Identification of the protein products of the rrnC, ilv, rho region of the Escherichia coli K-12 chromosome

Identification of a cloned cytokinin biosynthetic gene

A small region of the Ti plasmid (the tmr locus), thought to be involved in phytohormone metabolism in Agrobacterium tumefaciens-transformed plant tissue, was cloned and expressed in Escherichia coli. By enzyme assay, the tmr locus was shown to encode isopentenyltransferase, an enzyme that catalyzes the first step in cytokinin biosynthesis.

Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol

Laboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited thus far by the inability of workers to readily detect mutations in evolved microbial strains on a genome scale. This limitation has now been overcome by recently developed genome sequencing technology that allows workers to identify all accumulated mutations that appear during laboratory adaptive evolution. In this study, we evolved Escherichia coli K-12 MG1655 with a nonnative carbon source, l-1,2-propanediol (l-1,2-PDO), for approximately 700 generations. We found that (i) experimental evolution of E. coli for approximately 700 generations in 1,2-PDO-supplemented minimal medium resulted in acquisition of the ability to use l-1,2-PDO as a sole carbon and energy source so that the organism changed from an organism that did not grow at all initially to an organism that had a growth rate of 0.35 h(-1); (ii) six mutations detected by whole-genome resequencing accumulated in the evolved E. coli mutant over the course of adaptive evolution on l-1,2-PDO; (iii) five of the six mutations were within coding regions, and IS5 was inserted between two fuc regulons; (iv) two major mutations (mutations in fucO and its promoter) involved in l-1,2-PDO catabolism appeared early during adaptive evolution; and (v) multiple defined knock-in mutant strains with all of the mutations had growth rates essentially matching that of the evolved strain. These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate.

Conversion of aldonic acids to their corresponding 2-keto-3-deoxy-analogs by the non-carbohydrate enzyme dihydroxy acid dehydratase (DHAD)

Aldonic acids containing four to six carbon atoms were tested as potential substrates of dihydroxy acid dehydratase (DHAD), an enzyme from the biosynthetic pathway of branched chain amino acids. Novel assay systems for observing the course of DHAD catalysed reactions were developed in order to adapt the enzyme to extended practical applications. Kinetic studies for the new substrates (12/13) as well as inhibitor kinetics for the substrate analogue 3-deoxy-aldonic acids (25, 27 and 29) were performed. These gave indications for the restrictions of substrate modifications and contributed to the understanding of the individual effects. Finally L-threonic acid (12) and D-erythronic acid (13) could be successfully applied as substrates for DHAD and this led to the chemoenzymatic synthesis of their 2-keto-3-deoxy-analogue (20) in a preparative scale.

Sequence and transcriptional activity of the Escherichia coli K-12 chromosome region between rrnC and ilvGMEDA

We previously identified a protein related to the expression of the ilvGMEDA cluster of Escherichia coli K-12. It was observed that this ilv-related protein was produced at higher levels in UV irradiated cells infected with lambda dilvGMEDA phage with specific ilvG mutations (ValR), compared to phage carrying the wild-type(ValS) ilvG allele. The gene encoding this protein was further localized to a region between rrnC and ilvGMEDA by analyzing restriction fragment subsets in maxicells. We have now determined the nucleotide (nt) sequence of the 3.5-kb segment between rrnC and ilvGMEDA, and two open reading frames (ORFs) are present in the region expected to contain the ilv-related gene. These ORFs predicts Mrs of 18,751 (ORFI) and 20,085 (ORFII) Da, and both ORFs have a strong probability to encode proteins based on codon frequency analysis. Maxicell analysis revealed that a 1319-bp HindIII-SmaI fragment containing ORFI encodes the ilv-related peptide. We deleted a ClaI fragment that removed a portion of ORFI encoding the C-terminal region of the peptide, and maxicell analysis revealed a decrease in the size of the protein produced in accord with the prediction. RNA slot blots and Northern blots were used to characterize transcripts encoding ORFI. A transcript initiated 112 nt from the ilvGp2 promoter, but proceeding in the opposite direction, may encode the ORFI peptide.

Suppression of the Escherichia coli dnaA46 mutation by a mutation in trxA, the gene for thioredoxin

The dasC mutation, an extragenic suppressor of dnaA46, was mapped by P1 transduction near the rep, trxA, rho region of the Escherichia coli chromosome. The dasC mutation could not be separated from trxA by P1 transduction indicating that dasC and trxA are allelic. Multicopy plasmids containing an intact trxA gene were able to reverse the suppressive effect of the dasC mutation on the dnaA46 mutation. Introduction of a frameshift mutation into the cloned trxA coding region abolished the ability of these recombinant plasmids to reverse the suppressive effect. These results indicate that dasC is allelic with trxA, the gene encoding thioredoxin.

