Structural Characterization of the Transfer Ribonucleic Acids From Halobacterium Volcanii and Other Archaebacteria

Gupta, Ramesh

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Description

Title

Structural Characterization of the Transfer Ribonucleic Acids From Halobacterium Volcanii and Other Archaebacteria

Author(s)

Gupta, Ramesh

Issue Date

1981

Department of Study

Microbiology

Discipline

Microbiology

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

Biology, Microbiology

Language

eng

Abstract

• The archaebacteria have been defined primarily on the basis of their ribosomal RNAs, as a primary kingdom, distinct from the eubacteria ('prokaryotes') and the eucaryotes. To help in evaluating the molecular affinities, we characterize here the transfer RNAs (tRNAs) in two ways. First, we describe the modification patterns of the tRNAs of ten archaebacteria (Halobacterium volcanii, Halococcus morrhuae, Methanobacterium bryantii, Methanobrevibacter smithii, Methanococcus vannielii, Methanococcus voltae, Methanomicrobium mobile, Methanosarcina barkeri, Thermoplasma acidophilum, and Sulfolobus acidocaldarius), as analyzed by two-dimensional thin layer chromatography of the ('32)P-labelled nucleotides. Second, we describe the sequences of seventeen H. volcanii tRNAs (tentative for two) as determined by the oligonucleotide cataloging methods. These sequences have been largely confirmed by sequencing 3'-end labelled tRNAs by gel methods.
• Al archaebacterial species tested lack ribothymidine (T) and 7-methylguanosine; dihydrouridine is absent from all but M. barkeri. Pseudouridine ((psi)), 2'-O-methylcytidine (Cm), 1-methylguanosine, and N('2),N('2)-dimethylguanosine are present in all of them. Except for M. barkeri and T. acidophilum, all have N('2)-methylguanosine (m('2)-G). All, except H. volcanii and H. morrhuae, contain 1-methyladenosine, and only these two organisms and S. acidocaldarius contain 5-methylcytidine. Some of the modified nucleotides could not be identified.
• The sequences have been determined for two tRNAs each for glutamic acid, leucine, methionine (initiator and noninitiator), proline and serine, and one tRNA each for arginine, aspartic acid, glutamine, isoleucine, lysine, tyrosine and valine. The amino acids are assigned to the tRNAs on the basis of their anticodon sequences, but these assignments were checked and confirmed in certain cases by aminoacylation of the tRNAs.
• All tRNAs except those for leucine and serine have short extra arms. One tRNA('Ser) has four base pairs in the b-stem (so-called 'D stem'). Isoacceptors for glutamic acid and serine show sequence similarity in several regions. The initiator has a triphosphate at the 5'-end, and the base at the 5'-end paris with the fifth base from the 3'-end. The c-stem (anticodon stem) in some tRNAs can be extended on the side away from anticodon, by an extra base pair and in several cases by another base pair on the anticodon side. Five tRNAs (arginine, glutamine, initiator methionine and two proline) show a G-C pair at the second position of the b-stem, instead of the semivariant pyrimidine-purine pair. In these cases, an alternate pairing is possible in the b-stem. The b-stem in tRNA('Ile) can be extended on the loop I (so-called 'D loop') side by an A-U pair.
• The region 53-61 of tRNAs (using the numbering system of yeast tRNA for phenylalanine) which includes the common T(psi)CG sequence of most organisms, shows a similar sequence for most of the H. volcanii tRNAs. Here T is replaced by a modified uridine (xU) or (psi). The sequence T(psi)CG is replaced by xU(psi)Cmm('2)G, xU(psi)CmG, (psi)(psi)Cmm('2)G or (psi)(psi)CmG.
• Most of the recognized common invariant and semivariant bases are present in H. volcanii tRNAs. Positions 13 and 22, the normal positions for the fourth pair in the b-stem, have high frequencies of (psi) and pyrimidines, respectively.
• This study was incapable of determining whether the distinctive features of the tRNA sequences of H. volcanii reflect their archaebacterial affinities or their halophilic habitats. However, the study indicates that the sequences and the modification patterns of the tRNAs in archaebacteria are distinct from those of eubacteria and eucaryotes. In some tRNA characters, the archaebacteria show more similarity to the eucaryotes than to the eubacteria. The differences in modification patterns among archaebacteria themselves can be interpreted along phylogenetic lines.

Graduation Semester

1981

Type of Resource

text

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