Genomes and Genes
Summary: A modified nucleoside which is present in the first position of the anticodon of tRNA-tyrosine, tRNA-histidine, tRNA-asparagine and tRNA-aspartic acid of many organisms. It is believed to play a role in the regulatory function of tRNA. Nucleoside Q can be further modified to nucleoside Q*, which has a mannose or galactose moiety linked to position 4 of its cyclopentenediol moiety.
- Van Lanen S, Reader J, Swairjo M, De Crecy Lagard V, Lee B, Iwata Reuyl D. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sci U S A. 2005;102:4264-9 pubmed..We report here in vitro and in vivo studies that demonstrate this catalytic activity, as well as preliminary biochemical and bioinformatics analysis that provide insight into the structure of this family of enzymes. ..
- Morris R, Galicia M, Clase K, Elliott M. Determination of queuosine modification system deficiencies in cultured human cells. Mol Genet Metab. 1999;68:56-67 pubmed..These techniques can be applied to any cultured cell types to determine specific lesions of the queuosine modification system, which have been suggested to be associated with neoplastic progression. ..
- Kinzie S, Thern B, Iwata Reuyl D. Mechanistic studies of the tRNA-modifying enzyme QueA: a chemical imperative for the use of AdoMet as a "ribosyl" donor. Org Lett. 2000;2:1307-10 pubmed..We report here the first mechanistic studies of this remarkable enzyme, and we propose a chemical mechanism for the reaction consistent with our experimental observations. ..
- Wilding B, Winkler M, Petschacher B, Kratzer R, Egger S, Steinkellner G, et al. Targeting the substrate binding site of E. coli nitrile reductase QueF by modeling, substrate and enzyme engineering. Chemistry. 2013;19:7007-12 pubmed publisher..Three non-natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild-type and mutant nitrile reductase. ..
- Ming X, Seela F. Efficient synthesis of the tRNA nucleoside preQ0, 7-cyano-7-deazaguanosine, via microwave-assisted iodo?carbonitrile exchange. Chem Biodivers. 2010;7:2616-21 pubmed publisher..The overall reaction yield was 30% starting with the glycosylation reaction of the nucleobase. Corresponding 2'-deoxyribonucleosides were prepared following the same route. ..
- Quaranta D, McCarty R, Bandarian V, Rensing C. The copper-inducible cin operon encodes an unusual methionine-rich azurin-like protein and a pre-Q0 reductase in Pseudomonas putida KT2440. J Bacteriol. 2007;189:5361-71 pubmed publisher..putida KT2440 under the conditions tested. Possible roles of CinA and CinQ to help pseudomonads adapt and survive under prolonged copper stress are discussed...
- Swairjo M, Reddy R, Lee B, Van Lanen S, Brown S, De Crecy Lagard V, et al. Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:945-8 pubmed..Guided by this insight, a second crystal form was grown that was strictly dependent on the presence of preQ0. This crystal form diffracted to 2.25 A resolution. ..
- Grosjean H, De Crecy Lagard V, Bjork G. Aminoacylation of the anticodon stem by a tRNA-synthetase paralog: relic of an ancient code?. Trends Biochem Sci. 2004;29:519-22 pubmed..This modified nucleoside might be a relic of an ancient code. ..
- Chiari Y, Dion K, Colborn J, Parmakelis A, Powell J. On the possible role of tRNA base modifications in the evolution of codon usage: queuosine and Drosophila. J Mol Evol. 2010;70:339-45 pubmed publisher..willistoni is in young females producing eggs. Because tRNAs laid down in eggs persist through the early stages of development, this implies that Q modification occurs earlier in development in D. willistoni than in other Drosophila...
- Costa A, Pais de Barros J, Keith G, Baranowski W, Desgres J. Determination of queuosine derivatives by reverse-phase liquid chromatography for the hypomodification study of Q-bearing tRNAs from various mammal liver cells. J Chromatogr B Analyt Technol Biomed Life Sci. 2004;801:237-47 pubmed..It is noteworthy that in all cases of Q-tRNA hypomodification, our analytical procedure showed that tRNA(Asp) is always the least affected by the hypomodification. The biological significance of this phenomenon is discussed. ..
- Boland C, Hayes P, Santa Maria I, Nishimura S, Kelly V. Queuosine formation in eukaryotic tRNA occurs via a mitochondria-localized heteromeric transglycosylase. J Biol Chem. 2009;284:18218-27 pubmed publisher..Confocal and immunoblot analysis suggest that TGT weakly interacts with the outer mitochondrial membrane possibly through association with Qv1, which was found to be stably associated with the organelle. ..
