The Sinorhizobium meliloti chemoreceptor McpU mediates positive and negative chemotaxis responses to dipeptides and competes with periplasmic solute-binding proteins for ligand binding

Abstract

ABSTRACT Many bacteria can utilize extracellular amino acids and peptides as nitrogen sources, metabolic energy, or as an indicator of the environment. Sinorhizobium meliloti, an endosymbiont of alfalfa, is attracted to host-exuded amino acids sensed by the chemoreceptor McpU, but the role of peptides in S. meliloti chemotaxis is unknown. A high-throughput screen using Biolog compound arrays confirmed efficient peptide utilization by S. meliloti with a preference toward nonpolar peptides. Differential scanning fluorimetry and isothermal titration calorimetry (ITC) demonstrated binding of non-aspartate dipeptides to the purified, periplasmic ligand-binding domain of McpU (McpULBD), which was abolished by a single amino acid substitution in the McpU ligand-binding pocket. S. meliloti wild-type, but not the mcpU, deletion strain elicited positive chemotaxis to specific dipeptides in a quantitative capillary assay. However, chemotactic responses of S. meliloti wild type to the dipeptides Ala-Ala, Arg-Trp, and Phe-Ala were observed at 10- to 100-fold higher concentrations as compared to its response to the prototypical McpU ligands, proline and alanine, while cells did not migrate into capillaries filled with Trp-Ala and Val-Phe. We showed that this shift in chemotaxis response might be explained by dipeptides binding to solute-binding proteins, thereby decreasing the concentration of free dipeptides in the periplasm. S. meliloti regulates chemotaxis responses by controlling its swimming velocity. Consequently, a repellent response is expected to result in a reduction in swimming speed. Swimming speed measurements of wild type and a strain deficient in chemotaxis revealed negative chemotaxis of S. meliloti toward dipeptides. However, the response at higher concentrations of Trp-Ala was dominated by a detrimental effect on swimming motility. Agarose chemical-in-plug assay confirmed negative chemotaxis to dipeptides mediated by McpU. This study provides the first report of negative chemotaxis responses in S. meliloti. IMPORTANCE Most gram-negative bacteria use small peptides as carbon sources and signaling molecules, which contributes to their survival in a wide range of environmental conditions. The ability to detect and navigate the environment for these peptides, along with the necessary systems for their metabolism, is crucial. Sinorhizobium meliloti, an endosymbiont of alfalfa, significantly enhances the growth of its host by fixing atmospheric nitrogen. This study provides firsthand information on peptide physiology and the possible role of dipeptide transporters in S. meliloti's chemotaxis to dipeptides. Furthermore, we provide the first description of negative chemotaxis in S. meliloti. Specifically, the S. meliloti chemoreceptor McpU transmits positive and negative chemotactic responses to dipeptides. Understanding the mechanisms that enable S. meliloti to adapt to and survive in its environment could have a significant impact on the development of commercial bacterial inoculants, reducing our dependence on synthetic fertilizers that harm the environment. Most gram-negative bacteria use small peptides as carbon sources and signaling molecules, which contributes to their survival in a wide range of environmental conditions. The ability to detect and navigate the environment for these peptides, along with the necessary systems for their metabolism, is crucial. Sinorhizobium meliloti, an endosymbiont of alfalfa, significantly enhances the growth of its host by fixing atmospheric nitrogen. This study provides firsthand information on peptide physiology and the possible role of dipeptide transporters in S. meliloti's chemotaxis to dipeptides. Furthermore, we provide the first description of negative chemotaxis in S. meliloti. Specifically, the S. meliloti chemoreceptor McpU transmits positive and negative chemotactic responses to dipeptides. Understanding the mechanisms that enable S. meliloti to adapt to and survive in its environment could have a significant impact on the development of commercial bacterial inoculants, reducing our dependence on synthetic fertilizers that harm the environment.