Arabinose-leucine deletion mutants of Escherichia coli B-r

Functional limits of the araIc promoter suggest an additional regulatory site for araBAD expression

The araBAD promoter is defined, in part, by two types of cis-acting constitutive mutations, araIc at position -35 and araXc at position -10. Subcloning experiments demonstrated that the araIc and araIcXc promoters require DNA sequence information out to position -53 to -56 for maximum constitutive expression. This is 8 to 10 base pairs more DNA than is generally thought to be necessary for RNA polymerase interaction. The -53 to -56 region is required for glucose repression, suggesting that an additional factor interacts in this region and is necessary for maximum expression.

Studying promoters and terminators by gene fusion

Prokaryotic gene control signals can be isolated, compared, and characterized by precise fusion in vitro to the Escherichia coli galactokinase gene (galK), which provides both a simple assay and genetic selection. This recombinant galK fusion vector system was applied to the study of promoters and terminators recognized by the Escherichia coli RNA polymerase. Three promoters created by mutation from DNA sequences having no promoter function were characterized. Mutations that inactivate promoter function were selected, structurally defined, and functionally analyzed. Similarly, transcription termination was examined, and mutations affecting terminator function were isolated and characterized.

DNA sequence of the araBAD-araC controlling region in Salmonella typhimurium LT2

The araB and araC genes of Salmonella typhimurium have been cloned onto the plasmid pBR322. Restriction analysis and subcloning of restriction fragments localized these genes to a 4.4 kb DNA fragment. Complementation analysis revealed that the cloned araB and araC genes from S. typhimurium complemented araB and araC mutant strains of escherichia coli. Conversely, cloned araB and araC genes from E. coli complemented araB and araC mutant strains of Escherichia coli. Conversely, cloned araB and araC genes from E. coli complemented araB and ara C mutant strains of S. typhimurium. The DNA sequence was determined for the S. typhimurium araB and araC controlling region and for the initially translated portions of these genes. The nucleotide sequence of the araB promoter was 87% homologous with the same region in E. coli and contained no deletions or insertions relative to the E. coli sequence. The presumed AUG codon corresponding to the amino terminus of the S. typhimurium araC protein was in the same location as in E. coli. There was, however, considerable divergence for the E. coli sequence preceding the translation start site. The nucleotide sequence of the initial 237 bp in the open reading frame of the S. typhimurium araC gene was 78% homologous with the same sequence in E. coli. By comparison, the amino acid sequence for this region was 91% conserved.

The araIc mutation in Escherichia coli B/r

The araIc allele is a cis-acting mutation which has been used to define the araBAD promoter in Escherichia coli B/r. Nineteen araIc mutants were originally isolated by Englesberg and co-workers as Ara+ "revertants" of an araC deletion mutant (Englesberg et al. J. Mol. Biol. 43:281-298, 1969). The mutants constitutively expressed araBAD gene products in the absence of functional araC activator protein. Eight of the araIc mutations have been cloned by in vivo recombination onto pBR322-ara hybrid plasmids. Restriction and DNA sequence analysis of these araIc mutations showed that they result from a single base-pair change located at -35 in the araBAD promoter.

Construction of pBR322-ara hybrid plasmids by in vivo recombination

In vivo recombination was used to clone deletions of the araBAD-araC genes of Escherichia coli onto a hybrid pBR322-ara plasmid. Genetic and physical analyses demonstrated that the desired deletions had been recombined onto the plasmid. In addition to permitting a detailed physical analysis of various ara deletions, this procedure has generated a series of plasmid cloning vehicles that can be used to clone, by in vivo recombination, any ara point mutation located within the region covered by the deletions. Hybrid plasmids containing the cloned point mutation can be distinguished from the original cloning vehicle by genetic complementation. The desired recombinant plasmid can be easily obtained because the frequency of recombination between the plasmid ara region and the chromosomal ara region is 0.025%--3%. A plasmid containing a deletion which removes the ara controlling site region and the araC gene was used to clone two types of araBAD promoter mutations and an araC mutation by in vivo recombination. Genetic and physical analysis of these plasmids established that the mutations in question had been recombined on to the ara deletion plasmid. The application of this procedure to the ara genes and to other genetic systems is discussed.

