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C Yanofsky

Publications and source records attributed to C Yanofsky.

At least 181 records · Page 10Linked to original sources
PubMed1980

A phenylalanine tRNA gene from Neurospora crassa: conservation of secondary structure involving an intervening sequence.

We have isolated and sequenced a tRNAPhe gene from Neurospora crassa. Hybridization analyses suggest that trnaPhe is the only tRNA encoded on the cloned 5 kb DNA fragment. The tRNAPhe gene contains an intervening sequence 16 nucleotides in length located one nucleotide 3' to the anticodon position. The tRNAPhe coding region of Neurospora and yeast are 91% conserved, whereas their intervening sequences are only 50% identical. The pattern of sequence conservation is consistent with a proposed secondary structure for the tRNA precursor in which the anticodon is base paired with the middle of the intervening sequence and the splice points are located in adjacent single-stranded loops. The DNA sequence following the tRNAPhe coding region is similar to sequences following other genes transcribed by RNA polymerase III in that it is AT-rich and includes a tract of A residues in the coding strand. In contrast, the sequence preceding the Neurospora tRNAPhe coding region does not resemble sequences preceding other sequenced tRNA genes.

Base Sequence↗
PubMed1980

Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor.

The nucleotide sequence of trpR of Escherichia coli was determined. This gene codes for a polypeptide (Mr 12,356) that is 108 amino acid residues in length. NH2-terminal, COOH-terminal, and total amino acid analyses of purified aporepressor agree with the deduced amino acid sequence and establish the translation start and stop codons of the structural gene. The transcription start site for trpR mRNA synthesis in vitro was shown to be 56 base pairs prior to the translation start site. The nucleotide sequence on either side of the transcription start site is homologous to the trp operon operator. Purified trp aporepressor, when activated by L-tryptophan, protects restriction sites in this region, the presumed trpR operator, from cleavage by the respective restriction endonucleases. Bound RNA polymerase protects the same restriction sites. These findings and the additional observation that trp repressor inhibits transcription initiation in vitro establish that there is a functional overlap of operator and promoter sequences in the regulatory region of the trpR operon. These findings indicate that expression of trpR is autoregulatory.

Apoproteins↗
PubMed1980

Structural and functional analysis of cloned DNA containing genes responsible for branched-chain amino acid transport in Escherichia coli.

The four genes encoding the components of the high-affinity branched-chain amino acid transport systems in Escherichia coli (livH, livG, livJ, and livK) have been cloned into lambda phage and subsequently into the plasmid vector pACYC184. The presence of the four structural genes and their accompanying regulatory regions on the resultant plasmid, pOXI, was confirmed by genetic complementation and analysis and by transport studies carried out on the appropriate transformed mutant strains. When pOX1 DNA was used to direct an in vitro transcription/translation system, four major polypeptide products were produced. Immunoprecipitation with antibody directed against the LIV-binding protein identified the two leucine-binding proteins as products of in vitro synthesis. The binding proteins were produced in precursor forms and had molecular weights approximately 2500 higher than the processed, mature forms. A minicell-producing strain transformed with plasmid pOX1 produced the binding proteins in the processed form.

Amino Acids, Branched-Chain↗
PubMed1980

Amino-terminal sequence and processing of the precursor of the leucine-specific binding protein, and evidence for conformational differences between the precursor and the mature form.

A 2.1-kilobase Bgl II DNA fragment from Escherichia coli containing livK, the gene coding for the leucine-specific binding protein, has been cloned into the BamHI site of the plasmid vector pBR322. The DNA sequence of segments of the resulting plasmid, pOX7, established the location of the livK gene and the direction of its transcription. In vitro protein synthesis directed by pOX7DNA yielded the Mr 42,000 precursor of the leucine-specific binding protein and a small amount of the Mr 39,000 mature protein. Continued incubation of the in vitro reaction mixture after DNase and RNase treatment resulted in additional processing. The DNA sequence of the beginning of livK suggested that 23 additional amino acid residues are present as an extension of the NH2 terminus of the mature protein. Amino acid sequence analysis established that the precursor has the predicted 23-residue extension. Proteolytic digestion studies with the precursor and mature forms of the leucine-specific binding protein indicate that there are conformational differences between the two. This suggests a possible role for the signal sequence in determining the conformation of the binding protein precursor that is recognized by the membrane.

Amino Acid Sequence↗
PubMed1980

Translational coupling during expression of the tryptophan operon of Escherichia coli.

E. coli trpE polar mutations are 10 time more polar on trpD gene expression than on downstream (trpC, B, or A) gene expression. This effects was shown to be the result of "translational coupling," in which efficient translation of trpE-trpD intercistronic punctuation region consists of overlapping stop and start codons, and the trpE and trpD gene products form a functional complex in the cell. In light observations and characteristics, several models for the mechanism of translational coupling are considered.

Escherichia coli↗
PubMed1980

Subunits of the adenosine triphosphatase complex translated in vitro from the Escherichia coli unc operon.

