1
|
Abstract
The separation of biologically active, pure, and specific tRNAs is difficult due to the overall similarity in secondary and tertiary structures of different tRNAs. Because prior methods do not facilitate high-resolution separations of the extremely complex mixture represented by a cellular tRNA population, global studies of tRNA identity and/or abundance are difficult. We have discovered that the enzymatic digestion of an individual tRNA by a ribonuclease (e.g., RNase T1) will generate digestion products unique to that particular tRNA, and we show that a comparison of an organism's complete complement of tRNA RNase digestion products yields a set of unique or "signature" digestion product(s) that ultimately enable the detection of individual tRNAs from a total tRNA pool. Detection is facilitated by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and proof-of-principle is demonstrated on the whole tRNA pool from Escherichia coli. This method will enable the individual identification of tRNA isoacceptors without requiring specific affinity purification or extensive chromatographic and/or electrophoretic purification. Further, experimental identifications of tRNAs or other RNAs will now be possible using this signature digestion product approach in a manner similar to peptide mass fingerprinting used in proteomics, allowing RNomic studies of RNA at the post-transcriptional level.
Collapse
MESH Headings
- Escherichia coli/chemistry
- Escherichia coli/genetics
- RNA, Bacterial/analysis
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Transfer/analysis
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acid-Specific/analysis
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/metabolism
- Reproducibility of Results
- Ribonuclease T1/metabolism
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Collapse
Affiliation(s)
- Mahmud Hossain
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, OH 45221-0172, USA
| | | |
Collapse
|
2
|
Kelly VP, Suzuki T, Nakajima O, Arai T, Tamai Y, Takahashi S, Nishimura S, Yamamoto M. The distal sequence element of the selenocysteine tRNA gene is a tissue-dependent enhancer essential for mouse embryogenesis. Mol Cell Biol 2005; 25:3658-69. [PMID: 15831471 PMCID: PMC1084291 DOI: 10.1128/mcb.25.9.3658-3669.2005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Appropriate expression of the selenocysteine tRNA (tRNA(Sec)) gene is necessary for the production of an entire family of selenoprotein enzymes. This study investigates the consequence of disrupting an upstream enhancer region of the mouse tRNA(Sec) gene (Trsp) known as the distal sequence element (DSE) by use of a conditional repair gene targeting strategy, in which a 3.2-kb insertion was introduced into the promoter of the gene. In the absence of DSE activity, homozygous mice failed to develop in utero beyond embryonic day 7.5 and had severely decreased levels of selenoprotein transcript. Cre-mediated removal of the selection cassette recovered DSE regulation of Trsp, restoring wild-type levels of tRNA(Sec) expression and allowing the generation of viable rescued mice. Further analysis of targeted heterozygous adult mice revealed that the enhancer activity of the DSE is tissue dependent since, in contrast to liver, heart does not require the DSE for normal expression of Trsp. Similarly, in mouse cell lines we showed that the DSE functions as a cell-line-specific inducible element of tRNA(Sec). Together, our data demonstrate that the DSE is a tissue-dependent regulatory element of tRNA(Sec) expression and that its activity is vital for sufficient tRNA(Sec) production during mouse embryogenesis.
Collapse
MESH Headings
- Animals
- Antioxidants/metabolism
- Base Sequence
- Embryo, Mammalian/cytology
- Embryo, Mammalian/enzymology
- Embryonic Development/genetics
- Embryonic Development/physiology
- Enhancer Elements, Genetic/genetics
- Enhancer Elements, Genetic/physiology
- Gene Expression Regulation, Developmental
- Gene Targeting
- Genes, Lethal/genetics
- Glutathione Peroxidase/genetics
- Glutathione Peroxidase/metabolism
- Heme Oxygenase (Decyclizing)/genetics
- Heme Oxygenase (Decyclizing)/metabolism
- Heme Oxygenase-1
- Liver/metabolism
- Membrane Proteins
- Mice/embryology
- Mice/genetics
- Molecular Sequence Data
- Myocardium/metabolism
- Proteins/genetics
- Proteins/metabolism
- RNA, Transfer, Amino Acid-Specific/analysis
- RNA, Transfer, Amino Acid-Specific/genetics
- Selenoproteins
- Tissue Distribution
- Up-Regulation
- Glutathione Peroxidase GPX1
Collapse
Affiliation(s)
- Vincent P Kelly
- Center for TARA, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
3
|
Abstract
Activity to convert serine to selenocysteine in B. subtilis was studied but no activity was detected. In addition, although we tried to find its selenocysteine tRNA (tRNA(SeCys)) gene from a total genome sequence (1) by the computer search with FASTA against E. coli selC (2), no convincing candidate was found. These results suggest that in B. subtilis, selenium-related system is considerably different from known one like E. coli.