Influence on immunoreactive folate-binding proteins of extracellular folate concentration in cultured human cells

The influence of extracellular folate concentration on cellular levels of the folate transport protein and its soluble product was studied directly in cultured human nasopharyngeal carcinoma (KB) cells. As determined by radioimmunoassay, levels of the folate transport protein and the soluble folate-binding protein were 58 +/- 17 (mean +/- SD) and 5 +/- 2 pmol/mg cell protein, respectively, in KB cells maintained in standard medium (containing 2,300 nM folic acid). These levels significantly increased to 182 +/- 34 and 26 +/- 6 pmol/mg cell protein, respectively, in KB cells serially passaged in low folate medium (containing 2-10 nM 5-methyltetrahydrofolate). Increases in folate-binding protein levels occurred more rapidly in KB cells serially passaged in very low folate medium containing less than 2 nM folate and were prevented by the addition of 100 nM 5-methyltetrahydrofolate or 0.1-1 microM 5-formyltetrahydrofolate to this medium. When KB cells which had been passaged in low folate medium were passaged back into either standard medium or low folate medium supplemented with reduced folates, the levels of both folate-binding proteins fell linearly towards the levels in KB cells continuously maintained in standard medium. The folate transport protein was identified in and underwent similar changes in human and mouse mammary tumor cells. These studies indicate that the folate transport system is probably regulated by the extracellular folate concentration through changes in intracellular metabolite levels.

Generation of a detailed physical and genetic map of the ilv-metE-udp region of the Escherichia coli chromosome

The entire ilv-metE-udp region of the Escherichia coli chromosome has been cloned in two steps using the lambda replacement vector EMBL4. A detailed restriction map for approximately 70 X 10(3) bases of DNA has been generated. The gpp and udp structural genes have been identified, the cya and metE genes have been physically located, and the direction of recQ gene transcription has been determined. By examining a variety of plasmid subclones, 44 polypeptides have been detected using maxicell and minicell analysis, accounting for 70% of the maximum coding capacity of the entire region. On the basis of the observed gene density in the ilv-metE-udp region, a total number of 3000 genes is predicted for the entire E. coli chromosome. In addition, anomalies in cotransduction frequencies that have been observed in this region have been interpreted by employing a new formula that incorporates the effects of different transducing fragment representations and recombination probabilities.

The complete nucleotide sequence of the ilvGMEDA operon of Escherichia coli K-12

In this report we present the complete nucleotide sequence of the ilvGMEDA operon of Escherichia coli. This operon contains five genes encoding four of the five enzymes required for the biosynthesis of isoleucine and valine. We identify and describe the coding regions for these five structural genes and the structural and functional features of the flanking and internal regulatory regions of this operon. This new information contributes to a more complete understanding of the overall control of the biosynthesis of isoleucine and valine.

The complete nucleotide sequence of the ilvGMEDA cluster of Escherichia coli K-12

The ilvGMEDA gene cluster of Escherichia coli K-12 has been the focus of intensive genetic and biochemical analysis for the past 30 years. Genetic regulation of the ilvGMEDA cluster involves attenuation, internal promoters, internal Rho-dependent termination sites, a site of polarity in the ilvG pseudogene of the wild-type organism, and autoregulation by the ilvA gene product, the biosynthetic L-threonine deaminase. We have now completed the nucleotide sequence of the 6600-bp cluster and have analyzed it, along with the ilvYC, ilvBN, and ilvIH genes, for codon frequencies and possible evolutionary relationships. The isoleucine content of each of the gene products of the ilvGMEDA cluster is quite similar (less than a two-fold variation), thus excluding one possible interpretation of the isoleucine-specific downstream amplification phenomenon. There is no evidence for retrograde evolution in the cluster since no significant homologies are detectable among genes that catalyze sequential reactions of the pathway. A highly significant homology does exist, however, between the threonine deaminases of yeast mitochondria and E. coli. The sequence at the boundary of the ilvA and ilvD genes is TAATAATG, so that the second TAA stop codon of ilvD overlaps the ATG initiation codon of ilvA.

