Altered expression of biodegradative threonine dehydratase in Escherichia coli mutants

Catabolism of Amino Acids and Related Compounds

This review considers the pathways for the degradation of amino acids and a few related compounds (agmatine, putrescine, ornithine, and aminobutyrate), along with their functions and regulation. Nitrogen limitation and an acidic environment are two physiological cues that regulate expression of several amino acid catabolic genes. The review considers Escherichia coli, Salmonella enterica serovar Typhimurium, and Klebsiella species. The latter is included because the pathways in Klebsiella species have often been thoroughly characterized and also because of interesting differences in pathway regulation. These organisms can essentially degrade all the protein amino acids, except for the three branched-chain amino acids. E. coli, Salmonella enterica serovar Typhimurium, and Klebsiella aerogenes can assimilate nitrogen from D- and L-alanine, arginine, asparagine, aspartate, glutamate, glutamine, glycine, proline, and D- and L-serine. There are species differences in the utilization of agmatine, citrulline, cysteine, histidine, the aromatic amino acids, and polyamines (putrescine and spermidine). Regardless of the pathway of glutamate synthesis, nitrogen source catabolism must generate ammonia for glutamine synthesis. Loss of glutamate synthase (glutamineoxoglutarate amidotransferase, or GOGAT) prevents utilization of many organic nitrogen sources. Mutations that create or increase a requirement for ammonia also prevent utilization of most organic nitrogen sources.

TdcA, a transcriptional activator of the tdcABC operon of Escherichia coli, is a member of the LysR family of proteins

The tdcB and tdcC genes of the tdcABC operon of Escherichia coli encode threonine dehydratase and a threonine-serine permease, respectively. These proteins are involved in transport and metabolism of threonine and serine during anaerobic growth. In this study, we functionally characterized tdcA, which encodes a 35 kDa polypeptide consisting of 312 amino acid residues. Non-polar and partially polar mutations introduced into tdcA drastically reduced the expression of the genes down-stream from tdcA. Complementation studies using single-copy chromosomal integrants of a tdcB-lacZ fusion harboring an in-frame deletion of tdcA with chromosomal or plasmid-borne tdcA+ in trans showed complete restoration of tdc operon expression in vivo. The amino acid sequence at the amino-terminal end of TdcA revealed a significant homology to the helix-turn-helix motifs of typical DNA binding proteins. Sequence alignment of TdcA with LysR also showed considerable sequence similarity throughout their entire lengths. Our results suggest that TdcA is related to the LysR family of proteins by common ancestry and, based on its functional role in tdc expression, belongs to the LysR family of transcriptional activators.

Amino acid sequence of the regulatory-site glyoxylate peptide of biodegradative threonine dehydratase of Escherichia coli

Incubation of purified Escherichia coli biodegradative threonine dehydratase with glyoxylate resulted in covalent binding of 1 mol of glyoxylate per mol of protein with concomitant loss of enzyme activity. The glyoxylate-binding site was identified as a heptapeptide representing amino acid residues Ser-33-Asn-Tyr-Phe-Ser-Glu-Arg-39 in the protein primary structure. Addition of glyoxylate to a culture of E. coli cells led to time-dependent enzyme inactivation. Immunoprecipitation with anti-dehydratase antibody of extract from [14C]glyoxylate-treated cells revealed labeled dehydratase polypeptide. These results are interpreted to mean that enzyme inactivation by glyoxylate in E. coli cells is associated with covalent protein modification.

Isolation, characterization, and nucleotide sequence of appY, a regulatory gene for growth-phase-dependent gene expression in Escherichia coli

A plasmid carrying a regulator gene, designated appY, was found in the screening of an Escherichia coli gene library for clones overproducing AppA, an acid phosphatase which is induced as a culture approaches the stationary phase. In cells containing multicopy plasmids carrying the appY gene, the expression of the chromosomal appY gene was stimulated 10- to 40-fold in the stationary phase and more than 100-fold during exponential growth. The appA plasmid also changed the rate of synthesis of more than 30 other proteins in a growth-phase-dependent way. The appY gene was mapped to 13 min on the E. coli genetic map. The position of the appY gene on the 4.9-kilobase HindIII fragment of the original clone was located by Tn5 mutagenesis and deletion analysis, and the nucleotide sequence of a 1.9-kilobase region containing the gene was determined. The appY gene product was identified as a weakly expressed 243-amino-acid polypeptide which contains a stretch of 20 amino acids showing very good similarity to the conserved DNA-binding domain of repressors and transcriptional activators.