The unc operon of Escherichia coli was split into two fragments by the restriction endonuclease HindIII. The operator-proximal portion was cloned into plasmid pACYC184, forming plasmid pAN51, which included the genes uncB, uncE, and uncA. When plasmid pAN51 was used as template in an in vitro transcription/translation system, the alpha subunit (from the uncA gene) and delta subunit of the F(1) adenosine triphosphatase (ATPase) were formed. In addition, three polypeptides of molecular weights 18,000, 17,000, and 14,000 were formed, and the significance of these polypeptides is discussed. The operator-distal portion of the unc operon was also cloned into plasmid pACYC184, forming plasmid pAN36, which included the uncD and uncC genes. When this plasmid was used as template in an in vitro transcription/translation system, the beta subunit (from the uncD gene) and the epsilon subunit (from the uncC gene) of the F(1) ATPase were formed. A polypeptide of a molecular weight similar to the epsilon subunit but of different net charge was also formed. Plasmid pAN45, carrying the complete unc operon, was isolated after digestion of a mixture of plasmids pAN51 and pAN36 with the restriction endonuclease HindIII and then religation with T4 deoxyribonucleic acid ligase. It was concluded that a HindIII restriction site occurred within the newly described uncG gene, which was shown, by complementation studies with Mu-induced mutants, to be located between the uncA and uncD genes to give the gene order uncBEAGDC. The uncG gene appears to code for the gamma subunit of the F(1) ATPase.

Adenosine Triphosphatases↗
PubMed1979

Nucleotide sequence and conserved features of the 5.8 S rRNA coding region of Neurospora crassa.

The nucleotide sequence of Neurospora crassa 5.8 S rDNA and adjacent regions has been determined. The deduced 5.8 S rRNA sequence of Neurospora differs from the 5.8 S rRNA sequence of Saccharomyces cerevisiae at 13 of 158 residues. Nine of these differences are clustered in a segment capable of forming a short hairpin secondary structure thought to be involved in the 28 S - 5.8 S rRNA complex. These differences occur in pairs such that the potential secondary structure is preserved.

Base Sequence↗
PubMed1979

Construction of plasmid cloning vehicles that promote gene expression from the bacteriophage lambda pL promoter.

Two multiple-copy, ColE1-type, plasmid cloning vehicles, pHUB2 and pHUB4, have been constructed that carry four different single restriction sites down-stream from the phage lambda promoter pL. The promoting activity of pL is switched off at low temperature in the presence of a cIts gene that specifies a temperature-sensitive repressor but could be activated by heat induction. cIts was located either on the host chromosome, or on a second plasmid pRK248 that is compatible with the cloning vehicle, or on the vehicle itself. Three different restriction fragments, each carrying the gene trpA of Salmonella typhimurium or Shigella dysenteriae, have been inserted into the EcoRI, BamHI and SalI sites, respectively, of these plasmids and pL dependent expression of the inserted gene in Escherichia coli was determined by measuring the enzymatic activity of the trpA gene product. Heat induction resulted in a level of expression of trpA corresponding to 1 to 6.6% of the total soluble cell protein as trpA protein. The level of trpA protein production depended on the particular insert and the plasmid used.

Bacterial Proteins↗
PubMed1979

Nucleotide sequences of trpA of Salmonella typhimurium and Escherichia coli: an evolutionary comparison.

The complete nucleotide sequences of trpA of Salmonella typhimurium and Escherichia coli were determined. The nucleotide sequences are 24.8% divergent, compared with amino acid sequence divergence of 14.9%. Over half of the codons of each gene contain synonymous nucleotide changes. The pattern of synonymous nucleotide changes is consistent with the interpretation that such changes result from random mutational events. We do not find any evidence indicating that codon selection or RNA structure is of major selective value. We conclude that polypeptide function is the primary basis of selection in trpA and that most synonymous codon changes are selectively neutral.

Base Sequence↗
PubMed1979

Attenuation in the Escherichia coli tryptophan operon: role of RNA secondary structure involving the tryptophan codon region.

The secondary structure of the terminated trp leader transcript from Escherichia coli was analyzed by RNase T1 partial digestion. Base-paired regions were recovered by nondenaturing gel electrophoresis and identified by denaturing gel electrophoresis and fingerprinting. The tandem tryptophan codons in the leader peptide coding region were found to be base paired with a more distal region of the transcript. This and other secondary structures that the trp leader RNA can form help explain the physiological response of the operon as well as the behavior of regulatory mutants.

Codon↗
PubMed1979

Structural and functional analysis of cloned deoxyribonucleic acid containing the trpR-thr region of the Escherichia coli chromosome.

Specialized transducing phages containing the thr-trpR region of the Escherichia coli chromosome were derived from a strain with lambda prophage inserted in thr. Cloning of segments of the chromosomal deoxyribonucleic acid of one such lambda thr + trpR+ phage in various plasmid vectors established that a 1.3-kilobase BamHI fragment carried trpR+ intact. Strains with a multicopy plasmid vector containing the BamHI insert produced 20-fold-higher levels of trp aporepressor than did the wild-type strain of Escherichia coli. Similarly, induction of lambda thr + trpR+ lysogens resulted in increased aporepressor levels. The 1.3-kilobase trpR+ BamHI fragment was inserted in either orientation downstream from lambda pLN in a plasmid vector in which transcription from lambda pL was under the control of a temperature-sensitive lambda repressor. Induction established the orientation of transcription of trpR and led to the production of 100-fold-increased levels of trp aporepressor. A presumptive 23,500-dalton trpR+ polypeptide was detected by using lambda pLNtrpR+ plasmid deoxyribonucleic acid in a cell-free transcription-translation system.

Bacterial Proteins↗
PubMed1978

The regulatory region of the trp operon of Serratia marcescens.

The nucleotide sequence of the regulatory region of the trp operon of Serratia marcescens is presented. It contains a transcription termination control site in the transcribed leader region preceding the first structural gene of the operon as well as a regulated promoter/operator transcription initiation region. The structural organisation of the leader region differs substantially from that of Escherichia coli.

Amino Acid Sequence↗