wobble hypothesis pdf

Microbe Notes

The Wobble Hypothesis: Definition, Statement, Significance

There are more than one codon for one amino acid . This is called degeneracy of genetic code. To explain the possible cause of degeneracy of codons, in 1966, Francis Crick proposed “the Wobble hypothesis”.

According to The Wobble 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).

The phenomenon permits a single tRNA to recognize more than one codon. Therefore, although there are 61 codons for amino acids, the number of tRNA is far less (around 40) which is due to wobbling.

Table of Contents

Interesting Science Videos

The Wobble Hypothesis Statement

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.

This leads to the following conclusions:

The first two bases of the codon make normal (canonical) H-bond pairs with the 2nd and 3rd bases of the anticodon.
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.
The relaxed base-pairing requirement, or “wobble,” allows the anticodon of a single form of tRNA to pair with more than one triplet in mRNA.
The rules: first base U can recognize A or G, first base G can recognize U or C, and first base I can recognize U, C or A.

Crick’s hypothesis hence predicts that the initial two ribonucleotides of triplet codes are often more critical than the third member in attracting the correct tRNA.

Wobble base pairs

A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules.
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.
Inosine displays the true qualities of wobble, in that if that is the first nucleotide in the anticodon then any of three bases in the original codon can be matched with the tRNA.

Significance of the Wobble Hypothesis

Our bodies have a limited amount of tRNAs, and wobble allows for broad specificity.
Wobble base pairs have been shown to facilitate many biological functions, most clearly proven in the bacterium Escherichia coli .
The thermodynamic stability of a wobble base pair is comparable to that of a Watson-Crick base pair.
Wobble base pairs are fundamental in RNA secondary structure and are critical for the proper translation of the genetic code.
Wobbling allows faster dissociation of tRNA from mRNA and also protein synthesis.
The existence of wobble minimizes the damage that can be caused by a misreading of the code; for example, if the Leu codon CUU were misread CUC or CUA or CUG during transcription of mRNA, the codon would still be translated as Leu during protein synthesis.
Verma, P. S., & Agrawal, V. K. (2006). Cell Biology, Genetics, Molecular Biology, Evolution & Ecology (1 ed.). S .Chand and company Ltd.
Klug, W. S., & Cummings, M. R. (2003). Concepts of genetics. Upper Saddle River, N.J: Prentice Hall.
https://www.slideshare.net/sweetmerrymindfreak/genetic-code-53764823
https://www.slideshare.net/ArchaDave/genetic-code-24735057
https://www.scribd.com/document/344722502/Wobble-hyothesis-pdf
https://en.wikipedia.org/wiki/Wobble_base_pair#Wobble_hypothesis

About Author

Sagar Aryal

2 thoughts on “The Wobble Hypothesis: Definition, Statement, Significance”

I need help to drow my method how i contact you my email is [email protected]

nice explaination

The Wobble Hypothesis: Importance and Examples

The “wobble hypothesis” refers to a concept in molecular biology that explains the degeneracy of codons.

Since there are only 20 amino acids and 64 possible codons, multiple codons may code for a single amino acid during protein synthesis. In molecular biology, this redundancy or multiplicity of codons is termed degeneracy.

This hypothesis helps explain how a relatively limited number of tRNA molecules can recognize and bind to multiple codons for the same amino acid, facilitating efficient and accurate protein synthesis. Experimental evidence has supported the wobble hypothesis, a fundamental concept in understanding the genetic code and translation machinery.\

Table of Contents

Importance of Wobble Hypothesis

Overall, the wobble hypothesis plays a fundamental role in understanding protein synthesis and the genetic code, with implications for various aspects of molecular biology, genetics, and biotechnology.

Examples of Wobble Hypothesis

Here are some examples of the wobble hypothesis in action:

Limitation of Wobble Hypothesis

Hello, I am Ashma Shrestha. I had recently completed my Masters degree in Medical Microbiology. Passionate about writing and blogging. Key interest in virology and molecular biology.

We love to get your feedback. Share your queries or comments Cancel reply

This site uses Akismet to reduce spam. Learn how your comment data is processed .

Celebrating wobble decoding: Half a century and still much is new

Paul f. agris.

a The RNA Institute, State University of New York, Albany, NY, USA

b Department of Biology, State University of New York, Albany, NY, USA

c Department of Chemistry, State University of New York, Albany, NY, USA

Emily R. Eruysal

Amithi narendran, ville y. p. väre, sweta vangaveti, srivathsan v. ranganathan.

A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.

Introduction

Translation of the Universal Genetic Code ( Fig. 1 ) into the amino acid sequence of proteins requires accurate and efficient decoding of mRNA (mRNA) on the ribosome by tRNA (tRNA). Sixty-one of 64 3-nucleoside codons of the mRNA, N1N2N3, are decoded in frame with a complementary sequence of the tRNA anticodon, N 34 N 35 N 36 . Three codons are recognized by protein factors and correspond to translation termination signals. Complementariness of base pairing between tRNA's anticodon and the mRNA codon, A•U, U•A, G•C and C•G where • denotes canonical Watson-Crick hydrogen bonding, does not explain how the 61 amino acid codons are decoded by far fewer tRNAs. Fifty years ago, Francis Crick published the Wobble Hypothesis. 1 At the time there was evidence to suggest that the first two positions, N1N2, of mRNA's 3-nucleoside codons were uniquely identified by the tRNA with some ambiguity in the third position. Crick offered the idea that uridine (U) at the first position of the anticodon, position 34 in tRNA ( Fig. 2 ), would base pair with guanosine (G) and that inosine (I), which at the time had only recently been found at position 34 in yeast tRNA Ala , 2 would base pair with uridine, cytidine (C) and adenosine (A). Thus, canonical, Watson-Crick base pairing with tRNA and mRNA on the ribosome was supplemented with non-canonical hydrogen bonding, ‘wobble’ base pairing, including that of a purine with another purine. Though conceding that the wobble position base pairing of two purines would widen the anticodon-codon double helix at the point of an I 34 ○A3 base pair where A3 is the third nucleoside of the codon and ○ denotes non-canonical hydrogen bonding, Crick excluded the possibility of a wobble position pyrimidine-pyrimidine base pairing. He argued that the narrowing of the helix would be too dramatic in comparison to the neighboring canonical purine-pyrimidine distances at the first and second positions.

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g001.jpg

The Universal Genetic Code. The Universal Genetic Code is shown in an atypical array to highlight those codons and their decoding by tRNAs discussed here. Fully degenerate codon boxes are shown in blue, split codon boxes in brown and stop codons in red.

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g002.jpg

The tRNA journey. The secondary structure of tRNA with its constituent domains marked in different colors (top left): Acceptor Stem (green); Dihydrouridine Stem and Loop, DSL (black); Anticodon Stem and Loop, ASL (red); Variable Stem and Loop, VSL (yellow); Thymidine Stem and Loop, TSL (blue). tRNA transcripts are processed by sizing and modification, some are spliced, before functioning in translation. Modification of tRNAs, particularly the anticodon stem and loop (ASL) domain at positions 32, 34, 37, 38 and 39, is an important step toward achieving functional chemistry and architecture. The wobble nucleoside, first of the anticodon, is position 34. Red and black highlights of mature tRNA after modification indicate the locations in the ASL where it is heavily modified.

The post-transcriptional modification of tRNA, the original soluble RNA, has been known for over 50 years pioneered by the extraction and characterization methods of Ross Hall in the 1960s. 3 At the time the Universal Genetic Code was unveiled, 4 there were several RNAs known to contain modified nucleosides, but their sequence locations and functions were a mystery before the evolution of RNA sequencing methods. By 1991, 25 years later, a sufficient number of modified nucleosides had been found to occupy the wobble position 34 of tRNA's anticodon that a Modified Wobble Hypothesis was advanced. 5 Biophysical and biochemical experiments had suggested and continue to support the principle that some position 34 modifications structure the architecture of the anticodon stem and loop (ASL) to counter wobble whereas other modifications shape the ASL to enable a tRNA to decode three or even four synonymous codons (codons differing only in the wobble position N3). 6 - 10

Of what importance are these ubiquitous and highly conserved anticodon modified nucleosides to the decoding of mRNA codons? In general, modified nucleosides of tRNA's anticodon stem and loop (ASL) domain are found within the stem at positions 27, 28, 31, 39, and 40 and at loop positions 32, 34, 35, 37, and 38 ( Fig. 2 ). 11 - 13 These ten nucleoside positions of the ASL are not simultaneously modified in any one tRNA, rather a set of 3–5 specific nucleosides are found to be modified in an individual tRNA. Many times in the sequencing of a tRNA species one finds that as many as three nucleoside positions of the seven residue loop are modified. Considering that the ASL of tRNA constitutes 17 of the molecule's ∼76 nucleosides and that the stem constitutes 5 base pairs, with 10 nucleosides, the modifications within the ASL loop represent a dense population of altered nucleoside chemistries. Often the modifications at wobble position 34 and 3′-adjacent to the anticodon at position 37 are the most chemically complex of all RNA modifications and are composed of hydrophobic aliphatic chains or aromatic substituents, or of highly hydrophilic or even charged functional groups participating in translational efficiency and fidelity. 11 Thus, posttranscriptional modifications of the ASL nucleosides emulate the chemistries of amino acid side chains. 14 Even what appears to be one of the simplest of modifications, such as the substitution of a sulfur atom for an oxygen, a thioketone for a carbonyl group, or the deamination of adenosine to inosine (I), takes on significance in the decoding of mRNA. The modification of wobble position U 34 to s 2 U 34 alters tRNA's ability to wobble to G3; 5 the modification of C 32 to s 2 C 32 negates the ability of tRNAs with I 34 to decode A3 of the codon. 6

The importance of being modified

The high percentage of anticodon modification and their composite chemistries provides different functionalities to tRNA in its role in decoding mRNA ( Fig. 3 ). Individual anticodon domain modified nucleosides are identity determinants for protein recognition, particularly aminoacylation, 15 - 17 increase accuracy and efficiency in codon recognition, 18 - 24 and pre-structure the ASL for translation. 9 , 25 - 30 Each of the modified nucleosides contribute distinct chemistries, nucleoside conformations and dynamics, and their contributions to decoding have been studied extensively over decades and most recently reviewed. 20 , 22 , 24 , 28 , 31 - 38 However, there is significant evidence that a combination of two or three anticodon domain modifications play a synergistic role in tRNA function where modification of a wobble position U is crucial. 9 , 20 , 24 , 39 - 46 Today, we know that certain modifications of U 34 enable expansion of codon from NNA/G recognition to synonymous codons ending in pyrimidines, N1-N2-Pyr, where N is any of the 4 nucleosides and Pyr is either U or C. 29 Yet, the anticodon domain of some tRNA species lack modification and can be totally devoid of modified nucleosides. Bacteriophage T4 tRNA Gly is an early example of a tRNA lacking modification. 47 The unmodified U 34 nucleosides of native mitochondrial alanine, leucine, threonine and valine tRNA species in vivo , and that of a totally unmodified tRNA transcript in vitro were shown to read codons ending in U3 and C3, as well as A3 and G3. 48 , 49 To understand the forces that maintained and propagated tRNAs' anticodon domain modifications throughout all life, first we will discuss the limited number of examples revealed over many years to have unmodified Us and As at wobble position 34, and the influence of position 32 nucleosides on decoding.

