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R J Planta

Publications and source records attributed to R J Planta.

At least 145 records · Page 8Linked to original sources
PubMed1983

The genes coding for histone H3 and H4 in Neurospora crassa are unique and contain intervening sequences.

Sequences coding for histone H3 and H4 of Neurospora crassa could be identified in genomic digests with the use of the corresponding genes from sea urchin and X. laevis as hybridization probes. A 2.6 kb HindIII-generated N. crassa DNA fragment, showing homology with the heterologous histone H3-gene probes was cloned in a charon 21A vector. Using DNA from this clone as a homologous hybridization probe a 6.9 kb SalI-generated DNA fragment was isolated which in addition to the histone H3-gene also contains the gene coding for histone H4. Several lines of evidence demonstrate the presence of only a single histone H3- as well as a single histone H4-gene in N. crassa. The two genes are physically linked on the genome. DNA sequencing of the N. crassa histone H3- and H4-genes confirmed their identity and, in addition, revealed the presence of one short intron (67 bp) within the coding sequence of the H3-gene and even two introns (68 and 69 bp) within the H4-gene. The amino acid sequences of the N. crassa histones H3 and H4, as deduced from the DNA sequences, and those of the corresponding yeast histones differ only at a few positions. Much larger sequence differences, however, are observed at the DNA level, reflecting a diverging codon usage in the two lower eukaryotes.

Amino Acid Sequence↗
PubMed1983

Molecular cloning of the rDNA of Saccharomyces rosei and comparison of its transcription initiation region with that of Saccharomyces carlsbergensis.

We have cloned one complete repeating unit of rDNA from Saccharomyces rosei and determined its physical and genetic organization. Heteroduplex analysis of the rDNA units from S. rosei and S. carlsbergensis shows that the nontranscribed spacers are largely nonhomologous in sequence, whereas the transcribed regions are essentially homologous. We also determined the transcription initiation site for the 37S precursor RNA on S. rosei rDNA. Sequence comparison of the region surrounding the site of transcription initiation for the 37S RNA with the corresponding region of S. carlsbergensis revealed extensive homology from position -9 downstream into the external transcribed spacer. Very little homology was observed between position -9 and -55, but some homologous tracts are present upstream from position -55.

Base Sequence↗
PubMed1982

The structure of the gene coding for the phosphorylated ribosomal protein S10 in yeast.

From previous studies on cloned yeast ribosomal protein genes we obtained evidence that a large number of them contain an intron [Bollen et al. (1982) Gene 18, 29-38]. In the temperature-sensitive rna2-mutant transcription of these genes leads to the accumulation of precursor RNAs at the restrictive temperature. These precursor mRNAs are several hundreds of nucleotides longer than the respective mature mRNAs. The split character of one of these ribosomal protein genes, viz. the gene coding for the major phosphorylated small-subunit protein S10, was further established by sequence analysis. The intervening sequence interrupts the coding sequence after the second codon and has a length of 352 nucleotides. Genomic Southern hybridizations with a DNA fragment carrying part of the S10-gene revealed that this gene is duplicated on the yeast genome. The molecular weight of S10 as deduced from the sequence analysis was estimated to be 31462 dal. Comparison of the N-terminal aminoacid sequence of the yeast ribosomal protein S10 with that of ribosomal protein S6 from rat liver revealed a striking homology between both proteins. Moreover, at the C-terminal end of the yeast ribosomal protein the sequence Arg-Ala-Ser-Ser-Leu-Lys is present which is very similar to the phosphorylation site of the rat liver protein S6.

Amino Acid Sequence↗
PubMed1982

Ribosomal protein genes of yeast contain intervening sequences.

From a colony bank of HindIII-generated yeast DNA fragments we have isolated a number of recombinant DNAs carrying genes for ribosomal proteins (e.g., S10, S16A, S20, S24, S31, S33, L16, L25 and L34) of the yeast Saccharomyces carlsbergensis. By electron microscopic analysis of the R-loops formed between various DNA fragments and yeast mRNA, we could locate the ribosomal protein genes on the physical maps of the cloned DNA fragments. The R-loop structures observed indicate that a number of the ribosomal protein genes contain an intervening sequence.

Base Sequence↗
PubMed1981

The primary and secondary structure of yeast 26S rRNA.

