1
|
Borland K, Diesend J, Ito-Kureha T, Heissmeyer V, Hammann C, Buck AH, Michalakis S, Kellner S. Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis. Genes (Basel) 2019; 10:E26. [PMID: 30621251 PMCID: PMC6356711 DOI: 10.3390/genes10010026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 12/04/2022] Open
Abstract
Post-transcriptional RNA modifications have been found to be present in a wide variety of organisms and in different types of RNA. Nucleoside modifications are interesting due to their already known roles in translation fidelity, enzyme recognition, disease progression, and RNA stability. In addition, the abundance of modified nucleosides fluctuates based on growth phase, external stress, or possibly other factors not yet explored. With modifications ever changing, a method to determine absolute quantities for multiple nucleoside modifications is required. Here, we report metabolic isotope labeling to produce isotopically labeled internal standards in bacteria and yeast. These can be used for the quantification of 26 different modified nucleosides. We explain in detail how these internal standards are produced and show their mass spectrometric characterization. We apply our internal standards and quantify the modification content of transfer RNA (tRNA) from bacteria and various eukaryotes. We can show that the origin of the internal standard has no impact on the quantification result. Furthermore, we use our internal standard for the quantification of modified nucleosides in mouse tissue messenger RNA (mRNA), where we find different modification profiles in liver and brain tissue.
Collapse
Affiliation(s)
- Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Jan Diesend
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Taku Ito-Kureha
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
| | - Vigo Heissmeyer
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
- Helmholtz Zentrum München, Research Unit Molecular Immune Regulation, Marchioninistr. 25, 81377 Munich, Germany.
| | - Christian Hammann
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Amy H Buck
- Institute of Immunology & Infection and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich CiPSM at the Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
| |
Collapse
|
2
|
Chambers AE, Richardson AE, Read DF, Waller TJ, Bernstein DA, Smaldino PJ. An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity. J Vis Exp 2018. [PMID: 30346392 DOI: 10.3791/58100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
N6-isopentenyladenosine RNA modifications are functionally diverse and highly conserved among prokaryotes and eukaryotes. One of the most highly conserved N6-isopentenyladenosine modifications occurs at the A37 position in a subset of tRNAs. This modification improves translation efficiency and fidelity by increasing the affinity of the tRNA for the ribosome. Mutation of enzymes responsible for this modification in eukaryotes are associated with several disease states, including mitochondrial dysfunction and cancer. Therefore, understanding the substrate specificity and biochemical activities of these enzymes is important for understanding of normal and pathologic eukaryotic biology. A diverse array of methods has been employed to characterize i6A modifications. Herein is described a direct approach for the detection of isopentenylation by Mod5. This method utilizes incubation of RNAs with a recombinant isopentenyl transferase, followed by RNase T1 digestion, and 1-dimensional gel electrophoresis analysis to detect i6A modifications. In addition, the potential adaptability of this protocol to characterize other RNA-modifying enzymes is discussed.
Collapse
Affiliation(s)
| | | | - David F Read
- Department of Genome Sciences, University of Washington
| | - Thomas J Waller
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan
| | | | | |
Collapse
|
3
|
Schweizer U, Bohleber S, Fradejas-Villar N. The modified base isopentenyladenosine and its derivatives in tRNA. RNA Biol 2017; 14:1197-1208. [PMID: 28277934 PMCID: PMC5699536 DOI: 10.1080/15476286.2017.1294309] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Base 37 in tRNA, 3′-adjacent to the anticodon, is occupied by a purine base that is thought to stabilize codon recognition by stacking interactions on the first Watson-Crick base pair. If the first codon position forms an A.U or U.A base pair, the purine is likely further modified in all domains of life. One of the first base modifications found in tRNA is N6-isopentenyl adenosine (i6A) present in a fraction of tRNAs in bacteria and eukaryotes, which can be further modified to 2-methyl-thio-N6-isopentenyladenosine (ms2i6A) in a subset of tRNAs. Homologous tRNA isopentenyl transferase enzymes have been identified in bacteria (MiaA), yeast (Mod5, Tit1), roundworm (GRO-1), and mammals (TRIT1). In eukaryotes, isopentenylation of cytoplasmic and mitochondrial tRNAs is mediated by products of the same gene. Accordingly, a patient with homozygous mutations in TRIT1 has mitochondrial disease. The role of i6A in a subset of tRNAs in gene expression has been linked with translational fidelity, speed of translation, skewed gene expression, and non-sense suppression. This review will not cover the action of i6A as a cytokinin in plants or the potential function of Mod5 as a prion in yeast.
