Identification of the key genes involved in the degradation of homocholine by Pseudomonas sp. strain A9 by using suppression subtractive hybridization

[Display omitted] •Homocholine share high structural and metabolic similarities with choline.•Microbial metabolism of homocholine affects all kingdoms of life.•This first genomic study elucidates the catabolic pathway of homocholine.•Complete sequence information of key homocholine degrading genes was obtained.•This work allows better understanding of microbial catabolism of homocholine. Microbial transformation of homocholine plays a central role in many biological systems and influence on all kingdoms of life. Here, we used suppression subtractive hybridization (SSH) approach to screen for genes that differentially expressed in response to homocholine by Pseudomonas sp. strain A9 and to gain deep acknowledge about the gene expression and sequences of homocholine degrading enzymes. Twenty-seven differentially expressed genes were identified and were found to involve in the uptake and metabolism of homocholine as well as physiological responses of strain A9 to this compound. Of them, fragments of homocholine dehydrogenase (hcdH), β-alanine betaine aldehyde dehydrogenase (bABALDH), β-alaninebetaine CoA transferase (hcdD), 3-hydroxypropionate dehydrogenase (hcdB), and malonate semialdehyde dehydrogenase (hcdC) genes were detected. After excessive experiments of PCR and sequencing, the full-length sequences of these key genes were identified. Interestingly, a complete sequence of a unique gene cluster (6.2kbp) of hcd (homocholine degrading) genes that contain the genes hcdD, hcdB, hcdC, and hcdR was obtained. The sequence information of these essential genes will enhance our understanding of homocholine catabolic pathway in microorganisms and will help in identifying better inhibitors or activators of these enzymes to either improve or suppress their activity depending on the importance of the formed metabolite.