Relevant bibliographies by topics / Dihydrouridine

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters

Academic literature on the topic 'Dihydrouridine'

Author: Grafiati
Published: 16 November 2024

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Journal articles on the topic "Dihydrouridine"

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Kasprzak, Joanna M., Anna Czerwoniec, and Janusz M. Bujnicki. "Molecular evolution of dihydrouridine synthases." BMC Bioinformatics 13, no. 1 (2012): 153. http://dx.doi.org/10.1186/1471-2105-13-153.

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Byrne, Robert T., Huw T. Jenkins, Daniel T. Peters, Fiona Whelan, James Stowell, Naveed Aziz, Pavel Kasatsky, et al. "Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases." Proceedings of the National Academy of Sciences 112, no. 19 (April 22, 2015): 6033–37. http://dx.doi.org/10.1073/pnas.1500161112.

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The reduction of specific uridines to dihydrouridine is one of the most common modifications in tRNA. Increased levels of the dihydrouridine modification are associated with cancer. Dihydrouridine synthases (Dus) from different subfamilies selectively reduce distinct uridines, located at spatially unique positions of folded tRNA, into dihydrouridine. Because the catalytic center of all Dus enzymes is conserved, it is unclear how the same protein fold can be reprogrammed to ensure that nucleotides exposed at spatially distinct faces of tRNA can be accommodated in the same active site. We show that the Escherichia coli DusC is specific toward U16 of tRNA. Unexpectedly, crystal structures of DusC complexes with tRNAPhe and tRNATrp show that Dus subfamilies that selectively modify U16 or U20 in tRNA adopt identical folds but bind their respective tRNA substrates in an almost reverse orientation that differs by a 160° rotation. The tRNA docking orientation appears to be guided by subfamily-specific clusters of amino acids (“binding signatures”) together with differences in the shape of the positively charged tRNA-binding surfaces. tRNA orientations are further constrained by positional differences between the C-terminal “recognition” domains. The exquisite substrate specificity of Dus enzymes is therefore controlled by a relatively simple mechanism involving major reorientation of the whole tRNA molecule. Such reprogramming of the enzymatic specificity appears to be a unique evolutionary solution for altering tRNA recognition by the same protein fold.
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Whelan, Fiona, Huw T. Jenkins, Samuel C. Griffiths, Robert T. Byrne, Eleanor J. Dodson, and Alfred A. Antson. "From bacterial to human dihydrouridine synthase: automated structure determination." Acta Crystallographica Section D Biological Crystallography 71, no. 7 (June 30, 2015): 1564–71. http://dx.doi.org/10.1107/s1399004715009220.

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The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically byphenix.mr_rosettastarting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.
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Dixit, Sameer, and Samie R. Jaffrey. "Expanding the epitranscriptome: Dihydrouridine in mRNA." PLOS Biology 20, no. 7 (July 20, 2022): e3001720. http://dx.doi.org/10.1371/journal.pbio.3001720.

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House, Christopher H., and Stanley L. Miller. "Hydrolysis of Dihydrouridine and Related Compounds." Biochemistry 35, no. 1 (January 1996): 315–20. http://dx.doi.org/10.1021/bi951577+.

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Savage, Dan F., Valérie de Crécy-Lagard, and Anthony C. Bishop. "Molecular determinants of dihydrouridine synthase activity." FEBS Letters 580, no. 22 (September 5, 2006): 5198–202. http://dx.doi.org/10.1016/j.febslet.2006.08.062.

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Dyubankova, N., E. Sochacka, K. Kraszewska, B. Nawrot, P. Herdewijn, and E. Lescrinier. "Contribution of dihydrouridine in folding of the D-arm in tRNA." Organic & Biomolecular Chemistry 13, no. 17 (2015): 4960–66. http://dx.doi.org/10.1039/c5ob00164a.