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g003.jpg

Modifications present in tRNA's anticodon stem and loop domain (ASL) featured in the text and displayed in their neutral state. A. Modified purines, adenosine (A) and guanosine (G). B. Modified pyrimidines, uridine (U) and cytidine (C). R = ribose.

Unmodified wobble position 34 and the importance of position 32

Bacteria, archaea and eukaryotes have some 40 tRNA species decoding the Universal Genetic Code. However, many times we find that in mammalian and yeast mitochondria, in chloroplasts, and in Mycoplasma ssp only a single tRNA species decodes all 4 codons of a fully degenerate codon box of the Universal codes ( Fig. 1 ). 49 - 57 Wobble codon recognition is at its extreme in these circumstances and has been referred to as ‘superwobble’. 58 An unmodified U in tRNA's wobble position 34 facilitates the use of far fewer tRNAs in organelles than the over 40 cytoplasmic species typically reading the 61 amino acid codes. Fewer tRNAs is certainly an advantage for the small genomes of the organelles and the minimal single cell organism, mycoplasma. An unmodified U 34 also abrogates the need for the extensive array of genes encoding the modified nucleoside pathways of enzymes and substrates required of the simplest to the most complex modifications of U 34 . 11 However, the superwobble reading of codons compromises translational efficiency. 58

An unmodified U 34 seems to be particularly efficient for the organellar tRNA Gly species. The codons for the amino acid glycine, GGA, GGG, GGU or GGC, are found in a 4-fold degenerate codon box, whose first two nucleosides are the same ( Fig. 1 ). They are read by as many as three different tRNA isoacceptors in bacteria with cognate and wobble anticodons. Early in the study of glycine tRNAs, the Escherichia coli tRNA Gly isoacceptors were grouped into 3 subspecies based on a chromatographic separation: tRNA Gly1 CCC , tRNA Gly2 UCC , and tRNA Gly3 GCC . 59 In an E. coli in which there were multiple copies of suppressors increasing the levels of wild-type tRNA Gly1 CCC , −1 translational frameshifting occurred at the 5′-GGG-3′ codon allowing the near-cognate tRNA to read GGA codons. 60 Surprisingly, experiments with E. coli tRNA Gly2 UCC demonstrated that the unmodified UCC anticodon discriminates among the four glycine codons depending on the nucleoside in position 32, an unmodified U 32 or C 32 ( Fig. 4A ). Thus, the unmodified UCC anticodon reads GGA and wobbles to GGG, but does not recognize GGU and GGC. 61

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g004.jpg

Sequences of unmodified ASL of tRNA Gly . A. ASLs of E. coli tRNA Gly1 CCC , tRNA Gly2 UCC , and tRNA Gly3 GCC indicating the changes in nucleoside position 32 and 34 (marked in red) from the tRNA Gly1 sequence. All 3 E. coli tRNA Gly have the same nucleoside at position 32 (U 32 ). The Mycoplasma mycoides tRNA Gly UCC differs from the E. coli tRNA Gly as a result of a cytidine at position 32 as well as the presence of inverted base pairs in the anticodon stem at positions 27•43 and 28•42. B. Three Dimensional Structure of the tRNA Gly GCC and tRNA Gly UCC ASLs of B. subtilis . The interactions between the U 32 •A 38 and C 32 ○A 38 nucleosides (PDB ID: 2LBJ and 2LBL) are shown. Both ASLs lack the sharp U-turn characteristic of ASLs of other tRNAs. Nucleosides of the anticodon are labeled 34 to 36.

Although the anticodon UCC could discriminate efficiently with a U in position 32, it loses its ability to differentiate when substituted with a C 32 as was also true for M. mycoides glycine tRNA. In wild type M. mycoides tRNA Gly , the anticodon UCC failed to discriminate between the glycine codons with a position 32 cytidine, but when changed to a U it acted like E. coli tRNAs and discriminated between the four glycine codons. 62 In M. mycoides , the single tRNA Gly UCC that decodes all four glycine codons is devoid of anticodon modifications and has a C 32 ○A 38 mismatch which leads to decreased fidelity in vivo ( Fig. 4 ). 63 The tRNA Gly UCC transcript without any modifications reads all 4 codons in vitro . 48 Ribosome binding experiments with U 32 /C 32 mutants of tRNA Gly showed an increased affinity of the C 32 mutant to the cognate codon and to codons with third position mismatches in the ribosome's A-site. 64 The rate of dissociation of the U 32 -containing tRNA Gly from the near-cognate GGC, GGA and GGU codons was much more rapid - 12-fold faster than from the GGG cognate codon - and stabilized the binding of tRNA to codons with third position mismatches. 64 In contrast, the mutated tRNA Gly1 with C 32 dissociated much more slowly from near-cognate codons. Analysis of the UV-thermal denaturation (melting) curves of the anticodon stem and loop domains demonstrated that tRNA Gly UCC with a protonated C 32 ○A + 38 non-canonical base pair melted at a temperature 10 °C lower than tRNA Gly GCC or np-tRNA Gly UCC , used exclusively for non-protein cell wall synthesis in Staphylococcus species, which exhibited a T m of 70 °C. 65 Although the sequences of these tRNA differed from one another, none of their solution structures formed the classical U-turn motif seen in other tRNA anticodon loops ( Fig. 4B ). tRNA molecules fulfill different functional roles by interacting with other cellular molecules, and the structural variations of the glycine ASL of S. aureus could contribute to its functional diversity. tRNA Gly GCC , without any base modification participates in transcriptional regulation and transcription. The tRNA Gly UCC which more often contains a U 34 modification except in some organisms including M. mycoides , participates in translation. The np-tRNA Gly UCC contains no base modification and participates in cell wall synthesis. 65 The presence of pyrimidine at position 37, along with a reduced affinity for EF-Tu, could limit their involvement in transcription and translation. Modifications of U 34 could increase or decrease the ability to wobble, thus enhancing discrimination. A more dynamic ASL tRNA Gly GCC was observed in the presence of multivalent cations, whereas tRNA Gly UCC and np-tRNA Gly UCC were more structurally ordered in their presence. A more dynamic loop structure would therefore, better accommodate the different functional roles of an unmodified tRNA Gly in protein translation, in tRNA-dependent gene regulation, and cell wall biosynthesis. 65

The nucleoside at position 32 of the tRNA's anticodon loop is recognized as important for translation, though the position 32 nucleoside is remote from the anticodon. The intraloop hydrogen bonding between the nucleosides at 32 and 38 strongly influences the affinity of tRNA to the A-site. 64 tRNA species other than those for glycine also have an unmodified wobble position U 34 , and the nature of the N 32 ○N 38 intraloop hydrogen bonding in these tRNAs does appear to regulate expansion/discrimination of codon reading. The A 32 •U 38 interaction, highly conserved in tRNA Ala and also seen in tRNA Pro , decreases the tRNA affinity to the ribosomal A-site compared with other N 32 ○N 38 intraloop hydrogen bonding nucleosides. 66 Five Mycoplasma capricolum tRNA species with the unmodified anticodon UNN and decoding for five different amino acids have anticodon loop sequences with C 32 ○A 38 . In addition, tRNA Ala UGC has an intraloop interaction of C 32 ○C 38 . Because these 6 tRNA species have a C 32 and an unmodified U 34 , in theory they could efficiently read all four synonymous codons for leucine, valine, proline, alanine, glycine and serine. 67 Although tRNA Thr UGU was shown to translate the codons ACU, ACA and ACG, it was inefficient in reading the codon ACC.