Collapse
Affiliation(s)
- Ulrich Schweizer
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
| | - Simon Bohleber
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
| | - Noelia Fradejas-Villar
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
| |
Collapse
|
4
|
Brencicova E, Diebold SS. Nucleic acids and endosomal pattern recognition: how to tell friend from foe? Front Cell Infect Microbiol 2013; 3:37. [PMID: 23908972 PMCID: PMC3726833 DOI: 10.3389/fcimb.2013.00037] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 07/10/2013] [Indexed: 12/18/2022] Open
Abstract
The innate immune system has evolved endosomal and cytoplasmic receptors for the detection of viral nucleic acids as sensors for virus infection. Some of these pattern recognition receptors (PRR) detect features of viral nucleic acids that are not found in the host such as long stretches of double-stranded RNA (dsRNA) and uncapped single-stranded RNA (ssRNA) in case of Toll-like receptor (TLR) 3 and RIG-I, respectively. In contrast, TLR7/8 and TLR9 are unable to distinguish between viral and self-nucleic acids on the grounds of distinct molecular patterns. The ability of these endosomal TLR to act as PRR for viral nucleic acids seems to rely solely on the mode of access to the endolysosomal compartment in which recognition takes place. The current dogma states that self-nucleic acids do not enter the TLR-sensing compartment under normal physiological conditions. However, it is still poorly understood how dendritic cells (DC) evade activation by self-nucleic acids, in particular with regard to specific DC subsets, which are specialized in taking up material from dying cells for cross-presentation of cell-associated antigens. In this review we discuss the current understanding of how the immune system distinguishes between foreign and self-nucleic acids and point out some of the key aspects that still require further research and clarification.
Collapse
Affiliation(s)
- Eva Brencicova
- Peter Gorer Department of Immunobiology, Guy's Hospital, King's College London, London, UK
| | | |
Collapse
|
5
|
Su AAH, Randau L. A-to-I and C-to-U editing within transfer RNAs. BIOCHEMISTRY (MOSCOW) 2011; 76:932-7. [DOI: 10.1134/s0006297911080098] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
6
|
Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, Fahlman RP. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 2009; 37:2461-70. [PMID: 19255090 PMCID: PMC2677864 DOI: 10.1093/nar/gkp093] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous non-identical small RNA sequences. Investigating the sites and identities of substitution errors reveal that many potentially originate as a result of post-transcriptional modifications or RNA editing. Modifications include N1-methyl modified purine nucleotides in tRNA, potential deamination or base substitutions in micro RNAs, 3′ micro RNA uridine extensions and 5′ micro RNA deletions. Additionally, further analysis of large sequencing datasets reveal that the combined effects of 5′ deletions and 3′ uridine extensions can alter the specificity by which micro RNAs associate with different Argonaute proteins. Hence, we demonstrate that not all sequencing errors in small RNA datasets are technical artifacts, but that these actually often reveal valuable biological insights to the sites of post-transcriptional RNA modifications.
Collapse
Affiliation(s)
- H Alexander Ebhardt
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
| | | | | | | | | | | |
Collapse
|
7
|
Todorov KA, Tan XJ, Nonekowski ST, Garcia GA, Carlson HA. The role of aspartic acid 143 in E. coli tRNA-guanine transglycosylase: insights from mutagenesis studies and computational modeling. Biophys J 2005; 89:1965-77. [PMID: 15951383 PMCID: PMC1366699 DOI: 10.1529/biophysj.105.059576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
tRNA guanine transglycosylase (TGT) is a tRNA-modifying enzyme which catalyzes the posttranscriptional exchange of guanine in position 34 of tRNA(Y,H,N,D) with the modified base queuine in eukaryotes or its precursor, preQ(1) base, in eubacteria. Thus, TGT must recognize the guanine in tRNA and the free base queuine or preQ(1) to catalyze this exchange. The crystal structure of Zymomonas mobilis TGT with preQ(1) bound suggests that a key aspartate is critically involved in substrate recognition. To explore this, a series of site-directed mutants of D143 in Escherichia coli TGT were made and characterized to investigate heterocyclic substrate recognition. Our data confirm that D143 has significant impact on K(M) of guanine; however, the trend in the K(M) data (D143A < D143N < D143S < D143T) is unexpected. Computational studies were used to further elucidate the interactions between guanine and the D143 mutants. A homology model of E. coli TGT was created, and the role of D143 was investigated by molecular dynamic simulations of guanine bound to the wild-type and D143-mutant TGTs. To validate the model systems against our kinetic data, free energies of binding were fit using the linear interaction energy (LIE) method. This is a unique application of the LIE method because the same ligand is bound to several mutant proteins rather than one protein binding several ligands. The atomic detail gained from the simulations provided a better understanding of the binding affinities of guanine with the mutant TGTs, revealing that water molecules enter the active site and hydrogen bond to the ligand and compensate for lost protein-ligand interactions. The trend of binding affinity for wild-type > D143A > D143N > D143S > D143T appears to be directly related to the degree of hydrogen bonding available to guanine in the binding site.
