Pseudogene YdfW in Escherichia coli decreases hydrogen production through nitrate respiration pathways

Escherichia coli has approximately 4300 open reading frames and about 178 of them are annotated as pseudogenes. The existence of the pseudogenes in E. coli had raised the question of whether they contribute to any cell function. Recently, several pseudogenes have been studied; however, these genes are still considered rare and tend to be ignored as so-called junk. Our recent study has shown several pseudogenes in E. coli are essential in hydrogen metabolism. ydfW is one of the pseudogenes associated with hydrogen metabolism. Here, we found carbon dioxide and nitrate in the fermentation medium of mutant ydfW suggesting that this strain may induce nitrate pathways. The Fdh-N complex is comprised of FdnG, FdnH, and FdnI subunits which correspond to the nitrate-nitrite pathway. This finding is supported by transcription analysis that shows formate dehydrogenase (fdnG) and nitrate reductase (narG) are significantly induced (25- and 18-fold, respectively). FdnG and NarG play a significant role in the reduction of nitrate into nitrite; hence, their genes are induced by the build-up of nitrate. Based on in silico docking analysis, we predict that YdfW is covalently bound to the Fdh-N complex in the cytoplasm. Hence, deletion of ydfW is expected has influenced the nitrate-nitrite pathway. Subsequently, the situation will affect the hydrogen production in E. coli.