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Journal articles on the topic 'TRNA-modification'

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Published: 4 June 2021

Last updated: 4 February 2022

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1

Winkler, Malcolm E. "Requisite tRNA modification." Molecular Microbiology 10, no. 3 (1993): 697. http://dx.doi.org/10.1111/j.1365-2958.1993.tb00941.x.

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2

Hori, Hiroyuki, Takuya Kawamura, Takako Awai, et al. "Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA." Microorganisms 6, no. 4 (2018): 110. http://dx.doi.org/10.3390/microorganisms6040110.

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To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Othe

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3

Yi, Xiaohua, Shuai He, Shuhui Wang, et al. "Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene <i>TRDMT1</i>." Archives Animal Breeding 64, no. 1 (2021): 147–55. http://dx.doi.org/10.5194/aab-64-147-2021.

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Abstract. The tRNA modification gene in eukaryotes is relatively conservative. As an important modification gene, the TRDMT1 gene plays an important role in maintaining tRNA structural maintenance and reducing mistranslation of protein translation by methylation of specific tRNA subpopulations. Mouse and zebrafish TRDMT1 knockout experiments indicate that it may mediate growth and development through tRNA modification. However, there are no systematic reports on the function of tRNA-modified genes in livestock. In this study, Qinchuan cattle DNA pool sequencing technology was used. A G>C mu

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4

Tomikawa, Chie. "7-Methylguanosine Modifications in Transfer RNA (tRNA)." International Journal of Molecular Sciences 19, no. 12 (2018): 4080. http://dx.doi.org/10.3390/ijms19124080.

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More than 90 different modified nucleosides have been identified in tRNA. Among the tRNA modifications, the 7-methylguanosine (m7G) modification is found widely in eubacteria, eukaryotes, and a few archaea. In most cases, the m7G modification occurs at position 46 in the variable region and is a product of tRNA (m7G46) methyltransferase. The m7G46 modification forms a tertiary base pair with C13-G22, and stabilizes the tRNA structure. A reaction mechanism for eubacterial tRNA m7G methyltransferase has been proposed based on the results of biochemical, bioinformatic, and structural studies. How

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Kimura, Satoshi, and Matthew K. Waldor. "The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNA." Proceedings of the National Academy of Sciences 116, no. 4 (2019): 1394–403. http://dx.doi.org/10.1073/pnas.1814130116.

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The factors and mechanisms that govern tRNA stability in bacteria are not well understood. Here, we investigated the influence of posttranscriptional modification of bacterial tRNAs (tRNA modification) on tRNA stability. We focused on ThiI-generated 4-thiouridine (s4U), a modification found in bacterial and archaeal tRNAs. Comprehensive quantification ofVibrio choleraetRNAs revealed that the abundance of some tRNAs is decreased in a ΔthiIstrain in a stationary phase-specific manner. Multiple mechanisms, including rapid degradation of a subset of hypomodified tRNAs, account for the reduced abun

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6

Keffer-Wilkes, Laura Carole, Govardhan Reddy Veerareddygari, and Ute Kothe. "RNA modification enzyme TruB is a tRNA chaperone." Proceedings of the National Academy of Sciences 113, no. 50 (2016): 14306–11. http://dx.doi.org/10.1073/pnas.1607512113.

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Cellular RNAs are chemically modified by many RNA modification enzymes; however, often the functions of modifications remain unclear, such as for pseudouridine formation in the tRNA TΨC arm by the bacterial tRNA pseudouridine synthase TruB. Here we test the hypothesis that RNA modification enzymes also act as RNA chaperones. Using TruB as a model, we demonstrate that TruB folds tRNA independent of its catalytic activity, thus increasing the fraction of tRNA that can be aminoacylated. By rapid kinetic stopped-flow analysis, we identified the molecular mechanism of TruB’s RNA chaperone activity:

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7

Krutyhołowa, Rościsław, Karol Zakrzewski, and Sebastian Glatt. "Charging the code — tRNA modification complexes." Current Opinion in Structural Biology 55 (April 2019): 138–46. http://dx.doi.org/10.1016/j.sbi.2019.03.014.

