Secretome of Hydrocarbon-Oxidizing Bacteria Tsukamurella tyrosinosolvens PS2: In silico Prediction and Experimental Evaluation

Abstract Secreted proteins play an important role in the adaptation of bacteria to changing environmental conditions by contributing to intercellular communication, resistance to unfavorable factors, and the breakdown of substrates. In this work, we comprehensively characterized the secretome of the strain Tsukamurella tyrosinosolvens PS2 capable of utilizing alkanes as the sole source of carbon and energy. Prediction of the secretome composition of several members of the genus Tsukamurella allowed us to identify approximately 140 genes, including laccase and poly-(3-hydroxybutyrate) depolymerase genes unique to the strain under study. Up to 46% of the genes in the predicted secretome were genes of unknown function. The use of multiple databases for annotation allowed us to determine the functional role of some protein-coding genes. Proteomic profiling of culture liquid samples of strain PS2 grown on mineral medium with sucrose or hexadecane showed that most proteins did not have a signal peptide. Cultivation on a medium containing hexadecane induced an increase in the abundance of proteins that mediate the transport and metabolism of fatty acids and amino acids, as well as those involved in energy production and translation processes. Among proteins featuring a signal peptide, elevated abundance was observed for proteins involved in the transport of hydrophobic molecules and phosphate metabolism. Decreased abundance was observed for MspA porins, lipid metabolism enzymes, and peptide metabolism enzymes. The obtained data on potential secreted proteins and experimental evaluation of the secretome of the strain T. tyrosinosolvens PS2 contribute to the fundamental knowledge concerning the diversity of secreted proteins in actinobacteria.