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Journal articles on the topic 'Dihydrouridine'

Author: Grafiati

Published: 16 November 2024

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1

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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2

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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3

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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4

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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5

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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6

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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7

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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8

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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9

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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10

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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11

House, Christopher H., and Stanley L. Miller. "The hydrolysis of dihydrouridine and related compounds." Origins of Life and Evolution of the Biosphere 26, no. 3-5 (October 1996): 357–58. http://dx.doi.org/10.1007/bf02459807.

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12

Lombard, Murielle, Colbie J. Reed, Ludovic Pecqueur, Bruno Faivre, Sabrine Toubdji, Claudia Sudol, Damien Brégeon, Valérie de Crécy-Lagard, and Djemel Hamdane. "Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family." Biomolecules 12, no. 12 (November 26, 2022): 1760. http://dx.doi.org/10.3390/biom12121760.

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Dihydrouridine (D) is an abundant modified base found in the tRNAs of most living organisms and was recently detected in eukaryotic mRNAs. This base confers significant conformational plasticity to RNA molecules. The dihydrouridine biosynthetic reaction is catalyzed by a large family of flavoenzymes, the dihydrouridine synthases (Dus). So far, only bacterial Dus enzymes and their complexes with tRNAs have been structurally characterized. Understanding the structure-function relationships of eukaryotic Dus proteins has been hampered by the paucity of structural data. Here, we combined extensive phylogenetic analysis with high-precision 3D molecular modeling of more than 30 Dus2 enzymes selected along the tree of life to determine the evolutionary molecular basis of D biosynthesis by these enzymes. Dus2 is the eukaryotic enzyme responsible for the synthesis of D20 in tRNAs and is involved in some human cancers and in the detoxification of β-amyloid peptides in Alzheimer’s disease. In addition to the domains forming the canonical structure of all Dus, i.e., the catalytic TIM-barrel domain and the helical domain, both participating in RNA recognition in the bacterial Dus, a majority of Dus2 proteins harbor extensions at both ends. While these are mainly unstructured extensions on the N-terminal side, the C-terminal side extensions can adopt well-defined structures such as helices and beta-sheets or even form additional domains such as zinc finger domains. 3D models of Dus2/tRNA complexes were also generated. This study suggests that eukaryotic Dus2 proteins may have an advantage in tRNA recognition over their bacterial counterparts due to their modularity.

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13

Chen, Minghao, Jian Yu, Yoshikazu Tanaka, Miyuki Tanaka, Isao Tanaka, and Min Yao. "Structure of dihydrouridine synthase C (DusC) fromEscherichia coli." Acta Crystallographica Section F Structural Biology and Crystallization Communications 69, no. 8 (July 27, 2013): 834–38. http://dx.doi.org/10.1107/s1744309113019489.

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14

Dalluge, J. "Conformational flexibility in RNA: the role of dihydrouridine." Nucleic Acids Research 24, no. 6 (March 15, 1996): 1073–79. http://dx.doi.org/10.1093/nar/24.6.1073.

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15

Draycott, Austin, Matthew C. Wang, Diana Martínez Saucedo, Luisa Escobar-Hoyos, and Wendy Gilbert. "Abstract LB299: Dihydrouridine synthase 2 sustains levels of tRNACys and prevents ferroptosis in lung cancer." Cancer Research 84, no. 7_Supplement (April 5, 2024): LB299. http://dx.doi.org/10.1158/1538-7445.am2024-lb299.

