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Urbonavičius J, Tauraitė D. Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea. Biomolecules 2020; 10:E1627. [PMID: 33276555 PMCID: PMC7761594 DOI: 10.3390/biom10121627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023] Open
Abstract
Tricyclic wyosine derivatives are present at position 37 in tRNAPhe of both eukaryotes and archaea. In eukaryotes, five different enzymes are needed to form a final product, wybutosine (yW). In archaea, 4-demethylwyosine (imG-14) is an intermediate for the formation of three different wyosine derivatives, yW-72, imG, and mimG. In this review, current knowledge regarding the archaeal enzymes involved in this process and their reaction mechanisms are summarized. The experiments aimed to elucidate missing steps in biosynthesis pathways leading to the formation of wyosine derivatives are suggested. In addition, the chemical synthesis pathways of archaeal wyosine nucleosides are discussed, and the scheme for the formation of yW-86 and yW-72 is proposed. Recent data demonstrating that wyosine derivatives are present in the other tRNA species than those specific for phenylalanine are discussed.
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Affiliation(s)
- Jaunius Urbonavičius
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223 Vilnius, Lithuania;
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Urbonavičius J, Rutkienė R, Lopato A, Tauraitė D, Stankevičiūtė J, Aučynaitė A, Kaliniene L, van Tilbeurgh H, Meškys R. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. RNA (NEW YORK, N.Y.) 2016; 22:1871-1883. [PMID: 27852927 PMCID: PMC5113207 DOI: 10.1261/rna.057059.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/19/2016] [Indexed: 06/06/2023]
Abstract
Tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNAPhe In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. We have suggested previously that a peculiar methyltransferase (aTrm5a/Taw22) likely catalyzes two distinct reactions: N1-methylation of guanosine to yield m1G; and C7-methylation of imG-14 to yield imG2. Here we show that the recombinant aTrm5a/Taw22-like enzymes from both Pyrococcus abyssi and Nanoarchaeum equitans indeed possess such dual specificity. We also show that substitutions of individual conservative amino acids of P. abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m1G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37. We further demonstrate that aTrm5a-type enzyme SSO2439 from Sulfolobus solfataricus, which has no N1-methyltransferase activity, exhibits C7-methyltransferase activity, thereby producing imG2 from imG-14. We thus suggest renaming such aTrm5a methyltransferases as Taw21 to distinguish between monofunctional and bifunctional aTrm5a enzymes.
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Affiliation(s)
- Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius 10223, Lithuania
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Anželika Lopato
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius 10223, Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Jonita Stankevičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Herman van Tilbeurgh
- Institut de Biologie Intégrative de la Cellule, I2BC, CNRS Université Paris-Sud UMR9198, Orsay, France
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
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Urbonavičius J, Meškys R, Grosjean H. Biosynthesis of wyosine derivatives in tRNA(Phe) of Archaea: role of a remarkable bifunctional tRNA(Phe):m1G/imG2 methyltransferase. RNA (NEW YORK, N.Y.) 2014; 20:747-753. [PMID: 24837075 PMCID: PMC4024628 DOI: 10.1261/rna.043315.113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The presence of tricyclic wyosine derivatives 3'-adjacent to anticodon is a hallmark of tRNA(Phe) in eukaryotes and archaea. In yeast, formation of wybutosine (yW) results from five enzymes acting in a strict sequential order. In archaea, the intermediate compound imG-14 (4-demethylwyosine) is a target of three different enzymes, leading to the formation of distinct wyosine derivatives (yW-86, imG, and imG2). We focus here on a peculiar methyltransferase (aTrm5a) that catalyzes two distinct reactions: N(1)-methylation of guanosine and C(7)-methylation of imG-14, whose function is to allow the production of isowyosine (imG2), an intermediate of the 7-methylwyosine (mimG) biosynthetic pathway. Based on the formation of mesomeric forms of imG-14, a rationale for such dual enzymatic activities is proposed. This bifunctional tRNA:m(1)G/imG2 methyltransferase, acting on two chemically distinct guanosine derivatives located at the same position of tRNA(Phe), is unique to certain archaea and has no homologs in eukaryotes. This enzyme here referred to as Taw22, probably played an important role in the emergence of the multistep biosynthetic pathway of wyosine derivatives in archaea and eukaryotes.
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Affiliation(s)
- Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, LT-08662 Vilnius, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, LT-08662 Vilnius, Lithuania
| | - Henri Grosjean
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Associée à l'Université Paris-Sud 11, FRC 3115, 91190 Gif-sur-Yvette, France
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Waas WF, de Crécy-Lagard V, Schimmel P. Discovery of a Gene Family Critical to Wyosine Base Formation in a Subset of Phenylalanine-specific Transfer RNAs. J Biol Chem 2005; 280:37616-22. [PMID: 16162496 DOI: 10.1074/jbc.m506939200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A large number of post-transcriptional base modifications in transfer RNAs have been described (Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., and Steinberg, S. (1998) Nucleic Acids Res. 26, 148-153). These modifications enhance and expand tRNA function to increase cell viability. The intermediates and genes essential for base modifications in many instances remain unclear. An example is wyebutosine (yW), a fluorescent tricyclic modification of an invariant guanosine situated on the 3'-side of the tRNA(Phe) anticodon. Although biosynthesis of yW involves several reaction steps, only a single pathway-specific enzyme has been identified (Kalhor, H. R., Penjwini, M., and Clarke, S. (2005) Biochem. Biophys. Res. Commun. 334, 433-440). We used comparative genomics analysis to identify a cluster of orthologous groups (COG0731) of wyosine family biosynthetic proteins. Gene knock-out and complementation studies in Saccharomyces cerevisiae established a role for YPL207w, a COG0731 ortholog that encodes an 810-amino acid polypeptide. Further analysis showed the accumulation of N(1)-methylguanosine (m(1)G(37)) in tRNA from cells bearing a YPL207w deletion. A similar lack of wyosine base and build-up of m(1)G(37) is seen in certain mammalian tumor cell lines. We proposed that the 810-amino acid COG0731 polypeptide participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
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MESH Headings
- Chromatography, High Pressure Liquid
- Chromatography, Thin Layer
- Gene Deletion
- Gene Expression Regulation, Fungal
- Genetic Complementation Test
- Guanosine/analogs & derivatives
- Guanosine/biosynthesis
- Guanosine/chemistry
- Heterocyclic Compounds, 3-Ring/chemistry
- Hydrolysis
- Molecular Structure
- Multigene Family
- Phylogeny
- RNA Processing, Post-Transcriptional/genetics
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
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Affiliation(s)
- William F Waas
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Abstract
The nucleotide sequence of Xenopus laevis phenylalanine tRNA extracted from oocytes was determined to be: pGCCGAAAUAm2GCUCm1AG DDGGGAGAGCm22 G psi psi AGACmUGmAAYA psi C UAAAGm7GDCm5CCUGGT psi CGm1AUCCCGG GUUUCGGCACCAoH. This result was achieved by analysing, with classical procedures [6], the oligonucleotides obtained after digestion by T1 or pancreatic ribonuclease. This sequence is identical to the mammalian sequence. It has been entirely conserved during 10(8) years, the time lapse between the divergence of amphibians and mammals in evolution. In contrast to 5S RNA, no important heterogeneity has been found in the oocyte sequence, suggesting that there is only a single sequence for tRNAphe in X. laevis. Small differences are seen in the elution pattern from RPC-5 columns for immature oocyte and somatic tRNAphe. They are probably due to a submodification of methyl-5-cytidine residues, which appear to be about half methylated in tRNAphe as well as in total tRNA from immature oocytes.
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