Deoxyribonucleic acid sequence of araBAD promoter mutants of Escherichia coli

The controlling site region for the araBAD operon is defined, in part, by two classes of cis-acting constitutive mutations. The aralc mutations allow low-level constitutive expression of ara-BAD in the absence of the positive regulatory protein coded for by the araC gene, whereas the araXc mutations allow expression of araBAD in the absence of the cyclic adenosine monophosphate receptor protein. Six independently isolated aralc mutations and three independently isolated araXc mutations were cloned onto the plasmid pBR322 using in vitro recombinant deoxyribonucleic acid techniques and in vivo recombination between plasmid and chromosomal deoxyribonucleic acid. The location of these mutations was determined by deoxyribonucleic acid sequence analysis. All of the aralc mutations occurred at position -35 within the araBAD promoter (+1 = messenger ribonucleic acid start for araBAD) and resulted from an AT leads to GC transition. All of the araXc mutations occurred at position -10 within the araBAD promoter and resulted from a GC leads to AT transition. Models are presented to explain the mode of action of the aralc and araXc mutations.

In vivo titration of araC protein

The requirement for araC protein in the induction of the araBAD operon was investigated. Strains of Escherichia coli carrying an araC(Am) mutation and temperature-sensitive amber suppressors were used to vary the intracellular level of araC protein. The levels of araC protein studied ranged from 0.007 to 1.8 times the normal amount. The results indicate that the normal level of araC protein is just sufficient to provide maximal expression of the araBAD operon.

The araC promoter: transcription, mapping and interaction with the araBAD promoter

The start sites of the araC and araBAD gene messenger of E. coli were located by transcription in vitro from short DNA fragments, by high magnification electron microscopy and by genetic mapping. Transcription for these messengers proceeds in opposite directions from the start sites that are 150 base pairs apart. Transcription from the araBAD promoter requires araC protein plus arabinose and CAP protein plus cyclic AMP. In the experiments performed in vitro, inducing the araBAD promoter represses activity of the araC promoter.

Functional expression of cloned yeast DNA in Escherichia coli

A collection of hybrid circular DNAs was constructed in vitro using the poly(dA-dT) "connector" method: each hybrid circle contained one molecule of poly(dT)-tailed DNA of plasmid ColE1 (made linear by digestion with EcoRI endonuclease) annealed to a poly(dA)-tailed fragment of yeast (Saccharomyces cerevisiae) DNA, produced originally by shearing total yeast DNA to an average size of 8 X 10(6) daltons. This DNA preparation was used to transform E. coli cells, selecting colicin-E1-resistant clones that contain hybrid ColE1-yeast DNA plasmids. Sufficient numbers of transformant clones were obtained to ensure that the hybrid plasmid population was representative of the entire yeast genome. Various hybrid ColE1-yeast DNA plasmids capable of complementing E. coli auxotrophic mutations were selected from this population. Plasmid pYeleu 10 complements several different point or deletion mutations in the E. coli or S. typhimurium leuB gene (beta-isopropylmalate dehydrogenase); plasmids pYeleu11, pYeleu12, and pYeleu17 are specific suppressors of the leuB6 mutation in E. coli C600. Plasmid pYehis2 complements a deletion in the E. coli hisB gene (imidazole glycerol phosphate dehydratase). Complementation of bacterial mutations by yeast DNA segments does not appear to be a rare phenomenon.

Constitutive mutations in the controlling site region of the araBAD operon of Escherichia coli B/r that decrease sensitivity to catabolite repression

Strains of Escherichia coli B/r containing a deletion of the regulatory gene araC are Ara-. Slow-growing revertants of these strains were isolated and designated aralc because they contain a second mutation in a controlling site, aral, that allows for a low level of constitutive expression of the araBAD operon (Englesbert et al., 1969). We mutagenized aralc delta C strains and selected mutants that grow faster in mineral L-arabinose medium. The new mutations, called araXc, map very close to the original aralc mutations and are in the controlling site region between araB and araC. The aralcXc delta C strains have a higher constitutive level of expression of the araBAD operon than the aralc delta C parents. The araXc mutations are cis acting and decrease the araBAD operon's sensitivity to catabolite repression. The araBAD operon is expressed equally well in ara delta C and ara C cya crp backgrounds. The repressor form of ara C protein is able to repress the constitutive synthesis due to the ara Xc allele.