We present the sequence of the 26S rRNA of the yeast Saccharomyces carlsbergensis as inferred from the gene sequence. The molecule is 3393 nucleotides long and consists of 48% G+C; 30 of the 43 methyl groups can be located in the sequence. Starting from the recently proposed structure of E. coli 23S rRNA (see ref. 25) we constructed a secondary structure model for yeast 26S rRNA. This structure is composed of 7 domains closed by long-range base pairings as n the bacterial counterpart. Most domains show considerable conservation of the overall structure; unpaired regions show extended sequence homology and the base-paired regions contain many compensating base pair changes. The extra length of the yeast molecule is due to a number of insertions in most of the domains, particularly in domain II. Domain VI, which is extremely conserved, is probably part of the ribosomal A site. alpha-Sarcin, which apparently inhibits the EF-1 dependent binding of aminoacyl-tRNA, causes a cleavage between position 3025 and 3026 in a conserved loop structure, just outside domain VI. Nearly all of the located methyl groups, like in E. coli, are present in domain II, V and VI and clustered to a certain extent mainly in regions with a strongly conserved primary structure. The only three methyl groups of 26S rRNA which are introduced relatively late during the processing are found in single stranded loops in domain VI very close to positions which have been shown in E. coli 23S rRNA to be at the interface of the ribosome.

Base Sequence↗
PubMed1981

The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript.

We have determined the nucleotide sequence of part of a cloned yeast ribosomal RNA operon extending from the 5.8S RNA gene downstream into the 5' -terminal region of the 26S RNA gene. We mapped the pertinent processing sites, viz. the 5' end of 26S rRNA and the 3'ends of 5.8S rRNA and its immediate precursor, 7S RNA. At the 3' end of 7S RNA we find the sequence UCGUUU which is very similar to the type I consensus sequence UCAUUA/U present at the 3' ends of 17S, 5.8S and 26S rRNA as well as 18S precursor rRNA in yeast. At the 5' end of the 26S RNA gene we find a sequence of thirteen nucleotides which is homologous to the type II sequence present at the 5' termini of both the 17S and the 5.8S RNA gene. These findings further support the suggestion put forward earlier (G.M. Veldman et al. (1980) Nucl. Acids Res. 8, 2907-2920) that both consensus sequences are involved in the recognition of precursor rRNA by the processing nuclease(s). We discuss a model for the processing of yeast rRNA in which a processing enzyme sequentially recognizes several combinations of a type I and a type II consensus sequence. We also describe the existence of a significant base complementarity between sequences in the 5' -terminal region of 26S rRNA and the 3' -terminal region of 5.8S rRNA. We suggest that base pairing between these sequences contributes to the binding between 5.8S and 26S rRNA.

Base Sequence↗
PubMed1981

Reconstitution of biologically active 50S ribosomal subunits with artificial 5S RNA molecules carrying disturbances in the base pairing within the molecular stalk.

Bacillus stearothermophilus 50S ribosomal subunits were reconstituted in vitro using artificial 5S RNA molecules constructed by combining parts of major and minor type (Raué et al. (1976) Europ. J. Biochem. 68, 169-176) B. licheniformis 5S RNA. The artificial 5S RNA molecules carry defined disturbances (A.C juxtapositions and extra G.U pairs) in the base pairing between the 5'- and 3'-terminal sequences of the molecule (the molecular stalk region). The biological activity of the reconstituted subunits was determined in an E. coli cell-free system programmed with poly-U. The results show that conservation of the base pairing within the molecular stalk is not required for biological activity of 5S RNA. Disturbances of the base pairing within this region do reduce the rate of reconstitution, however. Normal base pairing in the molecular stalk is thus required to ensure efficient ribosome assembly.

Bacillus↗
PubMed1981

Hydrogen-1 and phosphorus-31 nuclear magnetic resonance study of the solution structure of Bacillus licheniformis 5S ribonucleic acid.

The conformation of Bacillus licheniformis 5S RNA in solution has been studied by using 360-MHz 1H NMR and 40.5-MHz 31P NMR spectroscopy. The 1H NMR spectra, which are well resolved, have been compared with theoretical spectra derived by ring-current shift calculations for various models proposed in the literature for the secondary structure of 5S RNA. The total amount of base pairs is estimated to be around 36. NMR melting experiments indicate that both the molecular stalk and the prokaryotic loop [Fox, G. E., & Woese, C. R. (1975) Nature (London) 256, 505] are present in the solution structure. On this basis, some models proposed for the secondary structure of 5S RNA not containing these structural features can be rejected. Several resonances are observed around 10.7 ppm that can be ascribed to protons involved in non-Watson-Crick base pairing most likely present in tertiary interactions in the 5S RNA molecule or to ring N protons of nonpaired bases which as a result of the molecular folding are shielded from the solvent. Under our solution conditions, these structural features disappear at physiological temperature, the process being uncoupled from the collapse of the secondary structure. Using 31P NMR, we demonstrate that the number of phosphate conformations in the sugar phosphate backbone of 5S RNA, deviating from the g-,g- conformation normally found in double helices, is far les than in tRNA.

Bacillus↗
PubMed1981

Isolation of cloned ribosomal protein genes from the yeast Saccharomyces carlsbergensis.