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Abstract Dihydrouridine is a universally conserved tRNA modification installed by enzymes that are important for human health. High expression of dihydrouridine synthase 2 (DUS2) predicts poor patient outcomes in lung adenocarcinoma (LUAD) for reasons that are not yet clear. Here, we show in human cells and mouse xenografts that DUS2 suppresses ferroptosis, a metal-dependent non-apoptotic form of cell death that is emerging as a therapeutic target in lung cancer. Elevated DUS2 correlates with resistance to ferroptosis inducers and loss of DUS2 causes increased sensitivity with concomitant accumulation of toxic lipid peroxides. Mechanistically, DUS2 is required to maintain tRNA CysGCA levels, supporting translation of cysteine-rich proteins including metallothioneins, key regulators of metal and redox homeostasis Notably, DUS2 KO cells cannot sustain normal levels of metallothioneins, a class of very cysteine rich proteins that serve as key regulators of both metal and redox homeostasis. Accordingly, DUS2 knockout cells are more susceptible to zinc intoxication and have lower levels of reduced glutathione, which partially explains their sensitivity to ferroptosis. Our findings demonstrate that DUS2 is required to support tRNACys levels and fend off ferroptosis in lung cancer cells. This highlights that individual tRNA substrates can play an outsized role in the biological functions of tRNA modifying enzymes, and demonstrates the therapeutic potential of targeting DUS2 in cancer. Citation Format: Austin Draycott, Matthew C. Wang, Diana Martínez Saucedo, Luisa Escobar-Hoyos, Wendy Gilbert. Dihydrouridine synthase 2 sustains levels of tRNACys and prevents ferroptosis in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB299.

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16

Kaur, J., M. Raj, and B. S. Cooperman. "Fluorescent labeling of tRNA dihydrouridine residues: Mechanism and distribution." RNA 17, no. 7 (May 31, 2011): 1393–400. http://dx.doi.org/10.1261/rna.2670811.

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17

Luvino, Delphine, Michael Smietana, and Jean-Jacques Vasseur. "Selective fluorescence-based detection of dihydrouridine with boronic acids." Tetrahedron Letters 47, no. 52 (December 2006): 9253–56. http://dx.doi.org/10.1016/j.tetlet.2006.10.150.

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18

Gong, Nian, Lin Yang, and Xiang-Sheng Chen. "Structural Features and Phylogenetic Implications of Four New Mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha)." International Journal of Molecular Sciences 22, no. 3 (January 29, 2021): 1348. http://dx.doi.org/10.3390/ijms22031348.

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To explore the differences in mitogenome variation and phylogenetics among lineages of the Hemiptera superfamily Fulgoroidea, we sequenced four new mitogenomes of Caliscelidae: two species of the genus Bambusicaliscelis (Caliscelinae: Caliscelini), namely Bambusicaliscelis flavus and B. fanjingensis, and two species of the genus Youtuus (Ommatidiotinae: Augilini), namely Youtuus strigatus and Y. erythrus. The four mitogenomes were 15,922–16,640 bp (base pair) in length, with 37 mitochondrial genes and an AT-rich region. Gene content and arrangement were similar to those of most other sequenced hexapod mitogenomes. All protein-coding genes (PCGs) started with a canonical ATN or GTG and ended with TAA or an incomplete stop codon single T. Except for two transfer RNAs (tRNAs; trnS1 and trnV) lacking a dihydrouridine arm in the four species and trnC lacking a dihydrouridine stem in the Youtuus species, the remaining tRNAs could fold into canonical cloverleaf secondary structures. Phylogenetic analyses based on sequence data of 13 PCGs in the 28 Fulgoroidea species and two outgroups revealed that Delphacidae was monophyletic with strong support. Our data suggest that Fulgoridae is more ancient than Achilidae. Furthermore, Flatidae, Issidae, and Ricaniidae always cluster to form a sister group to Caliscelidae.

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19

Xing, Feng, Shawna L. Hiley, Timothy R. Hughes, and Eric M. Phizicky. "The Specificities of Four Yeast Dihydrouridine Synthases for Cytoplasmic tRNAs." Journal of Biological Chemistry 279, no. 17 (February 16, 2004): 17850–60. http://dx.doi.org/10.1074/jbc.m401221200.

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20

Bou-Nader, Charles, Damien Brégeon, Ludovic Pecqueur, Marc Fontecave, and Djemel Hamdane. "Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases." Biochemistry 57, no. 37 (August 27, 2018): 5407–14. http://dx.doi.org/10.1021/acs.biochem.8b00584.