The site for catabolite deactivation in the L-arabinose BAD operon in Escherichia coli B/r

A series of deletions beginning in the leu operon and continuing into the araC gene and also into the ara controlling site region were analyzed in reciprocal merodiploids, e.g., F' A2Cc67/B24delta719, F' B24delta719/A2Cc67, for their effects on catabolite deactivation (CD). The results of these experiments are consistent with placing the catabolite gene activator-cyclic AMP sensitive site in the controlling site region between araB and araO. With a deletion mutant, delta1109, that places araBAD under leu control when transcription begins at leuP, the araBAD operon is immune to CD even though araCGA, araP and araI are intact and functional. To focus attention on the fine structure and related functions of this region we propose that the three proteins that function therein have separate sites of action: araI (initiator-site for activator), araP (promoter-site for RNA polymerase) and ara(CGA) (catabolite gene activator-site for CGA-cAMP). None of the eighteen initiator constitutive mutants (Ic) tested have any significant effect on catabolite derepression or on the maximal level of expression of the operon supporting the view that the araI site may be distinct from araP and ARA(CGA). A series of constitutive mutants in the araC gene (Cc) also have no pronounced effect on catabolite deactivation.

Mutations affecting catabolite repression of the L-arabinose regulon in Escherichia coli B/r

Expression of the L-arabinose regulon in Escherichia coli B/r requires, among other things, cyclic adenosine-3', 5'-monophosphate (cAMP) and the cAMP receptor protein (CRP). Mutants deficient in adenyl cyclase (cya-), the enzyme which synthesizes cAMP, or CRP (crp-) are unable to utilize a variety of carbohydrates, including L-arabinose. Ara+ revertants of a cya-crp- strain were isolated on 0.2% minimal L-arabinose plates, conditions which require the entire ara regulon to be activated in the absence of cAMP and CRP. Evidence from genetic and physiological studies is consistent with placing these mutations in the araC regulatory gene. Deletion mapping with one mutant localized the site within either araO or araC, and complementation tests indicated the mutants acted trans to confer the ability to utilize L-arabinose in a cya-crp- genetic background. Since genetic analysis supports the conclusion, that the mutant sites are in the araC regulatory gene, the mutants were designated araCi, indicating a mutation in the regulatory gene affecting the cAMP-CRP requirement. Physiological analysis of one mutant, araCi1, illustrates the trans-acting nature of the mutation. In a cya-crp- genetic background, araCi1 promoted synthesis of both isomerase, a product of the araBAD operon, and permease, a product of the araE operon. Isomerase and permease levels in araCi1 cya+ crp+ were hyperinducible, and the sensitivity of each to cAMP was altered. Two models are presented that show the possible mutational lesion in the araCi strains.

Electron microscopy of gene regulation: the L-arabinose operon

Unlike normal cells, malignant rat and two simian virus 40-transformed human cell lines can neither grow nor survive in B12- and folate-supplemented media in which methionine is replaced by homocysteine. Yet three lines of evidence indicate that the malignant and transformed cells synthesize large amounts of methionine endogenously through the reaction catalyzed by 5-methyltetrahydropterolyl-L-glutamate: L-homocysteine S-methyltransferase (EC 2.1.1.13). (1) The activities of this methyltransferase were comparable in extracts of malignant and normal cells. (2) The uptake of radioactive label from [5-14C]methyltetrahydropteroyl-L-glutamic acid (5-Me-H4PteGlu) was at least as great in the malignant cells as in the normals and was nearly totally dependent on the addition of homocysteine, the methyl acceptor; furthermore, 59-84% of the label incorporated by cells was recovered as methionine.

Fusion of the Escherichia coli lac genes to the ara promoter: a general technique using bacteriophage Mu-1 insertions

The lac genes were fused to the ara promoter by means of phage phi 80 translocations of the lac and ara genes to att80. Homology for a crossover between the nonhomologous ara and lac operons was provided by mu insertions. Selection for recombinants within the mu insertions generated strains that had the ara promoter on one side of a mu insertion and the lac genes on the other side. ara-lac fusions were obtained from these strains by deleting the mu insertion. These fusions extend the techniques available for studies on the lac operon to studies on the ara operon. It should be possible to fuse other operons by this method.

Transcriptional control in the L-arabinose operon of Escherichia coli B-r

The structural genes involved in l-arabinose metabolism are regulated by the protein product of the araC gene. This protein functions as both an activator and repressor of enzyme synthesis in this gene complex. Using lambdah80dara deoxyribonucleic acid in hybridization studies, we have shown that the ara operon, including structural genes araB, araA, and araD, is transcribed in the direction araB to araD and that initiation of transcription of these genes requires an active araC gene. The half-life of this message, approximately 3 min at 30 C, is the same in the presence or absence of the araC protein in the activator state. However, an unexplained 2-min lag in decay of ara messenger ribonucleic acid that does not occur in decay of lac messenger ribonucleic acid is observed. This lag period requires activated araC protein.

