Introduction to the Biochemistry and Molecular Biology of Denitrification

This chapter provides an overview of the biochemistry and genetics of denitrification in such organisms. It considers the aspects of denitrification that occur in archaea and certain fungi. Denitrification has been mostly studied in Paracoccus denitrificans and Pseudomonas stutzeri and so it describes denitrification for each of these organisms in turn before considering to what extent general principles can be discerned. In recent years, high-resolution crystal structures have become available for these enzymes with the exception of the structure for NO-reductase. In general, the proteins required for denitrification are only produced under (close to) anaerobic conditions, and if anaerobically grown, cells are exposed to O₂ and then the activities of the proteins are inhibited. Specialized denitrifiers, such as P. denitrificans and the denitrifying Pseudomonads, contain more than 40 genes, which encode the proteins that make up a full denitrification pathway. They include the structural genes for the enzymes and e^- donors, their regulators as well as many accessory genes required for assembly, cofactor synthesis, and insertion into the enzymes. In contrast, some denitrifiers can only carry out the two central reactions of the pathway and use these activities to support growth, but the cost of maintaining this capability is a very small amount of genome space. It provides insights into the regulation of gene expression and the way in which some denitrification enzymes play different roles in bacteria.