- Iwata Reuyl D. An embarrassment of riches: the enzymology of RNA modification. Curr Opin Chem Biol. 2008;12:126-33 pubmed publisher..The discovery and mechanistic characterization of a new enzyme activity in the queuosine pathway is discussed. ..
- Phillips G, El Yacoubi B, Lyons B, Alvarez S, Iwata Reuyl D, De Crecy Lagard V. Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role for GTP cyclohydrolase I. J Bacteriol. 2008;190:7876-84 pubmed publisher..These results link the production of a tRNA-modified base to primary metabolism and further clarify the biosynthetic pathway for these complex modified nucleosides. ..
- Szulik M, Voehler M, Ganguly M, Gold B, Stone M. Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine. Biochemistry. 2013;52:7659-68 pubmed publisher..These results argue against the notion that electrostatic interactions with DNA are entirely entropic and suggest that major groove cations can stabilize DNA via enthalpic contributions to the free energy of duplex formation. ..
- Frey B, McCloskey J, Kersten W, Kersten H. New function of vitamin B12: cobamide-dependent reduction of epoxyqueuosine to queuosine in tRNAs of Escherichia coli and Salmonella typhimurium. J Bacteriol. 1988;170:2078-82 pubmed..Under these conditions, the biosynthesis of cobalamin was induced. The results suggest that oQ is derived from ribose and that oQ is finally reduced to Q by a cobamide-dependent enzyme. ..
- Kirtland G, Morris T, Moore P, O Brian J, Edmonds C, McCloskey J, et al. Novel salvage of queuine from queuosine and absence of queuine synthesis in Chlorella pyrenoidosa and Chlamydomonas reinhardtii. J Bacteriol. 1988;170:5633-41 pubmed..In mammalian cells, queuine salvage occurs by the specific cleavage of queuine from Q-5'-phosphate. The present data also support the hypothesis that plants, like animals, cannot synthesize Q de novo. ..
- Mueller S, Slany R. Structural analysis of the interaction of the tRNA modifying enzymes Tgt and QueA with a substrate tRNA. FEBS Lett. 1995;361:259-64 pubmed
- Slany R, Bosl M, Crain P, Kersten H. A new function of S-adenosylmethionine: the ribosyl moiety of AdoMet is the precursor of the cyclopentenediol moiety of the tRNA wobble base queuine. Biochemistry. 1993;32:7811-7 pubmed..coli) is sufficient to act as the RNA substrate for oQ synthesis. We propose that QueA is an S-adenosylmethionine:tRNA ribosyltransferase-isomerase. ..
- Horie N, Yamaizumi Z, Kuchino Y, Takai K, Goldman E, Miyazawa T, et al. Modified nucleosides in the first positions of the anticodons of tRNA(Leu)4 and tRNA(Leu)5 from Escherichia coli. Biochemistry. 1999;38:207-17 pubmed..Because of the conformational rigidity of Cm and cmnm5Um in the first position of the anticodon, these tRNA(Leu) species recognize the leucine codons UUA++ and UUG correctly, but never recognize the phenylalanine codons UUU and UUC. ..
- Zallot R, Ross R, Chen W, Bruner S, Limbach P, De Crecy Lagard V. Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics. ACS Chem Biol. 2017;12:844-851 pubmed publisher..While QueH contains conserved cysteines that could be involved in the coordination of a Fe/S center in a similar fashion to what has been identified in QueG, no cobalamin was identified associated with recombinant QueH protein. ..
- Marchetti M, Capela D, Poincloux R, Benmeradi N, Auriac M, Le Ru A, et al. Queuosine biosynthesis is required for sinorhizobium meliloti-induced cytoskeletal modifications on HeLa Cells and symbiosis with Medicago truncatula. PLoS ONE. 2013;8:e56043 pubmed publisher..meliloti are under queuosine control. We discuss whether the symbiotic defect of que mutants may originate, at least in part, from an altered capacity to modify plant cell actin cytoskeleton. ..
- Morris R, Elliott M. Queuosine modification of tRNA: a case for convergent evolution. Mol Genet Metab. 2001;74:147-59 pubmed..This minireview describes the differences between these modification systems and points to a new direction for developing research on the molecular function queuosine-modified tRNA in diverse species. ..
- Van Lanen S, Iwata Reuyl D. Kinetic mechanism of the tRNA-modifying enzyme S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). Biochemistry. 2003;42:5312-20 pubmed
- Salazar J, Ambrogelly A, Crain P, McCloskey J, Soll D. A truncated aminoacyl-tRNA synthetase modifies RNA. Proc Natl Acad Sci U S A. 2004;101:7536-41 pubmed..Thus, this aminoacyl-tRNA synthetase fragment contributes to standard nucleotide modification of tRNA. ..
