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tRNA, Anticodons, and The Wobble Hypothesis
tRNA, Anticodons, and The Wobble Hypothesis
tRNA, Anticodons, and The Wobble Hypothesis
Codon wobble positions [1]
The wobble position of a codon refers to the 3rd nucleotide in a codon. – Binding of a codon in an mRNA the cognate tRNA is much “looser” in the third position of the codon
– The genetic code is redundant whereby several different codons code for the same amino acid. Often, this redundancy is specified in the third codon position such that several codons with the same first two nucleotides, but different third position nucleotides, code for the same amino acids.
Wobble base pair [2]
A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules.[1] The four main wobble base pairs are guanine-uracil (G-U), hypoxanthine-uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C). In order to maintain consistency of nucleic acid nomenclature, “I” is used for hypoxanthine because hypoxanthine is the nucleobase of inosine;[2] nomenclature otherwise follows the names of nucleobases and their corresponding nucleosides (e.g., “G” for both guanine and guanosine – as well as for deoxyguanosine)
Wobble base pairs are fundamental in RNA secondary structure and are critical for the proper translation of the genetic code.. In the genetic code, there are 43 = 64 possible codons (3 nucleotide sequences)
If each tRNA molecule is paired with its complementary mRNA codon using canonical Watson-Crick base pairing, then 64 types of tRNA molecule would be required. In the standard genetic code, three of these 64 mRNA codons (UAA, UAG and UGA) are stop codons
Wobble base pair [3]
A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules.[1] The four main wobble base pairs are guanine-uracil (G-U), hypoxanthine-uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C). In order to maintain consistency of nucleic acid nomenclature, “I” is used for hypoxanthine because hypoxanthine is the nucleobase of inosine;[2] nomenclature otherwise follows the names of nucleobases and their corresponding nucleosides (e.g., “G” for both guanine and guanosine – as well as for deoxyguanosine)
Wobble base pairs are fundamental in RNA secondary structure and are critical for the proper translation of the genetic code.. In the genetic code, there are 43 = 64 possible codons (3 nucleotide sequences)
If each tRNA molecule is paired with its complementary mRNA codon using canonical Watson-Crick base pairing, then 64 types of tRNA molecule would be required. In the standard genetic code, three of these 64 mRNA codons (UAA, UAG and UGA) are stop codons
The Wobble Hypothesis [4]
– To explain the possible cause of degeneracy of codons, in 1966, Francis Crick proposed “the Wobble hypothesis”.. – According to this hypothesis, only the first two bases of the codon have a precise pairing with the bases of the anticodon of tRNA, while the pairing between the third bases of codon and anticodon may Wobble (wobble means to sway or move unsteadily).
Therefore, although there are 61 codons for amino acids, the number of tRNA is far less (around 40) which is due to wobbling.. The wobble hypothesis states that the base at 5′ end of the anticodon is not spatially confined as the other two bases allowing it to form hydrogen bonds with any of several bases located at the 3′ end of a codon
– At the remaining position, less stringent rules apply and non-canonical pairing may occur. The wobble hypothesis thus proposes a more flexible set of base-pairing rules at the third position of the codon.
Degenerate Code Wobble Pairing [5]
The genetic code is degenerate, meaning that multiple codons can encode a single amino acid, because the base pairing between the third position in a mRNA codon and a tRNA anticodon is flexible, a phenomenon know as wobble pairing.. There are 64 possible codons in the genetic code, and 61 of these encode 20 different amino acids
Take a look at the chart below and you’ll see that many amino acids are encoded by two or more codons. For example, the codons UCU, UCC, UCA, and UCG all code for the amino acid serine.
There are many different tRNA molecules in a cell, each with its own anticodon sequence and associated amino acid. During the pairing between mRNA codons and tRNA anticodons, some tRNAs can form base pairs with more than one codon
Codon wobble positions [6]
The wobble position of a codon refers to the 3rd nucleotide in a codon. – Binding of a codon in an mRNA the cognate tRNA is much “looser” in the third position of the codon
– The genetic code is redundant whereby several different codons code for the same amino acid. Often, this redundancy is specified in the third codon position such that several codons with the same first two nucleotides, but different third position nucleotides, code for the same amino acids.
“Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code [7]
“Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code. The genetic code evolved around the reading of the tRNA anticodon on the primitive ribosome, and tRNA-34 wobble and tRNA-37 modifications coevolved with the code
The genetic code devolved in evolution of mitochondria to reduce the size of the tRNAome (all of the tRNAs of an organism or organelle). “Superwobbling” or four-way wobbling describes a major mechanism for shrinking the mitochondrial tRNAome
During code evolution, to suppress superwobbling in 2-codon sectors, U34 modification by methylation at the 5-carbon position appears essential. As expected, at the base of code evolution, tRNA-37 modifications mostly related to the identity of the adjacent tRNA-36 base
At which position on tRNA is the wobble base of the triplet anticodon? [8]
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tRNA’s wobble decoding of the genome: 40 years of modification [9]
tRNA’s wobble decoding of the genome: 40 years of modification. tRNA’s wobble decoding of the genome: 40 years of modification
In 1966, Francis Crick hypothesized that the cell’s limited number of tRNAs decoded the genome by recognizing more than one codon. The ambiguity of that recognition resided in the third base-pair, giving rise to the Wobble Hypothesis
The Modified Wobble Hypothesis proposed in 1991 that specific modifications of a tRNA wobble nucleoside shape the anticodon architecture in such a manner that interactions were restricted to the complementary base plus a single wobble pairing for amino acids with twofold degenerate codons. However, chemically different modifications at position 34 would expand the ability of a tRNA to read three or even four of the fourfold degenerate codons
Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code [10]
Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far
We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.
Modifications of RNA are carried out by complex cellular pathways, which involve countless protein enzymes and catalytic RNA–protein complexes, which primarily target tRNAs and, to a lesser extent, ribosomal RNA and mRNAs1. The observed trends suggest that many modification motifs and their sequence locations are conserved throughout Bacteria, Archaea and Eukarya; however, some kingdom-specific differences are documented as well.
The Contributions of Wobbling and Superwobbling to the Reading of the Genetic Code [11]
Reduced bacterial genomes and most genomes of cell organelles (chloroplasts and mitochondria) do not encode the full set of 32 tRNA species required to read all triplets of the genetic code according to the conventional wobble rules. Superwobbling, in which a single tRNA species that contains a uridine in the wobble position of the anticodon reads an entire four-fold degenerate codon box, has been suggested as a possible mechanism for how tRNA sets can be reduced
Here we report a complete experimental assessment of the decoding rules in a typical prokaryotic genetic system, the plastid genome. By constructing a large set of transplastomic knock-out mutants for pairs of isoaccepting tRNA species, we show that superwobbling occurs in all codon boxes where it is theoretically possible
Finally, our data provide experimental evidence of the minimum tRNA set comprising 25 tRNA species, a number lower than previously suggested. Our results demonstrate that all triplets with pyrimidines in third codon position are dually decoded: by a tRNA species utilizing standard base pairing or wobbling and by a second tRNA species employing superwobbling
Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids [12]
The transfer RNA (tRNA) is perhaps the most important molecule in the origin and evolution of the genetic code. Just two years after the discovery of the double helix structure of DNA, F
A small nucleic acid (perhaps RNA) could serve the role of an adaptor, one part of the adaptor molecule binding a specific amino acid and another part recognizing the nucleotide sequence encoding that amino acid in an mRNA [3. These adaptors, larger than predicted by Crick, are the tRNAs soon discovered in 1958 [5
The overall process of mRNA-guided protein synthesis is often referred to simply as translation. The coding properties of each tRNA are not determined by the amino acid it carries but by the interaction of the aminoacylated tRNA with the mRNA template
Sources
- https://genomevolution.org/wiki/index.php/Codon_wobble_positions#:~:text=The%20wobble%20position%20of%20a,at%20the%20third%20codon%20position.
- https://en.wikipedia.org/wiki/Wobble_base_pair#:~:text=Movement%20(%22wobble%22)%20of,5’%2DUUU%2D3′.
- https://en.wikipedia.org/wiki/Wobble_base_pair
- https://microbenotes.com/the-wobble-hypothesis/
- https://jackwestin.com/resources/mcat-content/genetic-code/degenerate-code-wobble-pairing
- https://genomevolution.org/wiki/index.php/Codon_wobble_positions
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8879553/
- https://biology-forums.com/index.php?topic=1399847.0
- https://pubmed.ncbi.nlm.nih.gov/17187822/
- https://www.nature.com/articles/ncomms10457
- https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003076
- https://www.mdpi.com/2075-1729/4/3/341