Assessment of plasmid profile, exoenzyme activity, and virulence in recent human isolates of Yersinia enterocolitica

We examined a group of 23 recent clinical isolates of Yersinia enterocolitica recovered from symptomatic patients residing in the New York, N.Y. area. These isolates were tested for the presence of plasmids, exoenzyme activity, mouse lethality, and phenotypic properties postulated to correlate with virulence. Of the 23 isolates, 17 harbored a 60- to 65-kilobase (kb) plasmid. Six isolates were lethal for white mice, showed the phenotypic markers of autoagglutination and calcium dependence for growth at 37 degrees C, and contained a 60- to 65-kb plasmid. Restriction endonuclease analysis with several different enzymes revealed the presence of three distinct plasmid profiles in these isolates. Isolates with a single plasmid of 60 to 70 kb, typical for this species, were detected, but these were of three distinct types as judged from restriction enzyme digestion. One strain was unusual among clinical isolates of Y. enterocolitica in that it contained at least four distinct plasmids. In addition, this nontypable strain showed exoenzymatic activity similar to that of serogroup O8 isolates, was not lethal to mice, and did not require calcium for growth at 37 degrees C.

Physical analysis of deletion mutations in the ilvGEDA operon of Escherichia coli K-12

DNA-DNA hybridization of cloned segments of the Escherichia coli K-12 ilvGEDA operon to genomic blots was used to determine the physical dimensions of a series of deletion mutations of the ilvGEDA operon. The smallest mutation resulted from the deletion of approximately 200 base pairs from within ilvD, whereas the largest mutation resulted from the deletion of 17 kilobases including the rep gene. The structure of three of these mutants indicates that formation of the deletions was mediated by Tn5 (or Tn5-131) that is retained in the chromosome. This is the first observation of this type of Tn5-mediated event. Our analysis of the total acetohydroxy acid synthase activity of strains containing deletions of ilvG indicates that the truncated ilvG polypeptide of wild-type E. coli K-12 lacks enzyme activity. The small 200-base-pair deletion of ilvD confirms the presence of a strong polar site 5' to ilvA. The detailed structure of these deletions should prove useful for the investigation of other genes in this region. This genomic analysis demonstrates that the ilv restriction site map that was established previously by the analysis of recombinant bacteriophage and plasmids is identical to that on the genome.

Internal promoter in the ilvGEDA transcription unit of Escherichia coli K-12

Segments of the ilvGEDA transcription unit have been cloned into the promoter tester plasmid pMC81. This vector contains cloning sites situated upstream of the lacZ gene coding for beta-galactosidase. Using this method we have quantitatively evaluated in vivo (i) the activity of previously described promoter, pG, preceding ilvG; (ii) the relative activity of pE promoter, previously postulated to be located between ilvG and ilvE; and (iii) the effect of the frameshift site present in the wild-type ilvG gene by comparison with mutant derivatives lacking this frameshift site. Isogenic derivatives of strain MC1000 were constructed by transduction with phage P1 grown on rho-120, delta(ilvGEDA), delta(ilvED), and ilvA538 hosts. The potential effects of these alleles that were previously postulated to affect ilvGEDA expression were assessed in vivo by monitoring beta-galactosidase production directed by ilv DNA fragments. Cloned ilv segments were also tested for activity in vitro with a DNA-directed coupled transcription and translation system. The production in vitro of ilv-directed ilv gene expression and beta-galactosidase expression with ara-ilv-lac fusions paralleled the in vivo activity.

Nucleotide sequence of the immunity region of Bacillus subtilis bacteriophage phi 105: identification of the repressor gene and its mRNA and protein products

A gene involved in the regulation of lysogeny in the temperate Bacillus subtilis phage phi 105 has been identified and isolated. A plasmid, pDC4, was constructed that contains a 740-bp HindIII-PvuII fragment that is derived from the phi 105 immunity region and is capable of rendering B. subtilis immune to infection by phi 105. Three different hybrid plasmids that contain the 740-bp fragment, pAG101 [Cully and Garro, J. Virol. 34 (1980) 789-791], pDC1 and pDC2, were found to synthesize a common 18-kDal polypeptide in B. subtilis minicells and Escherichia coli maxicells. The nucleotide (nt) sequence of this region revealed three open reading frames (ORFs) that predict proteins with Mrs of 16521, 7332, and 5516. In vivo synthesized phi 105 prophage RNA was mapped by primer extension and shown to be transcribed from the DNA strand coding for the Mr 16521 protein. The 5' end of the phi 105 lysogen RNA was mapped to a region that contains conserved sequences for RNA polymerase recognition.

Genetic and physical analysis of the thioredoxin (trxA) gene of Escherichia coli K-12

The trxA gene of Escherichia coli K-12 has been cloned into multicopy plasmids on DNA fragments of varying sizes. The smallest of these was a 1-kb fragment resulting from partial digestion with Sau3A (pBHK10). The complete nucleotide sequence of the trxA gene and its promoter was determined. Comparison of the DNA sequence with the published amino acid sequence revealed the inversion of two amino acid pairs and the possibility of a leader peptide 18 amino acids in length. Three-factor P1 transductional crosses and physical mapping experiments have determined a map order of ilv-trxA-uvrD-corA-metE.

