scholarly journals Clues to tRNA Evolution from the Distribution of Class II tRNAs and Serine Codons in the Genetic Code

Life ◽  
2016 ◽  
Vol 6 (1) ◽  
pp. 10 ◽  
Author(s):  
Harold Bernhardt
Keyword(s):  
Genetic Code ◽  
Class Ii ◽  
Trna Evolution ◽  
Serine Codons

scholarly journals The fidelity of the translation of the genetic code.

2001 ◽  
Vol 48 (2) ◽  
pp. 323-335 ◽  
Author(s):  
R Sankaranarayanan ◽  
D Moras
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Structural Information ◽  
Class Ii ◽  
Zinc Ion ◽  
Trna Synthetase ◽  
Class I ◽  
Structural Basis ◽  
Clear Understanding

Aminoacyl-tRNA synthetases play a central role in maintaining accuracy during the translation of the genetic code. To achieve this challenging task they have to discriminate against amino acids that are very closely related not only in structure but also in chemical nature. A 'double-sieve' editing model was proposed in the late seventies to explain how two closely related amino acids may be discriminated. However, a clear understanding of this mechanism required structural information on synthetases that are faced with such a problem of amino acid discrimination. The first structural basis for the editing model came recently from the crystal structure of isoleucyl-tRNA synthetase, a class I synthetase, which has to discriminate against valine. The structure showed the presence of two catalytic sites in the same enzyme, one for activation, a coarse sieve which binds both isoleucine and valine, and another for editing, a fine sieve which binds only valine and rejects isoleucine. Another structure of the enzyme in complex with tRNA showed that the tRNA is responsible for the translocation of the misactivated amino-acid substrate from the catalytic site to the editing site. These studies were mainly focused on class I synthetases and the situation was not clear about how class II enzymes discriminate against similar amino acids. The recent structural and enzymatic studies on threonyl-tRNA synthetase, a class II enzyme, reveal how this challenging task is achieved by using a unique zinc ion in the active site as well as by employing a separate domain for specific editing activity. These studies led us to propose a model which emphasizes the mirror symmetrical approach of the two classes of enzymes and highlights that tRNA is the key player in the evolution of these class of enzymes.

scholarly journals Type-II tRNAs and Evolution of Translation Systems and the Genetic Code

2018 ◽  
Vol 19 (10) ◽  
pp. 3275 ◽  
Author(s):  
Yunsoo Kim ◽  
Bruce Kowiatek ◽  
Kristopher Opron ◽  
Zachary Burton
Keyword(s):  
Genetic Code ◽  
Type I ◽  
Type Ii ◽  
Trna Synthetases ◽  
The Core ◽  
Cellular Life ◽  
Evolution Of Life ◽  
Trna Evolution ◽  
Life On Earth ◽  
Translation Systems

Because tRNA is the core biological intellectual property that was necessary to evolve translation systems, tRNAomes, ribosomes, aminoacyl-tRNA synthetases, and the genetic code, the evolution of tRNA is the core story in evolution of life on earth. We have previously described the evolution of type-I tRNAs. Here, we use the same model to describe the evolution of type-II tRNAs, with expanded V loops. The models are strongly supported by inspection of typical tRNA diagrams, measuring lengths of V loop expansions, and analyzing the homology of V loop sequences to tRNA acceptor stems. Models for tRNA evolution provide a pathway for the inanimate-to-animate transition and for the evolution of translation systems, the genetic code, and cellular life.

scholarly journals A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code

Life ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 37 ◽  
Author(s):  
Yunsoo Kim ◽  
Kristopher Opron ◽  
Zachary F. Burton
Keyword(s):  
Genetic Code ◽  
Class Ii ◽  
Trna Synthetase ◽  
Class I ◽  
Protein Fold ◽  
Standard Genetic Code ◽  
Structural Class ◽  
Trna Synthetases ◽  
Protein Fold Recognition ◽  
Coevolution Theory

Pathways of standard genetic code evolution remain conserved and apparent, particularly upon analysis of aminoacyl-tRNA synthetase (aaRS) lineages. Despite having incompatible active site folds, class I and class II aaRS are homologs by sequence. Specifically, structural class IA aaRS enzymes derive from class IIA aaRS enzymes by in-frame extension of the protein N-terminus and by an alternate fold nucleated by the N-terminal extension. The divergence of aaRS enzymes in the class I and class II clades was analyzed using the Phyre2 protein fold recognition server. The class I aaRS radiated from the class IA enzymes, and the class II aaRS radiated from the class IIA enzymes. The radiations of aaRS enzymes bolster the coevolution theory for evolution of the amino acids, tRNAomes, the genetic code, and aaRS enzymes and support a tRNA anticodon-centric perspective. We posit that second- and third-position tRNA anticodon sequence preference (C>(U~G)>A) powerfully selected the sectoring pathway for the code. GlyRS-IIA appears to have been the primordial aaRS from which all aaRS enzymes evolved, and glycine appears to have been the primordial amino acid around which the genetic code evolved.

Electron microscopy analysis of degenerating pancreatic ß cells in transgenic mice expressing the MHC Class I antigen Dd

1990 ◽  
Vol 48 (3) ◽  
pp. 548-549
Author(s):  
T. A. Stewart ◽  
D. Liggitt ◽  
S. Pitts ◽  
L. Martin ◽  
M. Siegel ◽  
...  
Keyword(s):  
Type I Diabetes ◽  
Disease Process ◽  
Class Ii ◽  
Class I ◽  
Type I ◽  
Aberrant Expression ◽  
Mhc Molecules ◽  
Endogenous Insulin ◽  
Class Ii Mhc ◽  
Ifn Γ

Insulin-dependant (Type I) diabetes mellitus (IDDM) is a metabolic disorder resulting from the lack of endogenous insulin secretion. The disease is thought to result from the autoimmune mediated destruction of the insulin producing ß cells within the islets of Langerhans. The disease process is probably triggered by environmental agents, e.g. virus or chemical toxins on a background of genetic susceptibility associated with particular alleles within the major histocompatiblity complex (MHC). The relation between IDDM and the MHC locus has been reinforced by the demonstration of both class I and class II MHC proteins on the surface of ß cells from newly diagnosed patients as well as mounting evidence that IDDM has an autoimmune pathogenesis. In 1984, a series of observations were used to advance a hypothesis, in which it was suggested that aberrant expression of class II MHC molecules, perhaps induced by gamma-interferon (IFN γ) could present self antigens and initiate an autoimmune disease. We have tested some aspects of this model and demonstrated that expression of IFN γ by pancreatic ß cells can initiate an inflammatory destruction of both the islets and pancreas and does lead to IDDM.

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