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Feng, Pengmian, Zhaochun Xu, Hui Yang, Hao Lv, Hui Ding, and Li Liu. "Identification of D Modification Sites by Integrating Heterogeneous Features in Saccharomyces cerevisiae." Molecules 24, no. 3 (January 22, 2019): 380. http://dx.doi.org/10.3390/molecules24030380.

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As an abundant post-transcriptional modification, dihydrouridine (D) has been found in transfer RNA (tRNA) from bacteria, eukaryotes, and archaea. Nonetheless, knowledge of the exact biochemical roles of dihydrouridine in mediating tRNA function is still limited. Accurate identification of the position of D sites is essential for understanding their functions. Therefore, it is desirable to develop novel methods to identify D sites. In this study, an ensemble classifier was proposed for the detection of D modification sites in the Saccharomyces cerevisiae transcriptome by using heterogeneous features. The jackknife test results demonstrate that the proposed predictor is promising for the identification of D modification sites. It is anticipated that the proposed method can be widely used for identifying D modification sites in tRNA.
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Yu, F., Y. Tanaka, K. Yamashita, T. Suzuki, A. Nakamura, N. Hirano, T. Suzuki, M. Yao, and I. Tanaka. "Molecular basis of dihydrouridine formation on tRNA." Proceedings of the National Academy of Sciences 108, no. 49 (November 28, 2011): 19593–98. http://dx.doi.org/10.1073/pnas.1112352108.

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Bishop, Anthony C., Jimin Xu, Reid C. Johnson, Paul Schimmel, and Valérie de Crécy-Lagard. "Identification of the tRNA-Dihydrouridine Synthase Family." Journal of Biological Chemistry 277, no. 28 (April 30, 2002): 25090–95. http://dx.doi.org/10.1074/jbc.m203208200.

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Dissertations / Theses on the topic "Dihydrouridine"

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Toubdji, Sabrine. "Biological and biochemical characterization of dihydrouridilation in bacterial ribosomal RNA." Electronic Thesis or Diss., Sorbonne université, 2024. http://www.theses.fr/2024SORUS236.

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La dihydrouridine (D) est une modification répandue et conservée au cours de l'évolution que l'on trouve principalement dans les ARNt et, dans une moindre mesure, dans les ARNm. Chez E. coli, elle s'étend jusqu'à la position 2449 de l'ARNr 23S, stratégiquement située près du centre peptidyltransférase du ribosome. Malgré l'existence de dihydrouridine synthases (DUS) connues, qui utilisent le NADPH et le FMN, l'enzyme responsable de la biosynthèse de D2449 est restée insaisissable.Cette étude présente une méthode rapide de détection de la D dans l'ARNr, impliquant le blocage de la transcriptase inverse sur le site D2449 marqué à la rhodamine, suivi d'une amplification par PCR (RhoRT-PCR). L'analyse de l'ARNr de diverses souches d'E. coli, y compris celles présentant des délétions chromosomiques et des mutations ponctuelles, a permis d'identifier le gène yhiN comme étant la dihydrouridine synthase ribosomique, désormais désignée sous le nom de RdsA.Les caractérisations biochimiques ont révélé que la RdsA était une nouvelle classe de flavoenzymes dépendant du FAD et du NADH et présentant une topologie structurelle complexe. Des essais in vitro ont montré que RdsA dihydrouridylait un transcrit d'ARNr, imitant un segment du centre peptidyltransférase, ce qui suggère une introduction précoce de cette modification avant l'assemblage du ribosome. Des études phylogénétiques ont révélé la distribution étendue du gène rdsA dans le règne bactérien, soulignant la conservation de la dihydrouridylation de l'ARNr.Ces résultats soulignent la préférence de la nature pour l'utilisation de la flavine réduite dans la réduction des uridines et de leurs dérivés, mettant en évidence l'importance de cette modification dans la biologie de l'ARN et la physiologie bactérienne, offrant de nouvelles voies pour explorer la signification biologique de la dihydrouridylation du CPT dans la fonction ribosomique
Dihydrouridine (D) is a prevalent and evolutionarily conserved modification found mainly in tRNAs and, to a lesser extent, in mRNAs. In E. coli, it extends to position 2449 of the 23S rRNA, strategically located near the ribosome's peptidyl transferase site. Despite the existence of known dihydrouridine synthases (DUS), which utilize NADPH and FMN, the enzyme responsible for biosynthesizing D2449 has remained elusive.This study introduces a rapid method for detecting D in rRNA, involving reverse transcriptase blockage at the rhodamine-labeled D2449 site followed by PCR amplification (RhoRT-PCR). Through analysis of rRNA from diverse E. coli strains, including those with chromosomal deletions and point mutations, the yhiN gene was pinpointed as the ribosomal dihydrouridine synthase, now designated as RdsA.Biochemical characterizations revealed RdsA as a novel class of flavoenzymes dependent on FAD and NADH, exhibiting a complex structural topology. In vitro assays demonstrated that RdsA dihydrouridylates an rRNA transcript, mimicking a segment of the peptidyl transferase site, suggesting an early introduction of this modification before ribosome assembly. Phylogenetic studies unveiled the widespread distribution of the rdsA gene in the bacterial kingdom, emphasizing the conservation of rRNA dihydrouridylation.These findings underscore nature's preference for utilizing reduced flavin in the reduction of uridines and their derivatives, highlighting the importance of this modification in RNA biology and bacterial physiology, offering new paths for exploring the biological significance of PTC dihydrouridylation in ribosomal function
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Lee, Ming-Hsun, and 李明訓. "Synthesis of 4'-α/β-aminomethyl dihydrouridine analogs construction of libraries via amide-bond formation." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/18482427631937005984.

