flrB, a regulatory locus controlling branched-chain amino acid biosynthesis in Salmonella typhimurium

Role of codon choice in the leader region of the ilvGMEDA operon of Serratia marcescens

Leucine participates in multivalent repression of the Serratia marcescens ilvGMEDA operon by attenuation (J.-H. Hsu, E. Harms, and H.E. Umbarger, J. Bacteriol. 164:217-222, 1985), although there is only one single leucine codon that could be involved in this type of control. This leucine codon is the rarely used CUA. The contribution of this leucine codon to the control of transcription by attenuation was examined by replacing it with the commonly used leucine codon CUG and with a nonregulatory proline codon, CCG. These changes left intact the proposed secondary structure of the leader. The effects of the codon changes were assessed by placing the mutant leader regions upstream of the ilvGME structural genes or the cat gene and measuring acetohydroxy acid synthase II, transaminase B, or chloramphenicol acetyltransferase activities in cells grown under limiting and repressing conditions. The presence of the common leucine codon in place of the rare leucine codon reduced derepression by about 70%. Eliminating the leucine codon by converting it to proline abolished leucine control. Furthermore, a possible context effect of the adjacent upstream serine codon on leucine control was examined by changing it into a glycine codon.

Enhancement of bacitracin biosynthesis by branched-chain amino acids in a regulatory mutant of Bacillus licheniformis

DL-4-Azaleucine-resistant mutant of Bacillus licheniformis azlr-1 isolated after N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis, was a better bacitracin producer than the parent strain. In the minimal medium, the antibiotic biosynthesis was 4 times higher in the mutant than in the parent strain and less dependent on L-leucine addition. In the complex fermentation medium, the yield was 18-20% higher in the mutant strain. Transaminase B activity measured in the crude extract revealed that the branched-chain amino acid biosynthetic enzymes were 5-10 times derepressed supplying bacitracin synthetase with enhanced quantity of isoleucine and leucine, the building units of bacitracin molecule.

Characterization of the 3' end of the leucine operon of Salmonella typhimurium

The nucleotide sequence of the leuD gene of Salmonella typhimurium and of the downstream flanking region are presented. S1 mapping experiments identified 3' endpoints of leu mRNA 140 and 285 nucleotides downstream of the UAA stop codon of leuD mRNA. Experiments employing pulse-labeled RNA suggest that these endpoints result from transcription termination rather than RNA processing. Our results indicate that the organization of the 3' non-translated region of the leu operon from S. typhimurium resembles that of the trp operon of Escherichia coli. Further, our results suggest that the leu operon of S. typhimurium does not contain structural genes other than those identified by genetic experiments, i.e. leu, A,B,C and D.

Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes

We present an approach for determining the in vivo distribution of a protein on specific segments of chromosomal DNA. First, proteins are joined covalently to DNA by irradiating intact cells with UV light. Second, these cells are disrupted in detergent, and a specific protein is immunoprecipitated from the lysate. Third, the DNA that is covalently attached to the protein in the precipitate is purified and assayed by hybridization. To test this approach, we examine the cross-linking in Escherichia coli of RNA polymerase to a constitutively expressed, lambda cI gene, and to the uninduced and isopropyl beta-D-thiogalactoside (IPTG)-induced lac operon. As expected, the recovery of the constitutively expressed gene in the immunoprecipitate is dependent on the irradiation of cells and on the addition of RNA polymerase antiserum. The recovery of the lac operon DNA also requires transcriptional activation with IPTG prior to the cross-linking step. After these initial tests, we examine the distribution of RNA polymerase on the leucine operon of Salmonella in wild-type, attenuator mutant, and promoter mutant strains. Our in vivo data are in complete agreement with the predictions of the attenuation model of regulation. From these and other experiments, we discuss the resolution, sensitivity, and generality of these methods.

Evidence that repression mechanisms can exert control over the thr, leu, and ilv operons of Escherichia coli K-12

Mutants of Escherichia coli K-12 resistant to either the threonine analog DL-alpha-amino-beta-hydroxyvaleric acid or the leucine analog 5',5',5'-trifluoro-DL-leucine were isolated. One DL-alpha-amino-beta-hydroxyvaleric acid-resistant mutant strain, designated SP572, constitutively expressed the thr and ilv operons. The mutant allele, avr-16, was localized between trpR and the thr operon at min 0. The wildtype allele of avr-16, designated ileR, is trans dominant. One 5',5',5'-trifluoro-DL-leucine-resistant mutant strain, designated FLR9, expressed the leu and ilv operons constitutively. The mutant allele, flr-9, is linked to entA at min 13. The constitutive expression of the thr, leu, and ilv operons in mutants avr-16 and flr-9 was partly reversed in cells harboring a plasmid, which leads to elevated levels of the trpR gene product, the Trp aporepressor protein. Operator-like sequences situated upstream from the transcription startpoints of the thr, leu, and ilv operons are plausible candidates for targets of systems of repressor-operator control functioning in parallel with attenuation.

