Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine
Modification of the cytidine in the first anticodon position of the AUA decoding tRNAIle [tRNA superscript Ile subscript 2] 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 cyti...
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| Format: | Article |
| Language: | en_US |
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National Academy of Sciences (U.S.)
2011
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| Online Access: | http://hdl.handle.net/1721.1/61373 https://orcid.org/0000-0002-4530-5647 |
| _version_ | 1826195481095569408 |
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| author | Rajbhandary, Uttam L Koehrer, Caroline Su, Dan Russell, Susan P. Krivos, Kady Castleberry, Colette M. Blum, Paul Limbach, Patrick A. Söll, Dieter Mandal, Debabrata |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Rajbhandary, Uttam L Koehrer, Caroline Su, Dan Russell, Susan P. Krivos, Kady Castleberry, Colette M. Blum, Paul Limbach, Patrick A. Söll, Dieter Mandal, Debabrata |
| author_sort | Rajbhandary, Uttam L |
| collection | MIT |
| description | Modification of the cytidine in the first anticodon position of the AUA decoding tRNAIle [tRNA superscript Ile subscript 2] 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 [tRNA superscript Ile subscript 2] 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 [tRNA superscript Ile subscript 2] 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 [tRNA superscript Ile subscript 2] and in Sulfolobus solfataricus total tRNA, indicating its probable occurrence in the AUA decoding tRNAIle [tRNA superscript 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. |
| first_indexed | 2024-09-23T10:13:21Z |
| format | Article |
| id | mit-1721.1/61373 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:13:21Z |
| publishDate | 2011 |
| publisher | National Academy of Sciences (U.S.) |
| record_format | dspace |
| spelling | mit-1721.1/613732022-09-26T16:32:34Z Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine Agmatidine, a modified cytidine in the anticodon of archaeal tRNA {superscript Ile], base pairs with adenosine but not with guanosine Rajbhandary, Uttam L Koehrer, Caroline Su, Dan Russell, Susan P. Krivos, Kady Castleberry, Colette M. Blum, Paul Limbach, Patrick A. Söll, Dieter Mandal, Debabrata Massachusetts Institute of Technology. Department of Biology Rajbhandary, Uttam L. Rajbhandary, Uttam L Koehrer, Caroline Mandal, Debabrata Modification of the cytidine in the first anticodon position of the AUA decoding tRNAIle [tRNA superscript Ile subscript 2] 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 [tRNA superscript Ile subscript 2] 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 [tRNA superscript Ile subscript 2] 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 [tRNA superscript Ile subscript 2] and in Sulfolobus solfataricus total tRNA, indicating its probable occurrence in the AUA decoding tRNAIle [tRNA superscript 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. National Institutes of Health (U.S.) (Grant GM17151) (Grant GM22854) (Grant RR19900) National Science Foundation (U.S.) (Grant CHE0602413) (Grant CHE0910751) United States. Dept. of Energy (Grant DE-FG36-08GO88055) 2011-03-02T17:03:29Z 2011-03-02T17:03:29Z 2010-01 2009-12 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/61373 Mandal, D. et al. “Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine.” Proceedings of the National Academy of Sciences 107.7 (2010): 2872-2877. Copyright ©2011 by the National Academy of Sciences https://orcid.org/0000-0002-4530-5647 en_US http://dx.doi.org/10.1073/pnas.0914869107 Proceedings of the National Academy of Sciences of the United States of America. (PNAS) Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) PNAS |
| spellingShingle | Rajbhandary, Uttam L Koehrer, Caroline Su, Dan Russell, Susan P. Krivos, Kady Castleberry, Colette M. Blum, Paul Limbach, Patrick A. Söll, Dieter Mandal, Debabrata Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine |
| title | Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine |
| title_full | Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine |
| title_fullStr | Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine |
| title_full_unstemmed | Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine |
| title_short | Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine |
| title_sort | agmatidine a modified cytidine in the anticodon of archaeal trna ile base pairs with adenosine but not with guanosine |
| url | http://hdl.handle.net/1721.1/61373 https://orcid.org/0000-0002-4530-5647 |
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