- Fontecave M, Atta M, Mulliez E. S-adenosylmethionine: nothing goes to waste. Trends Biochem Sci. 2004;29:243-9 pubmed..SAM presents a unique situation in which all constituent parts have a chemical use. ..
- Feng J, Walter N, Brooks C. Cooperative and directional folding of the preQ1 riboswitch aptamer domain. J Am Chem Soc. 2011;133:4196-9 pubmed publisher..This kinetically efficient folding mechanism suggests a fast ligand-binding response in competition with RNA elongation. ..
- Roth A, Winkler W, Regulski E, Lee B, Lim J, Jona I, et al. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nat Struct Mol Biol. 2007;14:308-17 pubmed..Relatively compact RNA structures can therefore serve effectively as metabolite receptors to regulate gene expression. ..
- Kang M, Peterson R, Feigon J. Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Mol Cell. 2009;33:784-90 pubmed publisher..In the absence of preQ(1), the A-rich tail forms part of the antiterminator. These structural studies provide insight into riboswitch transcriptional control of preQ(1) biosynthesis. ..
- Bandarian V. Radical SAM enzymes involved in the biosynthesis of purine-based natural products. Biochim Biophys Acta. 2012;1824:1245-53 pubmed publisher..This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology. ..
- Cicmil N, Shi L. Crystallization and preliminary X-ray characterization of queD from Bacillus subtilis, an enzyme involved in queuosine biosynthesis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008;64:119-22 pubmed publisher..5 at 291 K. The crystals diffract to 3.6 A resolution and belong to the cubic space group F4(1)32, with unit-cell parameter a = 240.88 A. ..
- Lee B, Van Lanen S, Iwata Reuyl D. Mechanistic studies of Bacillus subtilis QueF, the nitrile oxidoreductase involved in queuosine biosynthesis. Biochemistry. 2007;46:12844-54 pubmed..Based on our data we propose a chemical mechanism for the enzyme-catalyzed reaction, and a chemical rationale for the observation of covalent catalysis. ..
- Gaur R, Bjork G, Tuck S, Varshney U. Diet-dependent depletion of queuosine in tRNAs in Caenorhabditis elegans does not lead to a developmental block. J Biosci. 2007;32:747-54 pubmed..The inherent advantages of C.elegans as a model organism, and the simplicity of conferring a Q-deficient phenotype on it make it an ideal system to investigate the function of Q modification in tRNA. ..
- Slany R, Kersten H. The promoter of the tgt/sec operon in Escherichia coli is preceded by an upstream activation sequence that contains a high affinity FIS binding site. Nucleic Acids Res. 1992;20:4193-8 pubmed..An approximately two-fold activation of the promoter by the UAS element was observed. ..
- Slany R, Bosl M, Kersten H. Transfer and isomerization of the ribose moiety of AdoMet during the biosynthesis of queuosine tRNAs, a new unique reaction catalyzed by the QueA protein from Escherichia coli. Biochimie. 1994;76:389-93 pubmed..A model for the reaction catalyzed by the S-adenosylmethionine:tRNA ribosyltransferase-isomerase QueA is proposed. ..
- Aytac U, Gunduz U. Q-modification of tRNAs in human brain tumors. Cancer Biochem Biophys. 1994;14:93-8 pubmed..Increased Q deficiency was also observed in higher grade tumors. ..
- Gaur R, Varshney U. Genetic analysis identifies a function for the queC (ybaX) gene product at an initial step in the queuosine biosynthetic pathway in Escherichia coli. J Bacteriol. 2005;187:6893-901 pubmed..In addition, we discuss the possibilities of collaboration of QueC with other cellular proteins in the production of preQ0. ..
- Ishiwata S, Katayama J, Shindo H, Ozawa Y, Itoh K, Mizugaki M. Increased expression of queuosine synthesizing enzyme, tRNA-guanine transglycosylase, and queuosine levels in tRNA of leukemic cells. J Biochem. 2001;129:13-7 pubmed..To our knowledge, this is a first report of increased expression levels of TGT60KD in human cancer cells. ..
- Blaise M, Becker H, Keith G, Cambillau C, Lapointe J, Giege R, et al. A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNAAsp QUC anticodon. Nucleic Acids Res. 2004;32:2768-75 pubmed
- Phillips G, Grochowski L, Bonnett S, Xu H, Bailly M, Blaby Haas C, et al. Functional promiscuity of the COG0720 family. ACS Chem Biol. 2012;7:197-209 pubmed publisher..This study reveals an expanded versatility of the COG0720 family members and illustrates that for certain protein families extensive comparative genomic analysis beyond homology is required to correctly predict function. ..
