Lysine transfer RNA from liver: a sulfur-containing species that codes for AAG

Novel methyltransferase for modified uridine residues at the wobble position of tRNA

We have identified a novel tRNA methyltransferase in Saccharomyces cerevisiae that we designate Trm9. This enzyme, the product of the YML014w gene, catalyzes the esterification of modified uridine nucleotides, resulting in the formation of 5-methylcarbonylmethyluridine in tRNA(Arg3) and 5-methylcarbonylmethyl-2-thiouridine in tRNA(Glu). In intact yeast cells, disruption of the TRM9 gene results in the complete loss of these modified wobble bases and increased sensitivity at 37 degrees C to paromomycin, a translational inhibitor. These results suggest a role for this potentially reversible methyl esterification reaction when cells are under stress.

The effects of growth factors on tRNALys modification

The tRNALys population from tissue culture cells contains several isoaccepting species which are not present in the tRNALys population from tissue sources. These isoacceptors were isolated from mouse LM cells and tested for their coding properties in ribosomal binding assays and their ability to incorporate lysine into protein in a reticulocyte lysate. tRNALys5A and tRNALys6 eluted in the area of tRNALys5. All three species coded preferentially for AAA and bound with equal efficiency. tRNALys1, tRNALys3, tRNALys4, and tRNALys6 all transferred lysine into protein at a slower rate than tRNALys2 and tRNALys5, which are the native species. Several purified growth factors were tested for their ability to affect the levels of tRNALys4, a tRNA possibly associated with cell division. When Balb/c 3T3 cells were grown in medium containing plasma instead of serum, there was a decrease in tRNALys2, tRNALys3, tRNALys4 and an increase in tRNALys5 and tRNALys6. The addition of either FGF or PDGF returned the tRNALys profile to normal. The extent of the tRNALys changes depended upon the concentration of growth factor added. FGF was able to cause a 35% decrease in the tRNALys5 peak with a corresponding increase in tRNALys2 within 1 h of the addition of the factor. These data suggest that competence factors have the ability to stimulate the modification of specific tRNALys isoacceptors.

Perturbation of the mitochondrial lysine tRNA population by virus-induced transformation or stress of mammalian cells: functional properties and nucleotide sequence of a mitochondrially associated lysine tRNA

Eleven isoaccepting lysine tRNAs from mammalian sources are demonstrable by RPC-5 chromatography and polyacrylamide gel electrophoresis. The appearance and amounts of these isoacceptors varies with the source and growth state of cells. One isoacceptor, tRNALys6, observed in preparations of tRNA from some virus-transformed cells in culture, has been characterized by determining functional properties, cellular location, and its nucleotide sequence. tRNALys6 responds primarily to the lysine codon AAA, but it is not used efficiently in a wheat germ translational system in vitro. Compared with lysine isoacceptors 1, 2, 4, 5a, and 5, [3H]lysine appears in vivo in tRNALys6 with a delay of about 3 h. This delay may in part be a result of a less functional tRNA, but a compartmented state of tRNALys6 also appears to be important. tRNALys6 is associated with mitoplasts prepared from KA31 fibroblasts. The nucleotide sequence of tRNALys6 was determined by rapid postlabeling procedures involving limited hydrolysis in formamide, 32P-labeling of 5' ends of fragments with polynucleotide kinase, separation of the nested set of fragments in polyacrylamide denaturing gels, release of 5'-labeled nucleotides with RNase T2, and identification of the released nucleotides by chromatography on PEI cellulose. Confirmation of the positions of major nucleotides was done by using limited digestions by RNases of tRNALys6 labeled with 32P on the 3' terminus in a gel readout procedure. The nucleotide sequence of tRNALys6 differs from that of cytoplasmic lysine tRNAs and mammalian mitochondrial lysine tRNAs. It contains U*, an unidentified modified uridine occurring in the anticodon of some mitochondrial tRNAs. tRNALys6 appears to occur in very limited amounts, or not at all, in most cells unless stressed, but when present it is associated with mitochondria, although it is probably coded in the nucleus.

