Phylogenetic Analysis of the Aminoacyl-tRNA synthetases

Nagel, Glenn M.; Doolittle, Russell F.

doi:10.1007/bf00166617

Cited by 128 publications

(94 citation statements)

References 32 publications

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“…Phylogenetic analysis supports that, with few exceptions, each synthetase family was present at the time of the LUCA, and inherited by each of the 3 major domains of life (Nagel and Doolittle 1995). Consequently, within each synthetase class numerous divergence events happened before the LUCA, each one a point at which the genetic code may have increased in complexity, either adding a new amino acid (neofunctionalization), or resolving a previously ambiguous specificity into two distinct amino acids (subfunctionalization).…”

Section: The Question Becomes At What Point Did Protein Synthetases mentioning

confidence: 71%

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

Fournier

Andam

Alm

et al. 2011

Orig Life Evol Biosph

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Aminoacyl-tRNA synthetases (aaRS) consist of several families of functionally conserved proteins essential for translation and protein synthesis. Like nearly all components of the translation machinery, most aaRS families are universally distributed across cellular life, being inherited from the time of the Last Universal Common Ancestor (LUCA). However, unlike the rest of the translation machinery, aaRS have undergone numerous ancient horizontal gene transfers, with several independent events detected between domains, and some possibly involving lineages diverging before the time of LUCA. These transfers reveal the complexity of molecular evolution at this early time, and the chimeric nature of genomes within cells that gave rise to the major domains. Additionally, given the role of these protein families in defining the amino acids used for protein synthesis, sequence reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl-and valyl-RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor. The implications of this observation for the early evolution of RNA-directed protein biosynthesis are discussed.

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Section: The Question Becomes At What Point Did Protein Synthetases mentioning

confidence: 71%

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

Fournier

Andam

Alm

et al. 2011

Orig Life Evol Biosph

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“…As the clues to such a hypothetical mechanism are very scarce, it is common practice to look for patterns in either one of the key constituents of the codon identity, namely, tRNAs (Eigen et al 1989;Nicholas and McClain 1995) or aaRSs (Eriani et al 1990;Ribas de Pouplana and Schimmel 2001a), and their respective evolution deduced from phylogenetic methods (Nagel and Doolittle 1995;Woese et al 2000). In the case of aaRSs, the phylogeny is complicated by a number of horizontal transfers (Wolf et al 1999).…”

Section: Introductionmentioning

confidence: 99%

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Delarue¹

2006

RNA

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Aminoacyl-tRNA synthetases (aaRSs) are responsible for creating the pool of correctly charged aminoacyl-tRNAs that are necessary for the translation of genetic information (mRNA) by the ribosome. Each aaRS belongs to either one of only two classes with two different mechanisms of aminoacylation, making use of either the 29OH (Class I) or the 39OH (Class II) of the terminal A76 of the tRNA and approaching the tRNA either from the minor groove (29OH) or the major groove (39OH). Here, an asymmetric pattern typical of differentiation is uncovered in the partition of the codon repertoire, as defined by the mechanism of aminoacylation of each corresponding tRNA. This pattern can be reproduced in a unique cascade of successive binary decisions that progressively reduces codon ambiguity. The deduced order of differentiation is manifestly driven by the reduction of translation errors. A simple rule can be defined, decoding each codon sequence in its binary class, thereby providing both the code and the key to decode it. Assuming that the partition into two mechanisms of tRNA aminoacylation is a relic that dates back to the invention of the genetic code in the RNA World, a model for the assignment of amino acids in the codon table can be derived. The model implies that the stop codon was always there, as the codon whose tRNA cannot be charged with any amino acid, and makes the prediction of an ultimate differentiation step, which is found to correspond to the codon assignment of the 22nd amino acid pyrrolysine in archaebacteria.

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“…Because of their ancient history, well-understood role, and high degree of conservation, they have been natural choices for many phylogenetic studies (Brown and Doolittle 1995;DiazLazcoz et al 1998;Hashimoto et al 1998;Kim et al 1998;Nagel and Doolittle 1995;Shiba et al 1998;Taupin and Leberman 1999;Wolf et al 1999). Unfortunately (in some respects), it appears that the evolutionary history of aaRS genes has not always been straightforward, with several proposed examples of gene duplications, fusions, and gain by horizontal transfer (DiazLazcoz et al 1998;Doolittle and Handy 1998;Lamour et al 1994;Wolf et al 1999;Handy and Doolittle 1999).…”

Section: Introductionmentioning

confidence: 99%

Duplication and Quadruplication of Arabidopsis thaliana Cysteinyl- and Asparaginyl-tRNA Synthetase Genes of Organellar Origin

et al. 2000

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Abstract. Two cysteinyl-tRNA synthetases (CysRS) and four asparaginyl-tRNA synthetases (AsnRS) from Arabidopsis thaliana were characterized from genome sequence data, EST sequences, and RACE sequences. For one CysRS and one AsnRS, sequence alignments and prediction programs suggested the presence of an N-terminal organellar targeting peptide. Transient expression of these putative targeting sequences joined to jellyfish green fluorescent protein (GFP) demonstrated that both presequences can efficiently dual-target GFP to mitochondria and plastids. The other CysRS and AsnRSs lack targeting sequences and presumably aminoacylate cytosolic tRNAs. Phylogenetic analysis suggests that the four AsnRSs evolved by repeated duplication of a gene transferred from an ancestral plastid and that the CysRSs also arose by duplication of a transferred organelle gene (possibly mitochondrial). These case histories are the best examples to date of capture of organellar aminoacyltRNA synthetases by the cytosolic protein synthesis machinery.

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Phylogenetic Analysis of the Aminoacyl-tRNA synthetases

Cited by 128 publications

References 32 publications

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Duplication and Quadruplication of Arabidopsis thaliana Cysteinyl- and Asparaginyl-tRNA Synthetase Genes of Organellar Origin

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