Biosynthetic and Catabolic Features of Amino Acid Metabolism in Pseudomonas

Phillips, Allen T.

doi:10.1016/b978-0-12-307210-8.50017-8

Cited by 8 publications

(8 citation statements)

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“…L-Lysine has been proposed to enter into the periplasmic space through the OprD porin (43). Subsequently, it is transported to the cytoplasm (the present study) and is metabolized through two branches that converge at ␦-aminovaleric acid (12,35). Further metabolism of ␦-aminovaleric acid yields glutaric acid that is channeled to Krebs cycle intermediates.…”

Section: Methodsmentioning

confidence: 99%

The davDT Operon of Pseudomonas putida , Involved in Lysine Catabolism, Is Induced in Response to the Pathway Intermediate δ-Aminovaleric Acid

et al. 2004

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Pseudomonas putida KT2440 is a soil microorganism that attaches to seeds and efficiently colonizes the plant's rhizosphere. Lysine is one of the major compounds in root exudates, and P. putida KT2440 uses this amino acid as a source of carbon, nitrogen, and energy. Lysine is channeled to ␦-aminovaleric acid and then further degraded to glutaric acid via the action of the davDT gene products. We show that the davDT genes form an operon transcribed from a single 70 -dependent promoter. The relatively high level of basal expression from the davD promoter increased about fourfold in response to the addition of exogenous lysine to the culture medium. However, the true inducer of this operon seems to be ␦-aminovaleric acid because in a mutant unable to metabolize lysine to ␦-aminovaleric acid, this compound, but not lysine, acted as an effector. Effective induction of the P. putida P davD promoter by exogenously added lysine requires efficient uptake of this amino acid, which seems to proceed by at least two uptake systems for basic amino acids that belong to the superfamily of ABC transporters. Mutants in these ABC uptake systems retained basal expression from the davD promoter but exhibited lower induction levels in response to exogenous lysine than the wild-type strain.

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Section: Methodsmentioning

confidence: 99%

The davDT Operon of Pseudomonas putida , Involved in Lysine Catabolism, Is Induced in Response to the Pathway Intermediate δ-Aminovaleric Acid

et al. 2004

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“…This similarity, and the fact that rei-2 can use lysine as a nitrogen source to a certain extent, suggested that the product of this gene could act as a ␦-aminovalerate aminotransferase, the enzyme responsible for the conversion of ␦-aminovalerate (an intermediate in lysine metabolism) (Fig. 4) into glutaric acid semialdehyde (18). To test this hypothesis, P. putida KT2440, rei-2, and rei-2(pLYS24) were inoculated on plates containing 20 mM ␦-aminovalerate as a carbon and/or nitrogen source or 20 mM glutarate as a carbon source.…”

Section: Isolation Of Mutants In Root Exudate-inducible (Rei) Genesmentioning

confidence: 99%

“…Root exudates consist of a complex mixture of sugars, amino acids, vitamins, organic acids, and other compounds (15,16,18) that provide the necessary elements and energy sources to support bacterial growth in the rhizosphere.…”

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confidence: 99%

Expression of a Pseudomonas putida Aminotransferase Involved in Lysine Catabolism Is Induced in the Rhizosphere

Espinosa‐Urgel

Ramos

2001

Appl Environ Microbiol

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Using a transposon carrying a promoterless lux operon to generate transcriptional fusions by insertional mutagenesis, we have identified a Pseudomonas putida gene with increased expression in the presence of corn root exudates. Expression of the transcriptional fusion, induced by the amino acid lysine, was detected in P. putida in the rhizosphere of plants as well as in response to seed exudates. The mutant was unable to grow on lysine or ␦-aminovalerate as carbon sources, which indicates that the affected function is involved in the pathway for lysine catabolism. However, the mutant strain grew with glutaric acid, the product of ␦-aminovalerate metabolism via glutaric acid semialdehyde, as a C source. The translated sequence of the interrupted gene showed high levels of similarity with aminotransferases. These sets of data suggest that the product of this gene has ␦-aminovalerate aminotransferase activity. This is the first direct genetic evidence correlating a DNA sequence with such activity in Pseudomonadaceae.The surface of plant roots and the surrounding soil regions (rhizosphere) constitute an environment where nutrients are available for bacterial populations to be established at relatively high cell densities. Root exudates consist of a complex mixture of sugars, amino acids, vitamins, organic acids, and other compounds (15,16,18) that provide the necessary elements and energy sources to support bacterial growth in the rhizosphere.The molecular mechanisms involved in the colonization of plant roots by rhizobacteria are being extensively studied by two different but complementary approaches: (i) a random approach involving the isolation and characterization of mutants with reduced colonization capacities and (ii) a directed design, in which specific functions presumed to be important for colonization are tested and their roles in plant-bacterial interactions are assessed. These two approaches have allowed researchers to establish the importance of elements such as flagella, type IV pili, or chemotactic responses (11,12,23,24). Particular attention has been paid to the so-called plant growth-promoting rhizobacteria and, among them, to Pseudomonas spp. strains that exert beneficial effects on plant health. Pseudomonas spp. genes encoding functions involved in plant root and seed colonization have been identified, including an agglutination factor (8), a site-specific recombinase (9), and a series of proteins involved in adhesion to seeds (13).In recent years there have been increasing efforts in a third direction: the analysis of bacterial gene expression in the rhizosphere by techniques such as in vivo expression technology. Genes that respond to root exudates or that are preferentially expressed in the rhizosphere have been identified in Rhizobium sp. and Pseudomonas spp. among others (5,6,19,20). Some of the genes identified in Pseudomonas fluorescens are involved in sugar transport and metabolism, amino acid transport, secretion, and oxidative stress response (19).In the soil bacterium Pseudomonas putid...

