An increasing knowledge concerning the genetic code helped us to better understand the mechanisms of translation. Now being a text-book knowledge, the genetic code is made up of 64 codons, of which 61 code for amino acids and three for stop codons. Corresponding number of tRNAs is needed for pairing with complementary triplets in mRNA using canonical Watson-Crick base pairing. However, most organisms encode less than 45 types of tRNA, with some of them capable of pairing with multiple codons, all of which encode the same amino acid. This led to the proposition of the wobble hypothesis stating that the 5’ nucleotide of the anticodon which pairs with the 3’ nucleotide of the codon, unlike the other two bases, have non-standard base pairing. Moreover, the possibility of non-canonical base-pairing widens the range of codons one anticodon can decode.
For a long time, the genetic code was thought to be universally conserved in the extant life forms, ranging from viruses to whales. However, within the last several decades, over 30 alternative of the genetic code have been discovered, in which selected codons have been reassigned to code for amino acid different from the canonical code. There are three types of codon reassignment: sense-to-sense, sense-to-stop, and stop-to-sense. Codon reassignment can occur due to changes in tRNA anticodons, modifications of tRNA wobble nucleotides, recognition of cognate tRNAs by aminoacyl-tRNA synthetases, or the fidelity of stop codon recognition by eukaryotic release factors.
Several hypotheses have been proposed to explain this codon reassignment. One of them is the codon capture hypothesis which postulates that following a mutation bias that changes the GC content of a given genome, several codons and their corresponding cognate tRNAs are gradually eliminated. Alternatively, the ambiguous intermediate hypothesis assumes the presence of two competing tRNAs with the same anticodon but different backbone which are differently charged. While codon reassignment is significantly more frequent in the mitochondria, the mechanisms of reassignments in organisms, mostly protists, remain mostly unclear.
The alternative genetic code is widely prevalent across various eukaryotic organisms, including ciliates, diplomads, yeast, green algae, and more. In the case of the trypanosomatid parasite Blastocrithidia, all three stop codons have been reassigned as sense codons. While the genome contains fully cognate tRNAs for UAA and UAG, the tRNA responsible for reading UGA is a tryptophan tRNA with an unusual 4bp anticodon stem. This unique adaptation allows efficient binding at the in-frame UGA, facilitated by a mutation in eRF1, providing valuable mechanistic insights into stop codon reassignment.
However, this discovery raises intriguing questions. If these organisms reassign all stop codons, how does translation termination occur? Moreover, what implications does reassigning other sense codons have on the genetic code’s meaning? Understanding the mechanisms behind codon reassignment holds potential in medical research. Synthetic tRNAs designed to recognize premature stop codons could offer promising avenues for addressing certain genetic diseases.
Lastly, the evolution of genetics, once believed to be “frozen” within a certain timeframe, demonstrates the fallibility of our scientific discoveries, assumptions, and theories. Scientific facts are not immutable; they remain until better science emerges to challenge and refine our understanding.
References:
1- Kollmar, M., and Mühlhausen, S. (2017). Nuclear codon reassignments in the genomics era and mechanisms behind their evolution. Bioessays 39.
2- Kachale, A., Pavlíková, Z., Nenarokova, A., Roithová, A., Durante, I.M., Miletínová, P., Záhonová, K., Nenarokov, S., Votýpka, J., Horáková, E., et al. (2023). Short tRNA anticodon stem and mutant eRF1 allow stop codon reassignment. Nature 613, 751–758..
3- Crick, F.H.C. (1966). Codon—anticodon pairing: The wobble hypothesis. Journal of Molecular Biology 19, 548
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