Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria

Abstract

DNA template-dependent multi-subunit RNA polymerases (RNAPs) found in all three domains of life and some viruses are of the two-double-Ψ-β-barrel (DPBB) type. The 2-DPBB protein format is also found in some RNA template-dependent RNAPs and a major replicative DNA template-dependent DNA polymerase (DNAP) from Archaea (PolD). The 2−DPBB family of RNAPs and DNAPs probably evolved prior to the last universal common cellular ancestor (LUCA). Archaeal Transcription Factor B (TFB) and bacterial σ factors include homologous strings of helix-turn-helix units. The consequences of TFB-σ homology are discussed in terms of the evolution of archaeal and bacterial core promoters. Domain-specific DPBB loop inserts functionally connect general transcription factors to the RNAP active site. Archaea appear to be more similar to LUCA than Bacteria. Evolution of bacterial σ factors from TFB appears to have driven divergence of Bacteria from Archaea, splitting the prokaryotic domains.

“Superwobbling” and tRNA-34 wobble and tRNA-37 anticodon loop modifications in evolution and devolution of the genetic code

“…To potentially gain insights into tRNA-A37 and -G37 modifications, we visualized the genetic code for Archaea along with reported tRNA-37 modifications (Figure 8). We strongly support the idea that Archaea are the most ancient organisms on Earth and the most similar to LUCA [39,48,63]. Because of missing data, we combined results for tRNA-37 modifications from a number of archaeal species.…”

“…We advocate for the model that LUCA evolved first to Archaea. Archaea gave rise to Bacteria [39,48,63]. Fusion of an Asgard Archaea and an  -Proteobacteria (i.e., Rickettsiales) gave rise to Eukarya, with division and establishment of separate and partly overlapping translation systems for the eukaryotic cytosol and the mitochondria [6,10,43].…”

“…We consider analysis of the evolution of genetic codes and tRNA-34 modifications through Earth's history to support our narrative (Figures 2-6). The simplest genetic code is that of Archaea (Figure 2), indicating that Archaea is closest to LUCA [39,48,63]. Generally, unmodified A34 is not allowed in Archaea, and only G34 is utilized.…”

“…A simple narrative for evolution of life on Earth is proposed in which LUCA evolved to Archaea [39,48]. As a reference organism that is close to LUCA, we propose Pyrococcus furiosis.…”

“Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code

“…A simple narrative for evolution of life on Earth is proposed in which LUCA evolved to Archaea [41,50]. As a reference organism that is close to LUCA, we propose Pyrococcus furiosis that has a tRNAome that is very similar in sequence to tRNA Pri (a primordial tRNA) [40].…”