Higher-order structure of bovine mitochondrial tRNA^SerUGA: chemical modification and computer modeling

Abstract

ABSTRACT

Pyrrolysine is not hardwired for cotranslational insertion at UAG codons

“…As noted earlier (9,11,15), tRNA Pyl has an unusual structure shared with only one Bos taurus mitochondrial tRNA Ser isoacceptor (17). Neither tRNA CUA Ser nor a stabilized version of this RNA (see Materials and Methods) were substrates for any endogenous E. coli synthetase in vivo or for M. barkeri PylRS in vitro.…”

Dual Mode Recognition of Two Isoacceptor tRNAs by Mammalian Mitochondrial Seryl-tRNA Synthetase

“…To examine the recognition elements of mt tRNA UGA Ser , we constructed several variants carrying a mutation(s), mainly at bases in the T⌿C loop, which is one of the mt SerRS contact sites and is predicted to be involved in tertiary interactions according to a previously proposed model (31). The mutational variations are shown in Fig.…”

“…When compared with the canonical cloverleaf structure, mammalian mt tRNA UGA Ser lacks six conserved residues, at positions 8, 16, 17, 21, 47, and 48, but contains one extra base pair (⌿26a⅐A43a) in the anticodon stem so as to form a characteristic pseudo-cloverleaf structure (31). On the other hand, chicken mt tRNA UGA Ser possesses the canonical cloverleaf structure (34).…”

Search for characteristic structural features of mammalian mitochondrial tRNAs

“…A: From secondary to tertiary structures of "classical" tRNAs+ Positions of nucleotides are numbered according to conventional rules (Sprinzl et al+, 1998)+ Conserved elements in the cloverleaf are highlighted as well as their involvement in folding of the L-shaped tertiary structure+ Nomenclature is as follows: Y: pyrimidine; R: purine; ⌿: pseudouridine+ B: The particular case of bovine mt tRNA Ser(UCN) (Watanabe et al+, 1994a;Hayashi et al+, 1998)+ Notice the absence of the complete D-domain and its replacement by a connector+ Also, the length of the anticodon stem and the size of the T-loop are at variance with classical tRNAs+ C: The particular case of bovine mt tRNA Ser(AGY) (Ueda et al+, 1983;Hayashi et al+, 1997b). The main differences from the classical cloverleaf reside in the length of connector 1, an additional pair in the anticodon stem, and the short size of the variable region+ et al+, 1980;de Bruijn & Klug, 1983;Watanabe et al+, 1994a;Hayashi et al+, 1997bHayashi et al+, , 1998)+ Efforts to explain other similar deviations from the cloverleaf structure have focused on a computer-model-based structural rational (Steinberg et al+, 1997)+ Whereas the above discussed mt tRNAs, picked from various organisms, indeed show significant deviations from the classical cloverleaf structure, it remains to be analyzed whether all mt tRNAs deviate as well, and if so, to evaluate the degree of deviation+ Mammalian mt tRNAs form a family of molecules for which poor structural and functional knowledge is available+ This is a considerable drawback, especially at a time when a growing number of human diseases are found to be correlated to point mutations in mt tRNA genes (Wallace, 1992(Wallace, , 1999Larsson & Clayton, 1995;Schon et al+, 1997)+ Since the first description in 1990 (Goto et al+, 1990) of a correlation between the MELAS syndrome and point mutation at position 3243 in the tRNA Leu(UUR) gene, more than 70 mutations have been reported so far in 19 out of the 22 tRNA genes (Kogelnick et al+, 1998, and updated web site Mitomap)+ Understanding the functional properties of mammalian mt tRNAs requires an understanding of their underlying structural basis+ Thus, we present here a sequence alignment of the 22 tRNA genes in 31 fully sequenced mammalian mt genomes+ This survey has as a primary goal to decipher the differences and similarities to canonical tRNAs+ Any conserved structural features in the mt tRNAs that deviate from the canonical tRNAs would be of particular interest, because they constitute landmarks to distinguish these two types of tRNAs from one another in structure+ We have therefore paid special attention to the degree of evolutionary conservation of such deviations+ In a number of previously reported seque...…”