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

Modification of the cytidine in the first anticodon position of the AUA decoding tRNA super(Ile) ([image]) 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,...

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Published in:Proceedings of the National Academy of Sciences - PNAS 2010-01, Vol.107 (7), p.2872-2877
Main Authors: Mandal, Debabrata, Koehrer, Caroline, Su, Dan, Russell, Susan P, Krivos, Kady, Castleberry, Colette M, Blum, Paul, Limbach, Patrick A, Soell, Dieter, RajBhandary, Uttam L
Format: Article
Language:English
Subjects:
Archaea
Haloarcula marismortui
Methanococcus maripaludis
Sulfolobus solfataricus
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Summary:Modification of the cytidine in the first anticodon position of the AUA decoding tRNA super(Ile) ([image]) 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 [image] 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 [image] 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 super(+), for this modified cytidine. Agmatidine is also present in Methanococcus maripaludis [image] and in Sulfolobus solfataricus total tRNA, indicating its probable occurrence in the AUA decoding tRNA super(Ile) 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.
ISSN:0027-8424
DOI:10.1073/pnas.0914869107