Interestingly, the sufD42 mutant of E. coli tRNA Gly1 , encoded by glyU, is a derivative of tRNA Gly CCC with an extra C in the anticodon loop and contains no modification in the anticodon loop. 68 This mutant is considered dominant and contains four bases, 5′-CCCC-3′ that make up the anticodon and suppress +1 frameshift mutants with an extra G inserted into a GGN codon (GGGN). The quadruplet translocation theory is used to deduce the pairing of these four cytidines with four bases of the codon in the A site. The tRNA anticodon sequence has been suggested to act as a molecular ruler which determines the codon size during translation, within certain limits, 69 thereby restoring some ribosomes to the wild type frame. Thus, the nature of the N 32 ○N 38 base interaction affects the binding of the anticodon to the codon suggesting that the intraloop hydrogen bonding alters the conformation and dynamics of the anticodon stem and loop domain within the ribosomal complex. 62 , 70

Very few unmodified, wobble position A 34 have been found in tRNA sequences: a yeast mitochondrial tRNA Arg ACG 71 and Mycoplasma tRNA Thr AGU . 50 , 56 , 72 In all domains of life, A 34 of the tRNA transcript is almost always deaminated to form inosine at the wobble position (I 34 ). The modification to I 34 expands the coding capacity to read the bases U, C and A. In Mycoplasma the unmodified A 34 of tRNA Thr AGU efficiently translates the ACC codon, 67 but mutants of E. coli tRNA Ser and tRNA Gly with A 34 could only weakly read UCC and GCC in vitro , respectively. 73 , 74 In Salmonella typhimurium , tRNA Pro GGG is the only tRNA that reads the CCC codon. With G 34 replaced by an unmodified A, a mutant with no cognate codon for CCC, grew normally. 75 The mutant tRNA Pro AGG efficiently read the CCC codon similarly to its wild-type counterpart with a GGG. It formed a wobble base pair using a protonated A with the third position C in mRNA. Similarly, a mutant tRNA Gly1 with a UCC to ACC mutation containing an unmodified A 34 , lost its ability to discriminate between the third position nucleosides of the glycine codons. 73 The possibility of a purine○purine base pair being more stable than a pyrimidine○pyrimidine pair, 76 as well as the two out of three model 77 was suggested to explain the non-discrimination by A in the wobble position. 73 The presence of A in the wobble position could change the conformation of the anticodon by preventing hydrogen bonding between U 33 and the phosphate of nucleoside 36, 78 which stabilizes the U-turn conformation of the ASL. The rare occurrence of an unmodified A 34 is supported by the hypothesis that a wobble position A cannot discriminate and ensure translational fidelity of tRNAs reading split box codons. In contrast, the presence of A 34 would be advantageous in the reading of fully degenerate synonymous codons where there is a lack of discrimination and in cases where only a single tRNA exists for the reading all four codons. 73

In addition to their primary role of translation, some tRNAs have other functions including regulation of gene expression, bacterial cell wall synthesis, viral replication, antibiotic biosynthesis and suppression of alternative splicing. 64 , 65 In Bacillus subtilis and many other Gram-positive bacteria, tRNA molecules regulate gene expression by the tRNA dependent, ‘T-box’, mechanism of transcription attenuation to maintain a balanced pool of aminoacyl-tRNAs that is essential for cell viability. 79 , 80 The tRNA ligand for the T-box mechanism regulating the expression of glycyl-tRNA synthetase is tRNA Gly UCC with an unmodified U 34 . A Rho-independent, terminator helix in the 5′UTR of the leader mRNA of the glyQS operon for glycyl-tRNA synthetase prevents the operational binding of an aminoacylated glycyl-tRNA Gly UCC . 81 Conversely, the anticodon of an uncharged tRNA interacts with a loop, the Specifier Loop, containing the complementary codon and the tRNA's 3′-terminal CCA hydrogen bonds to an anti-terminator helix, re-conformed from the terminator helix. These interactions as well as others between the tRNA and the mRNA stabilize the anti-terminator conformation of the 5′UTR and allow transcription to proceed downstream through the coding sequence. Thus, the unacylated tRNA Gly UCC is similar to the much smaller metabolic products that affect the riboswitch mechanisms controlling gene expression; the 5′UTR undergoes a conformational change with the binding of the ligand. 82 The tRNA Gly UCC is also predicted to bind to the 5′-GGA-3′ Specifier codon in Bacillus and Staphylococcus species glycyl T-box riboswitches. 83

A third glycine tRNA (UCC) without a modified U 34 has been identified in Staphylococcus species as participating in cell wall biosynthesis, but not in protein translation, and was termed non-proteinogenic (np-tRNA Gly ). 84 - 87 These np-tRNA have an unmodified U 34 nucleoside and a cytidine rather than a purine at position 37. 88 In Thermus thermophiles , the np-tRNA Gly species are found to have reduced affinity for the elongation factor Tu (EF-Tu) due to base substitutions of A 51 -U 63 for G 51 -C 63 in the base of the T-stem, thus decreasing their involvement in ribosomal protein synthesis. 65 These weak EF-Tu binders could act as glycine donors in forming essential pentaglycine bridges which stabilize the staphylococcal cell wall. 85 , 89 - 91

The biosynthesis of peptidoglycan in S. aureus involves two uridine nucleotide substrates, UDP-MurNAc-pentapeptide and UDP-GlcNAc (N-acetyl glucosamine), which combine to form a lipid intermediate GlcNAc-MurNAC(pentapeptide)-P-P-lipid. The lipid intermediate gets further modified by amidation of the α-carboxylic group of glutamic acid and the addition of a pentaglycine chain to the ε-amino group of lysine. The weak EF-Tu binding glycyl tRNAs serve as intermediates in these reactions to form the pentaglycine bridges, that stabilize the peptidoglycan chains and are essential for cell viability. These short peptide bridges are synthesized in a non-ribosome catalyzed peptidyl transferase reaction, which uses the charged glycyl-tRNA, 1 np-tRNA Gly and a ‘pseudo’-tRNA Gly UCC as substrates. 65 , 85 , 92 Glycine and serine act as substrates that are successively added to form small peptide bridges which are catalyzed by a family of non-ribosomal peptidyl transferases known as FEM-XAB (Factors Essential for Methicillin Resistance) - mediated cell wall synthesis. 93 The incomplete formation of these interpeptide bridges can lead to increased antibiotic susceptibility or lethality. 85

The wobble hypothesis and the modulation of inosine wobbling

Though there are instances of unmodified nucleosides at tRNA's wobble position 34 as described, more often than not U 34 is post-transcriptionally modified and A 34 is deaminated to inosine. Using specific modifications of U and the modulation of I reading A, U and C, we illustrate here the importance of wobble position 34 modifications to tRNAs' accuracy and efficiency of translation. The modification of adenosine to inosine was first recognized by Francis Crick for enabling tRNA recognition of synonymous codons. 1 Inosine ( Fig. 3 ) results from the deamination of adenosine, a transformation that is facilitated by the adenosine deaminase (ADAR) family of enzymes that act on RNA. 94 Although inosine is a marker of damage or mutation in DNA, the presence of this very same modified nucleoside is considered to be essential in various RNAs. 95 Inosine plays a vital role in the function of tRNA, in particular. As the first recorded nucleoside modification within the sequence of an anticodon, 2 Crick introduced inosine in his 1966 Wobble Hypothesis. 1 While the first two bases of the codon undergo traditional base-pairing without exception, 96 Crick proposed the potential for non-canonical base pairs between the first base of the anticodon (“wobble” position 34) and the third base of the codon, U 34 ○G3, or I 34 ○A3/U3/C3 ( Fig. 5 ). 1 This flexibility of the genetic code is not without limitations; however, in accordance with this hypothesis, a given tRNA isoacceptor may recognize multiple codons, thus explaining the degeneracy of the genetic code.

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g005.jpg

Canonical and wobble base pairing of tRNA to mRNA. A. Canonical A•U and G•C base pairs. B. Wobble U 34 ○G3, I 34 ○A3, I 34 ○C3, and I 34 ○U3 base pairs. G 34 ○U3 pairings are virtually nonexistent; therefore, the pairing is not shown. The arrows point away from the hydrogen bond donor and toward the hydrogen bond acceptor.

The Wobble Hypothesis states that position 34 inosine may base pair with uridine, cytidine, and adenosine. The ability of inosine at the wobble position to promote the reading of multiple codons, in some cases, proves essential to survival. The heterodimeric enzyme consisting of the Tad2p and Tad3p subunits of Saccharomyces cerevisiae catalyzes the deamination of adenosine to inosine on tRNA. 97 A strain of Schizosaccharomyces pombe containing a mutant tad3–1 , the homolog of TAD3 , experienced temperature-dependent arrested growth at Gap 1 and Gap 2 of the cell cycle. 98 The S. pombe genome utilizes only 3 tRNA Ala isoacceptors for the 4 alanine codons GCU, GCC, GCG, and GCA: tRNA Ala IGC , tRNA Ala CGC , and tRNA Ala UGC . According to the wobble rules, tRNA Ala IGC must be responsible for decoding of the GCC codon. The otherwise unmodified tRNA Ala AGC would be able to decode its complementary GCU codon but could not wobble to GCC, inhibiting the translation of gene products vital to the G 1 /S and G 2 /M transitions of the cell cycle. 98

A tRNA Arg IGC may be modified from A 34 to I 34 yet still be unable to decode A3. The E. coli tRNA Arg1 ICG and tRNA Arg2 ICG isoacceptors should bind and effectively decode the CGU and CGC codons, and even the CGA codon. These wobble pairings were confirmed experimentally, as the singly modified anticodon stem and loop of tRNA Arg ICG , ASL Arg ICG , is able to bind the CGU, CGC, and CGA codons within the ribosomal A-site. 39 In fact, tRNA Arg1 ICG and tRNA Arg2 ICG are the only isoacceptors available to recognize the 3 aforementioned codons. Furthermore, adenosine must be modified to inosine at position 34 of the tRNA Arg1,2 ICG isoacceptors in order for wobble pairing to occur. Unmodified ASL Arg1,2 ACG is able to bind its cognate codon, CGU, but unable to bind CGC or CGA as expected, as Crick did not explicitly delineate any wobble capabilities of position-34 adenosine. 1 , 39

The tRNA Arg1,2 ICG decoding of the CGA codon is relatively inefficient compared with translation of the CGU. 99 , 100 Although the energy barrier for I○A base-pair formation is greater than those of I○C and I○U, the increased distance between the N-glycosyl bonds of I 34 and A3 required to accommodate the purine○purine wobble pair can be achieved when the nucleosides adopt an I anti ○A anti conformation. 1 , 44 , 101 Additional modifications at position 32 and 37 of the ASL Arg ICG may further contribute to the difficulties of I○A wobble pairing. The E. coli tRNA Arg1 ICG species contains the naturally-occurring 2-thiocytidine at position 32 (s 2 C 32 ) and 2-methyladenosine at position 37 (m 2 A 37 ). The thrice modified ASL construct could not be synthesized, but the doubly modified ASL Arg ICG -s 2 C 32 was unable to bind the CGA codon within the ribosomal A-site. 39 Here, the complete wobble capabilities of inosine do not apply due to the restrictive effects of the s 2 C 32 modification with respect to the otherwise feasible I○A wobble pair.