Codon binding and translational properties of an isoaccepting lysine tRNA peculiar to virus-transformed Cells

Isoaccepting lysyl-tRNAs from virus-transformed cells in culture were fractionated in the RPC-5 system into peaks 1, 2, 4, 5a, 5, and 6. tRNALys6 previously was found predominantly associated with transformed cells. The codon response of each peak was determined in an E. coli ribosomal binding assay. tRNALys1, tRNALys2, and tRNALys4 are highly specific for the 5'AAG3' codon. tRNALys5 and tRNALys5a preferentially bind in response to AAA. tRNALys6 binds in response to AAA 3-fold better than in response to AAG. The presence of thiolated nucleosides in the anticodon regions of tRNALys5a, tRNALys5, and tRNALys6 is indicated by I2-inactivation of aminoacylation ability with no effect on the other is isoacceptors. Functional abilities of the isoacceptors were compared in a wheat germ translational system with tobacco mosaic virus RNA as messenger. All of the isoacceptors function about equally well in translation except for tRNALys6, which is only 14 to 24% as effective as the other isoacceptors.

Selenium-containing tRNAs from Clostridium sticklandii: cochromatography of one species with L-prolyl-tRNA

75Se-Labeled tRNAs were synthesized by Clostridium sticklandii cultures supplemented with 1 microM sodium [75Se]selenite or [75Se]selenocysteine. This process is highly specific for selenium; it occurred in the presence of 1.2 mM sodium sulfide and was not decreased by the further addition of a 500-fold molar excess of cysteine. The 75Se in these tRNAs was located in the polynucleotide portion of the molecules and not in esterified (alkali-labile) selenocysteine. Inhibition of cell multiplication by antibiotics that block either protein synthesis or DNA-dependent RNA synthesis did not prevent this 75Se incorporation. Three [75Se]tRNAs were separated from C. sticklandii cells labeled in the presence of chloramphenicol and were partially purified by chromatography on benzoylated DEAE-cellulose and DEAE-Sephadex A-50 columns. These were designated seleno-tRNAs I, II, and III according to their elution sequence from benzoylated DEAE-cellulose. Cochromatography of purified seleno-tRNA II on DEAE-Sephadex A-50 with an L-proline-accepting species suggests that it is a selenium-containing L-prolyl-tRNA.

Aminoacylation of undermethylated mammalian transfer RNA

To study the role of 5-methylcytidine in the aminoacylation of mammalian tRNA, bulk tRNA specifically deficient in 5-methylcytidine was isolated from the livers of mice treated with 5-azacytidine (18 mg/kg) for 4 days. For comparison, more extensively altered tRNA was isolated from the livers of mice treated with DL-ethionine (100 mg/kg) plus adenine (48 mg/kg) for 3 days. The amino acid acceptor capacity of these tRNAs was determined by measuring the incorporation of one of eight different 14C-labeled amino acids or a mixture of 14C-labeled amino acids in homologous assays using a crude synthetase preparation isolated from untreated mice. The 5-methylcytidine-deficient tRNA incorporated each amino acid to the same extent as fully methylated tRNA. The tRNA from DL-ethionine-treated livers showed an overall decreased amino-acylation capacity for all amino acids tested. The 5-methylcytidine-deficient tRNA from DL-ethionine-treated mice were further characterized as substrates in homologous rate assays designed to determine the Km and V of the aminoacylation reaction using four individual 14C-labeled amino acids and a mixture of 14C-labeled amino acids. The Km and V of the reactions for all amino acids tested using 5-methylcytidine-deficient tRNA as substrate were essentially the same as for fully methylated tRNA. However, the Km and V were increased when liver tRNA from mice treated with DL-ethionine plus adenine was used as substrate in the rate reaction with [14C]lysine as label. Our results suggest that although extensively altered tRNA is a poorer substrate than control tRNA in both extent and rate of aminoacylation, 5-methylcytidine in mammalian tRNA is not involved in the recognition of the tRNA by the synthetase as measured by aminoacylation activity.