barrels). Between β sheets 2 and 3 of the β subunit type DPBB of all multi-subunit RNAPs is a sandwich barrel hybrid motif (SBHM) that interacts with conserved initiation and elongation factors required to utilize a DNA template. Analysis of RNAP core protein motifs, therefore, indicates that RNAP evolution can be traced from the RNA-protein world to LUCA (the last universal common ancestor) branching to LECA (the last eukaryotic common ancestor) and to the present day, spanning about 4 billion years. The New Testament: in the eukaryotic lineage, I posit that splitting RNAP functions into RNAPs I, II and III and innovations developed around the CTD heptad repeat of RNAP II and the extensive CTD interactome helps to describe how greater structural, cell cycle, epigenetic and signaling complexity co-evolved in eukaryotes relative to eubacteria and archaea.

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Figure 1. The active site of eubacterial Tt RNAP. The catalytic center is occupied by ATP-Mg (space-filling representation). β sheets are yellow. RNA is silver. DNA is gold (template strand) and green (non-template strand). The active site is wedged between the closed trigger loop (TL; silver), bridge helix (BH; orange) and two DPBBs. This image was drawn using PDB 205J42 with the program Visual Molecular Dynamics (used for all molecular graphics).43
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Figure 1: Figure 1. The active site of eubacterial Tt RNAP. The catalytic center is occupied by ATP-Mg (space-filling representation). β sheets are yellow. RNA is silver. DNA is gold (template strand) and green (non-template strand). The active site is wedged between the closed trigger loop (TL; silver), bridge helix (BH; orange) and two DPBBs. This image was drawn using PDB 205J42 with the program Visual Molecular Dynamics (used for all molecular graphics).43

Mentions: Multi-subunit RNA polymerases (RNAPs) synthesize a RNA polymer from a DNA template.1-3Figure 1 shows a partial RNAP image emphasizing the active site, which is wedged between two-double psi β barrels (DPBBs) and the long (~40 amino acid) bridge α-helix and the mobile trigger loop. Because RNAPs translocate (move) along a DNA template in single base steps to form the RNA polymer, RNAPs are referred to as “molecular motors.” The catalytic mechanism involves two clustered magnesium (Mg) atoms. Polymerization requires a nucleoside triphosphate (NTP) substrate (ATP, GTP, CTP or UTP) from which a nucleoside monophosphate (NMP) unit is added to the growing RNA polymer. The NTP substrate is specified by Watson-Crick base pairing to the DNA template strand. Because these RNAPs are dependent on a DNA template, they are considered to be DNA-dependent RNA polymerases or DDRPs.


The Old and New Testaments of gene regulation. Evolution of multi-subunit RNA polymerases and co-evolution of eukaryote complexity with the RNAP II CTD.

Burton ZF - Transcription (2014)

Figure 1. The active site of eubacterial Tt RNAP. The catalytic center is occupied by ATP-Mg (space-filling representation). β sheets are yellow. RNA is silver. DNA is gold (template strand) and green (non-template strand). The active site is wedged between the closed trigger loop (TL; silver), bridge helix (BH; orange) and two DPBBs. This image was drawn using PDB 205J42 with the program Visual Molecular Dynamics (used for all molecular graphics).43
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215175&req=5

Figure 1: Figure 1. The active site of eubacterial Tt RNAP. The catalytic center is occupied by ATP-Mg (space-filling representation). β sheets are yellow. RNA is silver. DNA is gold (template strand) and green (non-template strand). The active site is wedged between the closed trigger loop (TL; silver), bridge helix (BH; orange) and two DPBBs. This image was drawn using PDB 205J42 with the program Visual Molecular Dynamics (used for all molecular graphics).43
Mentions: Multi-subunit RNA polymerases (RNAPs) synthesize a RNA polymer from a DNA template.1-3Figure 1 shows a partial RNAP image emphasizing the active site, which is wedged between two-double psi β barrels (DPBBs) and the long (~40 amino acid) bridge α-helix and the mobile trigger loop. Because RNAPs translocate (move) along a DNA template in single base steps to form the RNA polymer, RNAPs are referred to as “molecular motors.” The catalytic mechanism involves two clustered magnesium (Mg) atoms. Polymerization requires a nucleoside triphosphate (NTP) substrate (ATP, GTP, CTP or UTP) from which a nucleoside monophosphate (NMP) unit is added to the growing RNA polymer. The NTP substrate is specified by Watson-Crick base pairing to the DNA template strand. Because these RNAPs are dependent on a DNA template, they are considered to be DNA-dependent RNA polymerases or DDRPs.

Bottom Line: The Old Testament: at their active site, one class of eukaryotic interfering RNAP and ubiquitous multi-subunit RNAPs each have two-double psi β barrel (DPBB) motifs (a distinct pattern for compact 6-β sheet barrels).Analysis of RNAP core protein motifs, therefore, indicates that RNAP evolution can be traced from the RNA-protein world to LUCA (the last universal common ancestor) branching to LECA (the last eukaryotic common ancestor) and to the present day, spanning about 4 billion years.The New Testament: in the eukaryotic lineage, I posit that splitting RNAP functions into RNAPs I, II and III and innovations developed around the CTD heptad repeat of RNAP II and the extensive CTD interactome helps to describe how greater structural, cell cycle, epigenetic and signaling complexity co-evolved in eukaryotes relative to eubacteria and archaea.

View Article: PubMed Central - PubMed

Affiliation: a Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing, MI USA.

ABSTRACT
I relate a story of genesis told from the point of view of multi-subunit RNA polymerases (RNAPs) including an Old Testament (core RNAP motifs in all cellular life) and a New Testament (the RNAP II heptad repeat carboxy terminal domain (CTD) and CTD interactome in eukarya). The Old Testament: at their active site, one class of eukaryotic interfering RNAP and ubiquitous multi-subunit RNAPs each have two-double psi β barrel (DPBB) motifs (a distinct pattern for compact 6-β sheet barrels). Between β sheets 2 and 3 of the β subunit type DPBB of all multi-subunit RNAPs is a sandwich barrel hybrid motif (SBHM) that interacts with conserved initiation and elongation factors required to utilize a DNA template. Analysis of RNAP core protein motifs, therefore, indicates that RNAP evolution can be traced from the RNA-protein world to LUCA (the last universal common ancestor) branching to LECA (the last eukaryotic common ancestor) and to the present day, spanning about 4 billion years. The New Testament: in the eukaryotic lineage, I posit that splitting RNAP functions into RNAPs I, II and III and innovations developed around the CTD heptad repeat of RNAP II and the extensive CTD interactome helps to describe how greater structural, cell cycle, epigenetic and signaling complexity co-evolved in eukaryotes relative to eubacteria and archaea.

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