ABSTRACT
The choice of an appropriate structure coding scheme is the secret to success in QSAR studies. Depending on the problem at hand, 2D or 3D descriptors have to be chosen; the consideration of electronic effects might be crucial, conformational flexibility has to be of special concern. Artificial neural networks, both with unsupervised and with supervised learning schemes, are powerful tools for establishing relationships between structure and physical, chemical, or biological properties. The EROS system for the simulation of chemical reactions is briefly presented and its application to the degradation of s-triazine herbicides is shown. It is further shown how the simulation of chemical reactions can be combined with the simulation of infrared spectra for the efficient identification of the structure of degradation products.
Subject(s)
Decision Support Techniques , Models, Chemical , Forecasting , Herbicides/adverse effects , Herbicides/pharmacology , Infrared Rays , Molecular Conformation , Structure-Activity Relationship , TriazinesABSTRACT
In the fission yeast Schizosaccharomyces pombe, the enzyme RNAse P copurifies with two RNAs, K1- and K2-RNA, which are identical except for their termini [1] and which are encoded by a single gene [2]. We have undertaken the cloning of the K-RNA genes in related organisms in order to gain comparative structural information. Because the K-RNA sequence is poorly conserved across species, we have cloned the K-RNA genes in the Schizosaccharomyces species S. malidevorans, S. japonicus, S. versatilis, and S. octosporus. Of the 4 species, only S. octosporus contains a K-RNA gene different from that in S. pombe; the gene diverges by 20%. Based on the two sequences, nuclease protection data and computer analysis, we have proposed a secondary structure model for the K-RNA. Northern analysis shows the K-RNA genes in all four Schizosaccharomyces species to be expressed as two RNAs, as in S. pombe.
Subject(s)
Endoribonucleases/chemistry , Genes, Fungal , RNA, Fungal/chemistry , Schizosaccharomyces/genetics , Base Sequence , Cloning, Molecular , Endoribonucleases/genetics , Molecular Sequence Data , Nucleic Acid Conformation , Phylogeny , RNA Probes , Ribonuclease P , Schizosaccharomyces/enzymologyABSTRACT
The nucleotide sequence of the gene encoding the Escherichia coli selenocysteine tRNA (tRNA(SeCys] predicts an unusually long acceptor stem of 8 base pairs (one more than other tRNAs). Here we show by in vivo experiments (Northern blots, primer extension analysis) and by in vitro RNA processing studies that E. coli tRNA(SeCys) does contain this additional basepair, and that its formation results from abnormal cleavage by RNase P.
Subject(s)
Endoribonucleases , Escherichia coli Proteins , Escherichia coli/genetics , RNA, Transfer, Amino Acid-Specific/genetics , Base Composition , Base Sequence , Escherichia coli/metabolism , Genes, Bacterial , Molecular Sequence Data , Nucleic Acid Conformation , Protein Precursors/genetics , RNA Processing, Post-Transcriptional , RNA, Transfer, Amino Acid-Specific/metabolism , Ribonuclease PABSTRACT
Among tRNA species histidine tRNAs possess the unique feature of having an additional nucleotide, a guanylate, at their 5'-end. In prokaryotes this G is encoded in the gene sequence and retained in the mature tRNA as result of an unusual cleavage by RNase P (Orellana, O., Cooley, L., and Söll, D. (1986) Mol. Cell. Biol. 6, 525-529), while in eukaryotes it is added post-transcriptionally by a special tRNA guanylyl transferase (Cooley, L., Appel, B., and Söll, D. (1982) Proc. Natl. Acad. Sci. U. S. A. 79, 6475-6479). Here we show that the additional G of chloroplast tRNAHis species is gene-encoded and retained in the tRNA by a processing step analogous to the prokaryotic one. However, the structural requirements for recognition by the different RNase P activities are not the same.
Subject(s)
Chloroplasts/analysis , Escherichia coli Proteins , Guanine Nucleotides , Guanosine Monophosphate , RNA, Transfer, Amino Acid-Specific/genetics , RNA, Transfer, His/genetics , Animals , Base Sequence , Cyanobacteria/enzymology , DNA, Recombinant , Endoribonucleases/metabolism , Escherichia coli/enzymology , Escherichia coli/genetics , Euglena gracilis/genetics , Molecular Sequence Data , Pentosyltransferases/metabolism , Plants/enzymology , Plants/genetics , RNA Precursors/genetics , RNA, Transfer, His/metabolism , Ribonuclease P , Saccharomyces cerevisiae/enzymology , VegetablesABSTRACT
The 5'-terminal guanylate residue (G-1) of mature Escherichia coli tRNA(His) is generated as a result of an unusual cleavage by RNase P (Orellana, O., Cooley, L., and Söll, D. (1986) Mol. Cell. Biol. 6, 525-529). We have examined the importance of the unique acceptor stem structure of E. coli tRNA(His) in determining the specificity of RNase P cleavage. Mutant tRNA(His) precursors bearing substitutions of the normal base G-1 or the opposing, potentially paired base, C73, can be cleaved at the +1 position, in contrast to wild-type precursors which are cut exclusively at the -1 position. These data indicate that the nature of the base at position -1 is of greater importance in determining the site of RNase P cleavage than potential base pairing between nucleotides -1 and 73. In addition, processing of the mutant precursors by M1-RNA or P RNA under conditions of ribozyme catalysis yields a higher proportion of +1-cleaved products in comparison to the reaction catalyzed by the RNase P holoenzyme. This lower sensitivity of the holoenzyme to alterations in acceptor stem structure suggests that the protein moiety of RNase P may play a role in determining the specificity of the reaction and implies that recognition of the substrate involves additional regions of the tRNA. We have also shown that the RNase P holoenzyme and tRNA(His) precursor of Saccharomyces cerevisiae, unlike their prokaryotic counterparts, do not possess these abilities to carry out this unusual reaction.