Trp repressor protein is capable of intruding into other amino acid biosynthetic systems

Escherichia coli strains with elevated intracellular levels of Trp repressor protein displayed complete growth inhibition on minimal media which contained high levels of tryptophan. The inhibition was attributable to the acquisition of a compound nutritional requirement, which could be satisfied by a combination of isoleucine, leucine, valine, threonine, serine, phenylalanine, and tyrosine. It is proposed that Trp repressor protein, at elevated levels, represses the transcription of those genes which encode enzymes for the biosynthesis of these particular amino acids. Data which support this model are presented, together with a discussion of its regulatory implications.

Transcription attenuation is the major mechanism by which the leu operon of Salmonella typhimurium is controlled

Three mutations, each causing constitutive expression of the Salmonella typhimurium leu operon, were cloned into phage vector lambda gt4 on EcoRI DNA fragments carrying all of that operon except for part of the promoter-distal last gene. Sequence analysis of DNA from these phage demonstrated that each contains a single base change in the leu attenuator. Transcription of mutant DNA in vitro resulted in transcription beyond the usual site of termination. The level of beta-IPM dehydrogenase, the leuB enzyme, was elevated 40-fold in a strain carrying one of these mutations, and starvation of this strain for leucine had little effect on the amount of activity expressed. Using a strain with a wild-type promoter-leader region of the leu operon, the rates of synthesis and degradation of leu leader RNA and readthrough RNA (leu mRNA) were measured by DNA-RNA hybridizations with specific DNA probes. The rate of synthesis of the leu leader was about the same in cells grown with excess or with limiting leucine. On the other hand, the rate of synthesis of leu mRNA was 12-fold higher for cells grown in limiting leucine as opposed to excess leucine. The rate of degradation of these RNA species was the same under both conditions of growth. Thus, the variation in expression of the leu operon observed for cells grown in minimal medium is, for the most part, not caused by control over the frequency of initiation or by the differential stability of these RNA species. Rather, the variation is a direct result of the frequency of transcription termination at an attenuator site. These results taken together suggest that transcription attenuation is the major mechanism by which leucine regulates expression of the leu operon of S. typhimurium for cells growing in a minimal medium.

A mutation in Salmonella typhimurium imparting conditional resistance to 5-fluorouracil and a bioenergetic defect: mapping of cad

The position of the genetic locus allelic with the cad-2 mutation has been located between units 14 and 15 of the linkage map of S. typhimurium. Fine structure mapping established the gene order as cad flrB nag. The genetic evidence coupled with biochemical evidence indicates that this cad locus is homologous to the ubiF gene of Escherichia coli.

Cloning of an EcoRI-generated fragment of the leucine operon of Salmonella typhimurium

Recombinant plasmids carrying part of the leucine operon of Salmonella typhimurium were isolated following transformation of an Escherichia coli leucine auxotroph to prototrophy with a ligated mixture of EcoRI-treated Salmonella DNA and plasmid pSC101 DNA. Plasmids pCV11 and pCV13, containing a 3.4-10(6) dalton DNA fragment ligated to the vector, had the leu operon oriented in opposite directions. The orientation of the leu operon relative to plasmid genes was determined. The 3.4-10(6) dalton fragment was ligated in to the EcoRI site of plasmid pMB9 yielding plasmids pCV12 (orientation as in pCV11) and pCV14 (orientation as in pCV13). The results of enzyme assays and complementation tests indicated that these plasmids carry functional leuA, leuB, and leuC genes but not a functional leuD gene. Furthermore, the following results indicated that they have a functional leu control region and promoter. Expression of plasmid leu genes was markedly enhanced under conditions of leucine limitation whereas introduction of a leu promoter mutation into the operon oriented in either direction with respect to plasmid genes had a strong negative effect upon leu operon expression. Transcriptional readthrough from plasmid promoters, if it occurs at all, must be small in comparison with transcription initiated at the leu promoter. RNA was isolated from leucine auxotrophs grown under conditions of repression and derepression and from prototrophic strains derepressed for the leucine operon as a result of mutations in leuO, leuS, and flrB. The rate of synthesis of leu mRNA, measured by hybridization to plasmid pCV12 DNA, was proportional in each case to leu enzyme levels.

leu operon of Salmonella typhimurium is controlled by an attenuation mechanism

The nucleotide sequence of the control region of the leu operon of Salmonella typhimurium was determined. A prominent feature of this region is a signal for termination of transcription. In vitro, transcription does terminate at this site, yielding a leader RNA of about 160 nucleotides as a major product. This leader RNA is potentially translatable into a peptide containing 28 amino acids, 4 of which are adjacent leucine residues. Several regions of base complementarity exist within the leader, positioned such that pairing of one region precludes pairing of another. The position of the four leucine codons relative to two regions of base complementarity suggest a model for the regulation of the leu operon similar to that proposed by Yanofsky and coworkers for the trp operon. In addition, a third region of base complementarity was identified which, when incorporated into the model, explains why premature termination is the usual outcome when transcription is initiated in vitro by purified RNA polymerase.

