Tryptophan metabolism in Klebsiella aerogenes: regulation of the utilization of aromatic amino acids as sources of nitrogen

Crystal structure of the aromatic-amino-acid aminotransferase from Streptococcus mutans

Streptococcus mutans, a facultatively aerobic and Gram-positive bacterium, is the primary causative agent of dental caries and contributes to the multispecies biofilm known as dental plaque. In this study, the aromatic-amino-acid aminotransferase from Streptococcus mutans (SmAroAT) was recombinantly expressed in Escherichia coli. An effective purification protocol was established. The recombinant protein was crystallized using the hanging-drop vapor-diffusion method with PEG 3350 as the primary precipitant. The crystal structure of SmAroAT was solved at 2.2 Å resolution by the molecular-replacement method. Structural analysis indicated that the proteins of the aromatic-amino-acid aminotransferase family have conserved structural elements that might play a role in substrate binding. These results may help in obtaining a better understanding of the catabolism and biosynthesis of aromatic amino acids.

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.

Histidine degradation via an aminotransferase increases the nutritional flexibility of Candida glabrata

The ability to acquire nutrients during infections is an important attribute in microbial pathogenesis. Amino acids are a valuable source of nitrogen if they can be degraded by the infecting organism. In this work, we analyzed histidine utilization in the fungal pathogen of humans Candida glabrata. Hemiascomycete fungi, like C. glabrata or Saccharomyces cerevisiae, possess no gene coding for a histidine ammonia-lyase, which catalyzes the first step of a major histidine degradation pathway in most other organisms. We show that C. glabrata instead initializes histidine degradation via the aromatic amino acid aminotransferase Aro8. Although ARO8 is also present in S. cerevisiae and is induced by extracellular histidine, the yeast cannot use histidine as its sole nitrogen source, possibly due to growth inhibition by a downstream degradation product. Furthermore, C. glabrata relies only on Aro8 for phenylalanine and tryptophan utilization, since ARO8, but not its homologue ARO9, was transcriptionally activated in the presence of these amino acids. Accordingly, an ARO9 deletion had no effect on growth with aromatic amino acids. In contrast, in S. cerevisiae, ARO9 is strongly induced by tryptophan and is known to support growth on aromatic amino acids. Differences in the genomic structure of the ARO9 gene between C. glabrata and S. cerevisiae indicate a possible disruption in the regulatory upstream region. Thus, we show that, in contrast to S. cerevisiae, C. glabrata has adapted to use histidine as a sole source of nitrogen and that the aromatic amino acid aminotransferase Aro8, but not Aro9, is the enzyme required for this process.

Agrobacterium Ti plasmid indoleacetic acid gene is required for crown gall oncogenesis

A gene (iaaP) necessary for virulence and indoleacetic acid (IAA) production has been located on a nopaline Ti plasmid of Agrobacterium tumefaciens C58. iaaP function was established by using transformation to insert nopaline or octopine Ti plasmids into an avirulent, Ti plasmid-free mutant 1D1293-3 that was defective in IAA synthesis (iaaC(-)). The resulting transformants produced increased levels of IAA and virulence was restored. When these transformants were cured of their Ti plasmid, virulence and high IAA production levels were concomitantly lost. A Tn5 mutagenized TiC58 plasmid, deficient in the ability to direct increased synthesis of IAA, was inserted by transformation into mutant 1D1293-3. The resulting transformants 1D1293-3 (TiC58::Tn5) remained avirulent and iaaP(-). Restriction analysis of the TiC58::Tn5 plasmid DNA identified the iaaP gene at 20.9 kilobases to the left of the T-DNA. A major aromatic-amino-acid aminotransferase is coded by the iaaC gene, but not by the iaaP gene. The possible reasons for the iaaP locus to be situated outside the T-DNA region are discussed.

