The evolution of aminoacyl-tRNA synthetases, the biosynthetic pathways of amino acids and the genetic code

The genetic code defines how information in the genome is translated into protein. Aside from a handful of isolated exceptions, this code is universal. Researchers have developed techniques to artificially expand the genetic code, repurposing codons and translational machinery to incorporate nonstandard amino acids (nsAAs) into proteins. A key challenge for robust genetic code expansion is orthogonality; the engineered machinery used to introduce nsAAs into proteins must co-exist with native translation and gene expression without cross-reactivity or pleiotropy. The issue of orthogonality manifests at several levels, including those of codons, ribosomes, aminoacyl-tRNA synthetases, tRNAs, and elongation factors. In this concept paper, we describe advances in genome recoding, translational engineering and associated challenges rooted in establishing orthogonality needed to expand the genetic code.

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Oxidation of cellular amino acid pools leads to cytotoxic mistranslation of the genetic code

eLife ◽

10.7554/elife.02501 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 56

Author(s):

Tammy J Bullwinkle ◽

Noah M Reynolds ◽

Medha Raina ◽

Adil Moghal ◽

Eleftheria Matsa ◽

...

Keyword(s):

Amino Acids ◽

Protein Synthesis ◽

Amino Acid ◽

Genetic Code ◽

Trna Synthetase ◽

Control Mechanisms ◽

Cellular Toxicity ◽

Trna Synthetases ◽

Aminoacyl Trna Synthetases ◽

The Cost

Aminoacyl-tRNA synthetases use a variety of mechanisms to ensure fidelity of the genetic code and ultimately select the correct amino acids to be used in protein synthesis. The physiological necessity of these quality control mechanisms in different environments remains unclear, as the cost vs benefit of accurate protein synthesis is difficult to predict. We show that in Escherichia coli, a non-coded amino acid produced through oxidative damage is a significant threat to the accuracy of protein synthesis and must be cleared by phenylalanine-tRNA synthetase in order to prevent cellular toxicity caused by mis-synthesized proteins. These findings demonstrate how stress can lead to the accumulation of non-canonical amino acids that must be excluded from the proteome in order to maintain cellular viability.

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Evolution of the genetic code based on conservative changes of codons, amino acids, and aminoacyl tRNA synthetases

Journal of Theoretical Biology ◽

10.1016/j.jtbi.2019.01.022 ◽

2019 ◽

Vol 466 ◽

pp. 1-10 ◽

Cited By ~ 16

Author(s):

Scott O. Rogers

Keyword(s):

Amino Acids ◽

Genetic Code ◽

Trna Synthetases ◽

Aminoacyl Trna Synthetases

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On the Classes of Aminoacyl-tRNA Synthetases, Amino Acids and the Genetic Code

Origins of Life and Evolution of Biospheres ◽

10.1023/b:orig.0000029881.14519.42 ◽

2004 ◽

Vol 34 (4) ◽

pp. 407-420 ◽

Cited By ~ 13

Author(s):

Andre R. O. Cavalcanti ◽

Elisa Soares Leite ◽

Benício B. Neto ◽

Ricardo Ferreira

Keyword(s):

Amino Acids ◽

Genetic Code ◽

Trna Synthetases ◽

Aminoacyl Trna Synthetases

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Aminoacyl-tRNA Synthetases and tRNAs for an Expanded Genetic Code: What Makes them Orthogonal?

International Journal of Molecular Sciences ◽

10.3390/ijms20081929 ◽

2019 ◽

Vol 20 (8) ◽

pp. 1929 ◽

Cited By ~ 6

Author(s):

Sergey V. Melnikov ◽

Dieter Söll

Keyword(s):

Amino Acids ◽

Synthetic Biology ◽

Genetic Code ◽

Unnatural Amino Acids ◽

Trna Synthetases ◽

Cross Reactions ◽

The Past ◽

Aminoacyl Trna Synthetases ◽

Expanded Genetic Code ◽

Fundamental Requirement

In the past two decades, tRNA molecules and their corresponding aminoacyl-tRNA synthetases (aaRS) have been extensively used in synthetic biology to genetically encode post-translationally modified and unnatural amino acids. In this review, we briefly examine one fundamental requirement for the successful application of tRNA/aaRS pairs for expanding the genetic code. This requirement is known as “orthogonality”—the ability of a tRNA and its corresponding aaRS to interact exclusively with each other and avoid cross-reactions with additional types of tRNAs and aaRSs in a given organism.

