Biosynthesis of wybutosine, a hyper‐modified nucleoside in eukaryotic phenylalanine tRNA

@article{Noma2006BiosynthesisOW,
  title={Biosynthesis of wybutosine, a hyper‐modified nucleoside in eukaryotic phenylalanine tRNA},
  author={A. Noma and Y. Kirino and Y. Ikeuchi and Tsutomu Suzuki},
  journal={The EMBO Journal},
  year={2006},
  volume={25}
}
Wybutosine (yW) is a tricyclic nucleoside with a large side chain found at the 3′‐position adjacent to the anticodon of eukaryotic phenylalanine tRNA. yW supports codon recognition by stabilizing codon–anticodon interactions during decoding on the ribosome. To identify genes responsible for yW synthesis from uncharacterized genes of Saccharomyces cerevisiae, we employed a systematic reverse genetic approach combined with mass spectrometry (‘ribonucleome analysis’). Four genes YPL207w, YML005w… Expand
Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4†
TLDR
The structures revealed that the C-terminal domain folds into a β-propeller structure, forming part of the binding pocket for the target nucleoside, and suggest that TYW4 catalyzes both methylation and methoxy carbonylation at a single catalytic site, and in the latter reaction, the methoxycarbonyl group is formed through the fixation of carbon dioxide. Expand
Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea.
TLDR
Four of the five wybutosine biosynthetic enzymes are ancient and may have been present in the last common ancestor of Archaea and Eucarya and the variations in the distribution pattern of biosynthesis enzymes reflect the diversity of the wyosine derivatives found in different Archaea. Expand
Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2
TLDR
These findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the “acp” group, and not the methyl group, from AdoMet to the nucleobase. Expand
Structure-Function Analysis of Human TYW2 Enzyme Required for the Biosynthesis of a Highly Modified Wybutosine (yW) Base in Phenylalanine-tRNA
TLDR
It is demonstrated here that human TYW2 (hTYW2) is active in yeast and can synthesize the yW of yeast tRNAPhe, indicating that hTYW 2 may have a role in tumorigenesis unrelated to yW biogenesis. Expand
Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA.
TLDR
Mutational analyses in yeast supported the validity of this complex model structure, which provides a structural insight into the radical reaction involving two [4Fe-4S] clusters to create a complex tricyclic base. Expand
Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis.
TLDR
The AdoMet molecule, which is necessary for the reactions of radical-AdoMet enzymes, was modelled in P. horikoshii TYW1 and revealed the highly conserved and positively charged active-site hollow. Expand
Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea
TLDR
In this review, current knowledge regarding the archaeal enzymes involved in this process and their reaction mechanisms are summarized and the experiments aimed to elucidate missing steps in biosynthesis pathways leading to the formation of wyosine derivatives are suggested. Expand
Structural studies of S-adenosyl-L-methionine radical enzymes involved in tRNA and natural product biosynthesis
Members of the S-adenosyl-L-methionine (AdoMet) radical enzyme superfamily catalyze a myriad of diverse and challenging biotransformations using a [4Fe-4S] cluster and a molecule of AdoMet toExpand
Dual pathways of tRNA hydroxylation ensure efficient translation by expanding decoding capability
TLDR
It is shown that the first step of cmo5U biosynthesis from uridine is mediated by either one of two parallel factors, TrhP or TrhO, and that cmo4U modification is required for efficient translation, confirming that tRNA hydroxylation ensures efficient decoding during protein synthesis. Expand
A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria
TLDR
It is suggested that the kinetoplastids pathways evolved via gene duplication and acquisition of an FMN-binding domain now prevalent in TyW1 of most eukaryotes, and may have provided selective pressure for maintenance of mitochondrial wyosine in this lineage. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 53 REFERENCES
Enzymatic conversion of guanosine 3′ adjacent to the anticodon of yeast tRNAPhe to N1‐methylguanosine and the wye nucleoside: dependence on the anticodon sequence.
TLDR
Results obtained by oocyte microinjection indicate that all the restructured yeast tRNAsPhe are efficient substrates for the tRNA (guanosine‐37 N1)methyltransferase, which means that the anticodon sequence is not critical forThe tRNA recognition by this enzyme. Expand
S-Adenosylmethionine-dependent Methylation in Saccharomyces cerevisiae
TLDR
Yeast disruption mutants of each of the genes encoding these sequences are prepared, and it is found that disruption of the YJL125c gene is lethal, whereas disruptions of YCR047c and YDR140w lead to slow growth phenotypes. Expand
A novel methyltransferase required for the formation of the hypermodified nucleoside wybutosine in eucaryotic tRNA.
TLDR
Using pulse-chase labeling of intact yeast cells with S-adenosyl-L-[methyl-(3)H]methionine, it is shown that the methylesterified form of yW is metabolically stable. Expand
Biosynthesis of the nucleoside y in yeast tRNAPhe: Incorporation of the 3‐amino‐3‐carboxypropyl‐group from methionine
TLDR
The nucleoside Y in yeast tRNAflle and in the tRNAPhe of several other organisms has one of the most complex structures of all modified nucleosides known and a part of the side chain might be derived from methionine, as represented by the large characters in fig. 1. Expand
Structures of two new "minimalist" modified nucleosides from archaeal tRNA.
TLDR
The structures of two minimally elaborated wye derivatives from archaea suggest a minimal role for wye methyl groups and side chains in maintenance of anticodon stem-loop structures, and support the concept that archaeal tRNA nucleoside modification motifs are generally simpler than those of their counterparts in eukarya and bacteria. Expand
A specific modification next to the anticodon of phenylalanine transfer ribonucleic acid.
TLDR
It can be concluded that Y and probably the whole anticodon loop are not essential parts of the synthetase recognition region of tRNAPhe in homologous charging reactions. Expand
MiaB Protein Is a Bifunctional Radical-S-Adenosylmethionine Enzyme Involved in Thiolation and Methylation of tRNA*
TLDR
It is demonstrated that MiaB protein is a bifunctional system, involved in both thiolation and methylation of i6A, and probably through reductive cleavage and intermediate formation ofa5′-deoxyadenosyl radical as observed in other “Radical-AdoMet” enzymes. Expand
Tandem Mass Spectrometry for Structure Assignments of Wye Nucleosides from Transfer RNA
The tricyclic wye nucleoside family of eight known members constitutes one of the most complex and interesting series of posttranscriptionally modified nucleosides in transfer RNA. The principalExpand
Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions.
TLDR
It is revealed that 2-thiouridine formation proceeds through a complex sulfur-relay system composed of multiple sulfur mediators that select and facilitate specific sulfur flow to 2- thiouridine from various pathways of sulfur trafficking. Expand
A primordial tRNA modification required for the evolution of life?
TLDR
The results suggest that m1G37 existed in tRNA before the divergence of the three domains, and that a tRNA(m 1G37)methyltrans ferase is part of the minimal set of gene products required for life. Expand
...
1
2
3
4
5
...