Azospirillum brasilense produces the auxin-like phenylacetic acid by using the key enzyme for indole-3-acetic acid biosynthesis

An antimicrobial compound was isolated from Azospirillum brasilense culture extracts by high-performance liquid chromatography and further identified by gas chromatography-mass spectrometry as the auxin-like molecule, phenylacetic acid (PAA). PAA synthesis was found to be mediated by the indole-3-pyruvate decarboxylase, previously identified as a key enzyme in indole-3-acetic acid (IAA) production in A. brasilense. In minimal growth medium, PAA biosynthesis by A. brasilense was only observed in the presence of phenylalanine (or precursors thereof). This observation suggests deamination of phenylalanine, decarboxylation of phenylpyruvate, and subsequent oxidation of phenylacetaldehyde as the most likely pathway for PAA synthesis. Expression analysis revealed that transcription of the ipdC gene is upregulated by PAA, as was previously described for IAA and synthetic auxins, indicating a positive feedback regulation. The synthesis of PAA by A. brasilense is discussed in relation to previously reported biocontrol properties of A. brasilense.

Characterization of the indole-3-acetic acid (IAA) biosynthetic pathway in an epiphytic strain of Erwinia herbicola and IAA production in vitro

An epiphytic strain of Erwinia herbicola (strain 299R) synthesized indole-3-acetic acid (IAA) from indole-3-pyruvic acid and indole-3-acetaldehyde, but not from indole-3-acetamide and other intermediates of various IAA biosynthetic pathways in enzyme assays. TLC, HPLC, and GC–MS analyses revealed the presence of indole-3-pyruvic acid, indole-3-ethanol, and IAA in culture supernatants of strain 299R. Indole-3-acetaldehyde was detected in enzyme assays. Furthermore, strain 299R genomic DNA shared no homology with the iaaM and iaaH genes from Pseudomonas syringae pv. savastanoi, even in Southern hybridizations performed under low-stringency conditions. These observations strongly suggest that unlike gall-forming bacteria which can synthesize IAA by indole-3-acetamide, the indole-3-pyruvic acid pathway is the primary route for IAA biosynthesis in this plant-associated strain. IAA synthesis in tryptophan-supplemented cultures of strain 299R was over 10-fold higher under nitrogen-limiting conditions, indicating a possible role for IAA production by bacterial epiphytes in the acquisition of nutrients during growth in their natural habitat.Key words: indole-3-acetic acid, Erwinia, tryptophan, indole-3-pyruvic acid, nitrogen.

Purification and properties of aromatic amino acid aminotransferases from Azospirillum brasilense UAP 14 strain

The purification and characterization of AAT1, one of two aromatic amino acid aminotransferase (EC 2.6.1.57) in Azospirillum brasilense, is described. Purified AAT1 had a subunit mass of 33 kDa and a nondenatured molecular mass of 66 kDa, suggesting a dimeric structure. Other properties include a pI of 5.04, an optimum temperature of 45 degrees C, and optimum pH of 8.5. AAT1 utilized all aromatic amino acids, the L-tryptophan derivatives such as L-5-methyl tryptophan and L-flour-tryptophan, and L-histidine. The apparent Km values for L-tyrosine, L-phenylalanine, and L-tryptophan were 0.19, 0.43, and 1.05 mM, respectively. The enzyme was competive inhibited by indole-3-pyruvic acid with a Ki of 0.17 mM.

Involvement of L-tryptophan aminotransferase in indole-3-acetic acid biosynthesis in Enterobacter cloacae