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Destruxin A Interacts with Aminoacyl tRNA Synthases in Bombyx mori

Journal of Fungi ◽

10.3390/jof7080593 ◽

2021 ◽

Vol 7 (8) ◽

pp. 593

Author(s):

Jingjing Wang ◽

Alexander Berestetskiy ◽

Qiongbo Hu

Keyword(s):

Amino Acids ◽

Protein Synthesis ◽

Bombyx Mori ◽

Metarhizium Anisopliae ◽

Free Amino ◽

Molecular Target ◽

Trna Synthetases ◽

Interaction Mode ◽

Aminoacyl Trna Synthetases ◽

Wide Range

Destruxin A (DA), a hexa-cyclodepsipeptidic mycotoxin produced by the entomopathogenic fungus Metarhizium anisopliae, exhibits insecticidal activities in a wide range of pests and is known as an innate immunity inhibitor. However, its mechanism of action requires further investigation. In this research, the interactions of DA with the six aminoacyl tRNA synthetases (ARSs) of Bombyx mori, BmAlaRS, BmCysRS, BmMetRS, BmValRS, BmIleRS, and BmGluProRS, were analyzed. The six ARSs were expressed and purified. The BLI (biolayer interferometry) results indicated that DA binds these ARSs with the affinity indices (KD) of 10−4 to 10−5 M. The molecular docking suggested a similar interaction mode of DA with ARSs, whereby DA settled into a pocket through hydrogen bonds with Asn, Arg, His, Lys, and Tyr of ARSs. Furthermore, DA treatments decreased the contents of soluble protein and free amino acids in Bm12 cells, which suggested that DA impedes protein synthesis. Lastly, the ARSs in Bm12 cells were all downregulated by DA stress. This study sheds light on exploring and answering the molecular target of DA against target insects.

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Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.64.1.202-236.2000 ◽

2000 ◽

Vol 64 (1) ◽

pp. 202-236 ◽

Cited By ~ 447

Author(s):

Carl R. Woese ◽

Gary J. Olsen ◽

Michael Ibba ◽

Dieter Söll

Keyword(s):

Genetic Code ◽

Phylogenetic Trees ◽

Genetic Material ◽

Evolutionary Process ◽

Group Iv ◽

Evolutionary Relationships ◽

Evolutionary Stage ◽

Trna Synthetases ◽

Aminoacyl Trna Synthetases ◽

The Individual

SUMMARY The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the “gemini group.” (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense.

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Measuring the tolerance of the genetic code to altered codon size

10.1101/2021.04.26.441066 ◽

2021 ◽

Author(s):

E. DeBenedictis ◽

D. Söll ◽

K. Esvelt

Keyword(s):

Genetic Code ◽

Protein Translation ◽

Single Amino Acid ◽

Trna Synthetases ◽

E Coli ◽

Aminoacyl Trna Synthetases ◽

Triplet Codon ◽

Orthogonal Set ◽

Expanded Genetic Code ◽

Primordial Earth

SummaryProtein translation using four-base codons occurs in both natural and synthetic systems. What constraints contributed to the universal adoption of a triplet-codon, rather than quadruplet-codon, genetic code? Here, we investigate the tolerance of the E. coli genetic code to tRNA mutations that increase codon size. We found that tRNAs from all twenty canonical isoacceptor classes can be converted to functional quadruplet tRNAs (qtRNAs), many of which selectively incorporate a single amino acid in response to a specified four-base codon. However, efficient quadruplet codon translation often requires multiple tRNA mutations, potentially constraining evolution. Moreover, while tRNAs were largely amenable to quadruplet conversion, only nine of the twenty aminoacyl tRNA synthetases tolerate quadruplet anticodons. These constitute a functional and mutually orthogonal set, but one that sharply limits the chemical alphabet available to a nascent all-quadruplet code. Our results illuminate factors that led to selection and maintenance of triplet codons in primordial Earth and provide a blueprint for synthetic biologists to deliberately engineer an all-quadruplet expanded genetic code.

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Chaos, Order and Systematics in Evolution of the Genetic Code

10.20944/preprints202009.0162.v2 ◽

2020 ◽

Author(s):

Lei Lei ◽

Zachary F. Burton

Keyword(s):

Genetic Code ◽

Life Transition ◽

Life World ◽

Phase Separations ◽

Fiber Production ◽

Trna Synthetases ◽

Cellular Life ◽

Aminoacyl Trna Synthetases ◽

Translation Systems ◽

Liquid Liquid Phase Separation

The genetic code evolved by parallel tracks of chaotic and ordered processes. Liquid-liquid phase separation (hydrogels), a chaotic process, constructs diverse membraneless compartments within cells, resulting in regulated hydration and sequestration and concentration of reaction components. Hydrogels relate to chaotic amyloid fiber production. We propose that polyglycine and related hydrogels (i.e. GADV; G is glycine), phase separations, membraneless droplets and amyloid accretions organized protocell domains to drive the earliest evolution of the genetic code and the pre-life to cellular life transition. By contrast, evolution of tRNA, tRNAomes, aminoacyl-tRNA synthetases and translation systems followed highly ordered and systematic pathways, described by well-defined mechanisms and rules. The pathway of evolution of aminoacyl-tRNA synthetases, which tracked evolution of the genetic code, is clarified. Hydrogels and amyloids form a chaotic component, therefore, that complemented otherwise systematic processes. We describe with detail a pre-life world in which hydrogels and amyloids provided the selections of the first life.

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