TRNA precursors structure

Figure 28-10 Sequence of an E. coli tyrosine tRNA precursor drawn in a hypothetical secondary structure. Nucleotides found modified in the mature tRNA are indicated with their modifications (S4, 4-thiouridine Gm, 2 -0-methylgua-nosine 1°, N6-isopentenyladenosine jt, pseudouridine T, ribothymidine see also Fig. 5-33).241 A partial sequence of the tRNA gene past the CCA end is also shown. Note the region of local 2-fold rotational symmetry (indicated by the bars and the dot). The anticodon 3 -CUA (shaded) of this suppressor tRNA pairs with termination codon 5 -UAG.

Figure 28-20 Composite structure representing several tRNA precursors arranged in a similar secondary structure (see also Fig. 5-30). The arrows indicate splice points. Variable positions are designated (O) for the mature tRNA and (X) for the intervening sequence and also in loops where insertions or deletions occur. From Ogden et al.603...

Pre-tRNAs. In the removal of type I introns the formation of specific stem and loop structures directs the splicing reactions (Fig. 28-18).47 597 Stems and loop structures already exist in tRNA precursors. Cleavage sites are usually located just to the 3 side of the anti-... 

RNase P cleaves a specific phosphodiester bond of tRNA precursors to form the mature 5 -end of tRNA. Bacterial RNase P is a natural occurring ribozyme composed of a catalytic RNA subunit and one or more proteins. Each bacterial RNAse P holoenzyme also consists of a small basic protein that stabilizes the folded structure of the RNA under physiological conditions. It may also help to discriminate pre-tRNA substrate from tRNA product and to mediate RNAse P dimerization. The three domains of life bacteria, Archaea, and Eukarya have similar structurally related RNAse P RNAs but different protein subunits this indicates that RNAse P is very ancient... 

We cannot implicate the genes for DNA-dependent RNA polymerase (types I, II and III), for ribosomal proteins, for enzymes that process rRNA and tRNA precursors, or for enzymes that activate amino acids. All of these genes encode products that are utilized for all protein synthesis. A significant defect in any of these genes would lead to a general failure of protein synthesis (see Fig. 5). Again, we are compelled to conclude that defects in protein synthesis result from a defect in the structural gene or its controls for the specific protein that contains the abnormality. 

Enzymatic Synthesis.—The total synthesis by chemical and enzymatic methods of the structural gene for the precursor of a tyrosine suppressor tRNA from E. coli, a DNA duplex that is 126 nucleotides long, has been described. This, Khorana s Meisterwerk to date, represents the highest state of the art, and proceeds by methods which are already famous, and the touchstone of those who wish to follow.135... 

About 20 species of amino acids are incorporated into polypeptides. The aaRSs that catalyze the formation of the corresponding aa-tRNAs are derived from two precursors that have no evolutionary linkage, as evidenced mostly by the fact that their structures have completely different topologies. and by phylogenetic analyses of the sequences of their amino acid residues. " This classification is also consistent with the differences observed in the interactions of these enzymes with modified substrates and in their reactions with reactive groups mounted on substrate analogues. ... 

The structure of the precursor to the minor E. coli tyrosine tRNA, is shown in Fig. 28-10. This is encoded by the amber suppressor gene SupF (see Chapter 29). Transcription of its gene is initiated by GTP 43 bp upstream of the 5 end of the mature tRNA and usually terminates at a p-dependent signal 225 bp beyond the CCA terminus of the tRNA. An endonuclease cuts the transcript a few nucleotides beyond the CCA end. It is then trimmed to an 130-nucleotide piece still containing 2-3 extra nucleotides at the 3 end. This intermediate is cut by RNase P at the 5 end after which final trimming is done at the 3 end (Fig. 28-10).226 227... 

The processing steps of E. coli tyrosine tRNATyr are diagrammed in figure 28.15. The initial transcript has, in addition to the 85 nucleotide residues of the final product, 41 residues at the 5 end and 225 residues at the 3 end it probably folds to form the typical cloverleaf structure of the mature tRNA prior to processing. Processing begins when a specific endonuclease called RNaseF cleaves the precursor... 

The ultimate precursor of all the carbon atoms in cholesterol and in the other steroids that are derived from cholesterol is the acetyl group of acetyl-GoA. There are many steps in the biosynthesis of steroids. The condensation of three acetyl groups produces mevalonate, which contains six carbons. Decarboxylation of mevalonate produces the five-carbon isoprene unit frequently encountered in the structure of lipids. The involvement of isoprene imits is a key point in the biosynthesis of steroids and of many other compounds that have the generic name terpenes. Vitamins A, E, and K come from reactions involving terpenes that humans cannot carry out. That is why we must consume these vitamins in our diets vitamin D, the remaining lipid-soluble vitamin, is derived from cholesterol (Section 8.8). Isoprene units are involved in the biosynthesis of ubiquinone (coenzyme Q) and of derivatives of proteins and tRNA with specific five-carbon units attached. Isoprene units are often added to proteins to act as anchors when the protein is attached to a membrane. 

The tRNA genes (30-33) identified in cpDNA code for functional tRNAs, which form the typical clovcrlcaf structure. It is of particular imerest that tRNA (UUQ not only participates in protein synthesis, but also acts as a cofactor for the formation of 5-aminolevulinic acid, which is a common precursor in heme and chlorophyll biosynthesis. cpDNA-encoded tRNAs suffice for translation of 61 codons if normal wobble base pairing occurs in codon-anticodon recognition. Although this hypothesis is experimentally supported, transport of the nuclear-encoded tRNA into the chloroplasts cannot be excluded. Thus, the Epifagus plastid DNA contains only 17 tRNA genes, which is indirect evidence for the transport of nuclear-encoded tRNAs involved in translation. ... 

Unlike prokaryotic cells, eukaryotes contain three DNA-dependent RNA polymerase activities. Polymerase I (or A) catalyses the synthesis of ribosomal RNA precursors. Polymerase II (or B) transcribes the structural genes for proteins and polymerase III (or C) transcribes the genes for tRNA and 5S RNA. Consequendy, it is expected that the activity of these enzymes will be controlled in different ways and modem techniques of genetic manipulation have enabled considerable strides in the study of putative control regions for each of them. It cannot be said, however, that a clear consensus has yet emerged for the binding to the DNA of any of the three enzymes. 

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