Agmatidine, a modified cytidine in the anticodon of archaeal tRNA Ile, base pairs with adenosine but not with guanosine

Debabrata Mandal, Caroline Köhrer, Dan Su, Susan P. Russell, Kady Krivos, Colette M. Castleberry, Paul Blum, Patrick A. Limbach, Dieter Söll, Uttam L. RajBhandary

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96 Scopus citations


Modification of the cytidine in the first anticodon position of the AUA decoding tRNAIle (tRNAIle2) of bacteria and archaea is essential for this tRNA to read the isoleucine codon AUA and to differentiate between AUA and the methionine codon AUG. To identify the modified cytidine in archaea, we have purified this tRNA species from Haloarcula marismortui, established its codon reading properties, used liquid chromatography-mass spectrometry (LC-MS) to map RNase A and T1 digestion products onto the tRNA, and used LC-MS/MS to sequence the oligonucleotides in RNase A digests. These analyses revealed that the modification of cytidine in the anticodon of tRNAIle2 adds 112 mass units to its molecular mass and makes the glycosidic bond unusually labile during mass spectral analyses. Accurate mass LC-MS and LC-MS/MS analysis of total nucleoside digests of the tRNAIle2 demonstrated the absence in the modified cytidine of the C2-oxo group and its replacement by agmatine (decarboxy-arginine) through a secondary amine linkage. We propose the name agmatidine, abbreviation C+, for this modified cytidine. Agmatidine is also present in Methanococcus maripaludis tRNAIle2 and in Sulfolobus solfataricus total tRNA, indicating its probable occurrence in the AUA decoding tRNAIle of euryarchaea and crenarchaea. The identification of agmatidine shows that bacteria and archaea have developed very similar strategies for reading the isoleucine codon AUA while discriminating against the methionine codon AUG.

Original languageEnglish (US)
Pages (from-to)2872-2877
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number7
StatePublished - Feb 16 2010
Externally publishedYes


  • Agmatine
  • Decoding
  • Rna modification
  • Trna
  • Wobble pairing

ASJC Scopus subject areas

  • General


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