Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases - PubMed (original) (raw)
Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases
Charles W Carter Jr et al. Nucleic Acids Res. 2018.
Abstract
Class I and II aaRS recognition of opposite grooves was likely among the earliest determinants fixed in the tRNA acceptor stem bases. A new regression model identifies those determinants in bacterial tRNAs. Integral coefficients relate digital dependent to independent variables with perfect agreement between observed and calculated grooves for all twenty isoaccepting tRNAs. Recognition is mediated by the Discriminator base 73, the first base pair, and base 2 of the acceptor stem. Subsets of these coefficients also identically compute grooves recognized by smaller numbers of aaRS. Thus, the model is hierarchical, suggesting that new rules were added to pre-existing ones as new amino acids joined the coding alphabet. A thermodynamic rationale for the simplest model implies that Class-dependent aaRS secondary structures exploited differential tendencies of the acceptor stem to form the hairpin observed in Class I aaRS•tRNA complexes, enabling the earliest groove discrimination. Curiously, groove recognition also depends explicitly on the identity of base 2 in a manner consistent with the middle bases of the codon table, confirming a hidden ancestry of codon-anticodon pairing in the acceptor stem. That, and the lack of correlation with anticodon bases support prior productive coding interaction of tRNA minihelices with proto-mRNA.
Figures
Figure 1.
tRNA acceptor-stem bases considered in the analysis of aaRS groove recognition. Pyrimidines are colored with primary colors, purines with their respective complements. Cubes adjacent to each tRNA represent the availability of aaRS•tRNA co-crystals showing productive acceptor-stem interactions in prokaryotes (open) or other (gray) organisms. The width of the circle for each discriminator base indicates its strength as compiled by Giegé and Eriani (50). Note the following idiosyncratic features: (i) tRNALeu, tRNAPhe, tRNAThr and tRNAHis have identical bases in all four positions; (ii) tRNAAsp and tRNASer similarly share identical signatures; (iii) tRNAHis has a unique extra G at position –1; (iv) tRNAIle has a completely ambiguous first base pair.
Figure 2.
Superposition of the acceptor stems available from co-crystals containing relevant configurations of the 3′-CCA terminus. The 3′-terminal adenosine is shown as colored spheres; Class I tRNAs are colored different shades of green; Class II different shades of blue. Those for aromatic amino acids (Phe, Trp) are colored shades of red as they penetrate the population of the opposite class.
Figure 3.
Regression model relating tRNA groove recognition to tRNA acceptor-stem bases. (A) Actual versus Predicted Groove values for the twenty amino acids. Blue dots designate minor groove (1), red diamonds designate major groove (–1) interaction. (B) Log(worth) values plotted for each predictor. Worth is equal to the negative log of the _P_-value. The blue vertical line indicates a probability of 0.01 of observing a Student's _t_-test as large as that actually found for the model.
Figure 4.
Distribution of _R_2 for 24 random 30% subsets of amino acids based on coefficients estimated for the complementary training set. All values were identically 1.0.
Figure 5.
Hierarchy in regression models for groove recognition. Coefficients are diagrammed schematically using a circle to represent each base, as indicated by the key at the bottom left. Each circle is divided into quadrants. The top two quadrants represent the choice between pyrimidine and purine; the bottom the number of hydrogen bonds made when the base pairs. Red arrows indicate two-way interactions. The grooves recognized by fourteen of the twenty aaRS can be predicted (perfectly) using only three coefficients (top). Additional amino acids (bold) require additional coefficients, indicated in the middle and bottom schemes. The hierarchy does not necessarily imply an evolutionary succession.
Figure 6.
AARS•tRNA complexes interacting from the minor groove side. PDB IDs and amino acids are as indicated. Active-site ligands are abbreviated as follows: LSS, 5′-_O_-(
l
-leucylsulfamoyl)adenosine; Arg, arginine; GSU, O5′-(
l
-glutamyl-sulfamoyl)-adenosine; FYA, adenosine-5′-[phenylalaninol-phosphate]. Class I secondary structures depicted by color include a homologous section of connecting peptide 1 (CP1), slate; the ‘specificity-determining helix’ teal; and the base of the helix from the second crossover of the Rossmann fold, containing the signature GxDQ, salmon), and in the case of PheRS the Motif-2 loop (slate) and Motif-3 (yellow). Electrostatic influences of the dipole moments of various helices are indicated on the helices of 5OMW_Leu. Side chains that interact with the tRNA 3′-terminal adenosine (A76) are indicated by number. Note that in the 1U0B (CysRS) complex the 3′-terminal adenosine occupies an unproductive position close to the HIGH catalytic signature, suggesting that in the absence of aminoacyl-5′-adenylate, the adenine ring finds a site similar to that normally occupied by the adenine ring of the adenylate, underscoring its potential binding affinity for the heterocycle. Inset in 2ER8_Gln shows the interaction between A76 and a conserved aromatic side chain at the N-terminus of the specificity-determining helix.
Figure 7.
Interactions of Class I aaRS with the phosphate group of the 3′-terminal adenosine. The hairpin structure orients this phosphate group so that it points toward the N-terminus of the specificity-determining helix. Hydrogen bond distances shown suggest that, except in the case of 5OMW_Leu, these interactions may be strong. In 1F7U_Arg, the interaction is reinforced by a salt bridge between the phosphate group and R350.
Figure 8.
AARS•tRNA complexes interacting from the major groove side. PDB IDs and amino acids are as indicated. Active-site ligands are abbreviated as follows: AMP, adenosine 5′ monophosphate; GAP, glycyl-adenosine-5′-phosphate; AMO, aspartyl-adenosine-5′-monophosphate; Trp,
l
-tryptophan. Class II secondary structures depicted by color include the Motif-2 loop (slate), Motif-3 (yellow), and a loop that occurs prior to Motif-2 (salmon), and in the case of TrpRS, the base of the helix from the second crossover of the Rossmann fold (salmon) and a segment of CP1 (slate). Side chains that interact with the tRNA 3′-terminal adenosine (A76) are indicated by number. Antiparallel helix directions of the Motif 2 loop and the 3′-CCA terminus are shown as dashed arrows on 5EM6_Gly. Helix dipoles indicated for 2DR2_Trp suggest that the reorientation of the tRNATrp acceptor stem has moved it to a position that minimizes electrostatic disruption of the RNA double helix. Insets in 1QF6_Thr and 5E6M_Gly show interactions of A76 with a conserved aromatic side chain N-terminal to the Motif 2 loop and a conserved arginine from Motif 3.
Figure 9.
Elements of the ‘Operational RNA Code’ (10,11). Coding properties of the tRNA acceptor stem are represented schematically, to illustrate graphically relationships from each regression model in Tables 2B and 6. Bases that do not contribute to the respective regression model are omitted. Interpretation of the schematic key is given in Figure 5.
References
- Giegé R. Thèse de Doctorat d’Etat. 1972; Strasbourg: Université Louis Pasteur.
- Martinez L., Jimenez-Rodriguez M., Gonzalez-Rivera K., Williams T., Li L., Weinreb V., Chandrasekaran S.N., Collier M., Ambroggio X., Kuhlman B. et al. Functional Class I and II amino acid activating enzymes can be coded by opposite strands of the same gene. J. Biol. Chem. 2015; 290:19710–19725. -PMC -PubMed
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