Was nitric oxide the first deep electron sink?

The self-organizing fractal theory as a universal discovery method: the phenomenon of life

A universal discovery method potentially applicable to all disciplines studying organizational phenomena has been developed. This method takes advantage of a new form of global symmetry, namely, scale-invariance of self-organizational dynamics of energy/matter at all levels of organizational hierarchy, from elementary particles through cells and organisms to the Universe as a whole. The method is based on an alternative conceptualization of physical reality postulating that the energy/matter comprising the Universe is far from equilibrium, that it exists as a flow, and that it develops via self-organization in accordance with the empirical laws of nonequilibrium thermodynamics. It is postulated that the energy/matter flowing through and comprising the Universe evolves as a multiscale, self-similar structure-process, i.e., as a self-organizing fractal. This means that certain organizational structures and processes are scale-invariant and are reproduced at all levels of the organizational hierarchy. Being a form of symmetry, scale-invariance naturally lends itself to a new discovery method that allows for the deduction of missing information by comparing scale-invariant organizational patterns across different levels of the organizational hierarchy.An application of the new discovery method to life sciences reveals that moving electrons represent a keystone physical force (flux) that powers, animates, informs, and binds all living structures-processes into a planetary-wide, multiscale system of electron flow/circulation, and that all living organisms and their larger-scale organizations emerge to function as electron transport networks that are supported by and, at the same time, support the flow of electrons down the Earth's redox gradient maintained along the core-mantle-crust-ocean-atmosphere axis of the planet. The presented findings lead to a radically new perspective on the nature and origin of life, suggesting that living matter is an organizational state/phase of nonliving matter and a natural consequence of the evolution and self-organization of nonliving matter.The presented paradigm opens doors for explosive advances in many disciplines, by uniting them within a single conceptual framework and providing a discovery method that allows for the systematic generation of knowledge through comparison and complementation of empirical data across different sciences and disciplines.

Serpentinization as a source of energy at the origin of life

For life to have emerged from CO₂, rocks, and water on the early Earth, a sustained source of chemically transducible energy was essential. The serpentinization process is emerging as an increasingly likely source of that energy. Serpentinization of ultramafic crust would have continuously supplied hydrogen, methane, minor formate, and ammonia, as well as calcium and traces of acetate, molybdenum and tungsten, to off-ridge alkaline hydrothermal springs that interfaced with the metal-rich carbonic Hadean Ocean. Silica and bisulfide were also delivered to these springs where cherts and sulfides were intersected by the alkaline solutions. The proton and redox gradients so generated represent a rich source of naturally produced chemiosmotic energy, stemming from geochemistry that merely had to be tapped, rather than induced, by the earliest biochemical systems. Hydrothermal mounds accumulating at similar sites in today's oceans offer conceptual and experimental models for the chemistry germane to the emergence of life, although the ubiquity of microbial communities at such sites in addition to our oxygenated atmosphere preclude an exact analogy.

In quest of the nitrogen oxidizing prokaryotes of the early Earth

The introduction of nitrite and nitrate to the relatively reduced environment of the early Earth provided impetus for a tremendous diversification of microbial pathways. However, little is known about the first organisms to produce these valuable resources. In this review, the latest microbial discoveries are integrated in the evolution of the nitrogen cycle according to the great 'NO-ON' time debate, as we call it. This debate hypothesizes the first oxidation of nitrogen as abiotic and anoxic ('NO') versus biological and aerobic ('ON'). Confronting ancient biogeochemical niches with extant prokaryotic phylogenetics, physiology and morphology, pointed out that the well-described ammonia and nitrite oxidizing Proteobacteria likely did not play a pioneering role in microbial nitrogen oxidation. Instead, we hypothesize ancestral and primordial roles of methanotrophic NC10 bacteria and ammonia oxidizing archaea, respectively, for early nitrite production, and of anammox performing Planctomycetes followed by Nitrospira for early nitrate production. Additional genomic and structural information on the prokaryotic protagonists but also on their phages, together with the continued search for novel key players and processes, should further elucidate nitrogen cycle evolution. Through the ramifications between the biogeochemical cycles, this will improve our understanding on the evolution of terrestrial and perhaps extraterrestrial life.

H-NOX regulation of c-di-GMP metabolism and biofilm formation in Legionella pneumophila

Haem Nitric oxide/OXygen (H-NOX) binding domains are a family of haemoprotein sensors that are widespread in bacterial genomes, but limited information is available on their function. Legionella pneumophila is the only prokaryote found, thus far, to encode two H-NOX proteins. This paper presents data supporting a role for one of the L. pneumophila H-NOXs in the regulation of biofilm formation.