Mutations in the L-arabinose operon of Escherichia coli B-r that result in hypersensitivity to catabolite repression

Two independent mutants resistant to l-arabinose inhibition only in the presence of d-glucose were isolated from an l-arabinose-sensitive strain containing the araD139 mutation. Preliminary mapping studies indicate that these mutations are closely linked to the araIOC region. Addition of d-glucose to growing cultures of these mutants results in a 95 to 98% repression of ara operon expression, as compared to a 50% repression of the parental control. Since cultures of both mutant and parental strains undergo a 50% repression of lac operon expression upon addition of glucose, the hypersensitivity to catabolite repression exhibited by these mutants is specific for the ara operon. Addition of cyclic adenosine monophosphate reverses the catabolite repression of the ara operon in both mutant and parent strains to 70 to 80% of the control. It is suggested that in these mutants the affinity of the ara operon initiator region for the cAMP-catabolite-activator protein complex may have been altered.

Genetic analysis of the leucine region in Escherichia coli B-r: gene-enzyme assignments

Genetic mapping by transduction and conjugation using F(-) and F' strains carrying either point mutations in the l-arabinose or leucine regions or ara-leu fusion-deletion mutations has resulted in a detailed genetic map of the arabinose-leucine region of Escherichia coli B/r. These studies have identified four genes in the leucine region having the same order as found in Salmonella typhimurium: ara... leuDCBA.

Genetic fine structure of the leucine operon of Escherichia coli K-12

The order of mutational sites in 10 independently isolated leucine auxotrophys of Escherichia coli K-12 was determined by three-point reciprocal transductions. The sites of mutation mapped in linear sequence in a cluster; all leucine auxotrophic mutations were cotransducible with mutations in the arabinose operon. The mutations were assigned to four complementation groups by abortive transduction tests, designated D, C, B, and A, reading in a clockwise direction from the arabinose operon. Enzyme analyses showed that strains with a mutation in gene A lacked alpha-isopropylmalate synthetase activity (EC 4.1.3), and those with a mutation in gene B lacked beta-isopropylmalate dehydrogenase activity (EC 1.1.1). It is concluded that the gross structure of the leucine operon in E. coli is closely similar to, if not identical with, the gross structure of the leucine operon in Salmonella typhimurium.

L-arabinose isomerase formation in a conditional mutant of gene araA of Escherichia coli B-r

A temperature-sensitive mutant of Escherichia coli in which the synthesis of l-arabinose isomerase is blocked during growth at 42 C was found to possess the following properties. (i) The mutation occurred in the structural gene for the isomerase, gene araA. (ii) During growth at elevated temperatures the mutant accumulates a product which is a precursor to the active enzyme. (iii) The precursor produced at 42 C is slowly converted to active enzyme at 28 C in the absence of protein and ribonucleic acid synthesis. It is concluded that the mutation results in a change in the structure of isomerase which causes formation of active enzyme to be thermolabile at a step beyond the level of translation.

Characterization of strong polar mutations in a region immediately adjacent to the L-arabinose operator in Escherichia coli B-r

Seven l-arabinose-negative mutations are described that map in three genetically distinct regions immediately adjacent to the araO (operator) region of the l-arabinose operon. All seven mutants revert spontaneously, exhibit a cis-dominant, trans-recessive polarity effect upon the expression of l-arabinose isomerase (gene araA), and fail to respond to amber, ochre, or UGA suppressors. Three of these mutants exhibit absolute polarity and are not reverted by the mutangens 2-aminopurine, diethyl sulfate, and ICR-191. These may have arisen as a consequence of an insertion mutation in gene araB or in the initiator region of the l-arabinose operon. The four remaining mutants exhibit strong but not absolute polarity on gene araA and respond to the mutagens diethyl sulfate and ICR-191. Three of these mutants are suppressible by two independently isolated suppressors that fail to suppress known nonsense codons. Partially polar Ara(+) revertants with lesions linked to ara are obtained from three of the same four mutants. These polar mutants, their external suppressors, and their partially polar revertants are discussed in terms of the mechanism of initiation of expression of the l-arabinose operon.

New amino acid regulatory locus having unusual properties in heterozygous merodiploids

Spontaneous mutants of Escherichia coli B/r resistant to 5',5',5',-trifluoro-dl-leucine contain defects in a gene which maps to the left of the threonine region. Low-level constitutive expression of the isoleucine-valine and leucine operons is caused by this mutation in haploid strains. This is in contrast to extremely high levels of gene expression in the heterozygous merodiploids (F' wild type/mutant allele). The properties of these mutants define a new locus and suggest that it encodes a subunit protein which is involved in the repression of the structural genes for the branched-chain amino acid pathways.