L-Tryptophan aminotransferase (L-tryptophan:2-oxoglutarate aminotransferase; EC 2.6.1.27) from Enterobacter cloacae was purified 62-fold and characterized to determine its role in indole-3-acetic acid biosynthesis. The enzyme reversibly catalyzed the transamination of L-tryptophan with 2-oxoglutarate as the amino acceptor to yield indole-3-pyruvic acid and L-glutamate, and the Km values for L-tryptophan and indole-3-pyruvic acid were 3.3 mM and 24 microM, respectively. In the indole-3-acetaldehyde synthesis experiments in vitro, 94% of L-tryptophan was efficiently converted to indole-3-acetaldehyde by the purified L-tryptophan aminotransferase plus indolepyruvate decarboxylase. Furthermore, the amounts of L-tryptophan decreased with increases in the indolepyruvate decarboxylase activity, while the amounts of indole-3-acetaldehyde increased with increases in this activity. In genetic experiments, the amounts of L-tryptophan produced by Enterobacter and Pseudomonas strains harboring the gene for indolepyruvate decarboxylase were lower than those produced by these same strains without the gene, while the amounts of indole-3-acetic acid produced by Enterobacter and Pseudomonas strains harboring the gene for indolepyruvate decarboxylase were higher than those produced by these same strains without the gene. These results clearly show that L-tryptophan aminotransferase is involved in the indole-3-acetic acid biosynthesis and that indolepyruvate decarboxylase is the rate-limiting step in this pathway.

Characterization of an aromatic amino acid aminotransferase from Rhizobium leguminosarum biovar trifolii

The most abundant aromatic amino acid aminotransferase of Rhizobium leguminosarum biovar trifolii was partially purified. The molecular mass of the enzyme was estimated to be 53 kDa by gel filtration. The enzyme transaminated aromatic amino acids and histidine. It used aromatic keto acids and alpha-ketoglutaric and oxalacetic acids as amino-group acceptors. The optimum temperature was 35 degrees C. Using phenylalanine and alpha-ketoglutaric acid as substrates the activation energy was 46.2 kJ.mol-1 and for the couple tryptophan:alpha-ketoglutaric acid it was 70.3 kJ.mol-1. The optimum pH was different for each substrate: 7.3 for phenylalanine, 7.9 for histidine and 8.7 for tryptophan.

Molecular cloning of the gene for indolepyruvate decarboxylase from Enterobacter cloacae

Although indole-3-acetic acid (IAA) is a well-known plant hormone, the main IAA biosynthetic pathway from L-tryptophan (Trp) via indole-3-pyruvic acid (IPyA) has yet to be elucidated. Previous studies have suggested that IAA is produced by Enterobacter cloacae isolated from the rhizosphere of cucumbers and its biosynthetic pathway may possibly be the same as that in plants. To elucidate this pathway, the IAA biosynthetic gene was isolated from a genomic library of E. cloacae by assaying for the ability to convert Trp to IAA. DNA sequence analysis showed that this gene codes for only one enzyme and its predicted protein sequence has extensive homology with pyruvate decarboxylase in yeast and Zymomonas mobilis. Cell-free extracts prepared from Escherichia coli harboring this gene could convert IPyA to indole-3-acetaldehyde (IAAld). These results clearly show that this pathway is mediated only by indolepyruvate decarboxylase, which catalyzes the conversion of IPyA to IAAld.

Role of the nac gene product in the nitrogen regulation of some NTR-regulated operons of Klebsiella aerogenes

A positive, genetic selection against the activity of the nitrogen regulatory (NTR) system was used to isolate insertion mutations affecting nitrogen regulation in Klebsiella aerogenes. Two classes of mutation were obtained: those affecting the NTR system itself and leading to the loss of almost all nitrogen regulation, and those affecting the nac locus and leading to a loss of nitrogen regulation of a family of nitrogen-regulated enzymes. The set of these nac-dependent enzymes included histidase, glutamate dehydrogenase, glutamate synthase, proline oxidase, and urease. The enzymes shown to be nac independent included glutamine synthetase, asparaginase, tryptophan permease, nitrate reductase, the product of the nifLA operon, and perhaps nitrite reductase. The expression of the nac gene was itself highly nitrogen regulated, and this regulation was mediated by the NTR system. The loss of nitrogen regulation was found in each of the four insertion mutants studied, showing that loss of nitrogen regulation resulted from the absence of nac function rather than from an altered form of the nac gene product. Thus we propose two classes of nitrogen-regulated operons: in class I, the NTR system directly activates expression of the operon; in class II, the NTR system activates nac expression and the product(s) of the nac locus activates expression of the operon.

