Interaction Network of Human Aminoacyl-tRNA Synthetases and Subunits of Elongation Factor 1 Complex

2002 ◽  
Vol 291 (1) ◽  
pp. 158-164 ◽  
Author(s):  
Jong Sang Lee ◽  
Sang Gyu Park ◽  
Heonyong Park ◽  
Wongi Seol ◽  
Sangwon Lee ◽  
...  
Keyword(s):  
Elongation Factor ◽  
Interaction Network ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
Elongation Factor 1

scholarly journals Exclusive Use of trans-Editing Domains Prevents Proline Mistranslation

2013 ◽  
Vol 288 (20) ◽  
pp. 14391-14399 ◽  
Author(s):  
Oscar Vargas-Rodriguez ◽  
Karin Musier-Forsyth
Keyword(s):  
Amino Acids ◽  
Catalytic Activity ◽  
Bioinformatics Analysis ◽  
Caulobacter Crescentus ◽  
Protein A ◽  
Elongation Factor ◽  
Single Domain ◽  
Elongation Factor Tu ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases

Aminoacyl-tRNA synthetases (ARSs) catalyze the attachment of specific amino acids to cognate tRNAs. Although the accuracy of this process is critical for overall translational fidelity, similar sizes of many amino acids provide a challenge to ARSs. For example, prolyl-tRNA synthetases (ProRSs) mischarge alanine and cysteine onto tRNAPro. Many bacterial ProRSs possess an alanine-specific proofreading domain (INS) but lack the capability to edit Cys-tRNAPro. Instead, Cys-tRNAPro is cleared by a single-domain homolog of INS, the trans-editing YbaK protein. A global bioinformatics analysis revealed that there are six types of “INS-like” proteins. In addition to INS and YbaK, four additional single-domain homologs are widely distributed throughout bacteria: ProXp-ala (formerly named PrdX), ProXp-x (annotated as ProX), ProXp-y (annotated as YeaK), and ProXp-z (annotated as PA2301). The last three are domains of unknown function. Whereas many bacteria encode a ProRS containing an INS domain in addition to YbaK, many other combinations of INS-like proteins exist throughout the bacterial kingdom. Here, we focus on Caulobacter crescentus, which encodes a ProRS with a truncated INS domain that lacks catalytic activity, as well as YbaK and ProXp-ala. We show that C. crescentus ProRS can readily form Cys- and Ala-tRNAPro, and deacylation studies confirmed that these species are cleared by C. crescentus YbaK and ProXp-ala, respectively. Substrate specificity of C. crescentus ProXp-ala is determined, in part, by elements in the acceptor stem of tRNAPro and further ensured through collaboration with elongation factor Tu. These results highlight the diversity of approaches used to prevent proline mistranslation and reveal a novel triple-sieve mechanism of editing that relies exclusively on trans-editing factors.

scholarly journals Adaptive Partitioning of the tRNA Interaction Interface by Aminoacyl-tRNA-Synthetases

2018 ◽  
Author(s):  
Andy Collins-Hed ◽  
David H. Ardell
Keyword(s):  
Feature Matching ◽  
Interaction Network ◽  
Interaction Networks ◽  
Dynamic Features ◽  
Macroscopic Theory ◽  
Trna Synthetases ◽  
Translational Accuracy ◽  
Aminoacyl Trna Synthetases ◽  
Genotype Frequencies ◽  
Selection For

AbstractWe introduce rugged fitness landscapes called match landscapes for the coevolution of feature-based assortative interactions between P ≥ 2 cognate pairs of tRNAs and aminoacyl-tRNA synthetases (aaRSs) in aaRS-tRNA interaction networks. Our genotype-phenotype-fitness maps assume additive feature-matching energies, a macroscopic theory of aminoacylation kinetics including proofreading, and selection for translational accuracy in multiple, perfectly encoded site-types. We compute the stationary genotype distributions of finite panmictic, asexual populations of haploid aaRs-tRNA interaction networks evolving under mutation, genetic drift, and selection for cognate matching and non-cognate mismatching of aaRS-tRNA pairs. We compared expected genotype frequencies under different matching rules and fitness functions, both with and without linked site-specific modifiers of interaction. Under selection for translational accuracy alone, our model predicts no selection on modifiers to eliminate non-cognate interactions, so long as they are compensated by tighter cognate interactions. Only under combined selection for both translational accuracy and rate do modifiers adaptively eliminate cross-matching in non-cognate aaRS/tRNA pairs. We theorize that the encoding of macromolecular interaction networks is a genetic language that symbolically maps identifying structural and dynamic features of genes and gene-products to functions within cells. Our theory helps explain 1) the remarkable divergence in how aaRSs bind tRNAs, 2) why interaction-informative features are phylogenetically informative, 3) why the Statistical Tree of Life became more tree-like after the Darwinian Transition, and 4) an approach towards computing the probability of the random origin of an interaction network.

scholarly journals Molecular evolution of protein-RNA mimicry as a mechanism for translational control

2013 ◽  
Vol 42 (5) ◽  
pp. 3261-3271 ◽  
Author(s):  
Assaf Katz ◽  
Lindsey Solden ◽  
S. Betty Zou ◽  
William Wiley Navarre ◽  
Michael Ibba
Keyword(s):  
Translational Control ◽  
Elongation Factor ◽  
Trna Synthetase ◽  
Post Translational Modification ◽  
Translation Control ◽  
Trna Synthetases ◽  
Ribosome Binding ◽  
Trna Recognition ◽  
Aminoacyl Trna Synthetases ◽  
Secondary Mechanism

Abstract Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by the lysyl-tRNA synthetase paralog PoxA. To investigate how recognition of EF-P by PoxA evolved from tRNA recognition by aminoacyl-tRNA synthetases, we compared the roles of EF-P/PoxA polar contacts with analogous interactions in a closely related tRNA/synthetase complex. PoxA was found to recognize EF-P solely via identity elements in the acceptor loop, the domain of the protein that interacts with the ribosome peptidyl transferase center and mimics the 3'-acceptor stem of tRNA. Although the EF-P acceptor loop residues required for PoxA recognition are highly conserved, their conservation was found to be independent of the phylogenetic distribution of PoxA. This suggests EF-P first evolved tRNA mimicry to optimize interactions with the ribosome, with PoxA-catalyzed aminoacylation evolving later as a secondary mechanism to further improve ribosome binding and translation control.

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