Location and orientation of the phoA locus on the Escherichia coli K-12 linkage map

The order of gene loci in the phoA-phoR region of the Escherichia coli K-12 linkage map was demonstrated to be lac phoA proC phoR. The end of the phoA locus corresponding to the amino terminus of alkaline phosphatase was shown to be the end nearer proC. Translation (and transcription) of phoA is therefore in the anticlockwise direction relative to the conventional E. coli linkage map.

Purification of the araC protein

The araC gene product, a regulatory protein required for expression of the L-arabinose operon, has been purified by affinity chromatography on Sepharose 4B to which 4-aminophenyl-beta-D-6-deoxygalactopyranoside (an anti-inducer of the L-arabinose operon) had been covalently attached by means of a 4-aminophenylbutanamido side chain. Evidence is presented showing that the protein binds specifically to ara DNA.

Hyperinducibility as a result of mutation in structural genes and self-catabolite repression in the ara operon

Mutations in gene araB producing an l-arabinose-negative phenotype cause either an increase (hyperinducible), decrease (polar), or have no effect at all on the inducible rate of expression of the l-arabinose operon. Fourteen araB gene mutants exhibiting such effects were shown to be the result of: nonsense, frameshift, or missense mutations. All missense mutants were hyperinducible, exhibiting approximately a twofold increase in rate of l-arabinose isomerase production. All frameshift and most nonsense mutants exhibited polar effect. One nonsense mutant was hyperinducible. The cis-dominant polar effect of nonsense and frameshift mutants (as compared to induced wild type) were more pronounced in arabinose-utilizing merodiploids and in araBaraC(c) double mutants where inducible and constitutive enzyme levels are respectively determined. On the other hand, in arabinose-utilizing merodiploids, missense mutations no longer exhibited hyperinducibility but displayed a wild-type level of operon expression. Increases in the wild type-inducible rate of expression of the operon were found when growth rate was dependent on the concentration of l-arabinose. Cyclic 3',5'-adenosine monophosphate also stimulated expression of the operon with the wild type in a mineral l-arabinose medium. These observations are explained on the basis that the steady-state expression of the l-arabinose operon OIBAD is dependent on the concentration of (i) l-arabinose, the effector of this system, which stimulates the expression of the operon, and (ii) catabolite repressors, produced from l-arabinose, which dampen the expression of the operon. We have termed the latter phenomenon "self-catabolite" repression.

Polarity in gene araB of the l-Arabinose operon in Escherichia coli B/r

A series of mutations are described which map in the araB gene of the l-arabinose operon and exert a polar effect on gene araA, the structural gene for the l-arabinose isomerase. Ten of the 20 araB point mutants examined exhibited absolute polarity and may represent insertions of genetic material into the araB gene. The remaining 10 point mutants exhibit strong polarity (less than 10% of the normal wild-type inducible level of isomerase) and may represent a class of externally suppressible polar mutations other than amber or ochre. Seven of the 12 araB deletion mutants examined, or 58%, exhibit polarity, suggesting that a shift in the reading frame has been generated in the polycistronic message for the l-arabinose operon. The remaining, presumably in-phase, deletion mutants exhibit hyperinducible levels of isomerase, an effect that is eliminated when an araB(+) gene is introduced in the trans position. The hyperinducibility effect is discussed in terms of a model for self-catabolite repression, originally proposed by Katz and Englesberg.

L-arabinose binding protein from Escherichia coli B-r

A protein which is capable of binding l-arabinose-1-(14)C has been isolated from l-arabinose-induced cultures of Escherichia coli B/r. Analysis for this l-arabinose-binding protein (ABP) in a number of l-arabinose-negative mutants suggests that the ABP is not coded for by any of the known genetic units of the l-arabinose complex yet is under the control of the regulator gene araC. The ABP has been purified and found to bind l-arabinose, d-fucose, d-xylose, and l-ribulose with decreasing affinities. The K(m) for l-arabinose is 5.7 x 10(-6)m. The molecular weight, as determined by equilibrium centrifugation, was found to be 32,000. The protein was observed to have many features that liken it to other recently isolated binding proteins that have been implicated in the active transport of small molecules.

Compounds which serve as the sole source of carbon or nitrogen for Salmonella typhimurium LT-2

About 600 compounds were screened as possible carbon or nitrogen sources for Salmonella typhimurium LT-2. About 100 utilizable compounds were found.