Aromatic aminotransferase activity and indoleacetic acid production in Rhizobium meliloti

Bacterial indoleacetic acid (IAA) production, which has been proposed to play a role in the Rhizobium-legume symbiosis, is a poorly understood process. Previous data have suggested that IAA biosynthesis in Rhizobium meliloti can occur through an indolepyruvate intermediate derived from tryptophan by an aminotransferase activity. To further examine this biosynthetic pathway, the aromatic aminotransferase (AAT) activity of Rhizobium meliloti 102F34 (F34) was characterized. At least four proteins were detected on nondenaturing gels of F34 protein extracts that exhibited AAT activity. All four of these AATs were constitutively produced and utilized the aromatic amino acids tryptophan, phenylalanine, and tyrosine as amino substrates. Two AATs were also capable of using aspartate. Plasmids from an F34 gene bank were identified that coded for the synthesis of at least three of these proteins, and the respective gene sequences were localized by transposon mutagenesis. Selected transposon insertions were recombined into the F34 genome to produce strains defective in two of these proteins (AAT1 and AAT2). Characterization of the mutants revealed that neither was essential for the biosynthesis of IAA in the absence of exogenous tryptophan, but that both contributed to IAA biosynthesis when high levels of exogenous tryptophan were present. AAT1 and AAT2 were also not required for the production of a minimal level of aromatic amino acids, but both were able to scavenge nitrogen from the aromatic amino acids during nitrogen deprivation. Neither AAT1 nor AAT2 was essential for symbiosis with alfalfa.

Nitrogen regulation system of Klebsiella aerogenes: the nac gene

In Klebsiella aerogenes, the product of a his-linked gene, nac, appears to play a crucial role in tying the synthesis of enzymes activated or repressed by ammonia deprivation, such as histidase and glutamate dehydrogenase, to the known regulators of nitrogen assimilation, the products of glnG and glnF.

Role of glnA-linked genes in regulation of glutamine synthetase and histidase formation in Klebsiella aerogenes

We isolated mutants of Klebsiella aerogenes with insertions of transposon Tn5 linked to the structural gene for glutamine synthetase, glnA. We found that K. aerogenes, like Escherichia coli and Salmonella typhimurium, contains a regulatory gene, glnG, which is closely linked to but distinct from glnA. The product of glnG is essential for normal regulation of the synthesis of glutamine synthetase and histidase. We analyzed two mutations which affected the regulation of the formation of these enzymes and appeared to be outside glnG. The results of our studies suggest the presence in K. aerogenes of at least two regulatory genes located in the glnA region, namely, glnG and another gene, the transcription of which can be initiated at the promoter of glnA.

Effects of glnL and other regulatory loci on regulation of transcription of glnA-lacZ fusions in Klebsiella aerogenes

Mutants of Klebsiella aerogenes containing genetic fusions of glnA to lacZ were isolated by using Mu dl (lac, bla) bacteriophage and a Mu Kmr helper phage with the host range of bacteriophage P1. Synthesis of beta-galactosidase in these strains is regulated in response to nitrogen metabolites and regulatory gln loci and is rendered constitutive by a mutation in the linked glnL gene. Complementation studies indicated that glnL is a separate locus from glnA and glnG and that insertions in glnA are partially polar on glnL expression. These results support the hypothesis that glnA, glnL, and glnG are organized in an operon with multiple promoters.

Purification and properties of aromatic amino acid aminotransferase from Klebsiella aerogenes

We describe the complete purification of aromatic aminotransferase I, the enzyme responsible for the ability of Klebsiella aerogenes to use tryptophan and phenylalanine as sole sources of nitrogen, as well as the partial purification of aromatic aminotransferase IV. An examination of the properties of these enzymes revealed that aminotransferase I had much greater affinity for the aromatic amino acids than aminotransferase IV, explaining the essential role of aminotransferase I in the utilization of exogenously supplied aromatic amino acids. The properties of aminotransferase IV suggest that this enzyme is actually an aspartate aminotransferase (EC 2.6.1.1), corresponding to the product of the aspC gene of Escherichia coli.