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

Abstract

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...

Gut and Root Microbiota Commonalities

“…Genes involved in root exudate usage, root attachment, and survival are induced in bacteria colonizing roots (120,121). In vitro expression technology (IVET) (122), proteomic analysis, microarray and RNA Seq transcriptomics, and genetic analysis have revealed rhizobial (120,121,123), Pseudomonas (124,125), Streptomyces (126), and other bacterial genes expressed on roots or rhizospheres. Similarly, bacteria may differentially express genes when in guts.…”

Cell Density-Dependent Gene Contributes to Efficient Seed Colonization by Pseudomonas putida KT2440

“…Mutants of Pseudomonas fluorescens unable to synthesize certain vitamins and amino acids also show reduced colonization capacity, indicating that the amounts of these compounds found in the rhizosphere are not sufficient to overcome some auxotrophies (28). The ability to utilize different nutrients, such as lysine and organic acids, is also important for competitive root colonization by Pseudomonas putida and P. fluorescens, respectively (18,28).…”

Multiple and Interconnected Pathways for l -Lysine Catabolism in Pseudomonas putida KT2440

“…The ability to assimilate these compounds confers on the strain a selective advantage to grow in the rhizosphere of a number of plants where these amino acids are part of the exudates (2,11,28,29).…”

“…The amaA, dkpA, and amaB genes, in contrast, encode proteins involved in the transformation of Pseudomonas putida KT2440, a derivative of P. putida mt-2 cured of the TOL plasmid, can grown on proline, lysine, glutamate, and other amino acids as the sole carbon and nitrogen source. The ability to assimilate these compounds confers on the strain a selective advantage to grow in the rhizosphere of a number of plants where these amino acids are part of the exudates (2,11,28,29).The catabolism of L-lysine by P. putida mainly involves the following steps: L-lysine 3 ␦-aminovaleramide 3 ␦-aminovalerate (AMV) 3 glutarate semialdehyde 3 glutarate, which is then channeled to the Krebs cycle. This pathway is known as the AMV pathway ( Fig.…”