In vitro transcription of a transfer RNA gene

In vitro transcription of E. coli tRNA genes

Transcription of tRNA genes carried by transducing bacteriophages phi80psu3+ (tRNA1Tyr) and lambdah80T (tRNA2Tyr, tRNA2Glysu36+, tRNA3Thr) was studied in vitro in a system consisting of whole bacteriophage DNA and purified RNA polymerase. In contrast to unusual requirements for tRNA1Tyr gene transcription from DNA fragments, the transcription on whole bacteriophage DNA was found to be relatively not salt sensitive, did not require glycerol and rifampicin-resistant complexes with RNA polymerase were formed in the absence of nucleoside triphosphates. Termination factor rho stimulated the transcription of the tRNA genes as well as that of 4S RNA on lambdah80T DNA template. The stimulatory effect of rho was abolished by rifampicin and seems to be due to the release of RNA polymerase and reinitiation of transcription.

In vitro synthesis of tRNA precursors and their conversion to mature size tRNA

Two Escherichia coli tRNA gene clusters, tRNA1Tyr (su3+ and su3-) and tRNA2Tyr, tRNA2Gly (su+36), tRNA3Thr, were transcribed in a purified in vitro system. Evidence indicates that the adjacent tRNA genes are transcribed together as a common precursor of large size, which, on incubation with crude cell extracts, yields mature tRNA molecules.

Biosynthesis of transfer RNA: in vitro conversion of transfer RNA precursors from Bombyx mori to 4S RNA by Escherichia coli enzymes

Evidence for the presence of rapidly labeled short-lived RNA species, presumed to be precursors to transfer RNA (tRNA), in the silk glands of Bombyx mori is presented. These precursors, which migrate between 4S and 5S markers on acrylamide gels, can be converted in vitro into molecules indistinguishable in size from tRNA. The conversion is also catalyzed by a crude enzyme fraction isolated from ribosomes of E. coli. Since a similar enzyme preparation cleaves the suppressor tRNA(Tyr) sequence of E. coli from its precursor molecule, it would appear that the precursor to E. coli tRNA(Tyr) and the precursors to silk-gland tRNAs share common structural features.

Mutants of Escherichia coli thermosensitive for the synthesis of transfer RNA

Using a simple three-step procedure, we have isolated thermosensitive mutants of E. coli that are specifically defective in transfer RNA (tRNA) synthesis. Our procedure was designed to identify mutants that are unable to make su(3) (+) tRNA(Tyr) or grow at the restrictive temperature, yet under the same conditions they retain the ability to make mRNA and protein. The mutants obtained have been analyzed, and they are defective in different steps in the synthesis of functional tRNA at the restrictive temperature. Some of them may fail to modify certain bases in the tRNA. Two mutants are unable to process the 5' end of tRNA precursor molecules. Three are unable to cleave precursor molecules at the 3' end. 11 Mutants can not synthesize any tRNA molecules or tRNA precursors. We speculate that these latter mutants may be defective in RNA polymerase or in an RNA polymerase factor specific for stable RNA synthesis.

Transfer RNA synthesis in vitro

During infection of Escherichia coli, bacteriophage T4 directs the synthesis of at least eight transfer RNAs and of two stable RNA species of low molecular weight, of unknown function. When T4 DNA is incubated with purified RNA polymerase and the appropriate substrates, a high molecular weight RNA is produced. This RNA, on further incubation with a supernatant fraction prepared from E. coli, is cleaved to several species of RNA. These cleaved RNAs were analyzed by gel electrophoresis and fingerprint techniques, and were found to be similar or identical to those made in vivo. The fingerprint analysis of one of these, a tRNA(Gly), is presented. The molecule made in vitro, except for the absence of modified bases, appears to be identical to the RNA made by T4-infected cells. Therefore, in this system the tRNA genes are transcribed with fidelity, the transcript is cleaved correctly, and the tRNAs are made in good yield.

Close linkage between ochre and missense suppressors in Escherichia coli

It was previously shown that the ochre suppressor mutation sup15B in Escherichia coli determines the accumulation of altered 30S ribosomal subunits and the presence of altered transfer ribonucleic acid (tRNA) capable of suppressing in vitro the UAG codon. This mutation has been mapped in the present study by means of conjugation and transduction experiments. After establishing the location of sup15B near argH, the following order was determined for the markers tested: metB-argH-(sup15B, supA36)-rif-thi. A comparison of location, growth rate, and suppressor pattern determined by sup15B and supM indicates the high probability that both suppressor mutations are identical. This study has also yielded a more precise location for the rifampin resistance gene. The most interesting finding is the very close (if not adjacent) location of the suppressor mutations sup15B and supA36, both of which determine tRNA alterations.

