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New peptide-RNA Theory of life

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New peptide-RNA Theory of life
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CollecemallPosts: 347Joined: Tue Aug 19, 2014 1:53 am

Post New peptide-RNA Theory of life

Anyone seen this? I haven't had time to track down the studies and put my feeble brain to them but any time I see this stuff I find it interesting.

http://news.unchealthcare.org/news/2017 ... rdial-muck
"Every man is a creature of the age in which he lives, and few are able to raise themselves above the ideas of their time."
“Those who can make you believe absurdities, can make you commit atrocities.” ~~Voltaire
Sun Nov 05, 2017 4:36 am
RumraketUser avatarPosts: 1174Joined: Fri Jun 25, 2010 7:49 am Gender: Male

Post Re: New peptide-RNA Theory of life

Yes I've seen it. I don't really have the qualifications to assess the merits of their calculations. First of all I have to agree that there can't have been a pure RNA world. But that is not a statement I derive from some computational approach, but simply because when it comes to prebiotic chemistry, amino acids seem to be abundant, while making RNA is very difficult. So I agree that in so far as something exists that can make RNA, there's going to be amino acids around and they probably help. So RNA and peptides probably coevolved and co-invented coded protein translation in some sense.

But there's something strange about the solution they propose. And I have my own thoughts about it.
There are some particular proteins, which are enzymes, involved in the translation system. These enzymes, called aminoacyl-tRNA-synthetases (aaRS), have some particular sequence of amino acids.

There are two classes of these enzymes, meaning two families of proteins, with about 10 members in each class.
So ten enzymes in Class-I aminoactyl-tRNA-synthetases.
and another ten enzymes in Class-II aminoacyl-tRNA-synthetases.

These enzymes are responsible for attaching amino acids to transfer-RNA (tRNA).

Both classes have a common ancestor molecule from which each class evolved. Meaning Class-I has a common ancestor aaRS molecule, and class-II has a common ancestor aaRS.

Here's where it gets interesting.

Imagine the DNA strand that contains the coding region that codes for the class-I ancestral aaRS.
Let's just pretend it has this short DNA sequence to make it simple:
3'-AGACTTGACTGAC-5'

The class-II aaRS ancestor, it has been found out, can be encoded by the complementary strand. Think about that for a moment.

So class-I has this DNA sequence:
3'-AGACTTGACTGAC-5'

And the complementary strand would be:
5'-TCTGAACTGACTG-3'

So they are each other's complementary DNA strands:
3'-AGACTTGACTGAC-5'
5'-TCTGAACTGACTG-3'

So the one strand codes for the common ancestor of Class-I, and the opposite strand codes for the common ancestor of Class-II.

Amazing. Absolutely amazing. That two DNA strands complementary to each other, happen to code for the same type of enzymes, each of which can charge tRNA with 10 different amino acids.

But now it gets weird. The problem is this: How would these enzymes, which are made of amino acids, be made if there is no translation system to make them? Remember, they are enzymes made of amino acids, which means the translation system has to be able correctly charge tRNA with amino acids, which is what the aaRS enzymes do.

So the primordial translation system would only have been able to encode proteins that contain either two amino acids (one from each class), or maybe it would have to be random. There could be a third option which I will go into below. But if it was random, how could it reliably make aaRS enzymes?

The only solution, it seems to me, is that it wasn't actually random. As in random with an equiprobably distribution.

My own suspicion is that the primordial aaRS enzymes had preferences. So while they were promiscuous and could charge tRNA with several different amino acids, some chemical reactions were favored over others. Perhaps the solution, at least in part, is that some amino acids were simply more abundant, which meant whatever proteins were made by the primordial translation system had a higher frequency of those amino acids.
Another factor that probably played into primordial translation would have been the chemical preference. Perhaps some amino acids simply associated more frequently with the two ancestors of aaRS.

So while primordial translation was stochastic in nature, it was probably highly biased in the distribution and frequency of certain amino acids. And, I speculate, this bias was towards the types and the distribution of amino acids that was significantly more likely to result in asRS-like protein enzymes.

In this respect it seems to me a great "help" to this speculative system, that in so far as you have the ancestor of either class-I or class-II aaRS encoded in DNA (or RNA), you will necessarily also have the other, as they are encoded by the opposite strand. So basically, either ancestor only has to emerge once, and you will automatically have the other one too.

I would very much like to see some work on the "preferences" of these ancestral enzymes. I know they have been resurrected using ancestral sequence reconstruction, and found to work, and that they were promiscuous. But I wonder about the nature of the translation system into which they were embedded. My own conjecture here would predict that the ancestral aaRS classes would both have a higher abundance of so-called "primordial" amino acids, and that they would also show a preference for charging tRNA with the amino acids necessary for their own synthesis.
"Nullius in verba" - Take nobody's word for it. https://en.wikipedia.org/wiki/Nullius_in_verba
Extraordinary claims require extraordinary evidence.
Sun Nov 05, 2017 12:25 pm
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