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21

Kato, Tatsuya, Yataro Daigo, Satoshi Hayama, Nobuhisa Ishikawa, Takumi Yamabuki, Tomoo Ito, Masaki Miyamoto, Satoshi Kondo, and Yusuke Nakamura. "A Novel Human tRNA-Dihydrouridine Synthase Involved in Pulmonary Carcinogenesis." Cancer Research 65, no. 13 (July 1, 2005): 5638–46. http://dx.doi.org/10.1158/0008-5472.can-05-0600.

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22

COONEY, MICHAEL G., and PAUL W. DOETSCH. "Molecular modeling Studies of a Deoxyoctanucleotide Containing a Dihydrouridine Lesion." Annals of the New York Academy of Sciences 726, no. 1 DNA Damage (July 1994): 299–302. http://dx.doi.org/10.1111/j.1749-6632.1994.tb52832.x.

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23

Jenkins, Huw, Fiona Whelan, Daniel Peters, Robert Byrne, Andrey Konevega, Eugene Koonin, and Fred Antson. "Recognition of Specific Uridines in tRNA Substrates by Dihydrouridine Synthases." Biophysical Journal 110, no. 3 (February 2016): 239a. http://dx.doi.org/10.1016/j.bpj.2015.11.1319.

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24

Goyal, Nainee, Anshuman Chandra, Imteyaz Qamar, and Nagendra Singh. "Structural studies on dihydrouridine synthase A (DusA) from Pseudomonas aeruginosa." International Journal of Biological Macromolecules 132 (July 2019): 254–64. http://dx.doi.org/10.1016/j.ijbiomac.2019.03.209.

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25

Suleman, Muhammad Taseer, Fahad Alturise, Tamim Alkhalifah, and Yaser Daanial Khan. "iDHU-Ensem: Identification of dihydrouridine sites through ensemble learning models." DIGITAL HEALTH 9 (January 2023): 205520762311659. http://dx.doi.org/10.1177/20552076231165963.

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Background Dihydrouridine (D) is one of the most significant uridine modifications that have a prominent occurrence in eukaryotes. The folding and conformational flexibility of transfer RNA (tRNA) can be attained through this modification. Objective The modification also triggers lung cancer in humans. The identification of D sites was carried out through conventional laboratory methods; however, those were costly and time-consuming. The readiness of RNA sequences helps in the identification of D sites through computationally intelligent models. However, the most challenging part is turning these biological sequences into distinct vectors. Methods The current research proposed novel feature extraction mechanisms and the identification of D sites in tRNA sequences using ensemble models. The ensemble models were then subjected to evaluation using k-fold cross-validation and independent testing. Results The results revealed that the stacking ensemble model outperformed all the ensemble models by revealing 0.98 accuracy, 0.98 specificity, 0.97 sensitivity, and 0.92 Matthews Correlation Coefficient. The proposed model, iDHU-Ensem, was also compared with pre-existing predictors using an independent test. The accuracy scores have shown that the proposed model in this research study performed better than the available predictors. Conclusion The current research contributed towards the enhancement of D site identification capabilities through computationally intelligent methods. A web-based server, iDHU-Ensem, was also made available for the researchers at https://taseersuleman-idhu-ensem-idhu-ensem.streamlit.app/ .

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26

Noon, Kathleen R., Rebecca Guymon, Pamela F. Crain, James A. McCloskey, Michael Thomm, Julianne Lim, and Ricardo Cavicchioli. "Influence of Temperature on tRNA Modification in Archaea: Methanococcoides burtonii (Optimum Growth Temperature [Topt], 23°C) and Stetteria hydrogenophila (Topt, 95°C)." Journal of Bacteriology 185, no. 18 (September 15, 2003): 5483–90. http://dx.doi.org/10.1128/jb.185.18.5483-5490.2003.