- Haumont E, Droogmans L, Grosjean H. Enzymatic formation of queuosine and of glycosyl queuosine in yeast tRNAs microinjected into Xenopus laevis oocytes. The effect of the anticodon loop sequence. Eur J Biochem. 1987;168:219-25 pubmed..In tRNAAsp (anticodon QUC) and tRNATyr (anticodon Q psi A) from certain eukaryotic cells, the nucleoside Q-34 is further hypermodified into a glycosylated derivative by tRNA-queuine glycosyltransferase...
- Morris R, Brown K, Elliott M. The effect of queuosine on tRNA structure and function. J Biomol Struct Dyn. 1999;16:757-74 pubmed..Therefore, the queuosine modification may have the potential to influence cellular growth and differentiation by codon bias-based regulation of protein synthesis for discrete mRNA transcripts. ..
- Carlson B, Kwon S, Lee B, Hatfield D. Yeast asparagine (Asn) tRNA without Q base promotes eukaryotic frameshifting more efficiently than mammalian Asn tRNAs with or without Q base. Mol Cells. 2000;10:113-8 pubmed..However, we cannot absolutely rule out a role of Q base in frameshifting as wheat germ extracts and a lysate depleted of most of its tRNA and supplemented with calf liver tRNA contain both Asn tRNA with or without Q base. ..
- Moeller K, Nguyen G, Hollmann F, Hanefeld U. Expression and characterization of the nitrile reductase queF from E. coli. Enzyme Microb Technol. 2013;52:129-33 pubmed publisher..The enzyme activity towards its natural substrate, preQ(0), was demonstrated and optimal working conditions were found to be at 37°C and at pH 7 with Tris buffer. ..
- Bucklin D, Wills N, Gesteland R, Atkins J. P-site pairing subtleties revealed by the effects of different tRNAs on programmed translational bypassing where anticodon re-pairing to mRNA is separated from dissociation. J Mol Biol. 2005;345:39-49 pubmed..The wild-type, GGA, matched codons are the most efficient in their gene 60 context in contrast to the relatively low value in the non-programmed bypassing study. ..
- McCarty R, Bandarian V. Biosynthesis of pyrrolopyrimidines. Bioorg Chem. 2012;43:15-25 pubmed publisher..This article will illustrate the structural diversity of these compounds and review the current state of knowledge on the biosynthetic pathways that give rise to them. ..
- Carlson B, Lee B, Hatfield D. Ribosomal frameshifting in response to hypomodified tRNAs in Xenopus oocytes. Biochem Biophys Res Commun. 2008;375:86-90 pubmed publisher..Both tRNAAsn+Q and tRNAAsn-Q were used indiscriminately in frameshifting, whether the frameshift site contained the wild-type AAC, or the mutant AAU codon, suggesting that Q base modification status does not influence this process. ..
- ..The study of the cellular dynamics of modified RNA remains a largely open area for new development, which underscores the rich potential for important advances as researchers drive this emerging field to the next level. ..
- Miles Z, McCarty R, Molnar G, Bandarian V. Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification. Proc Natl Acad Sci U S A. 2011;108:7368-72 pubmed publisher..Moreover, discovery of the elusive oQ reductase protein completes the biosynthetic pathway of Q. ..
- Pathak C, Jaiswal Y, Vinayak M. Hypomodification of transfer RNA in cancer with respect to queuosine. RNA Biol. 2005;2:143-8 pubmed..The activators NaPP and ATP enhance TGTase activity of normal and DLAT cancerous mouse, where as 7mG inhibits the TGTase activity. ..
- Klepper F, Jahn E, Hickmann V, Carell T. Synthesis of the transfer-RNA nucleoside queuosine by using a chiral allyl azide intermediate. Angew Chem Int Ed Engl. 2007;46:2325-7 pubmed
- Blaise M, Olieric V, Sauter C, Lorber B, Roy B, Karmakar S, et al. Crystal structure of glutamyl-queuosine tRNAAsp synthetase complexed with L-glutamate: structural elements mediating tRNA-independent activation of glutamate and glutamylation of tRNAAsp anticodon. J Mol Biol. 2008;381:1224-37 pubmed publisher..The analyses made on tRNA(Asp) and tRNA(Asn) show that the presence of a C in position 38 is crucial for glutamylation of Q34. The results are discussed in the context of the evolution and adaptation of the tRNA glutamylation system. ..