The AtlasAmino acidsWritten in a stop codon

PyrrolysinePyl · O

The twenty-second amino acid, which no human cell makes or uses, and which matters to us through the microbes that do.

Status Reference · not yet an episodeSources 21Reviewed October 2026

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Skeletal formula — every corner and every line end is a carbon, and the hydrogens on carbon are left implied.

Molecule · Pyl · 18 heavy atoms

Pyrrolysine

C₁₂H₂₁N₃O₃255.32 g/mol

The twenty-second amino acid, which no human cell makes or uses, and which matters to us through the microbes that do.

Built fromthe charted ones open their own entry

C12CarbonH21Hydrogen N3Nitrogen O3Oxygen

Codes: Pyl · O
Formula: C₁₂H₂₁N₃O₃
Molar mass: 255.32 g/mol
Systematic name: (2S)-2-amino-6-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrole-2-carbonyl]amino}hexanoic acid
Side chain: Lysine’s four-carbon chain, ending in an amide to a methylated pyrroline ring.
Class: Written in a stop codon
In the diet: Not used by humans
Carbon skeleton: Not applicable
Codons: UAG

Formula and mass computed from the structure.

In brief

What it is

Lysine with a ring bolted onto the end of its side chain: a methylated pyrroline carboxylate, joined by an amide bond to lysine’s ε-amino group ¹. It is the twenty-second amino acid of the genetic code, written as UAG ^2,3.

Why it matters

Archaea that make methane from methylamines cannot do it without pyrrolysine ¹. Some of them live in the human gut, where they consume trimethylamine, the compound the liver turns into TMAO ^4,5.

Where it runs short

There is no pyrrolysine deficiency in a person: the trait is confined to a few microbes, and in human genes UAG is only a stop ⁶.

Where it turns

Nor is there an excess. What varies between people is whether their gut carries the archaea that use it; the Methanomassiliicoccales turned up in microbiome data from eight countries, and are associated with older age ^4,7.

An amino acid humans do not use, which matters through the microbes that do.

The molecule

Pyrrolysine is two amino acids’ worth of atoms in one: lysine whose side-chain amino group is joined, through an amide bond, to a five-membered ring, a methylated pyrroline carboxylate ¹. At 255 daltons it is the largest of the twenty-two genetically encoded amino acids.

It was discovered by looking. In 2002 the structure of a methanogen’s monomethylamine methyltransferase, at 1.55 Å, showed electron density at the position of an in-frame UAG codon that matched none of the twenty-one known amino acids ³. In the same issue of Science, a second group showed that a tRNA with the anticodon CUA, which pairs with UAG, and a synthetase to charge it were encoded beside the methyltransferase genes ².

StereochemistryThree stereocentres. The lysine’s α-carbon is S, as in every L-amino acid but cysteine and selenocysteine; the two on the ring are both R, as the crystal structure that found it showed ³.

The genetic codePyrrolysine is written as UAG, which in our cells means stop. In the archaea that use it, UAG is read as pyrrolysine with or without a helping signal nearby, and in some of them every UAG is.

The 64 codons of the standard genetic code. Codons for pyrrolysine are marked.
1st ↓ 2nd →	U	C	A	G	3rd
U	UUUPhe	UCUSer	UAUTyr	UGUCys	U
	UUCPhe	UCCSer	UACTyr	UGCCys	C
	UUALeu	UCASer	UAAStop	UGAStop	A
	UUGLeu	UCGSer	UAGPyl	UGGTrp	G
C	CUULeu	CCUPro	CAUHis	CGUArg	U
	CUCLeu	CCCPro	CACHis	CGCArg	C
	CUALeu	CCAPro	CAAGln	CGAArg	A
	CUGLeu	CCGPro	CAGGln	CGGArg	G
A	AUUIle	ACUThr	AAUAsn	AGUSer	U
	AUCIle	ACCThr	AACAsn	AGCSer	C
	AUAIle	ACAThr	AAALys	AGAArg	A
	AUGMet	ACGThr	AAGLys	AGGArg	G
G	GUUVal	GCUAla	GAUAsp	GGUGly	U
	GUCVal	GCCAla	GACAsp	GGCGly	C
	GUAVal	GCAAla	GAAGlu	GGAGly	A
	GUGVal	GCGAla	GAGGlu	GGGGly	G

Two stop codons, two solutionsSelenocysteine and pyrrolysine both took over a stop codon. They did it in opposite ways.