A colony bank of yeast dna obtained by cloning HindIII-generated fragments of total yeast nuclear DNA in Escherichia coli K-12 with the vector pBR322, was screened with a radioactive RNA probe enriched for a subset of ribosomal protein mRNAs. The selected recombinant DNA molecules were hybridized with poly(A)-containing mRNA under R-loop conditions. From the DNA-RNA hybrids the respective mRNAs were melted off and translated in vitro in a rabbit reticulocyte cell-free system. The translational products were analyzed by immunoprecipitation with antibodies raised against ribosomal proteins. The identity of the ribosomal protein gene products was further established by electrophoresis on two-dimensional gels. At least 15 recombinant DNA molecules were shown to contain ribosomal protein genes. Four of them, i.e. Y65, Y89, Y113 and Y138, have been characterized preliminarily.

DNA, Fungal↗
PubMed1980

The transcription termination site of the ribosomal RNA operon in yeast.

The site at which transcription of the ribosomal RNA operon in yeast is terminated was precisely localized. First, the exact position of the 3' end of the 26S rRNA gene was mapped on the rDNA on the basis of RNA- and DNA sequence data. Next, the 3' terminus of the primary transcript, 37S precursor rRNA, was established by hybridization experiments and sequence analysis. 37S pre-rRNA appears to be just 7 nucleotides longer at its 3' end than 26S rRNA. The non-coding strand around the termination site is extremely T-rich: 15 out of 18 nucleotides are T-residues. An extensive dyad symmetry is present in the sequence downstream from the termination site; a possible role of this structure in the regulation of transcription termination is discussed. The 3'-terminal 110 nucleotides of yeast 26S rRNA have approx. 50% and 60% homology with the corresponding regions of E. coli 23S rRNA and Xenopus laevis 28S rRNA, respectively.

Animals↗
PubMed1980

Structural features of Bacillus precursor 5S RNA involved in the interaction with RNAase M5.

Mature 5S (m5S) RNA from Bacillus licheniformis specifically and almost completely inhibits in vitro maturation of bacillus precursor 5S (p5S) RNA, showing that the maturation enzyme RNAase M5 can recognize Bacillus m5S RNA. E. coli m5S RNA is a much less efficient inhibitor, whereas S. carlsbergensis 5S RNA inhibits maturation by about 70%. The differences in inhibition can be correlated with the position of the sequence UAGG (residues 101-104 in B. licheniformis m5S RNA) relative to the double-helical region formed by the 5'- and 3'-terminal sequences (molecular stalk) of m5S RNA. Recent experiments by Meyhack and Pace (Biochemistry 17 (1980) 5804-5810) demonstrated this UAGG sequence to be indispensable for processing of p5S RNA. Other elements of secondary and/or tertiary structure are also required, however. The effect of artificially constructed "5S RNA" molecules having defined disturbances in the base-pairing within the molecular stalk on in vitro maturation shows that base-pairing in the immediate neighbourhood of the bonds to be cleaved during maturation is crucial to recognition of p5S RNA by RNAase M5. G.U pairs are tolerated in this region, however, without loss of efficiency in maturation. Base-pairing does not have to extend throughout the complete molecular stalk. The introduction of an A/C combination at the end of the molecular stalk removed from the bonds cleaved by RNAase M5 does not significantly impair the efficiency of maturation.

Bacillus↗
PubMed1980

Nucleotide sequence analysis of precursor 5S RNA from Bacillus licheniformis.

The complete nucleotide sequences of the various precursor 5S RNA species occurring in Bacillus licheniformis have been elucidated. The B. licheniformis precursors contain a 5'-precursor-specific segment of 95 nucleotides which is four times as long as the corresponding segment of the p5S RNAs from the closely related strains B. subtilis (Sogin, M.L., Pace, N.R., Rosenberg, M., Weissman, S.M. (1976) J. Biol. Chem. 251, 3480-3488) and Bacillus Q (Stiekema, W.J., Raué, H.A., Planta, R.J. (1980) Nucl. Ac. Res. 8, 2193-2211). However, fourteen of the sixteen nucleotides at the 5'-end are identical in the precursors from all three strains. These conserved nucleotides can form a stem and loop structure which is likely to play an important role in the biosynthesis of 5S RNA. Extension secondary and tertiary structure is present in the 5'-precursor-specific segment as concluded from the results of digestion with RNAase T1 both of the isolated segment and the intact precursors. No sequence homology exists between the 3'-precursor-specific segments of the B. licheniformis precursors and those of the other two strains except for a stretch of U residues at the 3-terminus. This stretch of U residues is not immediately preceded by a hairpin loop, however, as expected for a transcription termination signal (20). The question whether the precursors have already undergone processing at the 3'-end, therefore, remains open. The total number of genetically distinct precursor species in B. licheniformis is at least five and at most ten. Most likely each ribosomal RNA cistron produces a separate p5S RNA as is also the case in Bacillus Q.