Collapse
Affiliation(s)
- J Matsugi
- Department of Biochemistry, Jichi Medical School, Tochigi, Japan
| | | |
Collapse
|
4
|
Diamond AM, Jaffe D, Murray JL, Safa AR, Samuels BL, Hatfield DL. Lovastatin effects on human breast carcinoma cells. Differential toxicity of an adriamycin-resistant derivative and influence on selenocysteine tRNAS. Biochem Mol Biol Int 1996; 38:345-355. [PMID: 8850530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Selenocysteine tRNA[Ser]Sec isoacceptors contain the modified nucleotide i6A immediately 3' to the anticodon. Because synthesis of i6A is expected to be inhibited by lovastatin, the status of tRNA[Ser]Sec isoacceptors was examined in human breast carcinoma cells. As part of the initial characterization of these cells, it was determined that an adriamycin resistant derivative of the MCF-7 cell line exhibited a dramatic increase in the sensitivity to the killing effects of lovastatin relative to the parental MCF-7 cells. When MCF-7Adr cells were incubated with high levels of lovastatin, there was a dramatic perturbation in the distribution of isoacceptors within the selenocysteine tRNA population. Lovastatin may therefore be a useful reagent for both the study of differential killing of drug-resistant tumor cells and selenoprotein biosynthesis.
Collapse
Affiliation(s)
- A M Diamond
- Department of Radiation and Cellular Oncology, University of Chicago, IL 60637, USA
| | | | | | | | | | | |
Collapse
|
5
|
Abstract
Two isoacceptors of selenocysteine tRNA[Ser]Sec are present in higher vertebrates which are responsible for donating selenocysteine to protein. One such selenocysteine containing protein, glutathione peroxidase, requires selenium for its translation and transcription. Since tRNA[Ser]Sec is a critical component of the glutathione peroxidase translational machinery, the levels and distributions of its isoacceptors were examined from both human and rat cells grown in chemically defined media with and without selenium. Not only did the level of the selenocysteine tRNA[Ser]Sec population increase approximately 20% in cells grown in the presence of selenium, but the distributions of the two isoacceptors also changed relative to each other.
Collapse
Affiliation(s)
- D Hatfield
- Laboratory of Experimental Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | | | | | | |
Collapse
|
6
|
Freist W, Cramer F. Valyl-tRNA synthetase from yeast. Discrimination between 20 amino acids in aminoacylation of tRNA(Val)-C-C-A and tRNA(Val)-C-C-A(3'NH2). Eur J Biochem 1990; 191:123-9. [PMID: 2199195 DOI: 10.1111/j.1432-1033.1990.tb19101.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
For discrimination between valine and the 19 naturally occurring noncognate amino acids, as well as between valine and 2-amino-isobutyric acid by valyl-tRNA synthetase from baker's yeast, discrimination factors (D) have been determined from kcat and Km values in aminoacylation of tRNA(Val)-C-C-A. The lowest values were found for Trp, Ser, Cys, Lys, Met and Thr (D = 90-870), showing that valine is 90-870 times more frequently attached to tRNA(Val)-C-C-A than the noncognate amino acids at the same amino acid concentrations. The other amino acids exhibit D values between 1,100 and 6200. Generally, valyl-tRNA synthetase is considerably less specific than isoleucyl-tRNA synthetase, but this may be partly compensated in the cell by valine concentrations higher than those of noncognate acids. In aminoacylation of tRNA(Val)-C-C-A(3'NH2) discrimination factors D1 are in the range of 40-1260. From D1 values and AMP formation stoichiometry, pretransfer proof-reading factors pi 1 were determined: post-transfer proof-reading factors II 2 were determined from D values and AMP formation stoichiometry in acylation of tRNA(Val)-C-C-A. II 1 values (7-168) show that pretransfer proof-reading is the main correction step, post-transfer proof-reading (II 2 approximately 1-7) is less effective and in some cases negligible. Initial discrimination factors were calculated from discrimination and proof-reading factors according to a two-step binding process. These factors, due to different Gibbs free energies of binding can be related to hydrophobic interaction forces, and a hypothetical 'stopper' model of the amino-acid-binding site is discussed.