	Pyrrolysine	Selenocysteine
Codon	UAG	UGA
How it is made	As a free amino acid, from two lysines, then loaded onto its tRNA ^1,8	On its tRNA: serine is loaded first and converted in place ⁹
What the message needs	A nearby signal helps but is not required ^10,11	A SECIS hairpin; without it UGA is read as stop ^11,12
Who uses it	Some methane-making archaea and a few bacteria; not humans ^2,6	All three domains of life, humans included ¹³
How many proteins	More than 1,800 known in archaea ¹⁴	25 in humans ¹⁵
What it does there	Takes the methyl group off methylamines, the first step in making methane from them ¹	Redox chemistry: peroxides, thioredoxin, thyroid hormone ¹³

Only one organism is known to use both ⁶.

Where it comes from

No human cell makes or uses pyrrolysine. The trait is confined to a few microbes, mostly methane-making archaea, with related genes in a Gram-positive bacterium ^2,6.

Those organisms make it from lysine alone, by three enzymes, PylB, PylC and PylD ¹. A dedicated synthetase, PylS, then attaches the finished amino acid to its tRNA; it activates pyrrolysine with ATP and does not accept lysine ^8,16. Moving five genes, pylTSBCD, into the bacterium Escherichia coli is enough to make it build pyrrolysine and put it into protein ¹.

Not used by humansNot a nutrient. Humans have none of the machinery to make it or build it into protein; the organisms that use it make it from lysine ^1,6.

How much

None. Humans do not use it ⁶.

Where it is in food

Not a dietary amino acid: the organisms that use it make their own from lysine ¹.

In the bottle · laboratory onlyNot sold as a supplement. Chemists synthesised it in 2004 to prove that its synthetase loads it directly ^8,16, and laboratories now use the pyrrolysine machinery to build proteins carrying new amino acids ¹⁷.

What the body does with it

Pyrrolysine is necessary for every known pathway by which methane is made from methylamines. Three methyltransferases start those pathways, one for each of the methylamines, and each is encoded with pyrrolysine at an in-frame UAG ¹.

For two decades it looked like a speciality of those enzymes: a 2005 survey of genomes found conserved pyrrolysine in only four protein families, chiefly the methylamine methyltransferases ⁶. In 2025, proteomics showed that some archaea read every UAG as pyrrolysine, an alternative genetic code with 62 sense codons for 21 amino acids, and found more than 1,800 archaeal proteins containing it ¹⁴.

That is where it touches human health. Trimethylamine is made only by gut microbes, from choline, carnitine, lecithin and TMAO in food, and the liver oxidises it to TMAO, which is associated with cardiovascular disease ^5,7. A group of gut archaea, the Methanomassiliicoccales, use methylamines to make methane; one of them, Methanomassiliicoccus luminyensis, first isolated from human faeces, depleted trimethylamine in culture by reducing it with hydrogen ^5,18.

In three sentences each

Made from two lysines

PylB rearranges one lysine into 3-methylornithine, PylC joins it to a second lysine, and PylD oxidises the result into pyrrolysine ¹.

Loaded as a finished amino acid

Unlike selenocysteine, pyrrolysine is made free and then attached to its own UAG-reading tRNA by a dedicated synthetase, which ignores lysine ^8,11,16.

A tool for writing new amino acids

Pyrrolysyl-tRNA synthetase is unusually tolerant of what it loads, and engineered versions have put more than 100 non-canonical amino acids into proteins at UAG codons ¹⁷.

How it is made, moved and broken down

Pyrrolysine’s pathway is short and entirely its own: lysine in, pyrrolysine out, onto its tRNA, into a methyltransferase ^1,8.

Making it from lysineLysine is the only precursor ¹.

Lysine
Lysine mutase (radical SAM)pylB · SAM
3-Methylornithine
LigasepylC
3-Methylornithyl-lysine
OxidasepylD
Pyrrolysine

Loading and reading itCharged as a free amino acid; read at UAG, helped but not dictated by its context ^8,10.

Pyrrolysine + tRNA(Pyl)
Pyrrolysyl-tRNA synthetasepylS · ATP
Pyrrolysyl-tRNA(Pyl)
The ribosomepylT · PYLIS helps
Pyrrolysine at UAG

Where it matters most

The human gut: Home to the Methanomassiliicoccales, found in microbiome data from eight countries and associated with older age ^4,7.
Other guts, soil and sediment: The same order lives outside the human gut, and the nearest relatives of the first human isolate came from the digestive tracts of a cockroach, a chicken and other mammals ^7,18.
The laboratory: The pyrrolysine synthetase and its tRNA are a standard tool for putting non-canonical amino acids into proteins ¹⁷.

When it goes wrong

Inherited

Trimethylaminuria (fish-odour syndrome)

FMO3 · hereditary

A hereditary defect in flavin-containing monooxygenase 3 leaves trimethylamine unoxidised, and bacterial trimethylamine from food is believed to contribute to the odour ⁵. Archaea that consume trimethylamine with pyrrolysine enzymes have been proposed as a treatment, so-called archaebiotics; it has been shown in culture, not in patients ⁵.