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8

Van Lanen, Steven G., Sylvia Daoud Kinzie, Sharlene Matthieu, Todd Link, Jeff Culp, and Dirk Iwata-Reuyl. "tRNA Modification byS-Adenosylmethionine:tRNA Ribosyltransferase-Isomerase." Journal of Biological Chemistry 278, no. 12 (2003): 10491–99. http://dx.doi.org/10.1074/jbc.m207727200.

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9

Hawer, Harmen, Alexander Hammermeister, Keerthiraju Ravichandran, Sebastian Glatt, Raffael Schaffrath, and Roland Klassen. "Roles of Elongator Dependent tRNA Modification Pathways in Neurodegeneration and Cancer." Genes 10, no. 1 (2018): 19. http://dx.doi.org/10.3390/genes10010019.

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Transfer RNA (tRNA) is subject to a multitude of posttranscriptional modifications which can profoundly impact its functionality as the essential adaptor molecule in messenger RNA (mRNA) translation. Therefore, dynamic regulation of tRNA modification in response to environmental changes can tune the efficiency of gene expression in concert with the emerging epitranscriptomic mRNA regulators. Several of the tRNA modifications are required to prevent human diseases and are particularly important for proper development and generation of neurons. In addition to the positive role of different tRNA

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Hoffmann, Anne, Lieselotte Erber, Heike Betat, Peter F. Stadler, Mario Mörl, and Jörg Fallmann. "Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum." Non-Coding RNA 7, no. 2 (2021): 32. http://dx.doi.org/10.3390/ncrna7020032.

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Dictyostelium discoideum is a social amoeba, which on starvation develops from a single-cell state to a multicellular fruiting body. This developmental process is accompanied by massive changes in gene expression, which also affect non-coding RNAs. Here, we investigate how tRNAs as key regulators of the translation process are affected by this transition. To this end, we used LOTTE-seq to sequence the tRNA pool of D. discoideum at different developmental time points and analyzed both tRNA composition and tRNA modification patterns. We developed a workflow for the specific detection of modifica

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11

Noon, Kathleen R., Rebecca Guymon, Pamela F. Crain, et al. "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 (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,

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Huber, Sabrina, Andrea Leonardi, Peter Dedon, and Thomas Begley. "The Versatile Roles of the tRNA Epitranscriptome during Cellular Responses to Toxic Exposures and Environmental Stress." Toxics 7, no. 1 (2019): 17. http://dx.doi.org/10.3390/toxics7010017.

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Living organisms respond to environmental changes and xenobiotic exposures by regulating gene expression. While heat shock, unfolded protein, and DNA damage stress responses are well-studied at the levels of the transcriptome and proteome, tRNA-mediated mechanisms are only recently emerging as important modulators of cellular stress responses. Regulation of the stress response by tRNA shows a high functional diversity, ranging from the control of tRNA maturation and translation initiation, to translational enhancement through modification-mediated codon-biased translation of mRNAs encoding str

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13

Kretz, K. A., J. R. Katze, and R. W. Trewyn. "Guanine analog-induced differentiation of human promyelocytic leukemia cells and changes in queuine modification of tRNA." Molecular and Cellular Biology 7, no. 10 (1987): 3613–19. http://dx.doi.org/10.1128/mcb.7.10.3613.

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Treatment of hypoxanthine-guanine phosphoribosyltransferase (HGPRT)-deficient human promyelocytic leukemia (HL-60) cells with 6-thioguanine results in growth inhibition and cell differentiation. 6-Thioguanine is a substrate for the tRNA modification enzyme tRNA-guanine ribosyltransferase, which normally catalyzes the exchange of queuine for guanine in position 1 of the anticodon of tRNAs for asparagine, aspartic acid, histidine, and tyrosine. During the early stages of HGPRT-deficient HL-60 cell differentiation induced by 6-thioguanine, there was a transient decrease in the queuine content of

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Kretz, K. A., J. R. Katze, and R. W. Trewyn. "Guanine analog-induced differentiation of human promyelocytic leukemia cells and changes in queuine modification of tRNA." Molecular and Cellular Biology 7, no. 10 (1987): 3613–19. http://dx.doi.org/10.1128/mcb.7.10.3613-3619.1987.