Collapse
Affiliation(s)
- Katherine Abold Todorov
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
| | | | | | | | | |
Collapse
|
8
|
Garcia GA, Kittendorf JD. Transglycosylation: a mechanism for RNA modification (and editing?). Bioorg Chem 2005; 33:229-51. [PMID: 15888313 PMCID: PMC2802272 DOI: 10.1016/j.bioorg.2005.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 01/11/2005] [Accepted: 01/11/2005] [Indexed: 11/22/2022]
Abstract
The vast majority of the ca. 100 chemically distinct modified nucleosides in RNA appear to arise via the chemical transformation of a genetically encoded nucleoside. Two notable exceptions are queuosine and pseudouridine, which are incorporated into tRNA via transglycosylation. Transglycosylation is an extremely efficient process for incorporating highly modified bases such as queuine into RNA. Transglycosylation is also a requisite process for "isomerizing" an N-nucleoside into a C-nucleoside as is the case for pseudouridine formation. Finally, transglycosylation is an attractive possibility for certain RNA editing events (e.g., pyrimidine to purine conversions) that cannot occur via the known, more straightforward enzymatic reactions (e.g., deaminations). This review discusses what is known about the mechanisms of transglycosylation for the queuine and pseudouridine RNA modifications and will speculate about a potential role for transglycosylation in certain RNA editing events.
Collapse
Affiliation(s)
- George A. Garcia
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
| | | |
Collapse
|
9
|
Phillips SE, Stockley PG. Structure and function of Escherichia coli met repressor: similarities and contrasts with trp repressor. Philos Trans R Soc Lond B Biol Sci 1996; 351:527-35. [PMID: 8735275 DOI: 10.1098/rstb.1996.0051] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Transcription of genes encoding enzymes for the biosynthesis of methionine and trytophan in Escherichia coli is regulated by the ligand-activated met and trp repressors. X-ray crystallographic studies show how these two small proteins, although similar in size and function, have totally different three-dimensional structures and specifically recognize their respective DNA operator sequences in different ways. A common feature is that both repressors bind as cooperative arrays to tandem repeats of 8 base-pair 'Met' or 'Trp boxes' respectively, and the consensus sequences share the rare tetranucleotide CTAG. A series of structural and functional studies have shown how the two repressors discriminate between their operators, using a combination of direct contacts between side chains and bases, and indirect sensing of conformational properties of the DNA.