Collapse
Affiliation(s)
- W Freist
- Max-Planck-Institut für experimentelle Medizin, Abteilung Chemie, Göttingen, Federal Republic of Germany
| | | |
Collapse
|
7
|
Sangaré A, Weil JH, Grienenberger JM. Maize and wheat mitochondrial tRNAPro coding regions have similar sequences but different organizations. Biochim Biophys Acta 1990; 1049:96-8. [PMID: 1694093 DOI: 10.1016/0167-4781(90)90089-k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The nucleotide sequences of two maize mitochondrial DNA regions containing a tRNAPro gene and an incomplete tRNAPro gene have been compared with the corresponding regions of wheat mitochondrial DNA. These regions have similar sequences but their organization is modified due to different recombination events involving the tRNAPro immediate environment.
Collapse
Affiliation(s)
- A Sangaré
- Institut de Biologie Moléculaire des Plantes du CNRS, Université Louis Pasteur, Strasbourg, France
| | | | | |
Collapse
|
8
|
Balestrieri C, Giovane A, Quagliuolo L, Servillo L. Fluorescent labeling of tRNA by 5-[2-(2-iodoacetamido) ethylamino]-1-naphthalenesulfonate (IAEDANS). Ital J Biochem 1990; 39:177A-178A. [PMID: 2202701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- C Balestrieri
- Dipartimento di Biochimica e Biofisica, Università, Napoli
| | | | | | | |
Collapse
|
9
|
Ciesiołka J, Wrzesinski J, Górnicki P, Podkowiński J, Krzyzosiak WJ. Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal-ion-induced cleavages. Eur J Biochem 1989; 186:71-7. [PMID: 2689176 DOI: 10.1111/j.1432-1033.1989.tb15179.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The specificity of cleavages in yeast and lupin initiator and elongator methionine tRNAs induced by magnesium, europium and lead has been analysed and compared with known patterns of yeast tRNA(Phe) hydrolysis. The strong D-loop cleavages occur in methionine elongator tRNAs at similar positions and with comparable efficiency to those found in tRNA(Phe), while the sites of weak anticodon loop cuts, identical in methionine elongator tRNAs, differ from those found in tRNA(Phe). Methionine initiator tRNAs differ from their elongator counterparts: (a) they are cleaved in the D-loop with much lower efficiency; (b) they are cleaved in the variable loop which is completely resistant to hydrolysis in elongator tRNAs; (c) cleavages in the anticodon loop are stronger in initiator tRNAs and they are located mostly at the 5' side of the loop whereas in elongator tRNAs they occur mostly at the opposite, 3' side of the loop. The distinct pattern of the anticodon loop cleavages is considered to be related to different conformations of the anticodon loop in the two types of methionine tRNAs.