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ABSTRACT We report the first study of tRNA modification in psychrotolerant archaea, specifically in the archaeon Methanococcoides burtonii grown at 4 and 23°C. For comparison, unfractionated tRNA from the archaeal hyperthermophile Stetteria hydrogenophila cultured at 93°C was examined. Analysis of modified nucleosides using liquid chromatography-electrospray ionization mass spectrometry revealed striking differences in levels and identities of tRNA modifications between the two organisms. Although the modification levels in M. burtonii tRNA are the lowest in any organism of which we are aware, it contains more than one residue per tRNA molecule of dihydrouridine, a molecule associated with maintenance of polynucleotide flexibility at low temperatures. No differences in either identities or levels of modifications, including dihydrouridine, as a function of culture temperature were observed, in contrast to selected tRNA modifications previously reported for archaeal hyperthermophiles. By contrast, S. hydrogenophila tRNA was found to contain a remarkable structural diversity of 31 modified nucleosides, including nine methylated guanosines, with eight different nucleoside species methylated at O-2′ of ribose, known to be an effective stabilizing motif in RNA. These results show that some aspects of tRNA modification in archaea are strongly associated with environmental temperature and support the thesis that posttranscriptional modification is a universal natural mechanism for control of RNA molecular structure that operates across a wide temperature range in archaea as well as bacteria.

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27

Hayakawa, Hiroyuki, Hiromichi Tanaka, and Tadashi Miyasaka. "Lithiation of 5,6-dihydrouridine: a new route to 5-substituted uridines." Tetrahedron 41, no. 9 (January 1985): 1675–83. http://dx.doi.org/10.1016/s0040-4020(01)96481-6.

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28

Deb, Indrajit, Joanna Sarzynska, Lennart Nilsson, and Ansuman Lahiri. "Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations." Biopolymers 101, no. 10 (July 23, 2014): 985–91. http://dx.doi.org/10.1002/bip.22495.

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29

Leon-Lai, Chui Har, Michael J. Gresser, and Alan S. Tracey. "Influence of vanadium(V) complexes on the catalytic activity of ribonuclease A. The role of vanadate complexes as transition state analogues to reactions at phosphate." Canadian Journal of Chemistry 74, no. 1 (January 1, 1996): 38–48. http://dx.doi.org/10.1139/v96-005.

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The interactions of vanadate and its complexes of uridine, 5,6-dihydrouridine, and methyl β-D-ribofuranoside with bovine pancreatic ribonuclease A (RNase A) (EC 3.1.27.5) were studied by 51V NMR spectroscopy and enzyme kinetics. From kinetic studies, it was found that neither inorganic vanadate nor the methyl β-D-ribofuranoside–vanadate complex significantly inhibited the RNase A catalyzed hydrolysis of uridine 2′,3′-cyclic monophosphate. The NMR binding studies were in full agreement with the kinetics studies and showed that neither inorganic vanadate nor the methyl β-D-ribofuranoside–vanadate complex was bound tightly by the enzyme. Approximate binding constants were (5.0 ± 1.0) × 10−7 M and (3.0 ± 0.6) × 10−6 M for the uridine–and 5,6-dihydrouridine–vanadate complexes, respectively. An induced-fit mechanism is suggested, in which the pyrimidine subsite of the active site of RNase A must be fully occupied for the enzyme to be able to tightly bind the transition state or transition state analog. Calculation of the binding energies of vanadate complexes in ribonuclease, phosphoglycerate mutase, and phosphoglucomutase revealed an excess of binding energy over the analogous phosphate derivative of about 25 kJ/mol for all enzymes, even though the binding constants themselves varied by about six orders of magnitude. This energy represents about 40% of that expected to be available for a trigonal-bipyramidal transition state and requires a reassessment of the role of vanadate as a transition state analogue for phosphate transfer. Key words: vanadate, ribonuclease, transition state, binding constants, phosphate analogues, kinetics.

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30

Depelley, Jean, Robert Granet, Pierre Krausz, Salomon Piekarski, Claudine Bosgiraud, and Sylvie Beaussoleil. "Synthesis and Antiretroviral Evaluation of Various 5-Alkyl-6-AZA-5,6-Dihydrouridine." Nucleosides and Nucleotides 13, no. 4 (May 1994): 1007–10. http://dx.doi.org/10.1080/15257779408011873.

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31

XING, FENG, MARK R. MARTZEN, and ERIC M. PHIZICKY. "A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA." RNA 8, no. 3 (March 2002): 370–81. http://dx.doi.org/10.1017/s1355838202029825.