Collapse
Affiliation(s)
- S E Phillips
- Department of Biochemistry and Molecular Biology, University of Leeds, U.K
| | | |
Collapse
|
10
|
Old IG, Phillips SE, Stockley PG, Saint Girons I. Regulation of methionine biosynthesis in the Enterobacteriaceae. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1991; 56:145-85. [PMID: 1771231 DOI: 10.1016/0079-6107(91)90012-h] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- I G Old
- Département de Bactériologie et Mycologie, Institut Pasteur, Paris, France
| | | | | | | |
Collapse
|
11
|
Steiman R, Seigle-Murandi F, Betina V. Biochemical variations related to morphogenesis inAureobasidium pullulans. Folia Microbiol (Praha) 1990. [DOI: 10.1007/bf02821280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
12
|
Chapter 1 Synthesis and Function of Modified Nucleosides in tRNA. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/s0301-4770(08)61487-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
13
|
Studies on Polynucleotides CIII. Total Synthesis of the Structural Gene for an Alanine Transfer Ribonucleic Acid from Yeast. Mol Biol 1989. [DOI: 10.1016/b978-0-12-131200-8.50035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
14
|
Ajitkumar P, Cherayil JD. Thionucleosides in transfer ribonucleic acid: diversity, structure, biosynthesis, and function. Microbiol Rev 1988; 52:103-13. [PMID: 3280963 PMCID: PMC372707 DOI: 10.1128/mr.52.1.103-113.1988] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
15
|
Dirheimer G. Chemical nature, properties, location, and physiological and pathological variations of modified nucleosides in tRNAs. Recent Results Cancer Res 1983; 84:15-46. [PMID: 6342070 DOI: 10.1007/978-3-642-81947-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
16
|
Mulligan JT, Margolin W, Krueger JH, Walker GC. Mutations affecting regulation of methionine biosynthetic genes isolated by use of met-lac fusions. J Bacteriol 1982; 151:609-19. [PMID: 6284705 PMCID: PMC220301 DOI: 10.1128/jb.151.2.609-619.1982] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Fusions of the lac genes to the promoters of four structural genes in the methionine biosynthetic pathway, metA, metB, metE, and metF, were obtained by the use of the Mu d(Ap lac) bacteriophage. The levels of beta-galactosidase in these strains could be derepressed by growth under methionine-limiting conditions. Furthermore, growth in the presence of vitamin B12 repressed the synthesis of beta-galactosidase in strains containing a fusion of lacZ to the metE promoter, phi(metE'-lacZ+). Mutations affecting the regulation of met-lac fusions were generated by the insertion of Tn5. Tn5 insertions were obtained at the known regulatory loci metJ and metK. Interestingly, a significant amount of methionine adenosyltransferase activity remained in the metK mutant despite the fact that the mutation was generated by an insertion. Several Tn5-induced regulatory mutations were isolated by screening for high-level beta-galactosidase expression in a phi(metE'-lacZ+) strain in the presence of vitamin B12. Tn5 insertions mapping at the btuB (B12 uptake), metH (B12 dependent tetrahydropteroylglutamate methyltransferase), and metF (5,10-methylenetetrahydrofolate reductase) loci were obtained. The isolation of the metH mutant was consistent with previous suggestions that the metH gene product is required for the repression of metE by vitamin B12. The metF::Tn5 insertion was of particular interest since it suggested that a functional metf gene product was also needed for repression of metE by vitamin B12.
Collapse
|
17
|
Berg BH, Pryme IF. Comparison of the rate of aminoacylation of tRNA isolated from NMRI mouse liver with tRNA isolated from Krebs II ascites or mouse plasmacytoma cells. Cancer Lett 1981; 12:209-15. [PMID: 6911051 DOI: 10.1016/0304-3835(81)90070-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A comparison of the initial rates of aminoacylation of tRNAs isolated from different sources for 17 amino acids was performed. tRNA was isolated from NMRI mouse liver (tRNA L) and from Krebs II ascites tumors (tRNA Asc), and aminoacyl-tRNA synthetases were prepared from the latter cells. The aminoacylation of tRNA Asc was 31-88% slower than the charging of tRNA L. In similar studies, tRNA from a mouse plasmacytoma tumor (tRNA Mt) and from suspension cultured cells of the same cell line (tRNA M) were compared to tRNA L in the aminoacylation reaction catalysed by synthetases isolated from tumor or suspension cultured cells. About half of the tRNAs (Mt or M) for the 17 amino acids tested differed in charging rate when compared to tRNA L, but the differences were not as great as those observed in the experiments where tRNA Asc and tRNA L were compared.
