Homocholine, a quaternary ammonium compound that resembles choline in many cholinergic metabolisms, is recently incorporated in many synthetic pharmaceuticals drugs targeting various types of cancer and bone marrow cells. Here, we used a proteomic approach (two-dimensional polyacrylamide gel electrophoresis and MALDI-TOF-MS) to elucidate profoundly the degradation pathway of homocholine by Pseudomonas sp. strain A9. Eighty-nine differentially abundant proteins were identified and were found to cover a broad range of biological processes and cellular responses of strain A9 to homocholine. Of them, most of the proteins involved in the direct uptake and catabolism of homocholine were identified. These results demonstrated that strain A9 uptake homocholine from the media with different transporting systems and then consequently catabolize it to acetyl-CoA and trimethylamine (TMA) by five enzymes namely homocholine dehydrogenase, beta-alaninebetaine aldehyde dehydrogenase, beta-alaninebetaine CoA transferase, 3-hydroxypropionate dehydrogenase, and methylmalonate semialdehyde dehydrogenase. The acetyl-CoA enters the TCA and glyoxylate pathways to generate energy and provide metabolic precursors for other pathways while TMA exclude out of the bacterial cells raising some environmental and health concerns. Overall, the findings of this study provide a first insight into the global proteomic changes occurring in the strain A9 cells under exposure to homocholine in the environment. (C) 2015 Elsevier Ltd. All rights reserved.