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32

Negishi, Kazuo, and Hikoya Hayatsu. "The Fluorescence Property of Dinucleoside Monophosphates Containing Ethenoadenosine and 5, 6-Dihydrouridine Derivatives." Nucleosides and Nucleotides 13, no. 6-7 (July 1994): 1551–55. http://dx.doi.org/10.1080/15257779408012170.

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33

Mittelstadt, M., A. Frump, T. Khuu, V. Fowlkes, I. Handy, C. V. Patel, and R. C. Patel. "Interaction of human tRNA-dihydrouridine synthase-2 with interferon-induced protein kinase PKR." Nucleic Acids Research 36, no. 3 (November 21, 2007): 998–1008. http://dx.doi.org/10.1093/nar/gkm1129.

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34

Chen, Jan-Kan, Jürgen H. Krauss, Stephen S. Hixson, and Robert A. Zimmermann. "Covalent cross-linking of tRNAGly1 to the ribosomal P site via the dihydrouridine loop." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 825, no. 2 (June 1985): 161–68. http://dx.doi.org/10.1016/0167-4781(85)90100-9.

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35

Basith, Shaherin, and Balachandran Manavalan. "How well does a data-driven prediction method distinguish dihydrouridine from tRNA and mRNA?" Molecular Therapy - Nucleic Acids 31 (March 2023): 744–45. http://dx.doi.org/10.1016/j.omtn.2023.02.026.

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36

Giel-Pietraszuk, M., M. Z. Barciszewska, P. Mucha, P. Rekowski, G. Kupryszewski, and J. Barciszewski. "Interaction of HIV Tat model peptides with tRNA and 5S rRNA." Acta Biochimica Polonica 44, no. 3 (September 30, 1997): 591–600. http://dx.doi.org/10.18388/abp.1997_4407.

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New data are presented on the interaction of model synthetic peptides containing an arginine-rich region of human immunodeficiency virus (HIV-Tat), with native RNA molecules: tRNA(Phe) of Saccharomyces cerevisiae and 5S rRNA from Lupinus luteus. Both RNA species form complexes with the Tat1 (GRKKRRQRRRA) and Tat2 (GRKKRRQRRRAPQDSQTHQASLSKQPA) peptides, as shown by electrophoretic gel shift and RNase footprint assays, and CD measurements. The nucleotide sequence UGGG located in the dihydrouridine loop of tRNAPhe as well as in the loop D of 5S rRNA is specifically protected against RNases. Our data indicate direct interactions of guanine of RNA moieties with arginine residues. These interactions seem similar to those observed in DNA-protein complexes, but different from those previously observed in the TAR RNA-Tat complexes.

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37

Finet, Olivier, Carlo Yague-Sanz, Florian Marchand, and Damien Hermand. "The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function." RNA Biology 19, no. 1 (May 30, 2022): 735–50. http://dx.doi.org/10.1080/15476286.2022.2078094.

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38

Finet, Olivier, Carlo Yague-Sanz, Lara Katharina Krüger, Phong Tran, Valérie Migeot, Max Louski, Alicia Nevers, et al. "Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation." Molecular Cell 82, no. 2 (January 2022): 404–19. http://dx.doi.org/10.1016/j.molcel.2021.11.003.

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39

Bou-Nader, Charles, Hugo Montémont, Vincent Guérineau, Olivier Jean-Jean, Damien Brégeon, and Djemel Hamdane. "Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario." Nucleic Acids Research 46, no. 3 (December 27, 2017): 1386–94. http://dx.doi.org/10.1093/nar/gkx1294.

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40

Griffiths, Sam, Robert T. Byrne, Alfred A. Antson, and Fiona Whelan. "Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase." Acta Crystallographica Section F Structural Biology and Crystallization Communications 68, no. 3 (February 22, 2012): 333–36. http://dx.doi.org/10.1107/s1744309112003831.

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41

Dalluge, J. "Quantitative measurement of dihydrouridine in RNA using isotope dilution liquid chromatography-mass spectrometry (LC/MS)." Nucleic Acids Research 24, no. 16 (August 15, 1996): 3242–45. http://dx.doi.org/10.1093/nar/24.16.3242.