Collapse
|
18
|
Characterization of a mutation in Saccharomyces cerevisiae that produces mutant isoaccepting tRNAs for several of its tRNA species. Curr Genet 1981; 3:73-82. [DOI: 10.1007/bf00419583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/1980] [Indexed: 10/26/2022]
|
19
|
Lack of cytokinin activity of Y-type bases isolated from phenylalanine specific tRNAs. ACTA ACUST UNITED AC 1981. [DOI: 10.1016/0304-4211(81)90255-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
20
|
Lu LJ, Chiang GH, Randerath K. Effects of 5-azacytidine on transfer RNA modification: comparative study on normal and malignant tissues. Life Sci 1980; 27:577-84. [PMID: 6158642 DOI: 10.1016/0024-3205(80)90307-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
21
|
|
22
|
Novel mechanism of post-transcriptional modification of tRNA. Insertion of bases of Q precursors into tRNA by a specific tRNA transglycosylase reaction. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)30183-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
23
|
Lu LJ, Tseng WC, Randerath K. Effects of 5-fluorocytidine on mammalian transfer RNA and transfer RNA methyltransferases. Biochem Pharmacol 1979; 28:489-95. [PMID: 371626 DOI: 10.1016/0006-2952(79)90241-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
24
|
Sommer S, Lavi U, Darnell JE. The absolute frequency of labeled N-6-methyladenosine in HeLa cell messenger RNA decreases with label time. J Mol Biol 1978; 124:487-99. [PMID: 712844 DOI: 10.1016/0022-2836(78)90183-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
25
|
Zoltewicz JA, Deady LW. Quaternization of Heteroaromatic Compounds: Quantitative Aspects. ADVANCES IN HETEROCYCLIC CHEMISTRY 1978. [DOI: 10.1016/s0065-2725(08)60103-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
|
26
|
Goddard JP. The structures and functions of transfer RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978. [DOI: 10.1016/0079-6107(78)90021-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
27
|
Kwong LK, Moore VG, Kaiser II. Pseudouridine-deficient transfer RNAs from Escherichia coli B and their use as substrates for pseudouridine synthetase. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)39957-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
28
|
Randerath E, Gopalakrishnan AS, Randerath K. Transfer RNA in hepatomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1977; 92:517-64. [PMID: 205108 DOI: 10.1007/978-1-4615-8852-8_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
MESH Headings
- Animals
- Base Sequence
- Carcinoma, Hepatocellular/analysis
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/metabolism
- Liver Neoplasms/analysis
- Liver Neoplasms/enzymology
- Liver Neoplasms/metabolism
- Methylation
- Neoplasms, Experimental/analysis
- Neoplasms, Experimental/enzymology
- Neoplasms, Experimental/metabolism
- Nucleosides/analysis
- RNA, Neoplasm/metabolism
- RNA, Transfer/analysis
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/analysis
- RNA, Transfer, Amino Acyl/metabolism
- Rats
- tRNA Methyltransferases/metabolism
Collapse
|
29
|
Sheid B, Pedrinan L. Transfer RNA methylase activity in normal and dystrophic chicken muscle. Biochem Biophys Res Commun 1977; 75:56-61. [PMID: 849309 DOI: 10.1016/0006-291x(77)91288-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
30
|
|
31
|
METZLER DAVIDE. Biochemical Genetics and the Synthesis of Nucleic Acids and Proteins. Biochemistry 1977. [DOI: 10.1016/b978-0-12-492550-2.50020-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
32
|
Pegg AE. Formation and metabolism of alkylated nucleosides: possible role in carcinogenesis by nitroso compounds and alkylating agents. Adv Cancer Res 1977; 25:195-269. [PMID: 326002 DOI: 10.1016/s0065-230x(08)60635-1] [Citation(s) in RCA: 247] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
33
|
Abstract
Foetal rat liver extracts were found to have higher tRNA methylene activities than corresponding extracts of adult liver. When the specific activities were expressed per mg of liver or per mg of protein, the foetal tRNA methylating enzymes were respectively 2.5 and 6 times higher than those of adult livers. The presence of an inhibitor in adult liver can be excluded, since the same recoveries of total tRNA methylase activity were obtained after partial purification of both adult and foetal liver extracts: yields were close to 100%. The apparent Km's for the substrates in the methylating reactions were the same when tRNA methylases from either adult or foetal liver were used: values were 0.2 muM for Escherichia coli tRNA and 2.1 muM for S-adenosyl-L-methionine. After T1-T2 ribonuclease digestion of an in vitro methylated tRNA, similar methyl nucleotide patterns were observed in foetal and adult enzymatic extracts. It is concluded that the same tRNA methylase pool is present in adult and foetal liver. In addition, it is hypothesized that the different reaction rates exhibited by these enzymes might be due to the tRNA functional requirements rather than to the presence of a tRNA methylase inhibitor.
