3 ms·

Variants on the genetic code are known to exist: https://en.wikipedia.org/wiki/Genetic_code#Alternative_genetic_codes https://en.wikipedia.org/wiki/Genetic_code

Variants on the genetic code are known to exist: https://en.wikipedia.org/wiki/Genetic_code#Alternative_genetic_codes https://en.wikipedia.org/wiki/Genetic_code#Alternative_genet... I don't think there are any known to be radically different. Note that it's possible that life arose several times but only the lineage of that one cell survived, perhaps? In any case, it's not like there's been no variation. Now, here's a mystery (AFAIK): Just where is the genetic code stored? I seem to recall reading an article a while back about how while this seems like an easy question it's actually not known. I can't seem to find it at the moment, though. Anyone know more about this?

fabian2k 7y ago
The mapping between base triplets and amino acids is encoded in the tRNAs. And the tRNAs themselves are of course again encoded in the DNA sequences used to produce them.
- Sniffnoy 7y ago
  I mean, that's the obvious answer, but I recall reading a thing about why it wasn't actually that simple, how swapping out the tRNAs didn't actually have the effect you would expect. Like, obviously the anticodons match the codons, no problem there, but there was some complicated confusing thing about how the rest of the tRNA matched the amino acid. Trying to find it. Hoping someone knows what I'm talking about.
  - learnstats2 7y ago
    Presumably, biology has a lot of safeguarding to prevent modified transfer-RNA from being functional. In terms of potential errors in gene expression, the genetic code is rarely discussed as a potential source of error.
    - Reelin 7y ago
      Not to be "that guy", but actually, it is. (https://elifesciences.org/articles/09945 https://elifesciences.org/articles/09945) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026258/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026258/) It's just difficult to study for various technical reasons related to how we sequence it. Sometime the mistranslation is even intentional! (https://www.ncbi.nlm.nih.gov/pubmed/25220850 https://www.ncbi.nlm.nih.gov/pubmed/25220850) As you mentioned though, there are also quite a few safeguards. * tRNA synthetase example: https://www.ncbi.nlm.nih.gov/pubmed/27226603 https://www.ncbi.nlm.nih.gov/pubmed/27226603 * trans-editing factor example: https://www.ncbi.nlm.nih.gov/pubmed/28737471 https://www.ncbi.nlm.nih.gov/pubmed/28737471 Damaged tRNA is even repaired (a bit, sometimes). (https://www.ncbi.nlm.nih.gov/pubmed/28901837 https://www.ncbi.nlm.nih.gov/pubmed/28901837) From an interesting (2018) review of tRNA in general (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103721/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103721/): > Surprisingly, a perfect proteome is not a pre-requisite for cellular viability even in the context of human cells. Lant et al. demonstrated that a single tRNA mutant can lead to significant mistranslation in human cells [17]. This was accomplished by expressing an Ala accepting tRNAPro G3:U70 variant in HEK 293 cells. The authors visualized a rate of ~ 3% mistranslation using a novel green fluorescent protein (D129P) reporter that fluoresces in response to mistranslation at proline codons. In contrast to previous studies in yeast [18], human cells in culture did not mount a detectable heat-shock response and tolerated the mistranslation without apparent impact on cell viability.
      - klmr 7y ago
        The eLife paper you link to discusses errors in RNA synthesis (transcription), not in tRNA-dependent protein synthesis (translation). The abstract mentions “translation”, but only as an amplifier of transcription errors: each mRNA transcript is translated into proteins thousandfold, so every error in a single mRNA molecule will be present in thousands of protein molecules. Translation errors also exist, and some people hypothesise that there is selective pressure on protein-coding genes to reduce this source of errors by selecting codons in a way that reduces the error rate (potentially by slowing down the polymerase). This results in something known as “codon bias” but so far there is no good evidence that codon bias has an actual effect on error rate (it does have an effect on correct protein folding), or is selected for (http://dx.doi.org/10.7554/eLife.27344 http://dx.doi.org/10.7554/eLife.27344, http://dx.doi.org/10.1371/journal.pgen.1006024 http://dx.doi.org/10.1371/journal.pgen.1006024).
- twic 7y ago
  I'd say it's encoded in the combination of the tRNAs and the aminoacyl-tRNA synthetases, which load the appropriate amino acids on to the tRNAs. There's nothing in the tRNAs themselves which picks out a specific amino acid - that happens because the synthetases recognise specific amino acids and specific tRNAs. The synthetases are also encoded in DNA, so the fundamental point, that the code is encoded in DNA, stands.
  - Sniffnoy 7y ago
    Aha! Thanks, hopefully with that search term I can maybe find what I was thinking of. :)

fabian2k 7y ago

The mapping between base triplets and amino acids is encoded in the tRNAs. And the tRNAs themselves are of course again encoded in the DNA sequences used to produce them.

