Table 3.
Structural features within tRNA involved in interactions with aminoacyl-tRNA synthetases and/or important for the specificity of tRNA aminoacylation
| Structural features | Effecta on | Comments and references | ||
|---|---|---|---|---|
| Interaction | Specificity | |||
| Shape of tRNA recognized by an aaRS | ||||
| Canonical L-shape | +++ | ± | *Under special conditions, all tRNAs can be recognized by certain aaRSs, but tRNA mischarging efficiency is low (37) | |
| Atypical shapes tRNAs with large variable region, tRNA-like domains, many mitochondrial tRNAs, etc | +++ | ++ | *For tRNAs with large variable region (e.g., tRNALeu) or atypical tertiary interaction networks (e.g., tRNACys) (268) *For tRNA mimics in mRNA, e.g., in E. coli mRNAThr (206)*Aminoacylation of tRNA mimics can be efficient, e.g., in viral tRNA-like structures (264) *For atypical mitochondrial tRNAs, e.g., reference (269) | |
| Determinants in tRNA for specific tRNA aminoacylation directly read by an aaRS | ||||
| Bases Restricted number (2–11) in identity sets; mainly in single-stranded regions; sometimes in WC pairs | +++ | +/+++++ | *System-specific contacts, e.g., in E. coli aspartate and glutamine system (149, 244) and identity sets (6, 188) *Atomic determinants in E. coli alanine system (270) | |
| Sugar (from identity bases) | + | + | *Few examples of direct contacts of ribose O2′ with aaRSs, e.g., in the E. coli aspartate system (149)*Only a few examples of ribose as identity determinant (271, 272) | |
| Modified residues | + | ++ | *Few documented system-specific examples (273) | |
| Determinants in tRNA for specific tRNA aminoacylation indirectly read by an aaRS | ||||
| Sequence-dependent Individual or collective | +/++ | +++ | *Recognition of idiosyncratic conformations in cognate tRNAs (266)*Water mediated recognition of individual identity determinants, e.g., in E. coli aspartate system (149) | |
| Antideterminants in tRNA for noncognate tRNA rejections by an aaRS | ||||
| Individual nucleosides WC or modified nucleosides; possibly idiosyncratic tRNA domains | − | ++++ | *Not systematically searched; only a few cases supported by experimental validation (188, 274, 275) | |
| Other nucleotidic constituents for stability of a given aaRS:tRNA complex and for tuning its specificity | ||||
| Bases | +/+++ | ±/++ | *System-specific contacts contributing to overall binding affinity, e.g., in the E. coli glutamine system (149, 244) | |
| Ribophosphate backbones | +/+++ | ±/++ | *System-specific contacts (as above), e.g., reference 266 | |
Effects: +++++, strongest;++++, very important; +++, important; ++, medium; +, weak; ±, low. WC, Watson-Crick; n.d., not determined. See the text for more detail. Note that the structural features in tRNA are mirrored by proteic elements in the aaRSs (less well defined and characterized than their counterparts on tRNA), notably amino acids that contact identity nucleotides (e.g., in the E. coli AspRS Arg76, Glu93, and Gln46 make hydrogen-bond interactions with identity determinants Q34 and U35 from the anticodon of cognate tRNAAsp [149]). Two of these amino acids (Gln46 and Glu93) are conserved through evolution in AspRSs (276) and therefore can be considered as aspartate identity amino acids.