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Treatment of hypoxanthine-guanine phosphoribosyltransferase (HGPRT)-deficient human promyelocytic leukemia (HL-60) cells with 6-thioguanine results in growth inhibition and cell differentiation. 6-Thioguanine is a substrate for the tRNA modification enzyme tRNA-guanine ribosyltransferase, which normally catalyzes the exchange of queuine for guanine in position 1 of the anticodon of tRNAs for asparagine, aspartic acid, histidine, and tyrosine. During the early stages of HGPRT-deficient HL-60 cell differentiation induced by 6-thioguanine, there was a transient decrease in the queuine content of

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15

Keffer-Wilkes, Laura Carole, Emily F. Soon, and Ute Kothe. "The methyltransferase TrmA facilitates tRNA folding through interaction with its RNA-binding domain." Nucleic Acids Research 48, no. 14 (2020): 7981–90. http://dx.doi.org/10.1093/nar/gkaa548.

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Abstract tRNAs are the most highly modified RNAs in all cells, and formation of 5-methyluridine (m5U) at position 54 in the T arm is a common RNA modification found in all tRNAs. The m5U modification is generated by the methyltransferase TrmA. Here, we test and prove the hypothesis that Escherichia coli TrmA has dual functions, acting both as a methyltransferase and as a tRNA chaperone. We identify two conserved residues, F106 and H125, in the RNA-binding domain of TrmA, which interact with the tRNA elbow and are critical for tRNA binding. Co-culture competition assays reveal that the catalyti

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16

Thongdee, Narumon, Juthamas Jaroensuk, Sopapan Atichartpongkul, et al. "TrmB, a tRNA m7G46 methyltransferase, plays a role in hydrogen peroxide resistance and positively modulates the translation of katA and katB mRNAs in Pseudomonas aeruginosa." Nucleic Acids Research 47, no. 17 (2019): 9271–81. http://dx.doi.org/10.1093/nar/gkz702.

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Abstract Cellular response to oxidative stress is a crucial mechanism that promotes the survival of Pseudomonas aeruginosa during infection. However, the translational regulation of oxidative stress response remains largely unknown. Here, we reveal a tRNA modification-mediated translational response to H2O2 in P. aeruginosa. We demonstrated that the P. aeruginosa trmB gene encodes a tRNA guanine (46)-N7-methyltransferase that catalyzes the formation of m7G46 in the tRNA variable loop. Twenty-three tRNA substrates of TrmB with a guanosine residue at position 46 were identified, including 11 nov

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17

Thanedar, Swapna, T. K. Dineshkumar, and Umesh Varshney. "The Mere Lack of rT Modification in Initiator tRNA Does Not Facilitate Formylation-Independent Initiation inEscherichia coli." Journal of Bacteriology 183, no. 24 (2001): 7397–402. http://dx.doi.org/10.1128/jb.183.24.7397-7402.2001.

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ABSTRACT Formylation of initiator methionyl-tRNA is essential for normal growth of eubacteria. However, under special conditions, it has been possible to initiate protein synthesis with unformylated initiator tRNA even in eubacteria. Earlier studies suggested that the lack of ribothymidine (rT) modification in initiator tRNA may facilitate initiation in the absence of formylation. In this report we show, by using trmA strains of Escherichia coli(defective for rT modification) and a sensitive in vivo initiation assay system, that the lack of rT modification in the initiators is not sufficient t

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18

Zhang, Jilei, Yong-guo Zhang, Yinglin Xia, and Jun Sun. "TRANSFER RNA QUEUOSINE MODIFICATION ENZYME MANIPULATES TIGHT JUNCTION PROTEINS IN INFLAMMATORY BOWEL DISEASE." Inflammatory Bowel Diseases 27, Supplement_1 (2021): S28. http://dx.doi.org/10.1093/ibd/izaa347.065.