Association

TMAO and cardiovascular risk

Trimethylamine from the gut becomes TMAO in the liver, and TMAO is associated with atherosclerosis ^5,7. Methanomassiliicoccales abundance correlated with lower faecal trimethylamine in an elderly cohort; whether these archaea lower TMAO or risk in people is untested ⁴.

Association

Colorectal cancer

In 2,101 stool metagenomes from eleven cohorts, the order Methanomassiliicoccales was depleted in colorectal cancer while Methanobrevibacter smithii was enriched ¹⁹. An association, not a cause, and not a test.

How it is foundResearch only ¹⁹.

How it is measured

Pyrrolysine is identified in proteins by crystallography and mass spectrometry ^3,14. In people, what can be measured is the archaea that make it, and only in research.

Stool metagenomicsSequencing the DNA in stool can find the Methanomassiliicoccales and their genes for using trimethylamine ⁴.Research only.In an elderly cohort, their abundance went with lower faecal trimethylamine ⁴.Shows who is present, not what they are doing at the time.
Breath methaneMethane in the breath is how gut methanogens were first noticed ⁷.It reports all methanogens together. The best-known methane producers of the gut, Methanobrevibacter smithii and Methanosphaera stadtmanae, belong to a different order from the pyrrolysine-using Methanomassiliicoccales ⁷.

Food, supplements and the evidence

Establishedreplicated in people, for a named outcome

Nothing in this column.

Uncertainsmall, short, mixed, surrogate or preclinical

Archaebiotics, gut archaea given to consume trimethylamine and so lower TMAO or treat trimethylaminuria: proposed in 2013, supported in culture, untested in people ^4,5.
Whether the apparent decline of gut methanogens with industrialisation has metabolic consequences ²⁰.

Sold asthe claim on the label, against the evidence

Nothing in this column.

What is strange about it

Some archaea have their own genetic code in which UAG never means stop. It was the first alternative genetic code found in archaea, and it appears to have arisen independently several times ¹⁴; one 2026 analysis argues instead that it may be ancestral ²¹.

Its synthetase is so undemanding about what it loads that it became one of the main tools of synthetic biology, used to write more than a hundred amino acids that nature never made into proteins ¹⁷.

Industrialised guts may be losing their methanogens along with the rest of their microbial diversity; whether that matters for human metabolism is an open question ²⁰.

Where it connects

In the Atlas

LysLysinePositively charged SecSelenocysteineWritten in a stop codon MetMethionineNonpolar, aliphatic NNitrogenElement

Topics on the map

On the map

A star in The rest of the amino acids, one of 6. The twenty-second, and not ours. Some methane-making archaea read UAG as an amino acid built from two lysines; in our cells that codon is still stop.

Find it on the map

Sources

21 sources, numbered as they are cited. Every one was checked against PubMed or its publisher before it was cited here; the note under each says what it shows and what it does not.