The tRNA Arg2 ICG species lacks the s 2 C 32 modification but does contain the m 2 A 37 modification. As evidenced by the aforementioned ribosomal binding study, m 2 A 37 prohibits I○A pairing. 39 However, reading of the CGA codon defaults to tRNA Arg2 ICG , as the inclusion of the s 2 C 32 modification disqualifies the tRNA Arg1 ICG from decoding of the CGA codon in vivo . Yet the E. coli genome still must compensate for the overall poor capacity of the tRNA Arg ICG isoacceptors to wobble to the CGA codon by biasing codon usage. The inclusion of CGA codons in mRNA transcripts increases energetic costs and decreases the efficiency of translation. The prevalence of the CGU, CGC, and CGA codons is heavily biased against the CGA codon and in favor of the CGU and CGC codons. 102 , 103

The modified wobble hypothesis and decoding at position 34

For many years, Crick's Wobble Hypothesis appeared to sufficiently explain the function of modified nucleosides at tRNA's wobble position without the need for alteration. However, the discovery of numerous new modifications, a large number of which are found exclusively at the wobble position, led to the development of a modified wobble hypothesis. 5 The first base of the anticodon is so often modified to either expand or restrict the binding abilities of the wobble nucleoside, therefore enabling the specific recognition of cognate and synonymous codons. As such, near-cognate codons can be selected against, or the recognition of multiple codons can be made feasible with various chemical moieties introduced onto the wobble base. 5 There are several examples of both expansion as well as restriction of codon recognition which are presented with a focus on the mechanistic details of both expansion and restriction of recognition, and the many factors that must come to play to make either possible.

Expansion of codon recognition through modified nucleosides pre-structuring of the ASL

The high freedom of rotation coupled with the limited chemical variation of the four major nucleosides enables RNAs to adopt multiple conformations with comparable stability yet limited chemistry. Modifications add to the chemistry and can either limit or expand the number of available conformations, thereby influencing the structure toward a more specific architecture or provide dynamics important to translational effectiveness. There are six amino acids represented by 4-fold degenerate codon boxes which include alanine, glycine, proline, serine, threonine, and valine, and are of particular interest in U 34 modification. As with S. pombe and the GCN alanine codon box, Salmonella enterica utilizes 3 distinct species of tRNA Pro for recognition of the entire CCN codon box: tRNA Pro CGG , tRNA Pro GGG , and tRNA Pro UGG . Deletion of the genes for tRNA Pro CGG and tRNA Pro GGG simultaneously is not lethal to S. enterica . 104 Only tRNA Pro UGG proves necessary for viability of the organism by surpassing its expected decoding capabilities due to the presence of the 5-oxyacetic acid modification (cmo 5 ) on position-34 uridine in the ASL. The cmo 5 U 34 modification is present in one species of each of the tRNA isoacceptors for alanine, proline, serine, threonine, and valine. Similarly, tRNA Val UAC -cmo 5 and tRNA Ala UGC -cmo 5 partially rescue the E. coli growth phenotype caused by knockout of the 2 tRNA Val GAC isoacceptors and the tRNA Ala GGC isoacceptor, respectively, indicating the ability of tRNA containing the cmo 5 U 34 modification to decode an entire codon box, albeit somewhat inefficiently. 105 The presence of the cmo 5 U 34 modification facilitates pre-structuring of the ASL Val UAC that enhances its ability to bind near cognate codons. When binding each of the GUN valine codons, the ribose of cmo 5 U 34 of the modified ASL Val UAC assumes the C3′- endo conformation. 29 Prevalent within A-type helical regions of tRNA, the C3′- endo sugar pucker is synonymous with stability and rigidity. 106 - 108 The existence of a hydrogen bond between the 2′-OH of the almost invariant U 33 of the ASL and O5 of the cmo 5 modification further constrains cmo 5 U 34 . 29 This intramolecular hydrogen bond in particular expands the ability of ASL Val UAC -cmo 5 U 34 to decode codons ending in U and C, pre-structuring the ASL such that the entropic cost of a pyrimidine○pyrimidine base pair, initially believed to be unfavorably short, is surpassed. 1 , 29

The cmo 5 modification has surprising implications for the U 34 •G3 wobble pair. Although this pairing was originally predicted without regard for the potential of modified uridines, the uridine at position 34 of the ASL must be modified in order for the U 34 •G3 pairing to occur. 18 , 105 Rather than enhancing the ability of U 34 to wobble to G3, cmo 5 merely enables the interaction. In a second divergence from the original Wobble Hypothesis, the modified cmo 5 U 34 •G3 does not adopt the predicted wobble geometry with two hydrogen bonds between the two bases. The cmo 5 U 34 instead forms three hydrogen bonds with G3 as in the traditional Watson-Crick geometry ( Fig. 6 ). 29 The steric and electronic properties of the cmo 5 modification are thought to promote the enol form of cmo 5 U 34 , thus allowing for the Watson-Crick geometry of the cmo 5 U 34 •G3 base pair reminiscent of a C•G base pair. 29 , 109

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g006.jpg

Watson-Crick geometry of the cmo 5 U 34 ○G3 base pair. A. The predicted geometry of the unmodified U 34 ○G3 base pair containing two hydrogen bonds. B. The observed geometry of cmo 5 U 34 ○G3 base pair containing three hydrogen bonds. For the cmo 5 U 34 ○G3 to resemble a C•G base pair, the cmo 5 modification is proposed to facilitate formation of the enol tautomer. The arrows point away from the hydrogen bond donor and toward the hydrogen bond acceptor.

Additionally, E. coli tRNA Val UAC containing the cmo 5 U 34 modification is also methylated at the position-37 adenosine to yield N 6 -methyladenosine (m 6 A). As seen with tRNA Arg1 ICG -s 2 C 32 ;m 2 A 37 and tRNA Arg2 ICG -m 2 A 37 , it is not uncommon for the ASL of a given tRNA to contain multiple modified nucleosides. Modifications written onto N6 of the universal purine located at position 37 of the ASL are proposed to interfere with intraloop hydrogen bonding and to enhance base-stacking, thereby promoting an open loop structure within the ASL. 18 The open loop structure of the ASL is a prerequisite for anticodon-codon binding within the ribosomal complex. 110 ASL Val UAC lacking both the cmo 5 U 34 and m 6 A modifications does not appreciably bind the GUU, GUC, or GUG codons within the 30S ribosomal subunit. 111

While G is able to base pair with both C as well as U, the interaction with the latter is thermodynamically less stable. As such, tRNAs coding for aspartate, asparagine, histidine, and tyrosine commonly contain 7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanine, queuosine or Q ( Fig. 3A ), at the wobble position, which enables recognition of codons ending in either C or U without favoring one or the other. 112 This is true even for the more simplistic and somewhat less commonly modified mitochondrial tRNAs, implying an evolutionary necessity for enhanced codon recognition that Q provides. 113 Q is synthesized by bacteria, and eukaryotes acquire Q either as a nutrient or from the intestinal flora as quenine, the free base form of Q, which is then directly inserted into the pertinent tRNAs through substitution of the base quenine. 114 Interestingly, the E. coli tRNA Tyr contains pseudouridine at position 35, the second position of the anticodon and adjacent to Q, ms 2 i 6 A at position 37, and Ψ at position 39. Loss of Ψ at the rarely modified position 35 compromises translational fidelity in vitro , implying that some ASLs need even more than three modified nucleosides for accurate function. 115 Like many other large modifications, Q causes a steric effect in the ASL, influencing the structure of the loop. The effect is largely mediated by hydrogen bonding within the ASL, which has been shown to maintain the structure of the ASL in silico , thus pre-structuring the ASL for codon recognition in the ribosome. The electrostatic potential of Q compared with G is important. Due to the intramolecular hydrogen bond between O6 and the quaternary amine of the aminomethyl side chain, the electronegativity of O6 in Q is reduced compared with O6 in G. In G, O6 acts as a hydrogen bond acceptor, however, this is not the case for Q. The two amines act as hydrogen bond donors in both species. The side-chain of Q can also engage in hydrogen bonding with the backbone of U 33 , which in turn enhances the U 33 ○C 36 interaction, stabilizing the ASL conformation. This same effect is absent or reduced if Q is replaced with G. 112 The pre-structuring is further enhanced by the large modification wyosine, (3,4-dihydro-4,6-dimethyl-3-β-D-ribofuranosyl-9 H -imidazo[1,2-α]purin-9-one), imG, also derived from G and found at position 37 along with other derivatives often paramount to tRNA structure and function. 112

The high degree of hydrophobicity of wyosine ( Fig. 3A ) and its derivatives enhances the nucleoside's ability to form hydrophobic interactions such as base stacking, which enhances codon binding stability. The bulky residue prevents the intraloop hydrogen bond between residues 32 and 37, thus promoting proper pre-structuring of the ASL. 116 , 117 In mitochondrial tRNAs, imG 37 or its derivatives are commonly replaced by i 6 A 37 or a derivative thereof, or by a methylated purine, therefore suggesting the evolution of an alternative strategy for establishing the same functional properties by using different chemical moieties in RNA modifications. 113 , 116

The nearly universal modification at position 37 that is required for decoding codons beginning with A, N 6-threonylcarbamoyladenosine, t 6 A 37 , may be further modified to 2-methylthio- N 6-threonylcarbamoyladenosine, ms 2 t 6 A 37 . 118 Interestingly, a cyclic derivative of t 6 A, ct 6 A, has also been shown to exist, functioning in a manner analogous to the more studied t 6 A. 118 , 119 Hydrogen bonding between N1 and N11 of t 6 A lead to a pseudocyclic conformation that enhances the rigidity of the conformation. 120 The same hydrogen bonding exists in ct 6 A, but a further isomerization occurs as well, where C10 and C13 are linked via an ether, thus forming a oxazolidine. 118 - 120 The C14 alcohol of ct 6 A can hydrogen bond with the N7 of the first codon, an A, increasing the stabilization that enhanced stacking alone provides. 118 , 120 , 121

