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

Research output: Contribution to journalArticle

76 Citations (Scopus)

Abstract

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
Volume107
Issue number7
DOIs
StatePublished - Feb 16 2010

Fingerprint

RNA, Transfer, Ile
Anticodon
Cytidine
Guanosine
Codon
Base Pairing
Adenosine
Transfer RNA
Liquid Chromatography
Mass Spectrometry
Archaea
Pancreatic Ribonuclease
Isoleucine
Methionine
Reading
Haloarcula marismortui
Methanococcus
Agmatine
Sulfolobus solfataricus
Ribonuclease T1

Keywords

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

ASJC Scopus subject areas

  • General

Cite this

Agmatidine, a modified cytidine in the anticodon of archaeal tRNA Ile, base pairs with adenosine but not with guanosine. / Mandal, Debabrata; Köhrer, Caroline; Su, Dan; Russell, Susan P.; Krivos, Kady; Castleberry, Colette M.; Blum, Paul; Limbach, Patrick A.; Söll, Dieter; RajBhandary, Uttam L.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 107, No. 7, 16.02.2010, p. 2872-2877.

Research output: Contribution to journalArticle

Mandal, Debabrata ; Köhrer, Caroline ; Su, Dan ; Russell, Susan P. ; Krivos, Kady ; Castleberry, Colette M. ; Blum, Paul ; Limbach, Patrick A. ; Söll, Dieter ; RajBhandary, Uttam L. / Agmatidine, a modified cytidine in the anticodon of archaeal tRNA Ile, base pairs with adenosine but not with guanosine. In: Proceedings of the National Academy of Sciences of the United States of America. 2010 ; Vol. 107, No. 7. pp. 2872-2877.
@article{67d23841ec234475aff9f3ac3a85b55e,
title = "Agmatidine, a modified cytidine in the anticodon of archaeal tRNA Ile, base pairs with adenosine but not with guanosine",
abstract = "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.",
keywords = "Agmatine, Decoding, Rna modification, Trna, Wobble pairing",
author = "Debabrata Mandal and Caroline K{\"o}hrer and Dan Su and Russell, {Susan P.} and Kady Krivos and Castleberry, {Colette M.} and Paul Blum and Limbach, {Patrick A.} and Dieter S{\"o}ll and RajBhandary, {Uttam L.}",
year = "2010",
month = "2",
day = "16",
doi = "10.1073/pnas.0914869107",
language = "English (US)",
volume = "107",
pages = "2872--2877",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "7",

}

TY - JOUR

T1 - Agmatidine, a modified cytidine in the anticodon of archaeal tRNA Ile, base pairs with adenosine but not with guanosine

AU - Mandal, Debabrata

AU - Köhrer, Caroline

AU - Su, Dan

AU - Russell, Susan P.

AU - Krivos, Kady

AU - Castleberry, Colette M.

AU - Blum, Paul

AU - Limbach, Patrick A.

AU - Söll, Dieter

AU - RajBhandary, Uttam L.

PY - 2010/2/16

Y1 - 2010/2/16

N2 - 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.

AB - 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.

KW - Agmatine

KW - Decoding

KW - Rna modification

KW - Trna

KW - Wobble pairing

UR - http://www.scopus.com/inward/record.url?scp=77649263055&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77649263055&partnerID=8YFLogxK

U2 - 10.1073/pnas.0914869107

DO - 10.1073/pnas.0914869107

M3 - Article

C2 - 20133752

AN - SCOPUS:77649263055

VL - 107

SP - 2872

EP - 2877

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 7

ER -