Biosynthesis of transfer RNA

Processing of tRNA in prokaryotes and eukaryotes

Considerable progress has been made in defining the steps in the conversion of a tRNA precursor to a mature tRNA. These steps, which differ in different systems, include removal of precursor-specific residues from the 5' and 3' termini of the initial transcript, addition of the 3'-C-C-A terminus, splicing of intervening sequences, and modification of nucleotide residues. Despite these advances in defining the "pathways" of tRNA processing, relatively little is known about most of the enzymes actually involved in these processing steps. In this article I describe the sequence of reactions needed to convert the initial tRNA transcript to a functional, mature tRNA, and discuss the specificity and properties of enzymes known to be involved in this process. In addition, I speculate on the expected specificities of other enzymes involved in tRNA processing which have not yet been identified, and on the structural organization of the processing machinery.

Temperature-inducible amber suppressor: construction of plasmids containing the Escherichia coli serU- (supD-) gene under control of the bacteriophage lambda pL promoter

An Escherichia coli DNA fragment containing the structural gene serU132 for the nonsense suppressor tRNASer2am was identified and purified by being cloned into a plasmid vector. Information obtained from DNA sequence analysis was used to select a serU132 fragment for insertion downstream from the bacteriophage lambda pL promoter in two pBR322-lambda derivatives. In nonsense mutant strains bearing the resulting serU132 hybrid plasmids, the presence of the lambda cI857 repressor gene carried on the same plasmid or in a prophage genome permits thermal regulation of suppressor synthesis.

Molecular cloning and sequencing of pheU, a gene for Escherichia coli tRNAPhe

A recombinant plasmid (designated pID2) carrying the E. coli gene for tRNAPhe has been isolated from a plasmid bank constructed by the ligation of a total EcoRI digest of E. coli K12 DNA into the EcoRI site of pACYC184 DNA. The plasmid was selected by virtue of its ability to complement a temperature-sensitive lesion in the gene (PheS) for the alpha-subunit of phenylalanyl-tRNA synthetase. Crude tRNA isolated from such transformants exhibited elevated levels of phenylalanine acceptor activity. The tRNAPhe gene has been localized within the first 300 base pairs of a 3.6 kb SalI fragment of pID2. The sequence of the gene and its flanking regions is presented.

A G43 to U43 mutation in E. coli tRNAtyrsu3+ which affects processing by RNase P

A novel mutation in the anticodon stem of E. coli tRNA1Tyrsu3+ (G43 to U43) has been characterized. The gene coding for the mutant tRNA, carried by phage phi 80DHA61.3 a derivative of phi 80psu3+su0, produces only 20% of mature suppressor tRNA as compared with phi 80psu3+. Both the mutant tRNA precursor and mature tRNA have an altered conformation. The precursor tRNA coded for by phi 80DHA61.3 is processed by RNase P more slowly than the su3+ precursor and does not form as stable an enzyme-substrate complex as does su3+ precursor. phi 80 DHA61.3 also contains a large deletion which begins in the spacer region between the su3+ gene and the su0- gene, extends through the su0- gene and includes most of the repeated region following the tRNA genes.

Subcellular localization of the tRNA processing enzyme, tRNA nucleotidyltransferase, in Xenopus laevis oocytes and in somatic cells

Earlier studies of the tRNA processing enzyme, tRNA nucleotidyltransferase, in rat liver cells suggested that the enzyme was absent from nuclei, whereas more recent studies with tRNA transcription-processing systems from Xenopus laevis oocytes indicated that the enzyme was present in germinal vesicles of these cells. In order to resolve this apparent discrepancy, the subcellular localization of tRNA nucleotidyltransferase in oocytes was directly determined, and its distribution in somatic cells was re-examined. Oocyte germinal vesicles, isolated manually, contained about 25% of the total tRNA nucleotidyltransferase activity of the cell, but the enzyme rapidly leaked out of these nuclei during storage. In contrast, purified nuclei isolated from rat or Xenopus liver using a variety of aqueous procedures were devoid of tRNA nucleotidyltransferase activity. Since rapidly-isolated, crude nuclear preparations from liver contained substantially more of the enzyme than could be accounted for by cytoplasmic contamination, it appears that the enzyme leaks out of the somatic cell nuclei during the lengthy times required for their purification. The implications of these results for the development of tRNA processing systems from somatic cell nuclei are discussed.

Processing of procaryotic ribonucleic acid

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The tyrT locus: termination and processing of a complex transcript

The tyrT locus of E. coli contains a 208 bp spacer region that separates two copies of sequence encoding tRNATyr1. The spacer includes a 120 bp sequence that is homologous to a sequence that is repeated three times in the distal portion of the tyrT locus. The tyrT locus possesses a graded set of transcription termination sites that are spaced at 180 base intervals, corresponding to the distal repeated gene structure. The major termination site occurs within the second repeat unit, 225 bases beyond the mature tRNA sequences. In the presence of a temperature-sensitive rho protein there is increased read-through at this site to a termination site located 180 bases downstream in the third repeat and to several termination sites even further downstream. The primary native transcript, in the region distal to the second tRNA, carries the information for a low molecular weight, extremely basic protein. Although analogous coding sequences are present in the spacer and other repeat units, because of single base substitutions these sequences are pseudogenes. The parallel between the tyrT and TyrU gene clusters is discussed in relation to dual function transcripts that specify both tRNA and protein.