Predicting regulatory binding sites for anaerobic vs. aerobic respiration in P. denitrificans

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About Predicting regulatory binding sites for anaerobic vs. aerobic respiration in P. denitrificans


P. denitrificans in culture. The image was taken by Richard Evans-Gowing at the University of East Anglia, Norwich, UK. Colorized by Leila Hornick.
Paracoccus denitrificans is a non-motile coccoid soil organism from the alpha subdivision of the proteobacteria, and was first isolated in 1908 by the Dutch microbiologist Martinus Beijerinck.   The original selection was on the basis of its ability to reduce nitrate to dinitrogen under anaerobic growth conditions, the pathway now known as denitrification. Paracoccus has been a model organism for the study of denitrification ever since.   All four oxido-reductases required for the denitrification pathway, along with their corresponding structural, accessory and regulatory genes, have been well characterized in P. denitrificans.  Besides its intrinsic interest, denitrification also represents a source of atmosphere damaging compounds (nitric oxide and nitrous oxide), is a route for the loss of nitrogen fertilizer from agricultural soil, and has potential applications in the water treatment industry.  The organism grows well under aerobic conditions, expressing a respiratory chain very similar to that of the eukaryotic mitochondrion.   P. denitrificans has been, and continues to be, the subject of many studies of the fundamental biochemical and bioenergetic properties of the aerobic electron transport chain. The evidence from 16S rRNA analysis indicates that the evolutionary pre-cursor of the mitochondrion was a close relative of P. denitrificans (both fall in the alpha sub-group of the proteobacteria), justifying the use of P. denitrificans as a model for the mitochondrial respiratory chain. The availability of an annotated genome sequence will shed further light on the diverse and unusual metabolic capabilities of P. denitrificans.

Focus of this project is to identify regulatory sequences in promoters that control the expression of proteins recruited for aerobic and anaerobic respiration. For this, all possible promoter regions need to be identified and archived along with their allocated genes. Next, an algorithm has to be developed to screen for possible binding sites for regulatory proteins within these promoter regions. As proof of principle the focus will be on the binding site for Fnr-like transcription activators (consensus TTGAT-N4-ATCAA). Reference Baker, S.C., Ferguson, S.J., Ludwig, B., Page, M.D., Richter, O.M., and van Spanning, R.J. (1998) Molecular genetics of the genus Paracoccus : metabolically versatile bacteria with bioenergetic flexibility.   Microbiology and Molecular Biology Reviews 62 : 1046-1078.

Information: Anton Feenstra (FEW,, Rob van Spanning (FALW,