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I know scientists have created synthetic bacteria, with a genetic code containing 6 letters instead of 4, with the aim of creating more complex proteins (using amino acids outside of the standard 20+2, the +2 being selanocysteine and pyrrolysine).

Are there any examples of already-known organisms that use more than the 20+2 commonly occurring amino acids, when translating from RNA codons to amino acid sequences using the ribosome? Post-translational modifications would not count, as the ribosome would not be directly responsible for the incorporation of the amino acid into the protein through that method.

Source: 22 proteinogenic amino acids
https://en.wikipedia.org/wiki/Proteinogenic_amino_acid

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    $\begingroup$ Are you asking only about proteinogenic amino acids? $\endgroup$
    – canadianer
    Dec 8, 2018 at 20:34
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    $\begingroup$ Yeah, I'm asking about proteinogenic amino acids. But if an amino acid is used (beyond the scope of the 22+2 common ones), that amino acid by definition should be "proteinogenic", right? $\endgroup$
    – wyc
    Dec 8, 2018 at 21:31
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    $\begingroup$ No, there are natural amino acids that are not used to build proteins. Ornithine, for example. $\endgroup$
    – canadianer
    Dec 9, 2018 at 4:04
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    $\begingroup$ New contributors are welcomed to SE Biology. Good questions aim for clarity, but inadvertant ambiguity is normal. Comments can suggest ways the poster can edit to remove such ambiguity: 1. State that the +2 refers to selanocysteine and pyrrolysine. 2. Reference, e.g. the Wikipedia page on the Genetic Code. 3. State, if that is what you mean by proteinogenic, that you are refering to amino acids incorporated into protein on the ribosome, and are not talking about post-translational modifications. (The answer is that no others are yet known — as your research should have indicated.) $\endgroup$
    – David
    Dec 10, 2018 at 15:43
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    $\begingroup$ Thanks @David, I've edited my post to reflect your suggestions. How should I mark this question as answered? $\endgroup$
    – wyc
    Dec 11, 2018 at 23:12

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At this point in time it appears that no known organisms use amino acids beyond the standard repertoire of the 20+2 common amino acids (the +2 being selanocysteine and pyrrolysine) to construct proteins directly from the ribosome. The extensive review provided by Ann Rev Genetics 2017 mentions only selanocysteine and pyrrolysine, and no other amino acids beyond that.

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Some methanogenic Archaea incorporate pyrrolysine in some of their proteins (methyltransferases).

Selenocysteine is another non-standard amino acid; proteins with selenocysteine are called selenoproteins. Both prokaryotes and eukaryotes produce selenoproteins.

Both these amino acids are incorporated at a reassigned UGA codon.

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    $\begingroup$ But aren't these the +2 of the question? $\endgroup$
    – David
    Dec 10, 2018 at 15:30
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    $\begingroup$ @David I thought the +2 are hydroxyproline and hydroxylysine but they are not considered proteinogenic because they are result due to PTM. $\endgroup$
    – WYSIWYG
    Dec 10, 2018 at 19:15
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    $\begingroup$ No. There are a host of post-translational modifications of amino acids. Those two are the ones coded by stop codons in certain contexts and — especially selenocysteine — have been well characterised, as you mention. $\endgroup$
    – David
    Dec 10, 2018 at 20:18

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