Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase

The preprint for the article I wrote about here(old thread locked due to lack of activity) now got published in American Chemical Society. Sadly you need a subscription to access the paper:

Here’s a new addition to the paper where the authors also detail and discuss some experiments they did on the possible functions of the primitive beta barrel fold (which supports my own suggestions in the previous thread):

Potential Functions of the Ancestral DPBB. The DPBB domains in RNA polymerases interact with the template DNA polymer. Homologous β-barrel groups also bind to DNA and RNA.30 Thus, the ancient DPBB may have had the ability to interact with nucleic acid polymers. To investigate such potential functions of the ancient DPBB, we examined the interactions between fluorescently labeled DNA polymers and mk2h_ΔMILPS, the simplest mutant that can fold under the conditions for the biochemical analysis (Figure 4B), by an electrophoresis mobility shift assay (EMSA). When doublestranded (ds) DNA was mixed with 5 μM mk2h_ΔMILPS, most of the dsDNA remained stacked in the well (Figure 5A). Additionally, the dsDNA band shifts were observed as the mk2h_ΔMILPS concentration was increased (Figure 5B), indicating that mk2h_ΔMILPS was bound to dsDNA. On the other hand, no band shift was detected for single-stranded (ss) DNA in the presence of 5 μM mk2h_ΔMILPS (Figure 5A). The interaction between ssDNA and mk2h_ΔMILPS could only be detected with protein concentrations over 20 μM (Figure S24). Therefore, mk2h_ΔMILPS preferentially binds to dsDNA over ssDNA. These results suggest the possibility that ancestral simple DPBB peptides also worked as nucleic acid-binding proteins (e.g., transcription factors and histonelike chromatin proteins).40−42
Another potential function of the ancient DPBB is to interact with negatively charged metabolites. We found that negatively charged ligands, such as sulfate ion, malonic acid, or malic acid, are bound within the conserved ligand pocket of DPBB in the crystal structures of some symmetrized or simplified designs (Figure S22). Significantly, malic acid is an essential chemical component in the TCA cycle. These organic acids can be synthesized by chemical evolution experiments and used for prebiotic peptide synthesis.43−45 Therefore, the primitive DPBB may have interacted with metabolites in early life and facilitated a certain catalytic activity like its modern descendants (Figure S1A,E).

There’s more on this in the discussion too.


I was able to download the article. If anyone would like a copy, please shoot me a direct message with your email address.

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