DNA-directed cell-free synthesis of biologically active transfer RNA: su + 3 tyrosyl-tRNA

Biologically active su(+) (III) tyrosyl-tRNA has been synthesized in a DNA-directed cell-free system from Escerichia coli. Such a system should be most useful for studying the mechanism of tRNA synthesis. This tRNA is capable of suppressing amber mutations in the gene coding for beta-galactosidase (EC 3.2.1.23) and, therefore, must be capable of being charged and transferring amino acids. A 4-fold stimulation in the activity of the tRNA formed de novo is obtained with isopentenyl pyrophosphate, a compound involved in the post-transcriptional acylation of an adenine base adjacent to the anticodon. It has been suggested elsewhere that formation of RNA subject to stringent control may be inhibited by guanosine tetraphosphate (ppGpp). However, guanosine tetraphosphate did not affect the synthesis of su(+)III tyrosyl-tRNA, even though the synthesis of this tRNA is subject to stringent control.

Purification and in vitro transcription of a transfer RNA gene

A gene specifying tyrosine transfer RNA has been purified and transcribed in vitro. The purification procedure made use of two specialized transducing phages carrying the tRNA(Tyr) gene of Escherichia coli inserted into their DNA in opposite orientations. The separated heavy strands of the two phages were annealed and the single-stranded tails of the resulting hybrid were removed by digestion with Neurospora endonuclease. The size of the purified double-stranded structures was determined by electron microscopy. These isolated duplexes served as template for the in vitro transcription of tRNA(Tyr)-like molecules.

Enzymatic modification of transfer RNA

The molecular events leading to the synthesis of mature tRNA are only now becoming amenable to experimental study. In bacterial and mammalian cells tRNA genes are transcribed into precursor tRNA. These molecules, when isolated, contain additional nucleotides at both ends (20) of the mature tRNA and lack most modified nucleosides. Presumably, specific nucleases ("trimming" enzymes) cut the precursor to proper tRNA size. The C-C-A nucleotide sequence of the amino acid acceptor end common to all tRNA's does not seem to be coded by tRNA genes (30), and may be added to the trimmed molecules by the tRNA-CMP-AMP-pyrophosphorylase (71). Modifications at the polynucleotide level of the heterocyclic bases or the sugar residues give rise to the modified nucleosides in tRNA. Although newly available substrates have allowed the detection of more of the enzymes involved in these reactions, there is still no knowledge about the sequence of modification or trimming events leading to the synthesis of active tRNA. Progress in these studies may not be easy because enzyme preparations free of nucleases or other tRNA modifying enzymes are required. The role of the modified nucleosides in the biological functions of tRNA is still unknown. Possibly pseudouridine is required for ribosome mediated protein synthesis; some other modified nucleosides in tRNA are not required for this reaction, but may enhance its rate. What might be the role of the large variety of modified nucleosides in tRNA? One is tempted to speculate that such nucleosides are important in other cellular processes in which tRNA is thought to participate such as virus infection, cell differentiation, and hormone action (2, 3). Mutants in a number of tRNA-modifying enzymes are needed in order to extend our knowledge of their purpose and of tRNA involvement in other biological processes. But unless tRNA-modifying enzymes specific for a particular tRNA species exist, no simple selection procedure can be devised. Possibly some of the regulatory mutants of amino acid biosynthesis may prove to affect tRNA-modifying enzymes (72). Transfer RNA's are macromolecules well suited for the study of nucleic acid-protein interactions. The tRNA molecules are structurally very similar, and they interact with a large number of enzymes or protein factors (2, 3). Each aminoacyl-tRNA synthetase, for instance, very precisely recognizes a set of cognate isoacceptor tRNA's (2, 73). The availability of the tRNA- modifying enzymes adds another dimension to the problem of the nature of specific recognition of tRNA by proteins. There are some tRNA-modifying enzymes, such as the uracil-tRNA methylase, which may recognize all tRNA species, while others, such as the isopentenyl-tRNA transferase, probably recognize only a selected set of tRNA molecules, even with different amino acid accepting capacities. With well-characterized RNA precursor and tRNA molecules we can hope to delineate those features of primary, secondary, and tertiary structure involved in the specific interactions of tRNA with these enzymes.