Collapse
MESH Headings
- Base Sequence
- Binding Sites
- Europium/metabolism
- Hydrolysis
- Lead/metabolism
- Magnesium/metabolism
- Nucleic Acid Conformation
- Peptide Elongation Factors/metabolism
- Peptide Initiation Factors/metabolism
- Plants
- RNA, Transfer, Amino Acid-Specific/analysis
- RNA, Transfer, Met/analysis
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/analysis
- RNA, Transfer, Phe/metabolism
- Saccharomyces cerevisiae
Collapse
Affiliation(s)
- J Ciesiołka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań
| | | | | | | | | |
Collapse
|
10
|
Thomann HU, Schmutzler C, Hüdepohl U, Blow M, Gross HJ. Genes, variant genes and pseudogenes of the human tRNA(Val) gene family. Expression and pre-tRNA maturation in vitro. J Mol Biol 1989; 209:505-23. [PMID: 2585499 DOI: 10.1016/0022-2836(89)90590-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nine different members of the human tRNA(Val) gene family have been cloned and characterized. Only four of the genes code for one of the known tRNA(Val) isoacceptors. The remaining five genes carry mutations, which in two cases even affect the normal three-dimensional tRNA structure. Each of the genes is transcribed by polymerase III in a HeLa cell nuclear extract, but their transcription efficiencies differ by up to an order of magnitude. Conserved sequences immediately flanking the structural genes that could serve as extragenic control elements were not detected. However, short sequences in the 5' flanking region of two genes show striking similarity with sequences upstream from two Drosophila melanogaster tRNA(Val) genes. Each of the human tRNA(Val) genes has multiple, i.e. two to four, transcription initiation sites. In most cases, transcription termination is caused by oligo(T) sequences downstream from the structural genes. However, the signal sequences ATCTT and CTTCTT also serve as effective polymerase III transcription terminators. The precursors derived from the four tRNA(Val) genes coding for known isoacceptors and those derived from two mutant genes are processed first at their 3' and subsequently at their 5' ends to yield mature tRNAs. The precursor derived from a third mutant gene is incompletely maturated at its 3' end, presumably as a consequence of base-pairing between 5' and 3' flanking sequences. Finally, precursors encoded by the genes that carry mutations affecting the tRNA tertiary structure are completely resistant to 5' and 3' processing.
Collapse
Affiliation(s)
- H U Thomann
- Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Würzburg, Federal Republic of Germany
| | | | | | | | | |
Collapse
|
11
|
Ciesiołka J, Marciniec T, Krzyzosiak W. Probing the environment of lanthanide binding sites in yeast tRNA(Phe) by specific metal-ion-promoted cleavages. Eur J Biochem 1989; 182:445-50. [PMID: 2661230 DOI: 10.1111/j.1432-1033.1989.tb14851.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Specific yeast tRNA(Phe) hydrolysis brought about by europium ions has been studied in detail using the 32P-end-labeled tRNA and polyacrylamide gel electrophoresis. The dependence of the induced cleavages on pH, temperature and concentration of the europium ions has been determined. Europium hydrolyzes yeast tRNA(Phe) in the D-loop at phosphates 16 and 18, and the anticodon loop of phosphates 34 and 36. The two D-loop cuts are thought to take place from two distinct europium binding sites, while the two anticodon loop cleavages from a single site. Eight other members of the lanthanide series and ytrium give basically the same pattern of cleavages as europium. The specific cleavages taking place in the anticodon loop occur in an intramolecular mode from the lanthanide binding site that has not been found in yeast tRNA(Phe) crystal structure. It appears from the comparison of the europium-promoted cuts with those generated by magnesium and lead that the former two ions give more similar but not identical cleavage patterns. The usefulness of the specific cleavages induced by lanthanides for probing their own and magnesium binding sites in tRNA is discussed.
Collapse
Affiliation(s)
- J Ciesiołka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań
| | | | | |
Collapse
|
12
|
Kalachniuk LG, Tukalo MA, Matsuka GK. [Primary structure of tRNA1ser from bovine liver]. Ukr Biokhim Zh (1978) 1989; 61:72-5. [PMID: 2741244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The primary structure of tRNA(1Ser) from the bovine liver has been studied. pG- A-C-G-A-G-G-U-G-G-C-ac4C-G-A-G-D-Gm-G-D-D-A-A-G-G- C-m2(2)-G-A-psi-G-G-A-m3C-U-G-C-U-A*-A-psi-C-C-A-U-Um-G-psi- G-C-U-m3C-U-G-C-A-C-G-m5C-G-U-G-G-G-T-psi-C-G-m1A-A- U-C-C-C-A-U-C-C-U-C-G-U-C-G-C-C-AOH. A comparison of the nucleotide sequence of tRNA(1Ser) from the bovine liver with already known sequences of serine tRNA revealed a number of common nucleotides, some of them, probably, participated in specific interaction with seryl-tRNA synthetase.