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Books on the topic "Dihydrouridine"

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Hydrolysis of dihydrouridine and related compounds. [Washington, DC: National Aeronautics and Space Administration, 1996.

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Book chapters on the topic "Dihydrouridine"

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"Dihydrouridine (5,6-dihydro-2,4-dihydroxyuracil nucleo-side)." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics, 509. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_4475.

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"Dd." In Biochemistry and Molecular biology, edited by Dr AD Smith, SP Datta, Dr G. H. Smith, P. N. Campbell, Dr R. Bentley, Dr HA McKenzie, Dr DA Bender, et al., 157–90. Oxford University PressOxford, 1997. http://dx.doi.org/10.1093/oso/9780198547686.003.0004.

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Abstract d- abbr. for dextro- used (formerly) as symbol denoting dextrorotatory;( + )- should now be used. See optical isomerism.D symbol for 1 a residue of the a-amino acid L-aspartic acid. 2 aresidue of an incompletely specified base in a nucleic-acid sequencethat may be adenine, guanine, or either thymine (inDNA) or uracil (in RNA). 3 a residue of the ribonucleoside(5,6-)dihydrouridine. 4 debye. 5 deuterium (use deprecated).D600 gallopamil, 5-methoxyverapamil, a-(3-{[2-(3,4-dimethoxyphenyl)ethyl] methylamino }propyl)-3,4,5-trimethoxy-a-(l-methylethyl) benzeneacetonitrile; a drug used in thelaboratory to block transport of calcium
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Draycott, Austin S., Cassandra Schaening-Burgos, Maria F. Rojas-Duran, and Wendy V. Gilbert. "D-Seq: Genome-wide detection of dihydrouridine modifications in RNA." In Methods in Enzymology. Elsevier, 2023. http://dx.doi.org/10.1016/bs.mie.2023.09.001.

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Marchand, Virginie, Valérie Bourguignon-Igel, Mark Helm, and Yuri Motorin. "Mapping of 7-methylguanosine (m7G), 3-methylcytidine (m3C), dihydrouridine (D) and 5-hydroxycytidine (ho5C) RNA modifications by AlkAniline-Seq." In Methods in Enzymology, 25–47. Elsevier, 2021. http://dx.doi.org/10.1016/bs.mie.2021.06.001.

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