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“…Since the dpkA gene product is induced in L-and D-lysine catabolism and the mRNA of the ORF encoding PP3590 forms part of the same transcript, we decided to explore whether PP3590, that exhibits similarity to amino acid aminotransferases (7,27), played a major role in D-lysine catabolism. We knocked out ORF3590 using the pCHESI derivative as described in Materials and Methods and tested growth of the mutant on L-and D-lysine as the sole carbon or nitrogen source.…”

Section: Resultsmentioning

confidence: 99%

Identification of the Initial Steps in d -Lysine Catabolism in Pseudomonas putida

2007

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Pseudomonas putida uses L-lysine as the sole carbon and nitrogen source which preferentially requires its metabolism through two parallel pathways. In one of the pathways ␦-aminovalerate is the key metabolite, whereas in the other L-lysine is racemized to D-lysine, and L-pipecolate and ␣-aminoadipate are the key metabolites. All the genes and enzymes involved in the D-lysine pathway, except for those involved in the conversion of D-lysine into ⌬ 1 -piperideine-2-carboxylate, have been identified previously (30). In this study we report that the conversion of D-lysine into ⌬ 1 -piperideine-2-carboxylate can be mediated by a D-lysine aminotransferase (PP3590) and a D-lysine dehydrogenase (PP3596). From a physiological point of view PP3596 plays a major role in the catabolism of D-lysine since its inactivation leads to a marked reduction in the growth rate with L-or D-lysine as the sole carbon and nitrogen source, whereas inactivation of PP3590 leads only to slowed growth. The gene encoding PP3590, called here amaC, forms an operon with dpkA, the gene encoding the enzyme involved in conversion of ⌬ 1 -piperideine-2-carboxylate to L-pipecolate in the D-lysine catabolic pathway. The gene encoding PP3596, called here amaD, is the fifth gene in an operon made up of seven open reading frames (ORFs) encoding PP3592 through PP3597. The dpkA amaC operon was transcribed divergently from the operon ORF3592 to ORF3597. Both promoters were mapped by primer extension analysis, which showed that the divergent ؊35 hexamers of these operon promoters were adjacent to each other. Transcription of both operons was induced in response to L-or D-lysine in the culture medium.Pseudomonas putida KT2440, a derivative of P. putida mt-2 from which the TOL plasmid was cured (15, 25), can grow on proline, lysine, glutamate, and other amino acids as the sole carbon and nitrogen source. The ability to assimilate these compounds confers a selective advantage by enabling the strain to grow in the rhizosphere of a number of plants, where these amino acids form part of the root exudates (4, 13, 21, 23).Pioneering work on bacterial lysine metabolism (17) helped establish two parallel catabolic pathways (Fig. 1), starting with the interconversion by a racemase of both enantiomers of lysine. L-Lysine catabolism proceeds through the so-called aminovalerate (AMV) pathway and involves the following steps: L-lysine 3 ␦-aminovaleramide 3 ␦-AMV 3 glutarate semialdehyde 3 glutarate, which is then channeled into the Krebs cycle via glutaryl-and acetyl-coenzyme A (CoA). On the other hand, D-lysine catabolism proceeds via a series of cyclized intermediates which are necessary to regenerate an ␣-amino acid and comprise the following metabolites (aminoadipate [AMA] pathway): D-lysine 3 ␣-keto-ε-amino caproate 3 ⌬ 1 -piperideine-2-carboxylate 3 pipecolate 3 ⌬ 1 -piperideine-6-carboxylate 3 ␣-amino-␦-formylcaproate 3 ␣-AMA 3 ␣-ketoadipate. The latter is transformed to ␣-ketoglutarate via a series of CoA derivatives. These steps were established at the biochemical le...

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Biosynthetic and Catabolic Features of Amino Acid Metabolism in Pseudomonas

Cited by 8 publications

References 176 publications

The davDT Operon of Pseudomonas putida , Involved in Lysine Catabolism, Is Induced in Response to the Pathway Intermediate δ-Aminovaleric Acid

The davDT Operon of Pseudomonas putida , Involved in Lysine Catabolism, Is Induced in Response to the Pathway Intermediate δ-Aminovaleric Acid

Expression of a Pseudomonas putida Aminotransferase Involved in Lysine Catabolism Is Induced in the Rhizosphere

Identification of the Initial Steps in d -Lysine Catabolism in Pseudomonas putida

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