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Abstract Background Transfer RNA (tRNA) queuosine (Q)-modification occur at the wobble anticodon position of four special cellular tRNAs. In eukaryotes, tRNA-Q modification relies on the intestinal microbial product queuine and eukaryotic tRNA-guanine transglycosylase complex contains of Q tRNA ribosyltransferase catalytic subunit 1 (QTRT1). Q-tRNA modification is critical for the fidelity and accuracy to translate RNA to protein. It is known that dysfunction of Q-tRNA associates with cancer proliferation and malignancy. However, mechanisms of how Q and Q-tRNA modifications influence intestina

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Ramos-Morales, Elizabeth, Efil Bayam, Jordi Del-Pozo-Rodríguez, et al. "The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination." Nucleic Acids Research 49, no. 11 (2021): 6529–48. http://dx.doi.org/10.1093/nar/gkab436.

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Abstract Post-transcriptional modification of tRNA wobble adenosine into inosine is crucial for decoding multiple mRNA codons by a single tRNA. The eukaryotic wobble adenosine-to-inosine modification is catalysed by the ADAT (ADAT2/ADAT3) complex that modifies up to eight tRNAs, requiring a full tRNA for activity. Yet, ADAT catalytic mechanism and its implication in neurodevelopmental disorders remain poorly understood. Here, we have characterized mouse ADAT and provide the molecular basis for tRNAs deamination by ADAT2 as well as ADAT3 inactivation by loss of catalytic and tRNA-binding determ

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20

Zhou, Jing-Bo, Yong Wang, Qi-Yu Zeng, Shi-Xin Meng, En-Duo Wang, and Xiao-Long Zhou. "Molecular basis for t6A modification in human mitochondria." Nucleic Acids Research 48, no. 6 (2020): 3181–94. http://dx.doi.org/10.1093/nar/gkaa093.

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Abstract N 6-Threonylcarbamoyladenosine (t6A) is a universal tRNA modification essential for translational accuracy and fidelity. In human mitochondria, YrdC synthesises an l-threonylcarbamoyl adenylate (TC-AMP) intermediate, and OSGEPL1 transfers the TC-moiety to five tRNAs, including human mitochondrial tRNAThr (hmtRNAThr). Mutation of hmtRNAs, YrdC and OSGEPL1, affecting efficient t6A modification, has been implicated in various human diseases. However, little is known about the tRNA recognition mechanism in t6A formation in human mitochondria. Herein, we showed that OSGEPL1 is a monomer an

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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 (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 fe

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Funk, Holly M., Ruoxia Zhao, Maggie Thomas, et al. "Identification of the enzymes responsible for m2,2G and acp3U formation on cytosolic tRNA from insects and plants." PLOS ONE 15, no. 11 (2020): e0242737. http://dx.doi.org/10.1371/journal.pone.0242737.

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Posttranscriptional modification of tRNA is critical for efficient protein translation and proper cell growth, and defects in tRNA modifications are often associated with human disease. Although most of the enzymes required for eukaryotic tRNA modifications are known, many of these enzymes have not been identified and characterized in several model multicellular eukaryotes. Here, we present two related approaches to identify the genes required for tRNA modifications in multicellular organisms using primer extension assays with fluorescent oligonucleotides. To demonstrate the utility of these a

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Khonsari, Bahar, Roland Klassen, and Raffael Schaffrath. "Role of SSD1 in Phenotypic Variation of Saccharomyces cerevisiae Strains Lacking DEG1-Dependent Pseudouridylation." International Journal of Molecular Sciences 22, no. 16 (2021): 8753. http://dx.doi.org/10.3390/ijms22168753.

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Yeast phenotypes associated with the lack of wobble uridine (U34) modifications in tRNA were shown to be modulated by an allelic variation of SSD1, a gene encoding an mRNA-binding protein. We demonstrate that phenotypes caused by the loss of Deg1-dependent tRNA pseudouridylation are similarly affected by SSD1 allelic status. Temperature sensitivity and protein aggregation are elevated in deg1 mutants and further increased in the presence of the ssd1-d allele, which encodes a truncated form of Ssd1. In addition, chronological lifespan is reduced in a deg1 ssd1-d mutant, and the negative genetic

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Hagervall, Tord G., Johanna U. Ericson, K. Birgitta Esberg, Li Ji-nong, and Glenn R. Björk. "Role of tRNA modification in translational fidelity." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1050, no. 1-3 (1990): 263–66. http://dx.doi.org/10.1016/0167-4781(90)90178-5.