Restriction of codon recognition and pre-structuring of the ASL

RNAs are highly flexible molecules with each base containing several bonds about which free rotation can take place. The flexibility and the possibility of not only Watson-Crick base pairing but also wobble or Hoogsteen interactions provide suitable conditions for multiple structures to form. Certain modifications restrict intraloop base pairing interactions, thus conforming the architecture to one suitable for ribosomal decoding. Restriction of codon recognition may become necessary in cases where an unmodified nucleoside could base pair with a near-cognate codon, therefore causing misreading of the codon. U, for instance, can base pair with all of the 4 major nucleosides with a strong preference to purines. 18 As such, modification can provide an enhanced specificity. As an example, isoleucine shares a codon box with methionine where AUA, AUC, and AUU code for isoleucine, and AUG codes for methionine, with the exception of mitochondria where AUA also codes for methionine. 6 , 113 , 122 Two codons can be read by tRNA Ile GAU , but the AUA codon requires a different isoacceptor that would also not read AUG as isoleucine. Eukaryotes commonly have a tRNA Ile IAU which can read all three codons, but not AUG. 122 The genomes of bacteria and some eukaryotic organelles encode a tRNA Ile GAU and tRNA Ile LAU where L is lysidine (k 2 C). 123 Modification of C to k 2 C ( Fig. 3B ) effectively changes the base pairing capabilities of the nucleoside, causing a switch in preference from G to A for tRNA Ile . The modification is required to prevent the recognition of the near-cognate AUG codon ( Fig. 7 ). 7 Lysidine is a modified cytidine containing a lysine residue in lieu of O2 at the wobble position. The modification lysidine is the recognition determinant for the amino acid specificity in isoleucyl-tRNA synthetase (IleRS) aminoacylation of tRNA Ile LAU and not tRNA Met CAU . An intriguing minor tRNA Ile ΨAΨ in yeast contains pseudouridine at position 34 instead of lysidine, 121 and many archeal species utilize agmatidine [N-(4-carbamimidamidobutyl)-4-imino-1-(b-D-ribofuranosyl)-1,4-dihydro-2-pyrimidinamine] ( Fig. 3B ) for decoding of the AUA isoleucine codon. Thus, there have been multiple and convergent evolutionary paths to accomplish specificity in decoding through restriction of codon recognition with the help of modified nucleosides. 122

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g007.jpg

Modifications influence protein and codon recognition of tRNA through altered hydrogen bonding. R represents the ribose sugar. Hydrogen bonding is indicated by arrows. A. Nucleosides commonly found at position 34 of tRNA Ile . All 4 bases are capable of recognition by isoleucyl-tRNA synthetase, IleRS. B. Two possible tautomers of lysidine. Structure on the right can be recognized by IleRS, and could putatively recognize A as shown. C. Possible tautomers of mnm 5 s 2 U 34 of E. coli tRNA Lys UUU . Likely interactions with A and G are shown.

Tautomerism: A chemical mechanism by which modified nucleosides restrict codon recognition

Tautomers and rare ionic forms of nucleosides have been shown to exist at low populations in vitro ; 124 it is commonly postulated that the existence of tautomers of modified nucleosides at the ribosome's decoding site has a strong effect on codon recognition, either preventing or enabling it. 28 The nature of the C5 modification affects the tautomerism of the uridine and 2-thio modified uridine 125 producing either an expanded codon recognition, or one which is restricted. Restriction of codon recognition is a common mechanism for fidelity when a tRNA anticodon can mistakably base pair with a near-cognate codon in a shared codon box. In contrast, expansion of codon recognition by tRNA is often required when an interaction of an unmodified nucleoside would either lack the base pairing ability, thermodynamic stability, or the required structural orientation to achieve accuracy and efficiency of translation. 18

Both lysidine and agmatidine can exist in several tautomeric forms. The exact tautomeric form through which cognate codon recognition can occur still needs to be elucidated. 122 However, it is a tautomer of lysidine that disallows recognition of the near-cognate AUG codon. The modification contains a secondary amine in place of oxygen at the two position of C, thus switching a hydrogen bond acceptor into a donor. The two tautomers ( Fig. 7B ) have different base pairing capabilities due to distinct local electron densities. Interestingly, neither tautomer is ideal for base pairing with G, but the non-aromatic tautomer is capable of recognizing A; the primary amine at position 4 on the ring is switched into an imine, thereby enabling it to function as a hydrogen bond acceptor. Similarly, N3 of the base becomes a hydrogen bond donor, thus enabling base pairing with A ( Fig. 7B ). 126 Agmatidine forms a similar tautomer as lysidine. 122 , 126 The hydrogen bonding capability of modified nucleosides commonly found at the wobble position of tRNA Ile illustrates how small changes in the chemistry of a single nucleoside can have broad and highly specific effects, in this case altering codon recognition and specificity while simultaneously preserving aaRS recognition. 121

Tautomers of modified nucleosides expand reading of synonymous codons

U•A base pairs are thermodynamically much weaker than C•G base pairs. In tRNAs such as tRNA Lys UUU this problem is exacerbated, as all anticodon to codon base pairs are U•A pairs. Furthermore, in the absence of modifications, the U-rich ASL cannot effectively form stacking interactions to stabilize its structure nor negate intraloop hydrogen bonding that effectively condenses the size of the ASL. 117 The nearly ubiquitously modified, invariable purine at position 37 can alleviate the thermodynamic penalty of a pyrimidine rich anticodon. In tRNA Lys UUU the purine at position 37 is modified to N 6 -threonylcarbamoyladenosine, t 6 A or a derivative thereof such as 2-methylthio- N 6 -threonylcarbamoyladenosine, ms 2 t 6 A 37 found in mammalian tRNA Lys3 UUU . Additionally, Ψ at position 39 is important for function. 127 The wobble position is extensively modified with an xm 5 s 2 U type of modification, illustrating the importance of having three modified nucleosides in the anticodon loop for at least this tRNA. 28 , 128

Lysine is coded by AAA and AAG codons. In many organisms, as well as in organelles, a single tRNA Lys UUU reads both codons. In mammals, two isoacceptors, tRNA Lys1,2 CUU , decode the AAG codon, and a third, tRNA Lys UUU , translates both codons. The wobble xm 5 s 2 U modification is required for the efficient and specific recognition of both lysine codons, and for translocation on the ribosome. 129 The xm 5 s 2 U 34 modifications, such as bacterial tRNA modification mnm 5 s 2 U 34 , can undergo keto-enol tautomerism ( Fig. 7C ), which allows recognition of both AAA and AAG by expanding the hydrogen bonding capabilities of the nucleoside. Similarly, expanded codon recognition could be achieved via ionization of the nucleoside. In the case of mnm 5 s 2 U, the secondary amine in the sidechain could be positively charged and the thio-group negatively charged. This zwitterion would have the same hydrogen bonding qualities as the tautomer ( Fig. 7C ). 130

Group (VI) elements at the 2 position of U – the influence of atom size

When U is found at tRNA's position 34 it is nearly always modified. Modifications of U at the wobble position include 2-thiouridine (s 2 U) and 2-selenouridine (se 2 U) ( Fig. 8 ) 131 that affect both ribose sugar pucker as well as the glycosidic χ angle resulting in a restrictive reading of codons. Both sulfur as well as selenium have similar chemical properties to the carbonyl oxygen at the C2 position of U. However, the larger size of sulfur and selenium elicit different steric properties on their environment, being approximately 40% and 100% larger than oxygen, respectively ( Fig. 8 ). Also the electronegativity of the substituent atoms (sulfur and selenium) is smaller than that of oxygen. As would be expected, the modified U exhibits a dominant anti conformation. The larger atomic radii of these modifications also affect the nucleoside's sugar pucker particularly when the glycosidic bond angle χ is in the anti conformation. While the ribose of unmodified uridines populate equally the C3′ and C2′ endo conformations, the ribose sugar pucker of s 2 U and se 2 U exist preferentially in the C3′ endo conformation only occasionally switching to the C2′ endo pucker. The large size difference in the Van der Waal radius of the group IV elements bonded to C2 of U forces the sugar to adopt the C’3 endo conformation; a conformation that has been principally associated with increased stability through enhanced stacking. 28 In the case of the unmodified uridine, the carbonyl oxygen at C2 can form a hydrogen bond with the 2′OH group on the ribose thus stabilizing the C2′ endo conformation of the ribose ( Fig. 8A ). The less electronegative S or Se have a reduced propensity for such hydrogen bond interactions, and combined with the steric effects introduced by the larger size of the atoms, these modifications push the sugar pucker distribution toward C3′ endo ( Fig. 8B and 8C ). Thus, the conformation of uridines at wobble position 34 and modified with s 2 and se 2 is anti , C3′ endo , and the base pairing is preferentially to A, rather than wobbling to G.

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g008.jpg

Sulfur and selenium atomic radii affect sugar pucker when modifying the C2 position of uridine. A. Uridine, B. 2-thiouridine and C. 2-selenouridine nucleosides are shown. All 3 nucleosides are depicted in their anti conformation. The plane defined by atoms C1′-O4′-C4′ of the sugar separates the endo face (the side in which C5′ projects from the plane) from the exo face. In the case of uridine, the sugar pucker is C2′ endo as indicated by atom C2′ in the endo face (above the C1′-O4′-C4′ plane), while in 2-thiouridine and 2-selenouridine, the relative increase in atomic radius of substituent atom X at position C2 and the weakening of the hydrogen bonding interaction between 2′OH and X (where X – O2, S 2 or Se 2 ) shifts the equilibrium toward a C3′ endo conformation.

