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As is often the case with titles like this, the answer is that all life doesn't use the same 20 amino acids. For example: Akaogi et al. (2006) Role of non-pro

As is often the case with titles like this, the answer is that all life doesn't use the same 20 amino acids. For example: Akaogi et al. (2006) Role of non-protein amino acid L-canavanine in autoimmunity. Autoimmun Rev. 5(6):429-35. https://www.ncbi.nlm.nih.gov/pubmed/16890899 https://www.ncbi.nlm.nih.gov/pubmed/16890899 Nunn et al. (2010) Toxicity of non-protein amino acids to humans and domestic animals. Nat Prod Commun. 5(3):485-504. https://www.ncbi.nlm.nih.gov/pubmed/20420333 https://www.ncbi.nlm.nih.gov/pubmed/20420333

respinal 7y ago
I don’t see your point. Could you elaborate some more?
- mirimir 7y ago
  Please see my reply to Sharlin.
Sharlin 7y ago
> non-protein The title, of course, refers to the 20 proteinogenic amino acids.
- mirimir 7y ago
  Except that some sorts of life, such as some sprouting plants, do incorporate those "non-proteinogenic" amino acids into proteins. Which then screw up animals that eat them. Because they, in turn, also incorporate them into proteins. And those tweaked proteins elicit immune responses, because they weren't present during immune system development. And some of that immune response cross reacts with the normal host proteins. So you get autoimmune disease.
  - Catsandkites 7y ago
    That makes lots of sense. Do you have any examples of sprouting plants that so this? I'm guessing ones we consider poisonous?
  - afarrell 7y ago
    woah that sounds interesting. Do you have some links to videos or articles which talk more about this?
  - krick 7y ago
    While somewhat true, essentially the question of 20 amino acids still holds and trying to answer it is still meaningful (and in the same way article addresses it). Consider this: how old are these plant insecticides (or whatever they are)? Maybe some 150 mln years old? (I'm only assuming, of course, but it seems like a plausible assumption.) Well, the life on Earth itself is about 3.5 bln years old, and as far as we know it mostly utilizes the same set of 20 proteinogenic amino acids it did back then. It is only natural that given time, constantly mutating and evolving organisms would eventually learn to produce whatever amino acids possible, if it is useful (and being insecticide is obviously useful, if you are a plant, and for reasons you mention yourself it is natural to use as insecticide some compound that is not normally utilized in the other organism). The question is how did it occur that these amino acids weren't present during immune system development? Why it was always the same 20?
    - respinal 7y ago
      Yup and those shared articles don’t make a good counterargument or point..They are off topic. A better article(s) would have addressed the point of the number of amino acids...
  - atombender 7y ago
    Are you talking about human autoimmune disease? If so, do you have an examples and/or links to papers? I've read a lot about autoimmune diseases, and this hypothesis is not something I've ever heard of. Edit: I see your earlier comment has some links. Thanks.
    - mirimir 7y ago
      Yeah, some sprouts are ~dangerous. That is, if you're unlucky to have an immune system that got self-deselected in the "wrong" way.
  - Reelin 7y ago
    This turned out to be an incredibly interesting (and educational) diversion! It seems these amino acids aren't typically incorporated, but rather appear to serve as defense (https://www.ncbi.nlm.nih.gov/pubmed/21529857 https://www.ncbi.nlm.nih.gov/pubmed/21529857) and signaling molecules (https://www.ncbi.nlm.nih.gov/pubmed/28218981 https://www.ncbi.nlm.nih.gov/pubmed/28218981). Apparently humans do that sometimes as well (https://www.ncbi.nlm.nih.gov/pubmed/18828673 https://www.ncbi.nlm.nih.gov/pubmed/18828673). Sometimes the insects even end up using the toxic compound (in the linked example the non-protein amino acid L-DOPA) for their own purposes (https://www.ncbi.nlm.nih.gov/pubmed/27006098 https://www.ncbi.nlm.nih.gov/pubmed/27006098), which I find quite amusing. More than just being eaten, apparently L-DOPA is released into the environment at an impressive rate in some cases (https://www.ncbi.nlm.nih.gov/pubmed/24598311 https://www.ncbi.nlm.nih.gov/pubmed/24598311).
    - mirimir 7y ago
