Plasmodium apicoplast tyrosyl-tRNA synthetase recognizes an unusual, simplified identity set in cognate tRNATyr

Cela, Marta; Paulus, Caroline; Santos, Manuel A. S.; Moura, Gabriela; Frugier, Magali; Rudinger-Thirion, Joëlle

doi:10.1371/journal.pone.0209805

Cited by 4 publications

(4 citation statements)

References 58 publications

(83 reference statements)

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“…In apicoplasts, identity rules are likely also simplified as found in the Tyr system. Here, charging of api-tRNA Tyr by cognate Plasmodium falciparum api-TyrRS is promoted by only three weak positive identity elements in the tRNA and likely relies on negative recognition determinants and on the idiosyncratic sequence insertions in api-aaRSs, notably in TyrRS (Cela et al, 2018). Other idiosyncrasies in tRNA-synthetase systems correlated with identity are linked to taxaspecific sequence variabilities in both canonical and atypical systems.…”

Section: Origin Ancestry Doubtful Coevolutions and Idiosyncrasiesmentioning

confidence: 95%

Transfer RNA Recognition and Aminoacylation by Synthetases

Giegé

Eriani

2021

Encyclopedia of Life Sciences

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Fidelity of transfer ribonucleic acid (tRNA) charging by amino acids ensures correct translation of the genetic code into proteins. Charging is catalysed by a set of enzymes known as aminoacyl-tRNA synthetases. Owing to the degeneracy of the genetic code, some of the different tRNAs have the same amino acid attached to them. Specificity of charging obeys universal rules and is ensured by positive elements, the identity determinants unique to each tRNA and responsible for its recognition by the cognate synthetase, and negative elements, the antideterminants that prevent false recognitions. To fulfil the aminoacylation specificity and prevent noncognate aminoacyl-tRNA delivery to the ribosome, some synthetases also mediate proofreading reactions that increase fidelity of the tRNA charging. In such reactions, misactivated amino acids or mischarged tRNAs are checked in specific sites and noncognate products are hydrolysed. However, mischarging is beneficial under certain stress circumstances or when catalysed by nondiscriminatory synthetases, and represents a driving force in evolution. Key Concepts:•Translational expression of the genetic code refers to aminoacyl-tRNA-and ribosomedependent decoding of genes into proteins, a process highly dependent on fidelity of tRNA aminoacylation by synthetases.•The rules that account for the aminoacylation identity of tRNAs are referred to as the second genetic code.•The RNA operational code is encoded in the acceptor stem of tRNA and is crucial for recognition by aminoacyl-tRNA synthetases and specific aminoacylation.•Allostery in tRNA-synthetase systems concerns long-range transfer of chemical information (up to 75 Å) to the synthetase catalytic site (through the body of tRNA and/or synthetase) triggered by contacts of tRNA identity determinants with the synthetase.•Engineering the identity of tRNA-synthetase systems allows reprogramming the genetic code.

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Section: Origin Ancestry Doubtful Coevolutions and Idiosyncrasiesmentioning

confidence: 95%

Transfer RNA Recognition and Aminoacylation by Synthetases

Giegé

Eriani

2021

Encyclopedia of Life Sciences

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“…This probably results from the high AT content of the Plasmodium apicoplast genome and the resulting mutational pressure on the tRNA Tyr gene. How efficiently and specifically tRNA Tyr is aminoacylated in the apicoplast could be explained by the presence of additional antideterminants in tRNA Tyr or additional idiosyncratic peptides in TyrRS ( 303 ).…”

Section: Identities In Atypical Trna Folds and Organellar Trnasmentioning

confidence: 99%

The tRNA identity landscape for aminoacylation and beyond

Giegé

Eriani

2023

Nucleic Acids Research

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tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.

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“…Recognition rules for non-metazoans are poorly understood but have been examined in an Apicomplexan tyrosine system from Plasmodium (Cela et al 2018 ). In that organism a minimalistic set of elements compared with the evolutionarily conserved positions was detected.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Adjustment of tRNA Identity Rules in Bacillariophyta for Recognition by an Aminoacyl-tRNA Synthetase Adds a Facet to the Origin of Diatoms

Igloi

2022

J Mol Evol

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Error-free protein synthesis relies on the precise recognition by the aminoacyl-tRNA synthetases of their cognate tRNAs in order to attach the corresponding amino acid. A concept of universal tRNA identity elements requires the aminoacyl-tRNA synthetases provided by the genome of an organism to match the identity elements found in the cognate tRNAs in an evolution-independent manner. Identity elements tend to cluster in the tRNA anticodon and acceptor stem regions. However, in the arginine system, in addition to the anticodon, the importance of nucleotide A20 in the tRNA D-loop for cognate enzyme recognition has been a sustained feature for arginyl-tRNA synthetase in archaea, bacteria and in the nuclear-encoded cytosolic form in mammals and plants. However, nuclear-encoded mitochondrial arginyl-tRNA synthetase, which can be distinguished from its cytosolic form by the presence or absence of signature motifs, dispenses with the A20 requirement. An examination of several hundred non-metazoan organisms and their corresponding tRNAArg substrates has confirmed this general concept to a large extent and over numerous phyla. However, some Stramenopiles, and in particular, Diatoms (Bacillariophyta) present a notable exception. Unusually for non-fungal organisms, the nuclear genome encodes tRNAArg isoacceptors with C or U at position 20. In this case one of two nuclear-encoded cytosolic arginyl-tRNA synthetases has evolved to become insensitive to the nature of the D-loop identity element. The other, with a binding pocket that is compatible with tRNAArg-A20 recognition, is targeted to organelles that encode solely such tRNAs.

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Plasmodium apicoplast tyrosyl-tRNA synthetase recognizes an unusual, simplified identity set in cognate tRNATyr

Cited by 4 publications

References 58 publications

Transfer RNA Recognition and Aminoacylation by Synthetases

Transfer RNA Recognition and Aminoacylation by Synthetases

The tRNA identity landscape for aminoacylation and beyond

Evolutionary Adjustment of tRNA Identity Rules in Bacillariophyta for Recognition by an Aminoacyl-tRNA Synthetase Adds a Facet to the Origin of Diatoms

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