Collapse
|
34
|
Fournier MJ, Webb E, Kitchingman GR. General and specific effects of amino acid starvation on the formation of undermodified Escherichia coli phenylalanine tRNA. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 454:97-113. [PMID: 791374 DOI: 10.1016/0005-2787(76)90358-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The heterogeneity of undermodified phenylalanine tRNA produced in relaxed control E. coli during amino acid starvation was investigated. Examination of the RPC-5 elution profiles of tRNAPhe prepared from non-starved cells and cells starved of a variety of amino acids, including some known to be involved in the formation of modified bases revealed that: (1) only one species of fully modified tRNAPhe appears to occur in cells grown in enriched medium; (2) at least two chromatographically unique isoacceptor species are observed in addition to the normal tRNAPhe in starved cells; (3) the unique, undermodified species of tRNAPhe from leucine-starved cells, known to be deficient in dihydrouridine, pseudouridine, 2-thiomethyl-N6-(delta2-isopentenyl) adenosine and 3-(3-amino-3-carboxypropyl) uridine, co-elute with the unique species produced in cells starved of histidine or arginine or treated with puromycin or chloramphenicol; (4) additional unique species of tRNAPhe can be detected in methyl- and sulfur-deficient tRNA from methionine- and cysteine-starved cells; (5) analysis of phenoxyacetylated tRNA revealed that the chromatographically unique and normal species from starved cells contain subspecies deficient in 3-(3-amino-3-carboxypropyl) uridine; and (6) using phenoxyacetylation as a means of effecting the resolution of undermodified subspecies, a total of at least ten chromatographically unique subspecies of rRNAPhe were detected in an organism that appears to posses only one gene for tRNAPhe. Taken together, the results support the view that there are both general and specific effects of amino acid starvation on the post-transcriptional modification of tRNA.
Collapse
|
35
|
Salas CE, Cummins CJ, Sellinger OZ. The developmental pattern of homologous and heterologous tRNA methylation in rat brain differential effect of spermidine. Neurochem Res 1976; 1:369-84. [DOI: 10.1007/bf00966229] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/1976] [Indexed: 10/26/2022]
|
36
|
Mullenbach GT, Kammen HO, Penhoet EE. A heterologous system for detecting eukaryotic enzymes which synthesize pseudouridine in transfer ribonucleic acids. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33240-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
37
|
Abstract
The methylation of tRNA is a post-transcriptional modification which is achieved by specific enzymes, the tRNA methylases, with S adenosylmethionine as a methyl donor. The level and pattern of methylation are characteristic of the tRNA species and origin. Abnormally methylated tRNAs have been obtained, in vivo and in vitro, by a variety of methods, and their properties have been studied. The tRNA methylases are found in all cells and tissues. Their activity varies with the differentiation state of the cells, and under the influence of many internal and external factors ; it is especially elevated in embryonic and cancerous tissues. These enzymes are very unstable, and none of them has been purified to homogeneity. We present here their known properties and we propose a theory concerning their specificity. Finally, after reviewing the few available experimental data, we discuss the current hypotheses and speculations about the roles and functions of tRNA methylation.
Collapse
|
38
|
Khorana HG, Agarwal KL, Besmer P, Büchi H, Caruthers MH, Cashion PJ, Fridkin M, Jay E, Kleppe K, Kleppe R, Kumar A, Loewen PC, Miller RC, Minamoto K, Panet A, RajBhandary UL, Ramamoorthy B, Sekiya T, Takeya T, van de Sande JH. Total synthesis of the structural gene for the precursor of a tyrosine suppressor transfer RNA from Escherichia coli. 1. General introduction. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33826-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
39
|
Smith JD. Transcription and processing of transfer RNA precursors. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1976; 16:25-73. [PMID: 766079 DOI: 10.1016/s0079-6603(08)60755-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
40
|
Daves GD, Cheng CC. The chemistry and biochemistry of C-nucleosides. PROGRESS IN MEDICINAL CHEMISTRY 1976; 13:303-49. [PMID: 801779 DOI: 10.1016/s0079-6468(08)70141-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
41
|
|
42
|
Varricchio F, Ernst HJ. Separation of low molecular weight RNA by polyacrylamide gel electrophoresis. Anal Biochem 1975; 68:485-92. [PMID: 925 DOI: 10.1016/0003-2697(75)90643-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
43
|
Björk GR, Neidhardt FC. Physiological and biochemical studies on the function of 5-methyluridine in the transfer ribonucleic acid of Escherichia coli. J Bacteriol 1975; 124:99-111. [PMID: 1100618 PMCID: PMC235870 DOI: 10.1128/jb.124.1.99-111.1975] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Matched pairs of transductant strains differing by the presence of absence of 5-methyluridine (ribothymidine) (m5U) in their transfer ribonucleic acid (tRNA) were used to study the function of this modified nucleoside in Escherichia coli. Ordinary measurements of growth rate in different media revealed no effect of the loss of m5U in tRNA. A gene located close to trmA (the structural cistron for the methyltransferase that produces m5U in tRNA), however, was found to reduce the growth rates significantly, depending on the medium and the temperature of cultivation. Measurement of codon recognition, macromolecular composition, tRNA binding to the ribosome, and the rate of protein chain elongation in vivo indicated no disadvantage caused by the lack of m5U. The regulation of ilv and his operons seemed also to be unaffected by the absence of m5U in the tRNA. In a mixed population experiment, however, cells possessing m5U in their tRNA seemed to have a distinct advantage over cells lacking this modified nucleoside. This experiment provides the first indication of the overall value of m5U in tRNA.
