The 3 A crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination.

Abstract

A significantly improved molecular model of yeast initiator tRNA (ytRNA(iMet) has been prepared that gives insight into the structural basis of eukaryotic initiator tRNA's unique function. This study was made possible by X‐ray data collected at synchrotron radiation sources with the newly developed technologies of ‘imaging plates’ and ‘storage phosphors’. These data extend beyond the resolution limit of 4.0 A reported previously to a current limit of 3.0 A and are considerably more accurate. Refinement of the model against the new data (R factor = 21.5%) clearly reveals a novel modification and a set of tertiary interactions involving sequence features characteristic of eukaryotic initiator tRNAs. We hypothesize these to be the structural elements responsible for part of the special function of yeast tRNA(iMET).

Conformational Change in Transfer RNA Is an Early Indicator of Acute Cellular Damage

“…An Anti-1-Methyladenosine Antibody Detects Both tRNA and tRNA-Derived Fragments To examine the involvement of tRNA in the stress response, we established a monoclonal antibody against mononucleoside 1-methyladenosine (m1A), a key eukaryotic tRNA-specific modified nucleoside 9 that is important for folding tRNA into a tertiary structure 10 ( Figure 1A). This antibody specifically recognizes m1A but no other nucleosides.…”

The essential Gcd10p–Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA

“…Thus, we conclude that initiator tRNA Met produced in gcd10⌬ cells lacks m 1 A58. Importantly, this residue plays a central role in determining a unique tertiary substructure not observed in elongator tRNAs, involving three residues unique to eukaryotic initiators, A60, A54, and A20 (Basavappa and Sigler 1991). Therefore, the absence of this modification might alter the tertiary structure of the initiator, and impair its processing and stability, without similarly affecting elongator tRNA Met and other tRNAs bearing m 1 A58.…”

Alternative designs for construction of the class II transfer RNA tertiary core

“…Transfer RNAs possess remarkable structural similarity (Kim et al+, 1974;Robertus et al+, 1974;Moras et al+, 1980;Woo et al+, 1980;Rould et al+, 1989;Basavappa & Sigler, 1991;Goldgur et al+, 1997;Cusack et al+, 1998;Nissen et al+, 1999;Sankaranarayanan et al+, 1999;Silvian et al+, 1999), yet within the common L-shaped framework, each tRNA retains specific identity nucleotides that ensure correct aminoacylation by the cognate aminoacyl-tRNA synthetase (Giegé et al+, 1998b)+ The identity elements are usually located in the spatially separated amino-acid acceptor and anticodon arms of the molecule+ The bridging, core region of the transfer RNA molecule can often be viewed as a scaffold for presentation of these specific elements to the cognate synthetase+ The scaffold is extraordinarily robust: a wide variety of sequence lengths and compositions are tolerated while retaining biological function in both aminoacylation and later stages of translation+ This is demonstrated by extensive variations within a common design framework (e+g+, the class I structure with a small variable arm), and by the existence of alternative folds such as the class II large-variable arm tRNAs and the unusual mitochondrial species+ There are also examples of RNAs that do not function conventionally in translation but are nevertheless capable of aminoacylation+ These include tmRNA as well as tRNA-like pseudoknots in plant viral RNAs (Giegé et al+, 1998a)+ The tRNA core region consists of portions of the D, T, and variable arms, as well as the short connector bridging the acceptor and D-stems+ Among these elements, the T-loop structure is by far the most highly conserved; it forms interdigitated base-stacking interactions with the conserved G18-G19 nucleotides in the D-loop to build the upper horizontal arm of the tRNA (domain II; Steinberg et al+, 1997)+ The upper portion of the vertical arm (domain I) is constructed from the D-stem together with nucleotides from the D-loop, variable arm, and acceptor/D connector, and represents the most variable portion of the structure+ It includes both basetriple interactions as well as noncanonical base pairings (Fig+ 1)+…”