6 ms·

> 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).

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).