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42

Reimer, Mark L. J., Karl H. Schram, Katsuyuki Nakano, and Toshio Yasaka. "The identification of 5,6-dihydrouridine in normal human urine by combined gas chromatography/mass spectrometry." Analytical Biochemistry 181, no. 2 (September 1989): 302–8. http://dx.doi.org/10.1016/0003-2697(89)90247-9.

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De-Hua, Chen, Lou Ju-Xing, Yang Bing-Hui, Wu Lian-Fen, Chen Fa-Xian, and Liu De-Fu. "Synthesis of nonanucleotide (14-20) of the dihydrouridine (D) loop of yeast alanine transfer RNA." Acta Chimica Sinica 3, no. 1 (March 1985): 71–81. http://dx.doi.org/10.1002/cjoc.19850030112.

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LU, XIANGYI, QIANWEN ZHANG, and XUN BIAN. "Study on the Chinese Subfamily Anabropsinae (Orthoptera: Anostostomatidae) VI: One new species of Anabropsis (Pteranabropsis) from Yunnan Province." Zootaxa 5178, no. 2 (August 25, 2022): 178–92. http://dx.doi.org/10.11646/zootaxa.5178.2.4.

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This paper is sixth study the Chinese Anabropsinae and reports one new species from Yunnan Province, China, viz. A. (Pteranabropsis) maguanensis sp. nov. (Chinese name: 马关黯螽). Meanwhile, the complete mitochondrical genome of the new species was determined and annotated. The 15, 962 bp circle genome consisted of 13 protein-coding, 22 transfer RNA, 2 ribosomal RNA genes, and an A+T-rich region. It has the typical invertebrate mitochondrial gene arrangement. All protein-coding genes (PCGs) were initiated by typical ATN codon. The nucleotide compositions were significant bias towards AT. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except trnS1 in which the base pairs of the dihydrouridine (DHU) arm was lacking. Overall, six domains and 49 helices were predicted for rrnL, and three structural domains and 27 helices were predicted for rrnS.

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Zheng, Fang-Yuan, Qiu-Yue Shi, Yao Ling, Jian-Yu Chen, Bo-Fan Zhang, and Xin-Jiang Li. "Comparative Analysis of Mitogenomes among Five Species of Filchnerella (Orthoptera: Acridoidea: Pamphagidae) and Their Phylogenetic and Taxonomic Implications." Insects 12, no. 7 (July 2, 2021): 605. http://dx.doi.org/10.3390/insects12070605.

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Mitogenomes have been widely used for exploring phylogenetic analysis and taxonomic diagnosis. In this study, the complete mitogenomes of five species of Filchnerella were sequenced, annotated and analyzed. Then, combined with other seven mitogenomes of Filchnerella and four of Pamphagidae, the phylogenetic relationships were reconstructed by maximum likelihood (ML) and Bayesian (BI) methods based on PCGs+rRNAs. The sizes of the five complete mitogenomes are Filchnerella sunanensis 15,656 bp, Filchnerella amplivertica 15,657 bp, Filchnerella nigritibia 15,661 bp, Filchnerella pamphagoides 15,661 bp and Filchnerella dingxiensis 15,666 bp. The nucleotide composition of mitogenomes is biased toward A+T. All tRNAs could be folded into the typical clover-leaf structure, except that tRNA Ser (AGN) lacked a dihydrouridine (DHU) arm. The phylogenetic relationships of Filchnerella species based on mitogenome data revealed a general pattern of wing evolution from long wing to increasingly shortened wing.

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Liu, Ning, Hao Wang, Lijun Fang, and Yalin Zhang. "Mitogenome of the Doleschallia bisaltide and Phylogenetic Analysis of Nymphalinae (Lepidoptera, Nymphalidae)." Diversity 15, no. 4 (April 14, 2023): 558. http://dx.doi.org/10.3390/d15040558.