We and others have extolled the virtues of modifications at wobble position 34 and the invariant purine 3′-adjacent to the anticodon at position 37. Wobble base pairing does not appear to occur at positions other than tRNA position 34 with rare exception such as arthropod mitochondrial translation of the codon AGG as lysine instead of serine (invertebrates) or arginine (standard Universal Genetic Code) in which there is position 35 wobble base pairing, U 35 ○G2. 132 Modifications at tRNA's nucleosides 34 and 37 frame the anticodon and pre-structure the ASL for decoding. In doing so, they reduce energy barriers to conformational change required for ribosomal A-site binding, maintain the translational reading frame and either expand or restrict cognate and wobble codon recognition. In S cerevisiae , loss of either the xm 5 or s 2 modifications of mcm 5 s 2 U 34 increases observation of +1 translational frameshifts, 133 probably caused by a decrease in the affinity of the tRNA for the ribosomal A-site and an impaired translocation. 9 , 129 The nearly ubiquitous t 6 A 37 modification at position 37 in tRNAs responding to codons beginning with A, ANN, enhances base stacking of U 36 with A1 of the codon, as well as prevents intraloop base pairing within the ASL. 115 Thereby, t 6 A 37 facilitates the U-turn and presentation of the anticodon to the codon on the ribosome. t 6 A 37 also facilitates ribosomal codon binding and maintains the translational frame. 26 , 126 Other modifications at position 37, particularly in tRNAs responding to codons beginning with U, UNN, such as wyosine, contribute similarly to base stacking, maintaining the open loop structure and by doing so maintain the translational reading frame. 26 , 126 The fact that the ASL can be stabilized by various purine 37 modifications implies convergent evolutionary pathways that relate not only to the identity of the codon, but also to that of the nucleoside at position 34 and perhaps additionally either 32 or 38/39.

Yet, there appears to be a need for some tRNAs to further modify the anticodon loop for acceptance on the ribosome and codon recognition. For instance, the nucleoside N3-methylcytidine (m 3 C) was first found in tRNA over 50 years ago 134 and appears to be located exclusively at position 32 of the anticodon loop in specific eukaryotic tRNAs. 20 In addition, 2-thiocytidine is found at position 32 of specific prokaryotic tRNAs. The s 2 C 32 modification is present in E. coli and Salmonella enterica tRNA Arg ICG which decodes CGU/C and CGA in the absence of s 2 C 32 , tRNA Arg CCG that decodes CGG, tRNA Arg with the modified anticodon mnm 5 UCU that decodes AGA/G, and tRNA Ser GCU decoding AGC/U. 19 , 39 The presence of s 2 C 32 negates I 34 wobbling to A3. 39 It may affect translational efficiency of rare codons that are intrinsically inefficient in decoding. 19 , 135 The s 2 C 32 modification has also been found in archaeal tRNA. 136 Pseudouridine, Ψ, although present at the anticodon wobble position 34, is another modification found predominantly at positions 32, 38 and 39. 137 Pseudouridine in the anticodon loop apparently increases thermal stability but does not affect ribosome mediated codon binding, nor is its N1 position used for hydrogen bonding. 127

Multiple modifications within the ASL may provide a redundancy to the structure and conformational dynamics not otherwise achievable by 40+ individual tRNAs meeting ribosome acceptance and unique codon recognition. 43 Modification of tRNAs anticodon loop positions 32, 38 or 39, along with positions 34 and 37, in effect complete a triangle of modified nucleosides ( Fig. 9 ). It is interesting that the three point presentation of ASL modifications has modified nucleosides spaced almost equally around the anticodon loop at approximately every other position 32, 34, and 37, or 34, 37 and 39. Looking back at tRNA Gly NCC , the strong anticodon-codon, C•G interactions require no modifications, whereas tRNA Lys UUU , tRNA Tyr NUA , and tRNA Ile NAU have at least three functionally and/or structurally essential modified nucleosides in the ASL. Weak interactions with the codon, such as multiple U•A base pairs, may require far more extensive modifications, where chemically diverse modifications affect similar biologic properties, often through structure.

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g009.jpg

ASL modification triangle. A combination of 3 positions in the ASL (nucleotides 32 through 38) of tRNAs are commonly modified to expand or restrict codon recognition. Position 32, 34 and 37 (light blue) or position 34, 37 and 38 (dark blue) form vertices of the triangle in which modifications work in a co-surgical manner to achieve desired ribosomal binding affinity of the tRNA to different codons. The anticodon is represented in red and the nucleosides in the ASL in black.

The ribosome bound structures of the tRNA ASLs containing post-transcriptional modifications offer molecular insights into their role in modulating structure, stability and interactions of the tRNA. While the uridine at wobble position 34 is the most heavily modified, positions 32, 37 and 38 also show significant levels of modifications. We have gathered the structures of five tRNAs bound to the ribosome at the A-site, and highlighted the interactions of their modifications ( Fig. 10 ). It is interesting to note that U 34 is primarily modified at C5 adjacent to the base-pairing face and hence the modifications do not interfere with its hydrogen bonding to the codon except in cases where the modifications introduce tautomerism. However, the modifications are either polar (as is true in case of tRNA Leu 138 and tRNA Val 11 ) or charged, (tRNA Lys ), 44 and therefore participate in hydrogen bonding with neighboring bases or charge-charge interactions with the backbone phosphate group. Modifications on the position 37 purine nucleobase are primarily involved in stacking with the base at position 36 and the base to which it is paired in codon recognition on the ribosome. These modifications are either methylations (tRNA Val ) or groups with complex chemistries, like t 6 A 37 , which significantly increases its stacking propensity. Enhanced base stacking of position 37 modified purines provides additional stability to the U-turn structure, and increases the binding strength of the ASL when U 34 pairs with a near-cognate or non-cognate codon.

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g010.jpg

Ribosome-bound structures of the ASLs of 5 tRNA species with modifications. tRNA modified nucleosides at positions 32, 34 and 37 are influential in creating the architecture of the anticodon domain accepted into the ribosome's A-site for cognate and wobble codon binding. The codon on the mRNA is shown in green, the ASL in cyan with the modifications labeled and the rRNA interactions shown in magenta. Possible interactions of the modified groups are represented using a dashed line. A. In ASL Val UAC bound to codon GUU, (PDB ID: 2UUB), the carboxyl oxygen of cmo 5 U 34 is within hydrogen bonding distance of the amine group on the neighboring A 35 . B. In ASL Leu UAA bound to codon UUG (PDB ID: 2VQF), two of the three oxygens bonded to the sulfur atom in the τm 5 U 34 can form hydrogen bonding interactions with A 35 and A 36 . C. In ASL Lys UUU bound to codon AAA (PDB ID: 1XMQ), there are a salt-bridge between the 5-methylaminomethyl group on U 34 and its phosphate group, an enhanced stacking interaction provided by t 6 A 37 , and a possible hydrogen bond between the threonyl group of t 6 A 37 and A1 on the mRNA. D. ASL Arg2 ICG bound to the codon CGC. The ASL has the two modifications I 34 , m 2 A 37 . E. ASL Arg1 ICG bound to the codon CGC. The ASL has the modifications s 2 C 32 , I 34 . When either of the modifications m 2 A 37 or s 2 C 32 are present, then the tRNA is unable to recognize the rare CGA codon. 39

The cross-loop interaction between the nucleosides at position 32 and 38 at the beginning of the ASL loop ( Fig. 4B ) is characterized by a single or bifurcated hydrogen bond. 139 The strength of this interaction appears to be carefully modulated. For instance, pseudouridine at position 32 uses a water mediated base-backbone interaction to stabilize the interaction between nucleosides 32 and 38. 138 While a stronger interaction, like that of a canonical base pair at this position could lead to a loss in flexibility of the loop domain, a weaker interaction could result in loss of stacking in the ASL resulting in a disruption of the functional U-turn conformation of the ASL. Modifications at the 32 nd and 38 th positions of the ASL may be important as a possible means of modulating the interaction between the two nucleosides and base stacking in the loop.

We hypothesize that the combined chemistries and conformational dynamics of modified nucleosides located at three positions, positions 34, 37 and one other within the ASL loop ( Fig. 9 ) transform the loop architecture and dynamics to that consistent with the constraints that the ribosome places on all tRNAs. It is important that a stable, yet adaptable, U-turn is maintained for presentation of the anticodon resulting in accurate and efficient codon recognition. Multiple modifications mold the anticodon loop architecture of specific tRNAs into thermally stable, malleable triangles of strength recognizable by mRNA-programmed ribosomes ( Fig. 9 ). In order for the architecture of the anticodon's loop to change, an edge of the triangle must collapse, as in an alteration of the 5′-side and U-turn. This is apparent in the three different anticodon loop conformers of tRNA Arg1,2 that are recognized by argininyl-tRNA synthetase with a disrupted U-turn, a solution structure that does not exhibit a U-turn and a conformation on the ribosome in the A-site that has the canonical U-turn. 39

Conjecture about the evolution of site- and chemically specific modifications within tRNA's ASL domain relative to their functions can yield insights into their future, investigator-designed applications. RNA polymerases, with few exceptions, in vivo and in vitro , do not accept modified nucleoside triphosphates as substrates for transcription, and if they did the modification would be randomly placed throughout the transcript in response to the template. Therefore, it is feasible to hypothesize that the evolution of post-transcriptionally modified nucleosides occurred after the appearance of proteins that could catalyze their limited existence at specific sites to which each modification would contribute chemistry and conformation to that tRNA's function in translation. In acknowledging today's understanding of the manner in which anticodon domain modifications both expand and restrict recognition of cognate and wobble codons, but not near-cognate codons, it is difficult to comprehend life in which new amino acids would be introduced with limited numbers of tRNAs and necessitating 2-fold degenerate codons. For instance, without the restrictions imposed by modifications, one could conceive of asparagine and lysine, aspartic and glutamic acids, and perhaps arginine and serine being mistakenly incorporated. More likely, tRNAs with unmodified anticodon domains much like the very limited number of 22 tRNAs transcribed in mammalian mitochondria decoded 4-fold degenerate codon boxes without error, but perhaps at reduced efficiencies. In contrast, cytoplasmic and mitochondrial translation of codons from 2-fold degenerate codon boxes ( Fig. 1 ) preceded in the absence of modification with significantly reduced translational fidelity and lack of efficiency until restrictive modifications had evolved. If tRNA anticodon domain modifications facilitated the accurate and efficient entry of new amino acids through split codon boxes in the evolution of proteins as we know them, then why couldn't the emergence of still other amino acid incorporations continue by re-appropriating sense codons? 140 , 141 The use of 4-fold degenerate sense codons to incorporate new amino acids would require the splitting of 4-fold degenerate codons. Perhaps, this could be accomplished by removal of cytoplasmic tRNAs from redundant codon recognition (which does not occur in the mitochondria), restructuring the modification enzyme recognition of specific tRNA species and aminoacyl-tRNA synthetase recognition of tRNA and the non-natural amino acid substrates. The introduction of novel amino acids into proteins portends applications to biomaterial science and medicine. New investigator-designed, protein-based materials and potential therapeutics would become available through biomanufacturing.

