This seems interesting - re: RNA World and OOL

The title of the news piece is provocative, and the paper itself has the potential to challenge a lot of what we think we know about the OOL and the RNA World. Enjoy!

https://www.science.org/content/article/scientists-stunned-fundamentally-new-way-life-produces-dna

The Abstract:

Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo–electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis.

We’ve known for awhile that proteins can mimic structural features in RNA. This study takes the concept in new directions that are at the very least thought-provoking.

The paper:

https://www.science.org/doi/10.1126/science.aed1656

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Very interesting. Not sure I understand what they mean. Are the amino acids in the active site of Drt3b functioning as a sort of “template” for the repeating AC single-stranded DNA? This is the sort of thing I think needs a drawing/picture to clarify.

Edit: Ah yes that is what they are saying in the news article. Active site amino acids are quite literally functioning as a template for the DNA strand.

This is very close to a kind of simple reverse self-translation.

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I didn’t notice this when you first posted.

Abstract
Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo–electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis.

I’ll look at it tomorrow and hope there are some stats I might understand. :wink:

So, Drt3a makes one DNA strand, called poly(GT), by copying a repeating ACACAC sequence found in the RNA.

Drt3b then makes the complementary strand, poly(AC), without using a nucleic-acid template. Instead, features of the protein active site itself force the enzyme to alternate A and C in the correct pattern, while the strand is also protein-primed.

What this shows is that some enzymes can make DNA—specifically, a simple alternating dinucleotide repeat—in a way scientists did not previously know about.

However, the mechanism presupposes a thick layer of evolved biochemical complexity. A sophisticated, extant molecular machine inside living bacteria is evidentially remote from the question of how the first self-replicating systems arose before such machinery existed.

While the discovery expands the known chemistry of polymerases, it doesn’t solve the transition from nonliving chemistry to integrated, self-maintaining, information-bearing cells.

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All true.

It does lend another small piece of support for the interesting possibility that the long speculated mechanism of a direct templating interaction between RNA and protein sequence (conjectured to have seeded the origin of the translation system and the genetic code), is actually possible.

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Another small step, but wouldn’t it be fun if life arose out of DiRTs? :wink:

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All true.

It does lend another small piece of support for the interesting possibility that the long speculated mechanism of a direct templating interaction between RNA and protein sequence (conjectured to have seeded the origin of the translation system and the genetic code), is actually possible.

At the category level? Sure, the paper modestly broadens what biology has shown to be chemically possible. In that abstract sense, one might say it slightly weakens overly rigid assumptions that sequence-specific nucleotide synthesis must always be directed by a nucleic-acid template alone. But that is still a long way from supporting the sort of direct RNA–protein sequence interaction you mention as a possible seedbed for translation and the genetic code.

Hi John, thanks for joining the conversation. Speaking only for myself, I think the idea that an enzyme can serve as a sort of template for new DNA synthesis is pretty interesting. In the context of OOL research, it has the potential to stand some models and hypotheses on their heads, so to speak.

Well, since the origins of self-replicating systems likely involved RNA and not DNA, this probably can go without saying. However, there are rather new and interesting directions that OOL research might take in light of this report. Mikkel has mentioned one. I guess the interesting idea I get from this is that it may be possible for catalysts (non-protein catalysts, at that) to synthesize non-random oligomers. There is a possible conceptual connection in this idea with a suggestion made by Maizels and Weiner more than 30 years ago (Proc. Nati. Acad. Sci. USA Vol. 91, pp. 6729-6734, July 1994).

But of course, the key contribution of this important finding is that it will generate new hypotheses to test.

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@Rumraket , I think this is quite a ways away from an enzyme synthesizing its own mRNA, or even a template for translation. I am more excited by the possibility that nucleotidyl transferase-like catalysts may be able to synthesize a non-random set of oligonucleotides in a de novo fashion. That would be pretty cool.

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I could be wrong here, but get the sense that you think it’s really important to state this. If so, can you elaborate on why?

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@Art seems to be asking how I locate this finding within origin-of-life discussions, while @Rumraket is asking why I felt the need to draw that limiting line in the first place. I think both of those can be answered together.

I do think it is important to state that limitation, though not because I find the discovery uninteresting. Quite the opposite—I think it is genuinely fascinating, and I would regret giving any other impression. I agree with @Art that it “has the potential to stand some models and hypotheses on their heads,” and that sort of result can be very fruitful for science. At the category level, this does broaden what biology has shown to be chemically possible, and in that respect it may well stimulate new hypotheses in origin-of-life research.

My caution is simply about a particular inferential step. There is a large distance between this discovery and saying, “This lends support to a proposed early mechanism of direct RNA-protein sequence interaction involved in the origin of translation and the genetic code.” Those are not the same claim, and I think it matters to keep them distinct.

I say that because the paper describes a highly specialized extant molecular system, operating in living bacteria, and producing a low-complexity alternating dinucleotide repeat. That alone is enough to make it very interesting. But the origin of translation and the origin of the genetic code would seem to require something much more specific and much more ambitious: some account of how sequence relations between nucleic acids and proteins could become stable, meaningful, heritable, and functionally integrated within a larger self-maintaining system. This finding does not yet get us there. It broadens the space of analogy, and perhaps of conceptual possibility, but that still seems to me a long way from positive support for a seedbed of translation or coding.

So my reason for stressing that point was mainly methodological. In origin-of-life discussions, people often move too quickly from “apparently this is possible” to “I bet this is what happened.” I just think possible and actual should be kept separate. The former is entirely fair; the latter requires a much tighter correspondence between the phenomenon observed and the explanatory task in view.

So, speaking only for myself, I would put it this way: The discovery may be suggestive in a broad heuristic sense, and it may indeed inspire worthwhile new hypotheses about non-random oligomer formation or other prebiotic possibilities. Even so, as things stand, I think it is better understood as an expansion of the known landscape of biochemical mechanism than as meaningful evidential support for any specific model of the origin of translation or the genetic code.

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