1
Gaston MA, Zhang L, Green-Church KB, Krzycki JA. The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine.Nature · 2011 · 471(7340):647–650doi:10.1038/nature09918 · PMID 21455182
PylB, PylC and PylD make pyrrolysine from two lysines; required for methane from methylamines.
2
Srinivasan G, James CM, Krzycki JA. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA.Science · 2002 · 296(5572):1459–1462doi:10.1126/science.1069588 · PMID 12029131
The pylT tRNA with a CUA anticodon and the pylS synthetase; homologs in a Gram-positive bacterium.
3
Hao B, Gong W, Ferguson TK, et al. A new UAG-encoded residue in the structure of a methanogen methyltransferase.Science · 2002 · 296(5572):1462–1466doi:10.1126/science.1069556 · PMID 12029132
The 1.55 Å structure of MtmB that revealed pyrrolysine.
4
Borrel G, McCann A, Deane J, et al. Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome.ISME J · 2017 · 11(9):2059–2074doi:10.1038/ismej.2017.72 · PMID 28585938
Methanomassiliicoccales in data from eight countries; abundance against faecal TMA in the ELDERMET cohort.
5
Brugère JF, Borrel G, Gaci N, et al. Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease.Gut Microbes · 2014 · 5(1):5–10doi:10.4161/gmic.26749 · PMID 24247281
Proposal; M. luminyensis depleted TMA in culture. Not tested in people.
6
Zhang Y, Baranov PV, Atkins JF, Gladyshev VN. Pyrrolysine and selenocysteine use dissimilar decoding strategies.J Biol Chem · 2005 · 280(21):20740–20751doi:10.1074/jbc.M501458200 · PMID 15788401
The pyrrolysine trait in a few microbes; one organism with both; four protein families.
7
Gaci N, Borrel G, Tottey W, et al. Archaea and the human gut: new beginning of an old story.World J Gastroenterol · 2014 · 20(43):16062–16078doi:10.3748/wjg.v20.i43.16062 · PMID 25473158
Review of gut archaea, the Methanomassiliicoccales, trimethylamine and TMAO.
8
Blight SK, Larue RC, Mahapatra A, et al. Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo.Nature · 2004 · 431(7006):333–335doi:10.1038/nature02895 · PMID 15329732
Synthetic pyrrolysine attached as a free molecule by PylS, with ATP.
9
Xu XM, Carlson BA, Mix H, et al. Biosynthesis of selenocysteine on its tRNA in eukaryotes.PLoS Biol · 2007 · 5(1):e4doi:10.1371/journal.pbio.0050004 · PMID 17194211
Selenocysteine is made on its tRNA from serine.
10
Longstaff DG, Blight SK, Zhang L, et al. In vivo contextual requirements for UAG translation as pyrrolysine.Mol Microbiol · 2007 · 63(1):229–241doi:10.1111/j.1365-2958.2006.05500.x · PMID 17140411
A downstream PYLIS enhances UAG translation; a UAG with no evolved context was still read at 20%.
11
Peiter N, Rother M, Krzycki JA. Recent developments in (archaeal) pyrrolysine and selenocysteine specification and metabolism.Cold Spring Harb Perspect Biol · 2026doi:10.1101/cshperspect.a041979 · PMID 41997725
Review contrasting how the two recoded amino acids are made and read.
12
Chavatte L, Lange L, Schweizer U, et al. Understanding the role of tRNA modifications in UGA recoding as selenocysteine in eukaryotes.J Mol Biol · 2025 · 437(16):169017doi:10.1016/j.jmb.2025.169017 · PMID 39988117
SECIS and the machinery of UGA recoding.
13
Labunskyy VM, Hatfield DL, Gladyshev VN. Selenoproteins: molecular pathways and physiological roles.Physiol Rev · 2014 · 94(3):739–777doi:10.1152/physrev.00039.2013 · PMID 24987004
Selenoproteins in all three domains of life; mostly oxidoreductases.
14
Kivenson V, Peters SL, Borrel G, et al. An archaeal genetic code with all TAG codons as pyrrolysine.Science · 2025 · 390(6775):eadu2404doi:10.1126/science.adu2404 · PMID 41264687
The Pyl code: 62 sense codons, 21 amino acids; more than 1,800 pyrrolysine proteins.
15
Kryukov GV, Castellano S, Novoselov SV, et al. Characterization of mammalian selenoproteomes.Science · 2003 · 300(5624):1439–1443doi:10.1126/science.1083516 · PMID 12775843
Twenty-five human selenoproteins.
16
Polycarpo C, Ambrogelly A, Bérubé A, et al. An aminoacyl-tRNA synthetase that specifically activates pyrrolysine.Proc Natl Acad Sci U S A · 2004 · 101(34):12450–12454doi:10.1073/pnas.0405362101 · PMID 15314242
PylS charges pyrrolysine and not lysine; named pyrrolysyl-tRNA synthetase.
17
Wan W, Tharp JM, Liu WR. Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool.Biochim Biophys Acta · 2014 · 1844(6):1059–1070doi:10.1016/j.bbapap.2014.03.002 · PMID 24631543
More than 100 non-canonical amino acids incorporated with engineered PylRS.
18
Dridi B, Fardeau ML, Ollivier B, et al. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces.Int J Syst Evol Microbiol · 2012 · 62(Pt 8):1902–1907doi:10.1099/ijs.0.033712-0 · PMID 22859731
The first human isolate of the order; relatives from cockroach, chicken and mammal guts.
19
Li T, Coker OO, Sun Y, et al. Multi-cohort analysis reveals altered archaea in colorectal cancer fecal samples across populations.Gastroenterology · 2025 · 168(3):525–538.e2doi:10.1053/j.gastro.2024.10.023 · PMID 39490771
2,101 metagenomes; Methanomassiliicoccales depleted in colorectal cancer.
20
Subrahmanian A, Patel A, Veerus L, et al. Methanogens: vital but threatened members of the human microbiome?Trends Microbiol · 2026doi:10.1016/j.tim.2026.08.008 · PMID 42692861
Review: evidence that methanogens may be declining with industrialisation.
21
Di Giulio M. The archaeal genetic code with all UAG codons as pyrrolysine might be an ancestral and not derived trait: the non-monophyletic origin of the genetic code.Biosystems · 2026 · 263:105787doi:10.1016/j.biosystems.2026.105787 · PMID 41985704
Theoretical analysis; a minority view.

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