Collapse
|
44
|
Chen C, Smith OC, McChesney J. Biosynthesis and cytokinin activity of 8-hydroxy and 2,8-dihydroxy derivatives of zeatin and N-6(increment-2-isopentenyl)adenine. Biochemistry 1975; 14:3088-93. [PMID: 1148191 DOI: 10.1021/bi00685a008] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
8-Hydroxy and 2,8-dihydroxy derivatives of the cytokinins, 6-(4-hydroxy-3-methyl-trans-2-butenylamino)purine and N-6-(increment -2-isopentenyl)adenine, have been biosynthesized by xanthine oxidase oxidation. 8-Hydroxy derivatives have been shown to be the major intermdeiates. These compounds were tested for cytokinin activity in the tobacco bioassay. The results suggest that substitution of the 8 position with a hydroxyl group causes less decrease of cytokinin activity than substitution of both the 2 and 8 positions with hydroxyl groups.
Collapse
|
45
|
|
46
|
|
47
|
Liacouras AS, Anderson EP. Uridine-cytidine kinase. Purification from a murine neoplasm and characterization of the enzyme. Arch Biochem Biophys 1975; 168:66-73. [PMID: 166617 DOI: 10.1016/0003-9861(75)90228-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
48
|
Fournier MJ, Peterkofsky A. Formation of chromatographically unique species of transfer ribonucleic acid during amino acid starvation of relaxed-control Escherichia coli. J Bacteriol 1975; 122:538-48. [PMID: 1092655 PMCID: PMC246089 DOI: 10.1128/jb.122.2.538-548.1975] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Examination of the transfer ribonucleic acid (tRNA) produced by starving, relaxed-control (rel minus) strains of Escherichia coli for required amino acids revealed the occurrence of a number of chromatographically unique subspecies. Leucine starvation results in the formation of new isoacceptor species of leucine-, histidine-, arginine-, valine-, and phenylalanine-specific tRNA and quantitative changes in the column profiles of serine, glycine, and isoleucine tRNA. Evidence that the unique tRNA species are synthesized de novo during amino acid starvation comes from the findings that the major unique leucine isoacceptor species is not formed in stringent control cells or in rel minus cells starved for uracil or treated with rifampin. Furthermore, heat treatment of the unique leucine tRNA does not alter its chromatographic behavior, indicating that the species is not an aggregate or nuclease-damaged form of a normal isoacceptor tRNA. The methyl acceptor activities of tRNA from leucine-starved and nonstarved rel+ or rel minus cells were found to be essentially the same. This result and the finding that the chromatographic behavior of the unique leucine-specific tRNA was not altered after treatment with tRNA methylase suggests that gross methyl deficiency is probably not the biochemical basis for the occurrence of the unique species.
Collapse
|
49
|
Abstract
Messenger RNAs from mouse myeloma cells contain N-6-methyl adenosine and novel 5' termini having 7-methy-guanosine in a 5', 5' triphosphate linkage with ribose-methylated nucleosides. Ten common 5'-terminal sequences of the forms m-7-G-5'-PPP-5'-NmpNp and m-7-G-5'-ppp-5'-NmpNmpNp are reported. Structures like this may be a general feature of mRNA in eukaryotes.
Collapse
|
50
|
Affiliation(s)
- R. Holliday
- Genetics Division, National Institute for Medical Research, Mill Hill, London NW7 1AA, England
| | - J. E. Pugh
- Genetics Division, National Institute for Medical Research, Mill Hill, London NW7 1AA, England
| |
Collapse
|