Bacillus↗
PubMed1980

Sequence analysis and in vitro maturation of five precursor 5S RNAs from Bacillus Q.

Bacillus Q, which is closely related to B. subtilis, contains at least six different precursors of 5S rRNA. The complete nucleotide sequences of four of these precursors, as well as the major part of the sequence of a fifth one, have been determined. They all contain the same 5'-terminal non-conserved segment which is to a large degree homologous with the corresponding segment of the B. subtilis p5S RNAs (Sogin, M.L., Pace, N.R., Rosenberg, M., Weissman, S.M. (1976) J. Biol. Chem. 251, 3480-3488). On the other hand the 3'-terminal non-conserved sequences of the various Bacillus Q precursors show considerable differences both in length and in nucleotide sequence, while there is also little or no homology with the 3'-terminal non-conserved sequence of the B. subtilis precursors. Bacillus Q p5S RNAs do not possess tetranucleotide repeats around the sites which are cleaved during maturation, as does B. subtilis p5S RNA. Like in B. subtilis, however, the cleavage sites are contained within a double-helical region of the precursor molecules. Crude RNAse M5 isolated from various Bacillus strains can maturate the Bacillus Q p5S RNAs with high efficiency. Despite considerable differences in primary structure between the precursors from the various strains, each RNAs M5 preparation can maturate all these precursors with about the same efficiency.

Bacillus↗
PubMed1980

Physical map of chloroplast DNA of Spirodela oligorrhiza; analysis by the restriction endonucleases PstI, xhoI, SacI.

Using the restriction endonucleases XhoI, SacI and PstI, physical maps of Spirodela oligorrhiza (duck weed) chloroplast DNA [with a relatively large m. wt. of 120 Md; see van Ee et al. (1980)] were constructed. The overall structural organization of S. oligorrhiza chloroplast DNA appears to be rather similar to that of chloroplast DNAs of other higher plants. It is composed of two invertedly repeated DNA segments of 17 Md, separated by a small single-copy region of 19 Md and a large single-copy region of 69 Md. Apparently the extra DNA (as compared with chloroplast DNAs of other higher plants) is present within the large single-copy region.

Chloroplasts↗
PubMed1980

Isolation and Characterization of Chloroplast DNA from the Duckweed Spirodela oligorrhiza.

Chloroplast DNA of the duckweed Spirodela oligorrhiza, isolated by CsCl gradient centrifugation, was characterized by its buoyant density, guanine + cytosine content, melting behavior, circularity, and contour length. In all these characteristics, chloroplast DNA of S. oligorrhiza is similar to the chloroplast genomes of other higher plants, except that it has a significantly larger size.

Journal Article↗
PubMed1980

Small-size mRNAs code for ribosomal proteins in yeast.

In order to identify and to study the ribosomal protein genes in yeast we have tried to purify the mRNA coding for ribosomal proteins. Poly(A)-containing RNA from the yeast Saccharomyces carlsbergensis was fractionated according to size using preparative sucrose gradient centrifugation. The various (size) fractions were translated in vitro in a wheat germ cell-free system. The products were analysed by sodium dodecylsulfate/polyacrylamide gradient gel electrophoresis as well as by acetic acid/urea gel electrophoresis. It was found that an mRNA fraction of about 9 S directs the synthesis in vitro of proteins that have properties characteristic of ribosomal proteins, i.e. they are both small and basic. The ribosomal nature of these proteins was further established by two-dimensional gel electrophoresis. This small-size mRNA fraction can be used as a probe for the identification of ribosomal protein genes in recombinant DNA molecules.

Electrophoresis, Polyacrylamide Gel↗
PubMed1979

Pseudouridylation of yeast ribosomal precursor RNA.

The pseudouridylation of ribosomal RNA of Saccharomyces carlsbergensis was investigated with respect to its timing during the maturation of rRNA and its sequence specificity. Analysis of 37-S RNA, the common precursor to 17-S, 5.8-S and 26-S rRNA and most probably the primary ribosomal transcript, shows that this RNA molecule contains already most if not all of the 36-37 pseudouridine residues found in the mature rRNAs. Thus pseudouridylation is, like 2'-0-ribosemethylation, an early event in the maturation of rRNA, taking place immediately after, or even during, transcription. The data presented show that the non-conserved sequences of 37-S precursor rRNA contain very few pseudouridine residues if any. The pseudouridine residues within the rRNA sequences are apparently clustered to a certain degree as can inferred from the occurrence of a single oligonucleotide containing 3 pseudouridines, which was obtained by digestion of 26-S rRNA with ribonuclease T1.

Base Sequence↗