Molecular characterization of the tdc operon of Escherichia coli K-12

The nucleotide sequence of a 2-kilobase DNA fragment of the tdc region of Escherichia coli K-12, previously cloned in this laboratory, revealed two open reading frames, tdcC and ORFX, downstream from the tdcB gene (formerly designated tdc) encoding biodegradative threonine dehydratase. A 24-base-pair sequence separated tdcC from the dehydratase coding region, and an untranslated region of 60 nucleotides, which contains a recognizable -10 consensus sequence, was found between tdcC and ORFX. The deduced amino acid sequence of tdcC showed it to be a large hydrophobic polypeptide of 431 amino acid residues, whereas ORFX coded for a small 135-residue polypeptide lacking glutamine and tryptophan. A computer-assisted sequence analysis revealed no similarity among the tdcB, tdcC, and ORFX polypeptides, and a search of the GenBank database failed to detect similarity with any other known proteins. The tdc genes and ORFX showed similar codon usage and, in analogy with other bacterial genes, showed codon usage typical for genes expressed at an intermediate level. Transcriptional analysis with S1 nuclease indicated two distinct transcription start sites upstream of the tdcB gene in regions previously identified as promoterlike elements P1 and P2. Interestingly, expression of tdcB and tdcC, but not ORFX, was contingent upon the presence of P1. These results taken together tend to suggest that the biodegradative threonine dehydratase is the second gene in a polycistronic transcription unit constituting a novel operon (tdcABC) in E. coli implicated in anaerobic threonine metabolism.

Genetic analysis of the tdcABC operon of Escherichia coli K-12

The biodegradative threonine dehydratase (tdc) operon was mapped at 68 min on the Escherichia coli K-12 chromosome. The order of markers in the clockwise direction was dnaG uxaA tdc argG. A tdc deletion was isolated and mapped to this region of the chromosome. By using a tdcB-lacZ fusion the clockwise direction of transcription of tdc was determined.

Novel regulatory loci controlling oxygen- and pH-regulated gene expression in Salmonella typhimurium

Three new loci were discovered, each of which participates in the regulation of anaerobic gene expression. The regulatory gene earA negatively regulates the expression of the anaerobiosis-inducible gene aniG as well as that of at least three other genes, as determined by two-dimensional polyacrylamide gel electrophoresis. The earA locus maps at 86 min. The expression of aniG was also shown to be controlled by changes in external pH under aerobic and anaerobic conditions. Maximal expression was observed under anaerobic conditions at an external pH of 6.0. Significant transcriptional activity was also observed under aerobic conditions at pH 6.0. This was in contrast to hyd, whose expression was dependent upon anaerobiosis and varied with external pH. The pH dependence disappeared under fully aerobic conditions. Mutations in earA had no effect upon hyd expression. The two other regulators identified were oxrF, which controls aniH, and oxrG, which, in concert with oxrA and oxrB, controls aniC and aniI. The oxrG locus was mapped to 88 min and appears to code for a positive regulator. Various oxr mutants were subjected to two-dimensional polyacrylamide electrophoretic analysis of anaerobiosis-inducible proteins. Several pathways of anaerobic control were observed by means of these techniques.

Two genetically distinct pathways for transcriptional regulation of anaerobic gene expression in Salmonella typhimurium

Expression of the tripeptide permease gene tppB is anaerobically induced. This induction is independent of the fnr (oxrA) gene product, which is known to be required for the anaerobic induction of several respiratory enzymes. We isolated, characterized, and mapped mutations in two genes, oxrC and tppR, which prevent the anaerobic induction of tppB expression. Mutations in oxrC were highly pleiotropic, preventing the anaerobic expression of the formate dehydrogenase component of formate hydrogen lyase (fhl), a tripeptidase (pepT), and two of the three known hydrogenase isoenzymes (hydrogenases 1 and 3). On the other hand, expression of nitrate reductase, fumarate reductase, and a number of other fnr (oxrA)-dependent enzymes was not affected by mutations in oxrC. Thus, there appeared to be at least two distinct classes of anaerobically induced genes, those which required fnr for their expression and those which required oxrC. It seems that fnr-dependent enzymes perform primarily respiratory functions, whereas oxrC-dependent enzymes served fermentative or biosynthetic roles. We found the primary defect of oxrC mutants to be a deficiency in phosphoglucose isomerase activity, implying that a product of glycolysis functions as an anaerobic regulatory signal. Mutations in tppR were specific for tppB and did not affect expression of other oxrC-dependent genes. However, tppR did exhibit phenotypes other than the regulation of tppB. Both oxrC and tppR mutants were hypersensitive to the toxic NAD analog 6-aminonicotinic acid. This suggests that oxrC and tppR may play a role in the regulation of NAD biosynthesis or, alternatively, that NAD or a related nucleotide serves as the anaerobic signal for oxrC-dependent enzymes.