Collapse
|
13
|
Theobald A, Springer M, Grunberg-Manago M, Ebel JP, Giege R. Tertiary structure of Escherichia coli tRNA(3Thr) in solution and interaction of this tRNA with the cognate threonyl-tRNA synthetase. Eur J Biochem 1988; 175:511-24. [PMID: 2457500 DOI: 10.1111/j.1432-1033.1988.tb14223.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The solution structure of Escherichia coli tRNA(3Thr) (anticodon GGU) and the residues of this tRNA in contact with the alpha 2 dimeric threonyl-tRNA synthetase were studied by chemical and enzymatic footprinting experiments. Alkylation of phosphodiester bonds by ethylnitrosourea and of N-7 positions in guanosines and N-3 positions in cytidines by dimethyl sulphate as well as carbethoxylation of N-7 positions in adenosines by diethyl pyrocarbonate were conducted on different conformers of tRNA(3Thr). The enzymatic structural probes were nuclease S1 and the cobra venom ribonuclease. Results will be compared to those of three other tRNAs, tRNA(Asp), tRNA(Phe) and tRNA(Trp), already mapped with these probes. The reactivity of phosphates towards ethylnitrosourea of the unfolded tRNA was compared to that of the native molecule. The alkylation pattern of tRNA(3Thr) shows some similarities to that of yeast tRNA(Phe) and mammalian tRNA(Trp), especially in the D-arm (positions 19 and 24) and with tRNA(Trp), at position 50, the junction between the variable region and the T-stem. In the T-loop, tRNA(3Thr), similarly to the three other tRNAs, shows protections against alkylation at phosphates 59 and 60. However, tRNA(3Thr) is unique as far as very strong protections are also found for phosphates 55 to 58 in the T-loop. Compared with yeast tRNA(Asp), the main differences in reactivity concern phosphates 19, 24 and 50. Mapping of bases with dimethyl sulphate and diethyl pyrocarbonate reveal conformational similarities with yeast tRNA(Phe). A striking conformational feature of tRNA(3Thr) is found in the 3'-side of its anticodon stem, where G40, surrounded by two G residues, is alkylated under native conditions, in contrast to other G residues in stem regions of tRNAs which are unreactive when sandwiched between two purines. This data is indicative of a perturbed helical conformation in the anticodon stem at the level of the 30-40 base pairs. Footprinting experiments, with chemical and enzymatic probes, on the tRNA complexed with its cognate threonyl-tRNA synthetase indicate significant protections in the anticodon stem and loop region, in the extra-loop, and in the amino acid accepting region. The involvement of the anticodon of tRNA(3Thr) in the recognition process with threonyl-tRNA synthetase was demonstrated by nuclease S1 mapping and by the protection of G34 and G35 against alkylation by dimethyl sulphate. These data are discussed in the light of the tRNA/synthetase recognition problem and of the structural and functional properties of the tRNA-like structure present in the operator region of the thrS mRNA.
Collapse
Affiliation(s)
- A Theobald
- Institut de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Strasbourg, France
| | | | | | | | | |
Collapse
|
14
|
Abstract
In contrast to the widespread ability of bacteria, plants, and animals to incorporate selenium nonspecifically into proteins in the form of selenomethionine residues, the selenoamino acid selenocysteine occurs as a highly specific component of a few selenium-dependent enzymes. Selenocysteine has been identified in glycine reductase, formate dehydrogenase, and hydrogenase of bacterial origin and glutathione peroxidase from mammalian and avian sources. In these enzymes there is evidence that the selenol group, which is largely ionized at physiological pH, functions as a redox center. It now seems clear, from studies with both prokaryotes and eukaryotes, that the UGA opal stop codon is used to specify the cotranslational insertion of selenocysteine into proteins. The factors that allow this unusual use of the stop codon are, however, unknown. The occurrence of selenium as a normal constituent of several bacterial tRNA species has been established. The presence of a selenonucleoside, 5-methylaminomethyl-2-selenouridine, in the first or wobble position of the anticodons of certain glutamate and lysine iso-acceptor species influences codon-anticodon interaction and thus may serve to regulate translational processes. The biosynthesis of the selenonucleoside appears to involve the ATP-dependent activation of the sulfur in a preformed 5-methylaminomethyl-2-thiouridine residue in tRNA and replacement of the sulfur with selenium.
Collapse
Affiliation(s)
- T C Stadtman
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892
| |
Collapse
|