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25

Persson, Britt C. "Modification of tRNA as a regulatory device." Molecular Microbiology 8, no. 6 (1993): 1011–16. http://dx.doi.org/10.1111/j.1365-2958.1993.tb01645.x.

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26

Rapino, Francesca, Sylvain Delaunay, Zhaoli Zhou, Alain Chariot, and Pierre Close. "tRNA Modification: Is Cancer Having a Wobble?" Trends in Cancer 3, no. 4 (2017): 249–52. http://dx.doi.org/10.1016/j.trecan.2017.02.004.

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27

Dalluge, J. J., T. Hamamoto, K. Horikoshi, R. Y. Morita, K. O. Stetter, and J. A. McCloskey. "Posttranscriptional modification of tRNA in psychrophilic bacteria." Journal of bacteriology 179, no. 6 (1997): 1918–23. http://dx.doi.org/10.1128/jb.179.6.1918-1923.1997.

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28

Ramírez, Vicente, Beatriz González, Ana López, et al. "A 2′-O-Methyltransferase Responsible for Transfer RNA Anticodon Modification Is Pivotal for Resistance to Pseudomonas syringae DC3000 in Arabidopsis." Molecular Plant-Microbe Interactions® 31, no. 12 (2018): 1323–36. http://dx.doi.org/10.1094/mpmi-06-18-0148-r.

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Transfer RNA (tRNA) is the most highly modified class of RNA species in all living organisms. Recent discoveries have revealed unprecedented complexity in the tRNA chemical structures, modification patterns, regulation, and function, suggesting that each modified nucleoside in tRNA may have its own specific function. However, in plants, our knowledge of the role of individual tRNA modifications and how they are regulated is very limited. In a genetic screen designed to identify factors regulating disease resistance in Arabidopsis, we identified SUPPRESSOR OF CSB3 9 (SCS9). Our results reveal S

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Delaunay, Sylvain, Francesca Rapino, Lars Tharun, et al. "Elp3 links tRNA modification to IRES-dependent translation of LEF1 to sustain metastasis in breast cancer." Journal of Experimental Medicine 213, no. 11 (2016): 2503–23. http://dx.doi.org/10.1084/jem.20160397.

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Quantitative and qualitative changes in mRNA translation occur in tumor cells and support cancer progression and metastasis. Posttranscriptional modifications of transfer RNAs (tRNAs) at the wobble uridine 34 (U34) base are highly conserved and contribute to translation fidelity. Here, we show that ELP3 and CTU1/2, partner enzymes in U34 mcm5s2-tRNA modification, are up-regulated in human breast cancers and sustain metastasis. Elp3 genetic ablation strongly impaired invasion and metastasis formation in the PyMT model of invasive breast cancer. Mechanistically, ELP3 and CTU1/2 support cellular

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Tang, Jun, Pengfei Jia, Peiyong Xin, Jinfang Chu, Dong-Qiao Shi, and Wei-Cai Yang. "The Arabidopsis TRM61/TRM6 complex is a bona fide tRNA N1-methyladenosine methyltransferase." Journal of Experimental Botany 71, no. 10 (2020): 3024–36. http://dx.doi.org/10.1093/jxb/eraa100.

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Abstract tRNA molecules, which contain the most abundant post-transcriptional modifications, are crucial for proper gene expression and protein biosynthesis. Methylation at N1 of adenosine 58 (A58) is critical for maintaining the stability of initiator methionyl-tRNA (tRNAiMet) in bacterial, archaeal, and eukaryotic tRNAs. However, although research has been conducted in yeast and mammals, it remains unclear how A58 in plant tRNAs is modified and involved in development. In this study, we identify the nucleus-localized complex AtTRM61/AtTRM6 in Arabidopsis as tRNA m1A58 methyltransferase. Defi

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Mangroo, Dev, Xin-Qi Wu, and Uttam L. Rajbhandary. "Escherichia coliinitiator tRNA: structure–function relationships and interactions with the translational machinery." Biochemistry and Cell Biology 73, no. 11-12 (1995): 1023–31. http://dx.doi.org/10.1139/o95-109.