Sniffnoy 7y ago
I mean, that's the obvious answer, but I recall reading a thing about why it wasn't actually that simple, how swapping out the tRNAs didn't actually have the effect you would expect. Like, obviously the anticodons match the codons, no problem there, but there was some complicated confusing thing about how the rest of the tRNA matched the amino acid. Trying to find it. Hoping someone knows what I'm talking about.
- learnstats2 7y ago
  Presumably, biology has a lot of safeguarding to prevent modified transfer-RNA from being functional. In terms of potential errors in gene expression, the genetic code is rarely discussed as a potential source of error.
  - Reelin 7y ago
    Not to be "that guy", but actually, it is. (https://elifesciences.org/articles/09945 https://elifesciences.org/articles/09945) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026258/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026258/) It's just difficult to study for various technical reasons related to how we sequence it. Sometime the mistranslation is even intentional! (https://www.ncbi.nlm.nih.gov/pubmed/25220850 https://www.ncbi.nlm.nih.gov/pubmed/25220850) As you mentioned though, there are also quite a few safeguards. * tRNA synthetase example: https://www.ncbi.nlm.nih.gov/pubmed/27226603 https://www.ncbi.nlm.nih.gov/pubmed/27226603 * trans-editing factor example: https://www.ncbi.nlm.nih.gov/pubmed/28737471 https://www.ncbi.nlm.nih.gov/pubmed/28737471 Damaged tRNA is even repaired (a bit, sometimes). (https://www.ncbi.nlm.nih.gov/pubmed/28901837 https://www.ncbi.nlm.nih.gov/pubmed/28901837) From an interesting (2018) review of tRNA in general (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103721/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103721/): > Surprisingly, a perfect proteome is not a pre-requisite for cellular viability even in the context of human cells. Lant et al. demonstrated that a single tRNA mutant can lead to significant mistranslation in human cells [17]. This was accomplished by expressing an Ala accepting tRNAPro G3:U70 variant in HEK 293 cells. The authors visualized a rate of ~ 3% mistranslation using a novel green fluorescent protein (D129P) reporter that fluoresces in response to mistranslation at proline codons. In contrast to previous studies in yeast [18], human cells in culture did not mount a detectable heat-shock response and tolerated the mistranslation without apparent impact on cell viability.
    - klmr 7y ago
      The eLife paper you link to discusses errors in RNA synthesis (transcription), not in tRNA-dependent protein synthesis (translation). The abstract mentions “translation”, but only as an amplifier of transcription errors: each mRNA transcript is translated into proteins thousandfold, so every error in a single mRNA molecule will be present in thousands of protein molecules. Translation errors also exist, and some people hypothesise that there is selective pressure on protein-coding genes to reduce this source of errors by selecting codons in a way that reduces the error rate (potentially by slowing down the polymerase). This results in something known as “codon bias” but so far there is no good evidence that codon bias has an actual effect on error rate (it does have an effect on correct protein folding), or is selected for (http://dx.doi.org/10.7554/eLife.27344 http://dx.doi.org/10.7554/eLife.27344, http://dx.doi.org/10.1371/journal.pgen.1006024 http://dx.doi.org/10.1371/journal.pgen.1006024).
twic 7y ago
I'd say it's encoded in the combination of the tRNAs and the aminoacyl-tRNA synthetases, which load the appropriate amino acids on to the tRNAs. There's nothing in the tRNAs themselves which picks out a specific amino acid - that happens because the synthetases recognise specific amino acids and specific tRNAs. The synthetases are also encoded in DNA, so the fundamental point, that the code is encoded in DNA, stands.
- Sniffnoy 7y ago
  Aha! Thanks, hopefully with that search term I can maybe find what I was thinking of. :)