IN SUMMARY

(i) unmarked deletions in the hnox1 gene do not affect growth rate in liquid culture or replication in permissive macrophages; (ii) the Δhnox1 strain displays a hyper-biofilm phenotype; (iii) the gene adjacent to hnox1 is a GGDEF-EAL protein, lpg1057, and overexpression in L. pneumophila of this protein, or the well-studied diguanylate cyclase, vca0956, results in a hyper-biofilm phenotype; (iv) the Lpg1057 protein displays diguanylate cyclase activity in vitro and this activity is inhibited by the Hnox1 protein in the Fe(II)-NO ligation state, but not the Fe(II) unligated state; and (v) consistent with the Hnox1 regulation of Lpg1057, unmarked deletions of lpg1057 in the Δhnox1 background results in reversion of the hyper-biofilm phenotype back to wild-type biofilm levels. Taken together, these results suggest a role for hnox1 in regulating c-di-GMP production by lpg1057 and biofilm formation in response to NO.

Anoxic nitric oxide cycling in plants: participating reactions and possible mechanisms

At sufficiently low oxygen concentrations, hemeproteins are deoxygenated and become capable of reducing nitrite to nitric oxide (NO), in a reversal of the reaction in which NO is converted to nitrate or nitrite by oxygenated hemeproteins. The maximum rates of NO production depend on the oxygen avidity. The hemeproteins with the highest avidity, such as hexacoordinate hemoglobins, retain oxygen even under anoxic conditions resulting in their being extremely effective NO scavengers but essentially incapable of producing NO. Deoxyhemeprotein-related NO production can be observed in mitochondria (at the levels of cytochrome c oxidase, cytochrome c, complex III and possibly other sites), in plasma membrane, cytosol, endoplasmic reticulum and peroxisomes. In mitochondria, the use of nitrite as an alternative electron acceptor can contribute to a limited rate of ATP synthesis. Non-heme metal-containing proteins such as nitrate reductase and xanthine oxidase can also be involved in NO production. This will result in a strong anoxic redox flux of nitrogen through the hemoglobin-NO cycle involving nitrate reductase, nitrite: NO reductase, and NO dioxygenase. In normoxic conditions, NO is produced in very low quantities, mainly for signaling purposes and this nitrogen cycling is inoperative.

Nitrite reduction: a ubiquitous function from a pre-aerobic past

In eukaryotes, small amounts of nitrite confer cytoprotection against ischemia/reperfusion-related tissue damage in vivo, possibly via reduction to nitric oxide (NO) and inhibition of mitochondrial function. Several hemeproteins are involved in this protective mechanism, starting with deoxyhemoglobin, which is capable of reducing nitrite. In facultative aerobic bacteria, such as Pseudomonas aeruginosa, nitrite is reduced to NO by specialized heme-containing enzymes called cd(1) nitrite reductases. The details of their catalytic mechanism are summarized below, together with a hypothesis on the biological role of the unusual d(1)-heme, which, in the reduced state, shows unique properties (very high affinity for nitrite and exceptionally fast dissociation of NO). Our results support the idea that the nitrite-based reactions of contemporary eukaryotes are a vestige of earlier bacterial biochemical pathways. The evidence that nitrite reductase activities of enzymes with different cellular roles and biochemical features still exist today highlights the importance of nitrite in cellular homeostasis.

Hydrothermal focusing of chemical and chemiosmotic energy, supported by delivery of catalytic Fe, Ni, Mo/W, Co, S and Se, forced life to emerge

Energised by the protonmotive force and with the intervention of inorganic catalysts, at base Life reacts hydrogen from a variety of sources with atmospheric carbon dioxide. It seems inescapable that life emerged to fulfil the same role (i.e., to hydrogenate CO(2)) on the early Earth, thus outcompeting the slow geochemical reduction to methane. Life would have done so where hydrothermal hydrogen interfaced a carbonic ocean through inorganic precipitate membranes. Thus we argue that the first carbon-fixing reaction was the molybdenum-dependent, proton-translocating formate hydrogenlyase system described by Andrews et al. (Microbiology 143:3633-3647, 1997), but driven in reverse. Alkaline on the inside and acidic and carbonic on the outside - a submarine chambered hydrothermal mound built above an alkaline hydrothermal spring of long duration - offered just the conditions for such a reverse reaction imposed by the ambient protonmotive force. Assisted by the same inorganic catalysts and potential energy stores that were to evolve into the active centres of enzymes supplied variously from ocean or hydrothermal system, the formate reaction enabled the rest of the acetyl coenzyme-A pathway to be followed exergonically, first to acetate, then separately to methane. Thus the two prokaryotic domains both emerged within the hydrothermal mound-the acetogens were the forerunners of the Bacteria and the methanogens were the forerunners of the Archaea.