Molecular cloning and expression of the biodegradative threonine dehydratase gene (tdc) of Escherichia coli K12

The biodegradative threonine dehydratase gene (tdc) of Escherichia coli was cloned by isolating a dehydratase negative mutant after Tn5 mutagenesis, cloning the tdc::Tn5 DNA into pBR322 and then replacing the Tn5 element on the plasmid in vivo. Subcloning and nucleotide sequence data revealed two distinct procaryotic promoter-like elements each containing a potential CAP-binding site and AT-rich regions, and a Shine-Dalgarno sequence. One of these putative promoters, P2, was located immediately upstream from the tdc coding region, and a second, P1, was approximately 1 kilobase upstream from P2. Deletion of the potential CAP-binding site from P1 prevented tdc gene expression. However, removal of P2 and a large segment of the upstream DNA had no discernible effect on dehydratase synthesis. A 936-base pair open reading frame was found between P1 and the tdc coding region, which produced a polypeptide of about 32 kilodaltons. The data suggest that P1, and not P2, is necessary for tdc gene expression, and that the DNA sequences coding for the 32 KD polypeptide and threonine dehydratase are part of a single transcriptional unit.

Escherichia coli K-12 mutation that inactivates biodegradative threonine dehydratase by transposon Tn5 insertion

From a collection of kanamycin-resistant mutants of Escherichia coli K-12 isolated by transposon Tn5 mutagenesis, we have identified a mutant that lacks functional biodegradative threonine dehydratase (EC 4.2.1.16) by direct enzyme assay and by the loss of cross-reacting material with affinity-purified antibodies against the purified enzyme. Aerobic and anaerobic growth of this strain on various carbon sources failed to reveal a phenotype. Evidence for the insertional inactivation of threonine dehydratase by Tn5 was obtained by cloning the DNA segments flanking the Tn5 insertion site into pBR322 and hybridizing the cloned DNA to a synthetic oligodeoxynucleotide probe complementary to the DNA segment coding for a unique hexapeptide at the amino terminus end of the enzyme; the region of homology to the synthetic cDNA sequence appears to be located within about 500 nucleotides from one end of Tn5. Genetic analysis with the transposon element that caused insertional inactivation located the tdc gene at min 67 on the E. coli chromosome.

Synthesis of biodegradative threonine dehydratase in Escherichia coli: role of amino acids, electron acceptors, and certain intermediary metabolites

The specific activity of inducible biodegradative threonine dehydratase (EC 4.2.1.16) in Escherichia coli K-12 increased significantly when the standard tryptone-yeast extract medium or a synthetic mixture of 18 L-amino acids was supplemented with 10 mM KNO3 or 50 mM fumarate and with 4 mM cyclic AMP. In absolute terms, almost four times as much enzyme was produced in the amino acid medium as in the tryptone-yeast extract medium. Enzyme induction in the amino acid medium was sensitive to catabolite repression by glucose, gluconate, glycerol, and pyruvate. An analysis of amino acid requirements for enzyme induction showed that a combination of only four amino acids, threonine, serine, valine, and isoleucine, produced high levels of threonine dehydratase provided that both fumarate and cyclic AMP were present. Immunochemical data revealed that the enzyme synthesized in the presence of these four amino acids was indistinguishable from that produced in the tryptone-yeast extract or the medium with 18 amino acids. We interpret these results to mean that not the amino acids themselves but some metabolites derived anaerobically in reactions involving an electron acceptor may function as putative regulatory molecule(s) in the anaerobic induction of this enzyme.