A new locus (leuK) affecting the regulation of branched-chain amino acid, histidine, and tryptophan biosynthetic enzymes

A locus (leuK) affecting regulation of the leucine operon was selected by isolating a spontaneous Ara+ derivative of an Escherichia coli B/r strain carrying an ara-leu fusion in which the arabinose operon is under leucine control. Genetic analyses by P1 transduction demonstrated that the lesion is located to the right of the galactose operon. Regulation of the biosynthetic enzymes for leucine, isoleucine-valine, histidine, and tryptophan was altered in a strain carrying leuK16. High-level gene expression in the heterozygous merodiploid strain F' leuK+/leuK16) demonstrated the dominance of the mutant allele to the wild-type allele. No apparent effect was observed in the mutant on N-acetylornithinase, a biosynthetic enzyme in the arginine pathway, nor on any of the 18 aminoacyl-tRNA synthetases examined. However, compared with that of the parent strain, the extent of the charging of leucyl-, isoleucyl-, valyl-, histidyl-, and arginyl-tRNA was decreased in the mutant.

Relationship between messenger ribonucleic acid and enzyme levels specified by the leucine operon of Escherichia coli K-12

The levels of leucine-forming enzymes in Escherichia coli K-12 varied over a several thousand-fold range, depending upon conditions of growth. The highest levels were achieved by growing auxotrophs in a chemostat under conditions of leucine limitation. Under such conditions, enzyme levels were increased 45- to 90-fold relative to cells grown in minimal medium containing leucine (the latter values arbitrarily called 1). Leucine operon-specific messenger ribonucleic acid levels were elevated to about the same extent as enzyme levels in cells grown in a chemostat. Growth in media of greater complexity resulted in progressively lower levels of leucine-forming enzymes, reaching a value of less than 0.02 for growth in a medium containing tryptone broth and yeast extract. The levels of leucine operon-specified enzymes and messenger ribonucleic acid were also measured in strains containing about 25 copies of plasmid pCV1(ColE1-leu) per chromosome. For such strains grown in minimal medium, enzyme levels were proportional to the number of plasmids per cell. Furthermore, they followed the same trends as those described above upon derepression in a chemostat or upon repression following growth in rich media. Leucine messenger ribonucleic acid, measured both by pulse-labeling and hybridization-competition experiments, was roughly proportional to enzyme levels over this entire range. For a plasmid-containing strain grown in a chemostat under conditions of leucine limitation (about 100 plasmids per chromosome), about 27% of pulse-labeled ribonucleic acid was coded for by genes in or adjacent to the leucine operon, and 10% of the total protein was beta-isopropylmalate dehydrogenase.

Detection of messenger RNA from the isoleucine--valine operons of Salmonella typhimurium by heterologous DNA-RNA hybridization: involvement of transfer RNA in transcriptional repression

A hybridization assay using Escherichia coli K-12 DNA isolated from the specialized transducing bacteriophage gammaCI857St68h80 dilv was used to examine the rate of synthesis of the messenger RNA's (mRNA) derived from the isoleucine-valine (ilv) gene cluster of Salmonella typhimurium. In all cases examined, changes in ilv enzyme levels could be correlated with changes in the rate of synthesis of ilv mRNA. Several well characterized regulatory mutants of S. typhimurium had rates of synthesis of ilv mRNA 3 to 8-fold higher than the repressed wild-type strain. The increased rates of ilv mRNA synthesis found in a hisT strain as well as in isoleucyl-and leucyl-tRNA SYNTHETASE MUTANTS, STRONGLY SUGGESTS A ROLE FOR BRANCHED-CHAIN AMINOACYL-TRNA's in transcriptional control.

Transcriptional control of the isoleucine-valine messenger RNA's in E. coli K-12

Hybridization of messenger ribonucleic acid (mRNA) isolated from Escherichia Coli K-12 to deoxyribonucleic acid (DNA) from lambdaCI857st68h80dilv was used to detect isoleucine-valine (ilv) specific mRNA. A number of strains partially constitutive for the isoleucine-valine enzymes had levels of ilv mRNA 2 to 3-fold higher than the parent strain. Starvation for any of the branched-chain amino acids resulted in a 20 to 23-fold increase in ilv mRNA as compared to repressed levels. These differences were not due to altered growth rates or to changes in the stability of ilv mRNA. These data indicate that regulation of the isoleucine-valine enzymes by multivalent repression occurs mainly at the level of transcription. Kinetics of elongation of ilv mRNA after repression are consistent with the assumption that the mechanism of multivalent repression involves the prevention of further initiations by RNA polymerase.