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We showed previously that the sequence and (or) structural elements important for specifying the many distinctive properties of Escherichia coli initiator tRNA are clustered in the acceptor stem and in the anticodon stem and loop. This paper briefly describes this and reviews the results of some recently published studies on the mutant initiator tRNAs generated during this work. First, we have studied the effect of overproduction of methionyl-tRNA transformylase (MTF) and initiation factors IF2 and IF3 on activity of mutant initiator tRNAs mat are defective at specific steps in the initiation

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Strobel, M. C., and J. Abelson. "Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo." Molecular and Cellular Biology 6, no. 7 (1986): 2663–73. http://dx.doi.org/10.1128/mcb.6.7.2663.

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The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base

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Strobel, M. C., and J. Abelson. "Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo." Molecular and Cellular Biology 6, no. 7 (1986): 2663–73. http://dx.doi.org/10.1128/mcb.6.7.2663-2673.1986.

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The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base

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Paris, Zdeněk, and Juan D. Alfonzo. "How the intracellular partitioning of tRNA and tRNA modification enzymes affects mitochondrial function." IUBMB Life 70, no. 12 (2018): 1207–13. http://dx.doi.org/10.1002/iub.1957.

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Krutyhołowa, Rościsław, Alexander Hammermeister, Rene Zabel, et al. "Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator." Nucleic Acids Research 47, no. 9 (2019): 4814–30. http://dx.doi.org/10.1093/nar/gkz190.

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Noller, Harry F., Rachel Green, Gabriele Heilek, et al. "Structure and function of ribosomal RNA." Biochemistry and Cell Biology 73, no. 11-12 (1995): 997–1009. http://dx.doi.org/10.1139/o95-107.

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A refined model has been developed for the folding of 16S rRNA in the 30S subunit, based on additional constraints obtained from new experimental approaches. One set of constraints comes from hydroxyl radical footprinting of each of the individual 30S ribosomal proteins, using free Fe2+–EDTA complex. A second approach uses localized hydroxyl radical cleavage from a single Fe2+tethered to unique positions on the surface of single proteins in the 30S subunit. This has been carried out for one position on the surface of protein S4, two on S17, and three on S5. Nucleotides in 16S rRNA that are ess

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Fradejas, Noelia, Bradley A. Carlson, Eddy Rijntjes, Niels-Peter Becker, Ryuta Tobe, and Ulrich Schweizer. "Mammalian Trit1 is a tRNA[Ser]Sec-isopentenyl transferase required for full selenoprotein expression." Biochemical Journal 450, no. 2 (2013): 427–32. http://dx.doi.org/10.1042/bj20121713.

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Selenoproteins are proteins carrying the rare amino acid Sec (selenocysteine). Full expression of selenoproteins requires modification of tRNA[Ser]Sec, including N6-isopentenylation of base A37. We show that Trit1 is a dimethylallyl:tRNA[Ser]Sec transferase. Knockdown of Trit1 reduces expression of selenoproteins. Incubation of in vitro transcribed tRNA[Ser]Sec with recombinant Trit1 transfers [14C]dimethylallyl pyrophosphate to tRNA[Ser]Sec. 37A>G tRNA[Ser]Sec is resistant to isopentenylation by Trit1.

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Pereira, Marisa, Diana R. Ribeiro, Miguel M. Pinheiro, Margarida Ferreira, Stefanie Kellner, and Ana R. Soares. "m5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs." International Journal of Molecular Sciences 22, no. 6 (2021): 2941. http://dx.doi.org/10.3390/ijms22062941.