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The complete mitogenome of Doleschallia bisaltide was sequenced with a size of 16,389 bp. Gene orientation and arrangement in the newly sequenced mitogenome are the same as other mitogenomes in Lepidoptera. Except for trnS1(AGN), which lacks the dihydrouridine (DHC) arm, the other 21 tRNA genes all contain a typical cloverleaf structure. Ka/Ks ratio analysis of 13 protein-coding genes (PCGs) from 23 Nymphalinae species indicates that the evolutionary rate of COX1 was slowest, while that of ATP8, ND5, and ND6 was substantially high. Phylogenetic analysis revealed that Nymphalinae and Kallimini were nonmonophyletic. Trees constructed only from the nuclear DNA (nDNA) dataset had lower support than mitochondrial or combined datasets. The addition of RNA genes did not improve the phylogenetic signal, and nodal support decreased. These data provide important information for future studies into the phylogeny of Nymphalinae.

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Buskiewicz, Iwona, Malgorzata Giel-Pietraszuk, Piotr Mucha, Piotr Rekowski, Gotfryd Kupryszewski, and Miroslawa Z. Barciszewska. "Interaction of HIV Tat Peptides With tRNAPhe from Yeast." Collection of Czechoslovak Chemical Communications 63, no. 6 (1998): 842–50. http://dx.doi.org/10.1135/cccc19980842.

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We present data on the interaction of arginine-rich peptides of human immunodeficiency virus (HIV-Tat) with tRNAPhe of Saccharomyces cerevisiae. We have found that tRNA forms complexes with the Tat1 peptide of amino acid sequence GRKKRRQRRRA and its mutants where R is replaced by D-arginine, citrulline or ornithine. The structure of tRNA-Tat1 complex was probed by specific RNases digestions and Pb2+-induced cleavage of phosphodiester bond of guanosine. The nucleotide sequence UGGG located in the dihydrouridine loop of tRNAPhe binds to Tat peptide and therefore is specifically protected against RNases and is not hydrolyzed by Pb2+ ion. It seems that the peptide-RNA complex formation depends on direct recognition of guanine moieties of tRNA with arginine residues. These interactions are similar to those observed in many DNA-protein complexes, but are different from those previously observed for TAR RNA-Tat complexes.

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Yu, Futao, Yoshikazu Tanaka, Shiho Yamamoto, Akiyoshi Nakamura, Shunsuke Kita, Nagisa Hirano, Isao Tanaka, and Min Yao. "Crystallization and preliminary X-ray crystallographic analysis of dihydrouridine synthase fromThermus thermophilusand its complex with tRNA." Acta Crystallographica Section F Structural Biology and Crystallization Communications 67, no. 6 (May 25, 2011): 685–88. http://dx.doi.org/10.1107/s1744309111012486.

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Rider, Lance W., Mette B. Ottosen, Samuel G. Gattis, and Bruce A. Palfey. "Mechanism of Dihydrouridine Synthase 2 from Yeast and the Importance of Modifications for Efficient tRNA Reduction." Journal of Biological Chemistry 284, no. 16 (January 12, 2009): 10324–33. http://dx.doi.org/10.1074/jbc.m806137200.

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Suleman, Muhammad Taseer, Tamim Alkhalifah, Fahad Alturise, and Yaser Daanial Khan. "DHU-Pred: accurate prediction of dihydrouridine sites using position and composition variant features on diverse classifiers." PeerJ 10 (October 27, 2022): e14104. http://dx.doi.org/10.7717/peerj.14104.

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Background Dihydrouridine (D) is a modified transfer RNA post-transcriptional modification (PTM) that occurs abundantly in bacteria, eukaryotes, and archaea. The D modification assists in the stability and conformational flexibility of tRNA. The D modification is also responsible for pulmonary carcinogenesis in humans. Objective For the detection of D sites, mass spectrometry and site-directed mutagenesis have been developed. However, both are labor-intensive and time-consuming methods. The availability of sequence data has provided the opportunity to build computational models for enhancing the identification of D sites. Based on the sequence data, the DHU-Pred model was proposed in this study to find possible D sites. Methodology The model was built by employing comprehensive machine learning and feature extraction approaches. It was then validated using in-demand evaluation metrics and rigorous experimentation and testing approaches. Results The DHU-Pred revealed an accuracy score of 96.9%, which was considerably higher compared to the existing D site predictors. Availability and Implementation A user-friendly web server for the proposed model was also developed and is freely available for the researchers.

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