Reduced expression of the isoleucine and valine enzymes in integration host factor mutants of Escherichia coli

The level of the isoleucine and valine (Ilv) enzymes specified by the ilvB and ilvGEDA operons is reduced in integration host factor mutants (himA and himD) of Escherichia coli K-12. Growth inhibition of these strains in minimal medium can be explained by the decreased amounts of one of the Ilv enzymes, acetohydroxy acid synthase I (AHASI). No growth inhibition, or reduction in AHASI activity, was found in a himA derivative of a mutant strain containing high constitutive levels of AHASI. A strong correlation was observed in himA strains between the reduced amount of the Ilv enzymes and of Ilv-specific messenger RNA. These data suggest that integration host factor may be a positive effector for transcription of the ilvB and ilvGEDA operons.

Location of the rho gene and characterization of lambda ilv-gal derivatives of lambda ilv-rho bacteriophage

The location of the rho gene and its position relative to the ilv genes of Escherichia coli K-12 was analyzed using genetic criteria, restriction enzyme cleavage, and maxicell analysis. Plasmids were constructed with deletions of the rho gene introduced in vitro, and lambda ilv-gal derivatives of lambda ilv-rho bacteriophage were isolated by recombination in vivo. A HindIII restriction fragment of 8 kilobases (kb) previously shown to contain at least part of the rho gene (Gray et al. 1981) was cloned into plasmid pMC81. This vector has transcription stop sites that present read-through expression of cloned genes from either direction, and cloning sites upstream of the lacZ gene coding for beta-galactosidase. The position of the rho gene and flanking sequences required for its expression were further localized to a region of approximately 2 kb by introducing deletions using restriction enzyme treatment of these plasmids. A promoter in the rho region was found to direct beta-galactosidase synthesis in these plasmid derivatives. Derivatives of lambda ilv-rho phage were isolated in vivo by pyrophosphate chelation selection for phage with reduced genome size. Restriction enzyme analysis of twelve of these derivatives revealed an unexpected bias towards phage recombinants as opposed to simple internal deletions.

Autoregulation of the rho gene of Escherichia coli K-12

It has previously been proposed, based on indirect evidence, that the Rho protein may control the expression of the rho gene. Using an in vitro system for the transcription and translation of the rho gene cloned into plasmid pBR322, we tested this hypothesis directly by monitoring the effect in vitro of excess or limiting Rho protein. The addition of purified Rho protein suppresses Rho synthesis in vitro. The addition of antibody to Rho specifically stimulates Rho synthesis in vitro. The stimulation of Rho factor synthesis by antibody to Rho is reversed by Rho protein. Rho factor purified from a strain with a mutationally altered rho gene (rho-115) does not suppress Rho synthesis in vitro. These results provide convincing evidence that the rho gene is subject to autoregulation.

Identification and control of synthesis of the dsdC activator protein

Operon fusions between the D-serine deaminase regulatory and structural genes and lacZ were constructed and used to examine the control of expression of the positive regulatory gene, dsdC. Merodiploid strains containing both dsdCp::Mu d (lac Apr) and dsdC+A+ produced only one-fourth as much beta-galactosidase as did the haploid dsdCp::Mu d (lac Apr) strains, indicating that the dsdC+ product repressed its own synthesis. The repression was reversed by D-serine. dsdC expression was not depressed in a cya background. The basal level of D-serine deaminase was the same in wild-type and dsdCp fusion strains. The dsdC gene product was identified in maxicell strains harboring dsd plasmids as a 34,000-dalton protein. dsdC gene transcription proceeded clockwise; thus, its promoter is adjacent to that of dsdA.

Relative map location of the rep and rho genes of Escherichia coli

The rep gene of Escherichia coli was mapped between ilvC and rho by three-factor P1 transductional crosses and also by complementation with a set of lambda transducing phages that contain known amounts of bacterial DNA linked to ilvC. The physical distance between ilvC and rep and between rep and rho were calculated with an accuracy of +/- 0.4 kilobase to be 0 less than or equal to ilvC-rep less than or equal to 3.4 kilobases and 2.0 less than or equal to rep-rho less than or equal to 6.0 kilobases. It was shown that rho-15 is Gro+ for phage ST-1. An ilv::Tn10 mutation was located in ilvY.