      Yes, I was wrong about that. Alfalfa seeds and sprouts don't themselves use canavanine in their proteins. And yes, plants do seriously get into chemical warfare.
- Reelin 7y ago
  Even then it's an oversimplification. Selenocysteine (https://en.wikipedia.org/wiki/Selenocysteine https://en.wikipedia.org/wiki/Selenocysteine) occurs in proteins and is quite widespread. "Selenocysteine: the 21st amino acid." (https://www.ncbi.nlm.nih.gov/pubmed/1828528 https://www.ncbi.nlm.nih.gov/pubmed/1828528) It shows up in humans too (https://www.ncbi.nlm.nih.gov/pubmed/24194593 https://www.ncbi.nlm.nih.gov/pubmed/24194593). Pyrrolysine (https://en.wikipedia.org/wiki/Pyrrolysine https://en.wikipedia.org/wiki/Pyrrolysine) occurs in proteins in archaea and bacteria. "A new UAG-encoded residue in the structure of a methanogen methyltransferase." (https://www.ncbi.nlm.nih.gov/pubmed/12029132 https://www.ncbi.nlm.nih.gov/pubmed/12029132)
  - dmix 7y ago
    Also wasn't the answer always going to be they simply out-competed the other amino acids for that particular role? The research question is why they beat out similarly structured acids to become the consistently dominant ones in life. So in that context the fact they are so dominant is the key part of the question, not that they are the only ones capable?
    - wyattpeak 7y ago
      > wasn't the answer always going to be they simply out competed the other amino acids This is a tautological statement: the ones that still exist by definition are the ones which outcompeted the alternatives, because that's what outcompeting means. The question being addressed by the study is roughly "by what selection criterion did the survivors outcompete the others?"
      - dmix 7y ago
        Sure, my point is the fact that others are still capable of competing can always be assumed in a competitive environment. So in that context, where the question is inherently going to be why did these 20 amino acids out-compete the others, why bring up the fact others exist as a counter-point if the they aren't as dominant as the 20 primary ones? What's interesting is their dominance, not that they can play the game. I guess it's just nitpicking the headline and is not particularly relevant to the article or the research question (as the OP admitted).
appleflaxen 7y ago
Super interesting example! Nevertheless, even the organisms referenced in these papers don't have these amino acids in their DNA structure, and the meaning of the linked research really isn't affected by the point you are raising. Perhaps "non-proteinogenic" is a poor choice, or not exactly correct, but readers generally understand what is meant. It's a bit like responding to an article about "why do all pendulums keep the same frequency as they lose energy" with "but they are neglecting relativity!". It just isn't really relevant to the research question, which is "why are some amino acids present in the DNA code, and why is there consistency across species".
- mirimir 7y ago
  I'm not sure what you mean by "don't have these amino acids in their DNA structure". There are 64 codons that code for amino acids and start/stop signals. But there are only 20 common amino acids, so multiple codons typically code for the same amino acid. However, just exactly what happens depends on the set of tRNAs that are being expressed. Plus the enzymes that catalyze attachment of amino acids to tRNAs. That is, what's in the DNA is codons, and what amino acids get incorporated depends on tRNAs etc, plus what amino acids are around (synthesized or ingested). Anyway, I get that I was being a little pedantic. But in the paper referenced by TFA, I see that they studied three nonproteinaceous amino acids: ornithine, 2,4-diaminobutyric acid, and 2,3-diaminopropionic acid. Canavanine is much closer to arginine, with a methylene replaced with an ether bridge. I wonder how well it would have polymerized. 0) https://www.pnas.org/content/116/33/16338 https://www.pnas.org/content/116/33/16338 Edit: Upon reflection, "there are just 20 proteinaceous amino acids" and "AS/400 is a database" are ~similar simplifications.
dekhn 7y ago
articles like this are really talking about a standard that covers 99.9% of cases, not some sort of universal absolute. We know of many special cases which violate the standard (to the extent that 'life' has 'standards') but it's not clear how valuable it is to point out the exceptions here.

respinal 7y ago

I don’t see your point. Could you elaborate some more?

mirimir 7y ago
Please see my reply to Sharlin.

