Denitrification is a distinct
means
of energy conservation, making use of N oxides as terminal electron
acceptors
for cellular bioenergetics under anaerobic, microaerophilic, and
occasionally
aerobic conditions. The process is an essential branch of the global N
cycle, reversing dinitrogen fixation, and is associated with
chemolithotrophic,
phototrophic, diazotrophic, or organotrophic metabolism but generally
not
with obligately anaerobic life. Discovered more than a century ago and
believed to be exclusively a bacterial trait, denitrification has now
been
found in halophilic and hyperthermophilic archaea and in the
mitochondria
of fungi, raising evolutionarily intriguing vistas. Important advances
in the biochemical characterization of denitrification and the
underlying
genetics have been achieved with Pseudomonas stutzeri,
Pseudomonas
aeruginosa, Paracoccus denitrificans, Ralstonia eutropha,
and Rhodobacter sphaeroides. Pseudomonads represent one of the
largest
assemblies of the denitrifying bacteria within a single genus, favoring
their use as model organisms. Around 50 genes are required within a
single
bacterium to encode the core structures of the denitrification
apparatus.
Much of the denitrification process of gram-negative bacteria has been
found confined to the periplasm, whereas the topology and enzymology of
the gram-positive bacteria are less well established. The activation
and
enzymatic transformation of N oxides is based on the redox chemistry of
Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray
structures
of the two types of respiratory nitrite reductases and the isolation of
the novel enzymes nitric oxide reductase and nitrous oxide reductase,
as
well as their structural characterization by indirect spectroscopic
means.
This revealed unexpected relationships among denitrification enzymes
and
respiratory oxygen reductases. Denitrification is intimately related to
fundamental cellular processes that include primary and secondary
transport,
protein translocation, cytochrome c biogenesis, anaerobic gene
regulation,
metalloprotein assembly, and the biosynthesis of the cofactors
molybdopterin
and heme D1. An important class of regulators
for
the anaerobic expression of the denitrification apparatus are
transcription
factors of the greater FNR family. Nitrate and nitric oxide, in
addition
to being respiratory substrates, have been identified as signaling
molecules
for the induction of distinct N oxide-metabolizing enzymes.