In conclusion, The Wobble Hypothesis is being revised continually for as we learn more every year about modified nucleoside chemistry, structure and function and how it reflects on RNA chemistry, structure and function, we understand the subtleties of translation being able to manipulate and apply them. We have discussed the different instances in which wobble base pairs are used to expand/restrict codon recognition by tRNA's anticodon with modified and unmodified wobble position 34, and the importance of modified nucleoside positions outside of anticodon, 32, 37 and 38 ( Fig. 11 ). Wobble and non-canonical base pairs in the ASL domain of tRNA are integral to the translation of the genetic code. They are modulated either by unique structural and dynamic features introduced in a sequence dependent manner by unmodified bases (e.g., tRNA Gly with C 32 /U 32 ) or by nucleoside modifications that can expand or restrict decoding capacity of tRNAs by stabilizing or disrupting native interactions at the decoding center of the ribosome. An in-depth understanding of the origins and mechanisms of the variety of ways by which wobbling is achieved will equip us with the tools to tap into this often overlooked potential of using modified nucleoside contributions to translation for therapeutics and other applications.

An external file that holds a picture, illustration, etc.
Object name is krnb-15-4-5-1356562-g011.jpg

Wobble map. Anticodon domain modified nucleosides play an important role in the wobbling of tRNA's codon recognition, some expanding codon recognition to synonymous codons while others restrict recognition. The different cases of wobbling in the presence and absence of modifications as discussed in this paper, are shown. The black arrow represents no modifications, whereas a red arrow indicates the presence of one or more modifications. The tRNAs are shown in blue, the anticodons are indicated on the arrow and codons decoded by the tRNA bearing the anticodon are enclosed in white boxes.

Disclosure of potential conflicts of interest

The authors report no conflict of interest.

Research conducted by the authors is supported by grants to P.F.A. from the Department of Defense Medical Research Program under grant number W81XWH-16-1-0428, PR151248, the National Science Foundation under grant number CHE1407042 and the National Institutes of Health, National Institute of General Medical Sciences under grant number 5R01GM110588-03 to Manal Swairjo, P.F.A. co-investigator.

Wobble Hypothesis

December 2013
In book: Brenner's Encyclopedia of Genetics (pp.Volume 7:347-349)
Edition: Second
Publisher: Elsevier
Editors: Stanley Maloy and Kelly Hughes

University of Ottawa

Discover the world's research

25+ million members
160+ million publication pages
2.3+ billion citations

No full-text available

To read the full-text of this research, you can request a copy directly from the author.

BMC EVOL BIOL

NUCLEIC ACIDS RES

Stanislaw Dunin-Horkawicz
Elzbieta Purta
Kristian Rother

Christian Marck
M. G. Bulmer
F. H. C. Crick
Valery I Lim
A Czerwoniec
S Dunin-Horkawicz
Recruit researchers
Join for free
Login Email Tip: Most researchers use their institutional email address as their ResearchGate login Password Forgot password? Keep me logged in Log in or Continue with Google Welcome back! Please log in. Email · Hint Tip: Most researchers use their institutional email address as their ResearchGate login Password Forgot password? Keep me logged in Log in or Continue with Google No account? Sign up

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

View all journals
Explore content
About the journal
Publish with us
Sign up for alerts
News & Views
Published: 01 December 2004

Wobble during decoding: more than third-position promiscuity

Luisa Cochella 1 &
Rachel Green 1

Nature Structural & Molecular Biology volume 11 , pages 1160–1162 ( 2004 ) Cite this article

569 Accesses

11 Citations

Metrics details

Structural studies by the Ramakrishnan and Agris groups allow us to directly observe how the ribosome's decoding site accommodates non-Watson-Crick base pairs in the third position of the codon-anticodon triplet while maintaining the one-amino-acid-per-codon framework that is central to life.

This is a preview of subscription content, access via your institution

Access options

Subscribe to this journal

Receive 12 print issues and online access

176,64 € per year

only 14,72 € per issue

Buy this article

Purchase on Springer Link
Instant access to full article PDF

Prices may be subject to local taxes which are calculated during checkout

Accession codes

Protein data bank.

Bernfield, M.R. & Nirenberg, M.W. Science 147 , 479–484 (1965).

Article CAS Google Scholar

Söll, D. et al. J. Mol. Biol. 19 , 556–573 (1966).

Article Google Scholar

Kellogg, D.A., Doctor, B.P., Loebel, J.E. & Nirenberg, M.W. Proc. Natl. Acad. Sci. USA 55 , 912–919 (1966).

Crick, F.H. J. Mol. Biol. 19 , 548–555 (1966).

Agris, P.F. Nucleic Acids Res. 32 , 223–238 (2004).

Murphy, F.V. & Ramakrishnan, V. Nat. Struct. Mol. Biol. 11 , 1251–1252 (2004).

Murphy, F.V., Ramakrishnan, V., Malkiewicz, A. & Agris, P.F. Nat. Struct. Mol. Biol. 11 , 1186–1191 (2004).

Holley, R.W. JAMA 194 , 868–871 (1965).

Leonard, G.A., Booth, E.D., Hunter, W.N. & Brown, T. Nucleic Acids Res. 20 , 4753–4759 (1992).

Subramanian, E., Madden, J.J. & Bugg, C.E. Biochem. Biophys. Res. Commun. 50 , 691–696 (1973).

Carter, R.J., Baeyens, K.J., SantaLucia, J., Turner, D.H. & Holbrook, S.R. Nucleic Acids Res. 25 , 4117–4122 (1997).

Fuller, W. & Hodgson, A. Nature 215 , 817–821 (1967).

Ogle, J.M. et al. Science 292 , 897–902 (2001).

Mizuno, H. & Sundaralingam, M. Nucleic Acids Res. 5 , 4451–4461 (1978).

Holbrook, S.R., Sussman, J.L., Warrant, R.W. & Kim, S.H. J. Mol. Biol. 123 , 631–660 (1978).

LaRiviere, F.J., Wolfson, A.D. & Uhlenbeck, O.C. Science 294 , 165–168 (2001).

Yokoyama, S. & Nishimura, S. tRNA: Structure, Biosynthesis and Function (eds. Söll, D. & RajBhandary, U.) 207–223 (American Society for Microbiology, Washington, DC, 1995).

Book Google Scholar

Download references

Author information

Authors and affiliations.

Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland, USA

Luisa Cochella & Rachel Green

You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article.

Cochella, L., Green, R. Wobble during decoding: more than third-position promiscuity. Nat Struct Mol Biol 11 , 1160–1162 (2004). https://doi.org/10.1038/nsmb1204-1160

Download citation

Issue Date : 01 December 2004

DOI : https://doi.org/10.1038/nsmb1204-1160

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

This article is cited by

Role of taurine in the pathologies of melas and merrf.

Stephen W. Schaffer
Chian Ju Jong
Junichi Azuma

Amino Acids (2014)

Quick links

Explore articles by subject
Guide to authors
Editorial policies

BiologyDiscussion.com
Follow Us On:
Google Plus
Publish Now

Wobble Hypothesis (With Diagram) | Genetics

ADVERTISEMENTS:

In this article we will discuss about the concept of wobble hypothesis.

Crick (1966) proposed the ‘wobble hypothesis’ to explain the degeneracy of the genetic code. Except for tryptophan and methionine, more than one codons direct the synthesis of one amino acid. There are 61 codons that synthesise amino acids, therefore, there must be 61 tRNAs each having different anticodons. But the total number of tRNAs is less than 61.

This may be explained that the anticodons of some tRNA read more than one codon. In addition, identity of the third codon seems to be unimportant. For example CGU, CGC, CGA and CGG all code for arginine. It appears that CG specifies arginine and the third letter is not important. Conventionally, the codons are written from 5′ end to 3′ end.

Therefore, the first and second bases specify amino acids in some cases. According to the Wobble hypothesis, only the first and second bases of the triple codon on 5′ → ‘3 mRNA pair with the bases of the anticodon of tRNA i.e A with U, or G with C.

The pairing of the third base varies according to the base at this position, for example G may pair with U. The conventional pairing (A = U, G = C) is known as Watson-Crick pairing (Fig. 7.1) and the second abnormal pairing is called wobble pairing.

This was observed from the discovery that the anticodon of yeast alanine-tRNA contains the nucleoside inosine (a deamination product of adenosine) in the first position (5′ → 3′) that paired with the third base of the codon (5′ → 3′). Inosine was also found at the first position in other tRNAs e.g. isoleucine and serine.

The purine, inosine, is a wobble nucleotide and is similar to guanine which normally pairs with A, U and C. For example a glycine-tRNA with anticodon 5′-ICC-3′ will pair with glycine codons GGU, GGC, GGA and GGG (Fig 7.2). Similarly, a seryl-tRNA with anticodon 5′-IGA-3′ pairs with serine codons UCC, UCU and UCA (5-3′). The U at the wobble position will be able to pair with an adenine or a guanine.