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Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methylurid

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Edmonds, C. G., P. F. Crain, R. Gupta, et al. "Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria)." Journal of Bacteriology 173, no. 10 (1991): 3138–48. http://dx.doi.org/10.1128/jb.173.10.3138-3148.1991.

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Moukadiri, Ismaïl, Magda Villarroya, Alfonso Benítez-Páez, and M. Eugenia Armengod. "Bacillus subtilis exhibits MnmC-like tRNA modification activities." RNA Biology 15, no. 9 (2018): 1167–73. http://dx.doi.org/10.1080/15476286.2018.1517012.

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Zhang, Jilei, Rong Lu, Yongguo Zhang, et al. "tRNA Queuosine Modification Enzyme Modulates the Growth and Microbiome Recruitment to Breast Tumors." Cancers 12, no. 3 (2020): 628. http://dx.doi.org/10.3390/cancers12030628.

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Background: Transfer RNA (tRNA) queuosine (Q)-modifications occur specifically in 4 cellular tRNAs at the wobble anticodon position. tRNA Q-modification in human cells depends on the gut microbiome because the microbiome product queuine is required for its installation by the enzyme Q tRNA ribosyltransferase catalytic subunit 1 (QTRT1) encoded in the human genome. Queuine is a micronutrient from diet and microbiome. Although tRNA Q-modification has been studied for a long time regarding its properties in decoding and tRNA fragment generation, how QTRT1 affects tumorigenesis and the microbiome

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Kazuhito, Tomizawa, and Fan-Yan Wei. "Posttranscriptional modifications in mitochondrial tRNA and its implication in mitochondrial translation and disease." Journal of Biochemistry 168, no. 5 (2020): 435–44. http://dx.doi.org/10.1093/jb/mvaa098.

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Abstract A fundamental aspect of mitochondria is that they possess DNA and protein translation machinery. Mitochondrial DNA encodes 22 tRNAs that translate mitochondrial mRNAs to 13 polypeptides of respiratory complexes. Various chemical modifications have been identified in mitochondrial tRNAs via complex enzymatic processes. A growing body of evidence has demonstrated that these modifications are essential for translation by regulating tRNA stability, structure and mRNA binding, and can be dynamically regulated by the metabolic environment. Importantly, the hypomodification of mitochondrial

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Khonsari, Bahar, and Roland Klassen. "Impact of Pus1 Pseudouridine Synthase on Specific Decoding Events in Saccharomyces cerevisiae." Biomolecules 10, no. 5 (2020): 729. http://dx.doi.org/10.3390/biom10050729.

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Pus1-dependent pseudouridylation occurs in many tRNAs and at multiple positions, yet the functional impact of this modification is incompletely understood. We analyzed the consequences of PUS1 deletion on the essential decoding of CAG (Gln) codons by tRNAGlnCUG in yeast. Synthetic lethality was observed upon combining the modification defect with destabilized variants of tRNAGlnCUG, pointing to a severe CAG-decoding defect of the hypomodified tRNA. In addition, we demonstrated that misreading of UAG stop codons by a tRNAGlnCUG variant is positively affected by Pus1. Genetic approaches further

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Fu, Dragony, Jennifer A. N. Brophy, Clement T. Y. Chan, et al. "Human AlkB Homolog ABH8 Is a tRNA Methyltransferase Required for Wobble Uridine Modification and DNA Damage Survival." Molecular and Cellular Biology 30, no. 10 (2010): 2449–59. http://dx.doi.org/10.1128/mcb.01604-09.

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ABSTRACT tRNA nucleosides are extensively modified to ensure their proper function in translation. However, many of the enzymes responsible for tRNA modifications in mammals await identification. Here, we show that human AlkB homolog 8 (ABH8) catalyzes tRNA methylation to generate 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of certain tRNAs, a critical anticodon loop modification linked to DNA damage survival. We find that ABH8 interacts specifically with tRNAs containing mcm5U and that purified ABH8 complexes methylate RNA in vitro. Significantly, ABH8 depletion in human cell

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Liu, Ru-Juan, Tao Long, Mi Zhou, Xiao-Long Zhou, and En-Duo Wang. "tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily." Nucleic Acids Research 43, no. 15 (2015): 7489–503. http://dx.doi.org/10.1093/nar/gkv745.

