been the complementary (yin-yang) driving force facilitating the evolution of catalysis. It is thus no surprise to see that the complement of metalloenzymes involved in
the controlled transformations of NO is by far the greatest of all enzymes that
function in the extant N-cycle, facilitating one or two electron transfers in a single
reaction (see Fig. 9.1a, b).
Interestingly, while the flow of nitrogen and electrons in the extant nitrogen cycle
can be reconstructed by just examining microbes that utilize nitrogen in their
oxidative and reductive branches of catabolic electron flow, this does not prove
that all modules participating in the extant nitrogen cycle evolved in the ancestors of
extant nitrogen-centric bacteria (ammonia- and nitrite-oxidizing bacteria, anammox
bacteria) and archaea (ammonia-oxidizing Thaumarchaeota). In fact, it is more likely
that some of the modules that utilize nitrogen oxides as electron acceptors in the
reductive branch of catabolism evolved in microbes that harvest energy and reductant from reduced compounds that lack nitrogen, such as carbon-, sulfur- or ironcontaining compounds. Some of the N compound-reducing modules in the reductive
branch of catabolism are respiratory in that they contribute to the formation of
proton-motive force (i.e., NrfAH and NrfABC, reducing nitrite; NarGH, reducing
nitrate), while others do not contribute to the conservation of energy (i.e., nitrite
reductases NirK and NirS; nitrate reductases NasAB and NapABGH). On the other
end of the electron flow chain, it is unlikely that modules facilitating high-throughput
oxidation of catabolic substrates such as ammonium/ammonia or methylamine were
established before the modules providing detoxification of intermediates, and safe
channeling of the extracted electrons to final acceptors, were functional. Indeed, the
oxygen-dependent ammonia-oxidizing microbes utilize copper-containing membrane-bound monooxygenases (CuMMO), which were not functional as such in
anoxic environments. In contrast, the anammox bacteria catabolize their substrates at
considerably lower rates; the ammonium-oxidizing and hydrazine-forming module
is soluble, sequestered in an internal compartment, the anammoxosome, employs
iron as its catalytic transition metal, and it operates in the constraints of a fast
product-consuming redox gradient (without this gradient, the module operates in
the opposite direction, disproportionating hydrazine).
The nitrogen cycle with its many redox-active intermediates beautifully demonstrates how microorganisms evolved sophisticated metabolic inventory permitting
electron transfers between both benign and highly harmful nitrogen intermediates.
The modules are finely tuned to prevent accumulation of toxic intermediates near
susceptible intracellular targets and are redundant and diverse enough to provide an
opportunity to “call up” the module component to do the job under a range of
conditions. The acquisition of inventory enabling cells to exploit catabolically the
large diversity in oxidation states of nitrogen compounds including “mutagens,
radicals, rocket fuel, and laughing gas” and “stringing metabolic modules” to
support cellular metabolism provided a significant evolutionary avenue for organisms, successful in anoxic environments, to evolve and succeed (survive and prosper) in the expanding oxic surrounding of our blue planet. Dissection of the extant
biogeochemical nitrogen cycle and inference in the evolutionary history of the major
players in this cycle, organisms, and macromolecules, has, so far, provided beautiful
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M. G. Klotz and L. Y. Stein
the controlled transformations of NO is by far the greatest of all enzymes that
function in the extant N-cycle, facilitating one or two electron transfers in a single
reaction (see Fig. 9.1a, b).
Interestingly, while the flow of nitrogen and electrons in the extant nitrogen cycle
can be reconstructed by just examining microbes that utilize nitrogen in their
oxidative and reductive branches of catabolic electron flow, this does not prove
that all modules participating in the extant nitrogen cycle evolved in the ancestors of
extant nitrogen-centric bacteria (ammonia- and nitrite-oxidizing bacteria, anammox
bacteria) and archaea (ammonia-oxidizing Thaumarchaeota). In fact, it is more likely
that some of the modules that utilize nitrogen oxides as electron acceptors in the
reductive branch of catabolism evolved in microbes that harvest energy and reductant from reduced compounds that lack nitrogen, such as carbon-, sulfur- or ironcontaining compounds. Some of the N compound-reducing modules in the reductive
branch of catabolism are respiratory in that they contribute to the formation of
proton-motive force (i.e., NrfAH and NrfABC, reducing nitrite; NarGH, reducing
nitrate), while others do not contribute to the conservation of energy (i.e., nitrite
reductases NirK and NirS; nitrate reductases NasAB and NapABGH). On the other
end of the electron flow chain, it is unlikely that modules facilitating high-throughput
oxidation of catabolic substrates such as ammonium/ammonia or methylamine were
established before the modules providing detoxification of intermediates, and safe
channeling of the extracted electrons to final acceptors, were functional. Indeed, the
oxygen-dependent ammonia-oxidizing microbes utilize copper-containing membrane-bound monooxygenases (CuMMO), which were not functional as such in
anoxic environments. In contrast, the anammox bacteria catabolize their substrates at
considerably lower rates; the ammonium-oxidizing and hydrazine-forming module
is soluble, sequestered in an internal compartment, the anammoxosome, employs
iron as its catalytic transition metal, and it operates in the constraints of a fast
product-consuming redox gradient (without this gradient, the module operates in
the opposite direction, disproportionating hydrazine).
The nitrogen cycle with its many redox-active intermediates beautifully demonstrates how microorganisms evolved sophisticated metabolic inventory permitting
electron transfers between both benign and highly harmful nitrogen intermediates.
The modules are finely tuned to prevent accumulation of toxic intermediates near
susceptible intracellular targets and are redundant and diverse enough to provide an
opportunity to “call up” the module component to do the job under a range of
conditions. The acquisition of inventory enabling cells to exploit catabolically the
large diversity in oxidation states of nitrogen compounds including “mutagens,
radicals, rocket fuel, and laughing gas” and “stringing metabolic modules” to
support cellular metabolism provided a significant evolutionary avenue for organisms, successful in anoxic environments, to evolve and succeed (survive and prosper) in the expanding oxic surrounding of our blue planet. Dissection of the extant
biogeochemical nitrogen cycle and inference in the evolutionary history of the major
players in this cycle, organisms, and macromolecules, has, so far, provided beautiful
156
M. G. Klotz and L. Y. Stein