Sharlin 7y ago

> non-protein The title, of course, refers to the 20 proteinogenic amino acids.

mirimir 7y ago
Except that some sorts of life, such as some sprouting plants, do incorporate those "non-proteinogenic" amino acids into proteins. Which then screw up animals that eat them. Because they, in turn, also incorporate them into proteins. And those tweaked proteins elicit immune responses, because they weren't present during immune system development. And some of that immune response cross reacts with the normal host proteins. So you get autoimmune disease.
- Catsandkites 7y ago
  That makes lots of sense. Do you have any examples of sprouting plants that so this? I'm guessing ones we consider poisonous?
- afarrell 7y ago
  woah that sounds interesting. Do you have some links to videos or articles which talk more about this?
- krick 7y ago
  While somewhat true, essentially the question of 20 amino acids still holds and trying to answer it is still meaningful (and in the same way article addresses it). Consider this: how old are these plant insecticides (or whatever they are)? Maybe some 150 mln years old? (I'm only assuming, of course, but it seems like a plausible assumption.) Well, the life on Earth itself is about 3.5 bln years old, and as far as we know it mostly utilizes the same set of 20 proteinogenic amino acids it did back then. It is only natural that given time, constantly mutating and evolving organisms would eventually learn to produce whatever amino acids possible, if it is useful (and being insecticide is obviously useful, if you are a plant, and for reasons you mention yourself it is natural to use as insecticide some compound that is not normally utilized in the other organism). The question is how did it occur that these amino acids weren't present during immune system development? Why it was always the same 20?
  - respinal 7y ago
    Yup and those shared articles don’t make a good counterargument or point..They are off topic. A better article(s) would have addressed the point of the number of amino acids...
- atombender 7y ago
  Are you talking about human autoimmune disease? If so, do you have an examples and/or links to papers? I've read a lot about autoimmune diseases, and this hypothesis is not something I've ever heard of. Edit: I see your earlier comment has some links. Thanks.
  - mirimir 7y ago
    Yeah, some sprouts are ~dangerous. That is, if you're unlucky to have an immune system that got self-deselected in the "wrong" way.
- Reelin 7y ago
  This turned out to be an incredibly interesting (and educational) diversion! It seems these amino acids aren't typically incorporated, but rather appear to serve as defense (https://www.ncbi.nlm.nih.gov/pubmed/21529857 https://www.ncbi.nlm.nih.gov/pubmed/21529857) and signaling molecules (https://www.ncbi.nlm.nih.gov/pubmed/28218981 https://www.ncbi.nlm.nih.gov/pubmed/28218981). Apparently humans do that sometimes as well (https://www.ncbi.nlm.nih.gov/pubmed/18828673 https://www.ncbi.nlm.nih.gov/pubmed/18828673). Sometimes the insects even end up using the toxic compound (in the linked example the non-protein amino acid L-DOPA) for their own purposes (https://www.ncbi.nlm.nih.gov/pubmed/27006098 https://www.ncbi.nlm.nih.gov/pubmed/27006098), which I find quite amusing. More than just being eaten, apparently L-DOPA is released into the environment at an impressive rate in some cases (https://www.ncbi.nlm.nih.gov/pubmed/24598311 https://www.ncbi.nlm.nih.gov/pubmed/24598311).
  - mirimir 7y ago
    Yes, I was wrong about that. Alfalfa seeds and sprouts don't themselves use canavanine in their proteins. And yes, plants do seriously get into chemical warfare.
Reelin 7y ago
Even then it's an oversimplification. Selenocysteine (https://en.wikipedia.org/wiki/Selenocysteine https://en.wikipedia.org/wiki/Selenocysteine) occurs in proteins and is quite widespread. "Selenocysteine: the 21st amino acid." (https://www.ncbi.nlm.nih.gov/pubmed/1828528 https://www.ncbi.nlm.nih.gov/pubmed/1828528) It shows up in humans too (https://www.ncbi.nlm.nih.gov/pubmed/24194593 https://www.ncbi.nlm.nih.gov/pubmed/24194593). Pyrrolysine (https://en.wikipedia.org/wiki/Pyrrolysine https://en.wikipedia.org/wiki/Pyrrolysine) occurs in proteins in archaea and bacteria. "A new UAG-encoded residue in the structure of a methanogen methyltransferase." (https://www.ncbi.nlm.nih.gov/pubmed/12029132 https://www.ncbi.nlm.nih.gov/pubmed/12029132)
- dmix 7y ago
  Also wasn't the answer always going to be they simply out-competed the other amino acids for that particular role? The research question is why they beat out similarly structured acids to become the consistently dominant ones in life. So in that context the fact they are so dominant is the key part of the question, not that they are the only ones capable?
  - wyattpeak 7y ago
    > wasn't the answer always going to be they simply out competed the other amino acids This is a tautological statement: the ones that still exist by definition are the ones which outcompeted the alternatives, because that's what outcompeting means. The question being addressed by the study is roughly "by what selection criterion did the survivors outcompete the others?"
    - dmix 7y ago
      Sure, my point is the fact that others are still capable of competing can always be assumed in a competitive environment. So in that context, where the question is inherently going to be why did these 20 amino acids out-compete the others, why bring up the fact others exist as a counter-point if the they aren't as dominant as the 20 primary ones? What's interesting is their dominance, not that they can play the game. I guess it's just nitpicking the headline and is not particularly relevant to the article or the research question (as the OP admitted).