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COPELA, L. A. "The La protein functions redundantly with tRNA modification enzymes to ensure tRNA structural stability." RNA 12, no. 4 (2006): 644–54. http://dx.doi.org/10.1261/rna.2307206.

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Tsutsumi, Satoshi, Reiko Sugiura, Yan Ma, et al. "Wobble Inosine tRNA Modification Is Essential to Cell Cycle Progression in G1/S and G2/M Transitions in Fission Yeast." Journal of Biological Chemistry 282, no. 46 (2007): 33459–65. http://dx.doi.org/10.1074/jbc.m706869200.

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Inosine (I) at position 34 (wobble position) of tRNA is formed by the hydrolytic deamination of a genomically encoded adenosine (A). The enzyme catalyzing this reaction, termed tRNA A:34 deaminase, is the heterodimeric Tad2p/ADAT2·Tad3p/ADAT3 complex in eukaryotes. In budding yeast, deletion of each subunit is lethal, indicating that the wobble inosine tRNA modification is essential for viability; however, most of its physiological roles remain unknown. To identify novel cell cycle mutants in fission yeast, we isolated the tad3-1 mutant that is allelic to the tad3+ gene encoding a homolog of b

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Nakai, Yumi, Gorou Horiguchi, Kosei Iwabuchi, et al. "tRNA Wobble Modification Affects Leaf Cell Development in Arabidopsis thaliana." Plant and Cell Physiology 60, no. 9 (2019): 2026–39. http://dx.doi.org/10.1093/pcp/pcz064.

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Abstract The tRNA modification at the wobble position of Lys, Glu and Gln (wobbleU* modification) is responsible for the fine-tuning of protein translation efficiency and translation rate. This modification influences organism function in accordance with growth and environmental changes. However, the effects of wobbleU* modification at the cellular, tissue, or individual level have not yet been elucidated. In this study, we show that sulfur modification of wobbleU* of the tRNAs affects leaf development in Arabidopsis thaliana. The sulfur modification was impaired in the two wobbleU*-modificati

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Vothknecht, U. C., and D. Dörnemann. "Charging of Both, Plastidal tRNAgln and tRNAglu with Glutamate and Subsequent Amidation of the Misacylated tRNAgln by a Glutamyl-tRNA Amidotransferase in the Unicellular Green Alga Scenedesmus obliquus, Mutant C-2A'." Zeitschrift für Naturforschung C 50, no. 11-12 (1995): 789–95. http://dx.doi.org/10.1515/znc-1995-11-1209.

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Abstract , 1995 C5-Pathway, Glutamyl-tRNAglu-Synthetase (E.C.6.1.1.17), Misacylation of tR N A glu, Amidotransferase, Scenedesmus obliquus In a previous paper we described the purification of a glutamyl-tRNA synthetase from the unicellular green alga Scenedesmus obliquus, m utant C-2A'. We now dem onstrate that, firstly, this enzyme is capable of mischarging plastidal tR N A gln from barley with glutamate, as well as it regularly charges the plastidal tR N A glu from Scenedesmus. Secondly, we show that the mischarged glutamyl-tRNAgln is subsequently am idated by a glutamyl-tRNA am idotransfer

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Sun, Congliang, Patrick A. Limbach, and Balasubrahmanyam Addepalli. "Characterization of UVA-Induced Alterations to Transfer RNA Sequences." Biomolecules 10, no. 11 (2020): 1527. http://dx.doi.org/10.3390/biom10111527.

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Ultraviolet radiation (UVR) adversely affects the integrity of DNA, RNA, and their nucleoside modifications. By employing liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based RNA modification mapping approaches, we identified the transfer RNA (tRNA) regions most vulnerable to photooxidation. Photooxidative damage to the anticodon and variable loop regions was consistently observed in both modified and unmodified sequences of tRNA upon UVA (λ 370 nm) exposure. The extent of oxidative damage measured in terms of oxidized guanosine, however, was higher in unmodified RNA compared to its

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