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What would be the drawbacks of a genetic code with 6 nucleotides instead of 4, but each amino acid could be coded with 2 base pairs instead of 3 (so the genome could be 33% shorter)? (lemmy.world)
submitted 3 days ago* (last edited 3 days ago) by AbouBenAdhem@lemmy.world to c/askscience@lemmy.world
17 comments fedilink hide all child comments
 

Say, in the context of finding microbial life on Mars (i.e., organisms that evolved from the start with six nucleotides, not just taking current terrestrial organisms and swapping out the nucleic acids and ribosomes).

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[–] frongt@lemmy.zip 15 points 3 days ago (1 children)

Sounds like a greater risk of transcription errors. It's possible for RNA to be transcribed into erroneous DNA. Normal pairs are AT and GC. But if something goes wrong, you can see adenosine paired with cytosine, for example. Best case, it produces junk. Worst case, it's cancer.

Now instead of one to one match, it's a possible two to one. If a nucleotide gets damaged, but is still a valid combination, you can't tell it was damaged. That's a problem.

Additionally, you no longer have matching strands of DNA. Right now, if you have one strand, it encodes the same information as the other. Not only can you read either strand, but you can take two strands and rebuild them into two whole new strands. But if each nucleotide corresponds to two others, when you separate the strands, you don't have enough information to rebuild it. Nor can you necessarily build the protein you wanted, because you don't have that full information any more. A sequence doesn't have a corresponding sequence on the other strand.

[–] AbouBenAdhem@lemmy.world 6 points 3 days ago* (last edited 3 days ago) (2 children)

But if each nucleotide corresponds to two others

No, each nucleotide would still pair with one other—there would just be an additional possible purine/pyrimidine pair (i.e., A:T + G:C + X:Y).

As for transcription errors, you’d only have 36 potential codons (6^2^) instead of 64 (4^3^), so it seems like the process could be more robust.

[–] BussyCat@lemmy.world 1 points 2 days ago

Translation errors seem like biggest problem, with the current system you have some amount of redundancy where sometimes a single point mutation still gives the same codon but you would lose that with less base pairs per codon

[–] frongt@lemmy.zip 7 points 3 days ago

Oh, I misunderstood. Yeah, in that case there isn't such an increase in risk of transcription errors. I think it's still increased slightly, because each nucleotide could become one of five others instead of one of three others, so it might still be easier for a stray high-energy particle to cause a conversion. Depends on how they're formed.

But, I'm not any kind of biologist.

[–] arthur@lemmy.eco.br 4 points 2 days ago

Although the information could be the same, genetics happen in a "chemistry media" instead of a digital one, and most of the functionality of proteins is related to its physical structure, so I'm not sure if DNA could generate similar proteins with a different DNA encoding scheme.

[–] phdepressed@sh.itjust.works 8 points 3 days ago (1 children)

  1. Proteins aren't the only end product of DNA. RNA is also important. See point 2.

  2. Large parts of regulation are through structural elements at both DNA and RNA level that shortened genes would disrupt.

  3. While your rate of error per base wouldn't be higher. The chance of that error mattering is higher. With 3 base codons the third is a "wobble base" that if changed will still likely code for the correct product or at least a similar one. Whereas with 2 base codons there is no wobble, any base change is more likely to result in some functional difference.

  4. evolution is rarely concerned with being the most efficient but rather what works. Things are janky and a lot of the complexity of life stems from that jankiness.

[–] BussyCat@lemmy.world 1 points 2 days ago

Came to the comment section for your 3rd point, even with the “wobble” we have several single point mutations that are disastrous having only 2 BP per codon would be much worse and if anything I would assume the better medium would have more BP per codon with more redundancy

[–] WalrusDragonOnABike@reddthat.com 10 points 3 days ago (2 children)

With three, if two (at least if its the first two) are correct, you still have a decent chance of still making the same thing. If you only have 2 BPs, any mistake is very likely to change the protein produced.

[–] AbouBenAdhem@lemmy.world 2 points 3 days ago* (last edited 3 days ago) (1 children)

But wouldn’t that be offset by the potential errors avoided in reducing the size of the genome by a third?

[–] verdi@feddit.org 0 points 3 days ago (1 children)

No

[–] thebestaquaman@lemmy.world 2 points 3 days ago (1 children)

How so? If you have a certain probability of an erroneous match on each base pair, the probability of a successful transcription of a gene is just a binomial probability depending on the length of the gene and the probability of error on each base pair. If you reduce the length of the gene, you reduce the total probability of error.

[–] verdi@feddit.org 2 points 3 days ago (1 children)

Not all base pairs contribute equally to the result given the code is degenerate, by decreasing the codon size you're increasing the error probability regardless of gene size by reducing degeneracy. Since proteins would still functionally have the same number of aminoacids but now the signal to noise ratio of transcription would have a greater per aminoacid effect.

[–] thebestaquaman@lemmy.world 1 points 2 days ago (1 children)

the code is degenerate

I'm no biologist (I've only had some basic biochemistry), could you elaborate on this? As far as I can recall, each codon encodes a specific amino acid, which means that a single base pair being mistranscripted leads to the wrong amino acid, potentially breaking the protein.

the signal to noise ratio of transcription would have a greater per amino acid effect

Not sure I get what you mean here either? The difference is in whether each base(-pair) encodes a binary or a ternary bit. Lossless compression redundant data (i.e. what you do when moving from a binary to ternary format) doesn't change the signal-to-noise ratio.

[–] threelonmusketeers@sh.itjust.works 1 points 2 days ago

each codon encodes a specific amino acid

There are 4 × 4 × 4 = 64 possible codons, but only 20(-ish) amino acids. This leaves quite a few spares for some built-in redundancy.

For example, UCU, UCC, UCA, and UCG all code for Serine. The third letter can mutate or be mistranscribed, and still produce an identical protein.

[–] Donjuanme@lemmy.world 2 points 3 days ago

This was my first thought as well,

[–] notsosure@sh.itjust.works 4 points 3 days ago (1 children)

You seem to suggest a shorter genome is in all cases desirable. It certainly isn’t in e.g. higher organisms. With the gene as the corner stone of evolution, shorter genes are probably more advantageous.

[–] AbouBenAdhem@lemmy.world 3 points 3 days ago

Not shorter in the sense of less information—shorter in the sense of encoding the same proteins using fewer base pairs.