Mutations in genes cpxA and cpxB of Escherichia coli K-12 cause a defect in acetohydroxyacid synthase I function in vivo

Mutations in Escherichia coli genes cpxA and cpxB together cause a temperature-sensitive defect in isoleucine and valine syntheses that is related specifically to acetohydroxyacid synthase I. This enzyme catalyzes the first pair of homologous reactions required for the synthesis of these two amino acids. At both permissive and nonpermissive temperatures, mutant cells containing ilvB (the structural gene for acetohydroxyacid synthase I) cloned in a derivative of plasmid pBR322 synthesized comparable amounts of ilvB mRNA and contained several times the enzyme activity normally required to sustain exponential growth, yet these cells remained temperature sensitive for growth in the absence of isoleucine and valine. These observations suggest that the primary effect of the cpx mutations is to block enzyme function in vivo. The enzyme was unstable in mutant cells at growth temperatures above 37 degrees C, but this instability appeared to be a secondary effect on the cpx mutations.

Absence of significant membrane localization of the proteins coded by the ilvGEDAC genes of Escherichia coli K-12

We previously characterized a set of lambda dilv phages by genetic, restriction enzyme, and heteroduplex analyses and tentatively correlated isoleucine-valine gene products with specific ilv DNA segments by using cloned ilv segments in maxicells and lambda dilv phage infection of UV-irradiated cells. In this work, the identity of the ilvC gene product, alpha-acetohydroxy acid isomeroreductase, was confirmed by demonstrating its induction by the physiological inducers alpha-acetolactate and alpha-acetohydroxybutyrate. The identity of the ilvE gene product, transaminase, B, was confirmed by antibody precipitation of the purified enzyme. Phage derivatives with ilv regulatory mutations were found to have the predicted effect upon the ilvGEDA and ilvC protein products. The distribution of the ilvGEDA and ilvC gene products in the soluble, periplasmic, inner membrane, and outer membrane fractions was examined, and no significant membrane association was observed. The expression of the ilv genes in the lambda dilv phage from ilv and phage lambda promoters was compared in order to determine the fractional contribution of each to ilv gene expression. An additional protein of 54,000 daltons that was not detected in the previous analysis was observed to be coded by a bacterial gene but was produced only by readthrough from phage promoters.

Identification of a protein of 15,000 daltons related to isoleucine-valine biosynthesis in Escherichia coli K-12

The effect of the ilvG671, ilvG468, and ilvG603 mutations (phenotype, IlvG+ Valr; formerly ilvO) upon proteins synthesized was determined by infection of irradiated Escherichia coli K-12 cells, using specifically constructed derivatives of lambda dilv phage. These ilvG alleles are similar to the previously studied ilvG2096(Valr) allele in that they activate the latent ilvG gene which is present in the wild-type strain, leading to the synthesis of a 62,000-dalton protein. In addition, all of these ilvG (Valr) alleles increase the synthesis of a 15,000-dalton protein. To localize the gene coding for the 15,000-dalton protein, the proteins produced in maxicells containing plasmids with specific deletions of ilv and rrnX DNA segments were analyzed. The gene coding for the 15,000-dalton protein was located within a region about 1,000 base pairs long between ilv and trpT. The function of the 15,000-dalton protein is not known.

Cloning of the ilvA538 gene coding for feedback-hypersensitive threonine deaminase from Escherichia coli K-12

A variety of experimental results implicate the ilvA gene product, threonine deaminase, as an autoregulatory protein that affects the expression of its own gene and those coding for some related proteins. Some of the most direct evidence comes from the analysis of mutations in the ilvA gene with pleiotropic genetic regulatory effects. The most extensively documented mutation, ilvA538, lowers the expression of and abolishes repression control of the ilvGEDA transcription unit. A pleiotropic effect of the ilvA538 mutation, which may be either incidental or mechanistically related to the loss of repression control, renders threonine deaminase feedback hypersensitive to the inhibition of catalytic activity by the pathway end product, isoleucine. We transferred this mutation to lambda dilv phage and pBR322 derivatives. Direct enzyme assay of the plasmid- and phage-coded ilvA538 gene product in delta ilv hosts confirmed the feedback hypersensitivity of the enzyme product. In conjunction with the ilvG671 (phenotype, ILvG+ Valr; previously designated ilvO671) allele located in cis, high levels of the plasmid and lambda dilv phage-coded mutant enzyme suitable for protein purification were observed. Deletion mapping experiments with lambda dilv phage confirmed that the ilvA538 mutation, and not mutations promoter proximal to ilvD (transcription is from ilvG to ilvA), confer a loss of repression control. These genetic mapping studies indicate, however, that an additional mutation(s) may be present that contributes, at least in part, to the reduced enzyme levels in strains with the ilvA538 mutation.