(67d) Quantitative Proteomic Analysis of Interactions in a Binary Bacterial Culture

Classic studies of biological interactions have relied on simple descriptions such as competition and antagonism, but these terms convey only an effect and do not provide any information on how the interaction affects the organisms at a molecular level. Experimental systems biology methods have enormous potential to provide information about biological interactions. Among the different high-throughput technologies, proteomic approaches offer some advantages when compared to DNA or RNA-based methods, including the ability to provide protein-level functional information. To evaluate the complexity of molecular-level responses associated with interactions, a quantitative proteomics study was conducted on a constructed binary bacterial culture. An iTRAQ shotgun proteomics workflow was used to compare the protein profiles of the Gram-negative Pseudomonas putida strain KT2440 and Gram-positive Bacillus atrophaeus strain DSM675 with their co-culture. Sixty-three proteins were detected as differentially expressed (at least two-fold expression change) in the co-culture relative to the pure cultures. These differentially expressed proteins were classified according to the biological processes where they are involved using Gene Ontologies. As determined by the iTRAQ quantitative labeling approach, differential expression ratios (binary vs. pure culture) ranged from -10 to 9. When comparing the mixed culture to the base cultures, more proteins were up-regulated in response to the perturbation (38 in the perturbed B. atrophaeus culture and 48 in the P. putida perturbed culture). Among the proteins with the largest expression changes in B. atrophaeus are elongation factor G (9-fold lower in the binary culture), acetolactate synthase III large subunit (8.5-fold lower), quinone oxidoreductase (5.8-fold lower), putative cold-shock DNA-binding domain protein (4.6-fold higher), and heat shock protein Hsp20 (4.9-fold higher). For P. putida, the largest expression changes were found for outer membrane lipoprotein OprI (4.5-fold lower in the binary culture), isocitrate lyase (4.3-fold lower), and DNA-binding protein HU, form N (9.7-fold higher). Approximately two-thirds of the proteins identified were involved in metabolism, and the majority of those were related to amino acid and protein metabolism, and well as nucleic acid and DNA metabolism. This is the first use of proteomics to reveal the interactions between microorganisms.