:Wybutosine

Using an S. cerevisiae model, the biosynthetic pathway of wybutosine was proposed. Proceeding through a multi-enzymatic process, the first step of the synthesis involves the enzyme N1-methyltransferase TRM5 which methylates the G37 site of phenylalanine tRNA and converts it to m1G37. Then m1G37 acts as a substrate for the enzyme TYW1 and, using pyruvate as a C-3 source, forms the tricyclic core of wybutosine with flavin mononucleotide (FMN) as a cofactor. The enzyme TYW2 then transfers the α-amino-α-carboxypropyl group from Ado-Met, a common substrate involved in methyl group transfers, to the lateral side chain at the C-7 position of yW-187 to form yW-86. TYW3 acts as a catalyst for N-4 methylation of yW-86 to produce yW-72. TYW4 and Ado-Met-dependent carboxymethyltransferase then methylates the α-carboxy group of yW-72 to give yW-57. Finally by a predicted second function of TYW4 or other unidentified factors, the methoxycarbonylation of the α-amino group of the yW-58 side chain gives wybutosine.{{cite book |doi=10.1016/bs.mie.2018.04.024 |chapter=TYW1: A Radical SAM Enzyme Involved in the Biosynthesis of Wybutosine Bases |title=Radical SAM Enzymes |series=Methods in Enzymology |year=2018 |last1=Young |first1=Anthony P. |last2=Bandarian |first2=Vahe |volume=606 |pages=119–153 |pmid=30097090 |pmc=6448148 |isbn=978-0-12-812794-0 }}

File:Wybutosine.png

Wybutosine has been chemically synthesized.{{cite journal |vauthors=Itaya T, Kanai T, Iida T |title=Practical synthesis of wybutosine, the hypermodified nucleoside of yeast phenylalanine transfer ribonucleic acid |journal=Chem. Pharm. Bull. |volume=50 |issue=4 |pages=530–3 |year=2002 |pmid=11964003 |doi=10.1248/cpb.50.530 |doi-access=free }}{{cite journal |vauthors=Hienzsch A, Deiml C, Reiter V, Carell T |title=Total synthesis of the hypermodified RNA bases wybutosine and hydroxywybutosine and their quantification together with other modified RNA bases in plant materials |journal=Chemistry: A European Journal |volume=19 |issue=13 |pages=4244–8 |year=2013 |pmid=23417961 |doi=10.1002/chem.201204209 }}

Wybutosine and other unnatural nucleosides have been proposed to lead to a single outcome of hypermodification. This hypermodification at position 37 of tRNA^Phe may allow for base- stacking interactions which play a key role in maintenance of the reading frame.{{cite journal | last1 = Helm | first1 = M | last2 = Alfonzo | first2 = JD | year = 2014 | title = Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland | journal = Chem. Biol. | volume = 21 | issue = 2| pages = 174–85 | doi=10.1016/j.chembiol.2013.10.015| pmc = 3944000 | pmid=24315934}} Through its large aromatic groups, stacking interactions with adjacent bases A36 and A38 are enhanced, which help to restrict the flexibility of the anticodon.{{cite journal | last1 = Stuart | first1 = JW | last2 = Koshlap | first2 = KM | last3 = Guenther | first3 = R | last4 = Agris | first4 = PF | year = 2003 | title = Naturally-occurring modification restricts the anticodon domain conformational space of tRNA(Phe) | journal = J Mol Biol | volume = 334 | issue = 5| pages = 901–18 | doi=10.1016/j.jmb.2003.09.058| pmid = 14643656 }} It has been found that when tRNA^Phe lacks wybutosine, increased frameshifting occurs. Generally, modifications at position 37 prevent base pairing with neighboring nucleotides by helping to maintain and open the loop conformation, as well as generating an anticodon loop for decoding. The wybutosine modification of tRNA^Phe is found to be conserved in archaea and eukarya but is not found in bacteria.

Studies from the 1960s and 1970s noted that many mutations could lead to problems in translational accuracy. Further study of the mechanisms involved in translational accuracy revealed the importance of modifications on positions 34 and 37 of tRNA. Regardless of species, these sites of tRNA are almost always modified. The fact that wybutosine and its various derivatives are only found at position 37 may be indicative of the nature of the phenylalanine codons, UUU and UUC, and their predilection for ribosome slippage.{{cite journal | last1 = Christian | first1 = T | last2 = Lahoud | first2 = G | last3 = Liu | first3 = C | last4 = Hou | first4 = YM | year = 2010 | title = Control of catalytic cycle by a pair of analogous tRNA modification enzymes | journal = J Mol Biol | volume = 400 | issue = 2| pages = 204–17 | doi=10.1016/j.jmb.2010.05.003 | pmid=20452364 | pmc=2892103}} This has led to the assumption that tRNA^Phe modification at position 37 correlates with the amount of polyuridine slippery sequences found in genomes.{{cite journal | last1 = Jackman | first1 = JE | last2 = Alfonzo | first2 = JD | year = 2013 | title = Transfer RNA modifications: nature's combinatorial chemistry playground | journal = Wiley Interdiscip Rev RNA | volume = 4 | issue = 1| pages = 35–48 | doi=10.1002/wrna.1144| pmc = 3680101 | pmid=23139145}}

Wybutosine's role in prevention of frameshifts has raised some questions into its importance, as there are other strategies beside modification with yW to prevent a shift. In Drosophila there is no modification at position 37 while in mammals yW is modified there. To explain this variability the idea of frameshifting potential has come about. This implies that cells use frameshifting as a mechanism to regulate themselves rather than trying to avoid frameshifting at all times.{{cite journal |last1=Waas |first1=William F. |last2=Druzina |first2=Zhanna |last3=Hanan |first3=Melanie |last4=Schimmel |first4=Paul |title=Role of a tRNA Base Modification and Its Precursors in Frameshifting in Eukaryotes |journal=Journal of Biological Chemistry |date=September 2007 |volume=282 |issue=36 |pages=26026–26034 |doi=10.1074/jbc.m703391200 |pmid=17623669 |doi-access=free }} It has been suggested that frameshifting may be used in a programmed manner, possibly to increase coding diversity.{{cn|date=April 2025}}

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{{Nucleobases, nucleosides, and nucleotides}}

Category:Nucleosides

Category:Imidazopurines

Category:Hydroxymethyl compounds

Category:Carbamates

Category:Carboxylate esters

Category:Methyl esters