appleflaxen 7y ago

Super interesting example! Nevertheless, even the organisms referenced in these papers don't have these amino acids in their DNA structure, and the meaning of the linked research really isn't affected by the point you are raising. Perhaps "non-proteinogenic" is a poor choice, or not exactly correct, but readers generally understand what is meant. It's a bit like responding to an article about "why do all pendulums keep the same frequency as they lose energy" with "but they are neglecting relativity!". It just isn't really relevant to the research question, which is "why are some amino acids present in the DNA code, and why is there consistency across species".

mirimir 7y ago
I'm not sure what you mean by "don't have these amino acids in their DNA structure". There are 64 codons that code for amino acids and start/stop signals. But there are only 20 common amino acids, so multiple codons typically code for the same amino acid. However, just exactly what happens depends on the set of tRNAs that are being expressed. Plus the enzymes that catalyze attachment of amino acids to tRNAs. That is, what's in the DNA is codons, and what amino acids get incorporated depends on tRNAs etc, plus what amino acids are around (synthesized or ingested). Anyway, I get that I was being a little pedantic. But in the paper referenced by TFA, I see that they studied three nonproteinaceous amino acids: ornithine, 2,4-diaminobutyric acid, and 2,3-diaminopropionic acid. Canavanine is much closer to arginine, with a methylene replaced with an ether bridge. I wonder how well it would have polymerized. 0) https://www.pnas.org/content/116/33/16338 https://www.pnas.org/content/116/33/16338 Edit: Upon reflection, "there are just 20 proteinaceous amino acids" and "AS/400 is a database" are ~similar simplifications.

dekhn 7y ago

articles like this are really talking about a standard that covers 99.9% of cases, not some sort of universal absolute. We know of many special cases which violate the standard (to the extent that 'life' has 'standards') but it's not clear how valuable it is to point out the exceptions here.