According to Wobble hypothesis, allowed base pairings are given in Table 7.5:

Due to the Wobble base pairing one tRNA becomes able to recognise more than one codons for an individual amino acid. By direct sequence of several tRNA molecules, the wobble hypothesis is confirmed which explains the pattern of redundancy in genetic code in some anticodons (e.g. the anticodons containing U, I and G in the first position in 5’→ 3′ direction)

The seryl-tRNA anticodon (UCG) 5′-GCU-3′ base pairs with two serine codons, 5′-AGC-3′ and 5′-AGU-3′. Generally, Watson-Crick pairing occurs between AGC and GCU. However, in AGU and GCU pairing, hydrogen bonds are formed between G and U. Such abnormal pairing called ‘Wobble pairing’ is given in Table 7.5.

Three types of wobble pairings have been proposed:

(i) U in the wobble position of the tRNA anticodon pairs with A or G of codon,

(ii) G pairs with U or C, and

(iii) 1 pairs with A, U or C.

Short Notes on Anticodons | Genetics
Genetic Code: Degeneracy and Universality | Protein

Microbiology , Genetics , Wobble Hypothesis , Concept of Wobble Hypothesis

Anybody can ask a question
Anybody can answer
The best answers are voted up and rise to the top

Privacy Overview

Cookie	Duration	Description
cookielawinfo-checkbox-analytics	11 months	This cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Analytics".
cookielawinfo-checkbox-functional	11 months	The cookie is set by GDPR cookie consent to record the user consent for the cookies in the category "Functional".
cookielawinfo-checkbox-necessary	11 months	This cookie is set by GDPR Cookie Consent plugin. The cookies is used to store the user consent for the cookies in the category "Necessary".
cookielawinfo-checkbox-others	11 months	This cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Other.
cookielawinfo-checkbox-performance	11 months	This cookie is set by GDPR Cookie Consent plugin. The cookie is used to store the user consent for the cookies in the category "Performance".
viewed_cookie_policy	11 months	The cookie is set by the GDPR Cookie Consent plugin and is used to store whether or not user has consented to the use of cookies. It does not store any personal data.

DOI: 10.1016/B978-0-12-131200-8.50026-5
Corpus ID: 30840571

Codon--anticodon pairing: the wobble hypothesis.

Published in Journal of Molecular Biology 1 August 1966

Figures and Tables from this paper

1,692 Citations

Is there selection against wobble in codon-anticodon pairing, codon recognition: the allosteric ribosome hypothesis., wobble during decoding: more than third-position promiscuity, wobble position modified nucleosides evolved to select transfer rna codon recognition: a modified-wobble hypothesis., base pairing and fidelity in codon–anticodon interaction, recognition between codon and anticodon, how many anticodons, a minimum principle in codon-anticodon interaction, uga: a third nonsense triplet in the genetic code, conformation of the anticodon loop in trna, 12 references, genetic code: emergence of a symmetrical pattern, rna codewords and protein synthesis, vii. on the general nature of the rna code., specificity of srna for recognition of codons as studied by the ribosomal binding technique., structure of a ribonucleic acid, studies on polynucleotides, xlix. stimulation of the binding of aminoacyl-srna's to ribosomes by ribotrinucleotides and a survey of codon assignments for 20 amino acids., nucleotidsequenzen in serinspezifischen transfer-ribonucleinsäuren, rna codons and protein synthesis. ix. synonym codon recognition by multiple species of valine-, alanine-, and methionine-srna., rna codewords and protein synthesis. the nucleotide sequences of multiple codewords for phenylalanine, serine, leucine, and proline., studies on the structure of purified alanine and valine transfer rna from yeast, related papers.

Showing 1 through 3 of 0 Related Papers

IMAGES

The Wobble Hypothesis: How RNA’s 3D Structure Affects Protein Synthesis
(PDF) The wobble hypothesis revisited: Uridine-5-oxyacetic acid is
The Wobble Hypothesis: Definition, Statement, Significance
The Wobble Hypothesis: How RNA’s 3D Structure Affects Protein Synthesis
PPT
PPT

COMMENTS

The Wobble Hypothesis: Definition, Statement, Significance
There are more than one codon for one amino acid.This is called degeneracy of genetic code. To explain the possible cause of degeneracy of codons, in 1966, Francis Crick proposed "the Wobble hypothesis".. According to The Wobble 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 ...
PDF WOBBLE HYPOTHESIS
The Wobble Hypothesis •The first two bases of the codon make normal (canonical) H- bond pairs with the 2nd and 3rd bases of the anticodon •At the remaining position, less stringent rules apply and non- canonical pairing may occur •The rules: first base U can recognize A or G, first base G can recognize U or C, and first base I can recognize U, C or A (I
PDF Wobble Hypothesis
Wobble Hypothesis Proposed by Crick in 1966 According to this hypothesis, the base in the first position of anti-codon on tRNA is usually an abnormal base, like inosine, pseudouridine, tyrosine, etc. These abnormal bases are able to pair with more than one type of nitrogenous base in the third position of the codon on mRNA. eg.
The Wobble Hypothesis: Importance and Examples
Here are some examples of the wobble hypothesis in action: Arginine: The amino acid arginine is coded by six different codons: CGU, CGC, CGA, CGG, AGA, and AGG. However, no six different tRNA molecules correspond to each of these codons. Instead, one tRNA molecule with the anticodon 3′-CCU-5′ can recognize the codons CGU, CGC, and CGA ...
PDF kvmwai.edu.in
The wobble hypothesis thus proposes a more flexible set of base-pairing rules at the third position of the codon. The relaxed base-pairing requirement, or "wobble," allows the anticodon Of a single form Of tRNA to pair with more than one triplet in mRNA.
The wobble hypothesis revisited: Uridine-5-oxyacetic acid is critical
According to the wobble hypothesis , G34 base-pairs with C and U as the third nucleoside of the codon [denoted C(III) and U(III)], whereas C34 only base-pairs with G(III). Uridine as the wobble nucleoside cannot interact with a pyrimidine in the mRNA, since two pyrimidines are too "short" to form a base pair.
Celebrating wobble decoding: Half a century and still much is new
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's ...
PDF M.Sc. II Semester (2019-20) Paper BCH 201: Fundamentals of ...
The code is unambiguous. Each codon specifies no more than one amino acid. The code is degenerate. More than one codon can specify a single amino acid. All amino acids, except Met and tryptophan (Trp), have more than one codon. For those amino acids having more than one codon, the first two bases in the codon are usually the same.
PDF Hansraj College, University of Delhi
However, the wobble hypothesis can explain degeneracy only at the third position of the codon, and, at best this can account only for three codonsfor each amino acid. The remaining cases of degeneracy must be due to different varieties of tRNA for a single amino acid, but this type of degeneracy need not be limited to such cases only.
Wobble Hypothesis
Abstract. The original wobble hypothesis with its extended codon-anticodon base pairs played a crucial role in understanding the working of the messenger RNA (mRNA) translation machinery. Wobble ...
PDF Wobble during decoding: more than third-position promiscuity
original wobble hypothesis. Crick recognized that inosine had the potential for promiscu-ous interactions and proposed near-standard pairing with U and C and a slightly broader
Wobble Hypothesis (With Diagram)
In this article we will discuss about the concept of wobble hypothesis. Crick (1966) proposed the 'wobble hypothesis' to explain the degeneracy of the genetic code. Except for tryptophan and methionine, more than one codons direct the synthesis of one amino acid. There are 61 codons that synthesise amino acids, therefore, there must be 61 ...
PDF The wobble hypothesis revisited: Uridine-5-oxyacetic acid is critical
wobble nucleoside is almost always modified, and the cmo5-modification and the related modification 5-methoxy-uridine, mo5U, present in tRNA of Bacillus subtilis,is predicted to extend the wobble capacity to read not only A(III) and G(III), as predicted by the wobble hypothesis, but also U(III), but not C(III) (Yokoyama et al. 1985).
Transfer RNA in Decoding and the Wobble Hypothesis
This is achieved through an increased flexibility in the allowable base-pair interactions between the messenger RNA and the transfer RNA involving the third position of the codon and the first position of the corresponding anticodon. The rules governing this RNA:RNA interaction were originally summarised in Crick's 'wobble hypothesis'.
[PDF] Codon--anticodon pairing: the wobble hypothesis.
Base pairing and fidelity in codon-anticodon interaction. M. D. Topal J. R. Fresco. Biology, Chemistry. Nature. 1976. Base pairing in codon-anticodon interaction has been investigated in order to understand the basis on which particular base pairs have been selected for or against participation at the wobble…. Expand.
Wobbling of What
The wobble hypothesis, which was first proposed more than 40 years ago [1], can explain two events: 1) formation of the uracil-guanine pair as a result of codon-anticodon interaction in the third position and 2) encoding of isoleucine by three codons (for the universal genetic code). This hypothesis is based on two statements: in the third ...
Wobble base pair
Wobble base pairs for inosine and guanine. 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 ...
Celebrating wobble decoding: Half a century and still much is new
individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modiﬁed Wobble Hypothesis 25 years ago, some individual modiﬁcations at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons.
Codon—anticodon pairing: The wobble hypothesis
Codon—anticodon pairing: The wobble hypothesis. It is suggested that while the standard base pairs may be used rather strictly in the first two positions of the triplet, there may be some wobble in the pairing of the third base. This hypothesis is explored systematically, and it is shown that such a wobble could explain the general nature of ...
B.Sc. III B-302 Genetic CODE- Wobble Hypothesis PDF
Mendelian laws of Inheritance wobble hypothesis proposed crick in 1966 according to this hypothesis, the base in the first position of on trna is usually an. Skip to document. ... B.Sc. III B-302 Genetic CODE- Wobble Hypothesis PDF. Mendelian laws of Inheritance. Course. cell biology (msc 1) 48 Documents. Students shared 48 documents in this ...