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Nucleic Acids Research, 2001, Vol. 29, No. 22 4699-4706
© 2001 Oxford University Press

Post-transcriptional modification in archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales

James A. McCloskey*, David E. Graham1, Shaolian Zhou, Pamela F. Crain, Michael Ibba2, Jordan Konisky1, Dieter Söll2 and Gary J. Olsen1

Departments of Biochemistry and Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112-5820, USA, 1Department of Microbiology, University of Illinois, Urbana, IL 61801, USA and 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA

Post-transcriptional modifications in archaeal RNA are known to be phylogenetically distinct but relatively little is known of tRNA from the Methanococci, a lineage of methanogenic marine euryarchaea that grow over an unusually broad temperature range. Transfer RNAs from Methanococcus vannielii, Methanococcus maripaludis, the thermophile Methanococcus thermolithotrophicus, and hyperthermophiles Methanococcus jannaschii and Methanococcus igneus were studied to determine whether modification patterns reflect the close phylogenetic relationships inferred from small ribosomal subunit RNA sequences, and to examine modification differences associated with temperature of growth. Twenty-four modified nucleosides were characterized, including the complex tricyclic nucleoside wyosine characteristic of position 37 in tRNAPhe and known previously only in eukarya, plus two new wye family members of presently unknown structure. The hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, reported previously only in bacterial tRNA at the first position of the anticodon, was identified by liquid chromatography-electrospray ionization mass spectrometry in four of the five organisms. The ribose-methylated nucleosides, 2'-O-methyladenosine, N2,2'-O-dimethylguanosine and N2,N2,2'-O-trimethylguanosine, were found only in hyperthermophile tRNA, consistent with their proposed roles in thermal stabilization of tRNA.

* To whom correspondence should be addressed at: University of Utah, 30 South 2000 East, Room 311A, Salt Lake City, UT 84112-5820, USA. Tel: +1 801 581 5581; Fax: +1 801 581 7457; Email: james.mccloskey{at}m.cc.utah.eduPresent addresses:David E. Graham, Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, VA 24061-0308, USAMichael Ibba, Center for Biomolecular Recognition, IMBG, The Panum Institute, Blegdamsvej 3c, Copenhagen N, DK-2200, DenmarkJordan Konisky, Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005-1892, USA


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