Nitrogen is the major component of Earth's atmosphere and plays important roles in biochemistry. Biological systems have evolved a variety of mechanisms for fixing and recycling environmental nitrogen sources, which links them tightly with terrestrial nitrogen reservoirs. However, prior to the emergence of biology, all nitrogen cycling was abiological, and this cycling may have set the stage for the origin of life. It is of interest to understand how nitrogen cycling would proceed on terrestrial planets with comparable geodynamic activity to Earth, but on which life does not arise. We constructed a kinetic mass-flux model of nitrogen cycling in its various major chemical forms (e.g., N2, reduced (NHx) and oxidized (NOx) species) between major planetary reservoirs (the atmosphere, oceans, crust, and mantle) and included inputs from space. The total amount of nitrogen species that can be accommodated in each reservoir, and the ways in which fluxes and reservoir sizes may have changed over time in the absence of biology, are explored. Given a partition of volcanism between arc and hotspot types similar to the modern ones, our global nitrogen cycling model predicts a significant increase in oceanic nitrogen content over time, mostly as NHx, while atmospheric N2 content could be lower than today. The transport timescales between reservoirs are fast compared to the evolution of the environment; thus atmospheric composition is tightly linked to surface and interior processes.

Serine hydroxymethyltransferase catalyzes the cleavage of b-hydroxyamino acids into glycine and aldehydes in the absence of tetrahydrofolate. The enzyme accepts various b-hydroxyamino acids as the substrate of this reaction. The reaction rate varies depending on the substituent and stereochemistry at the Cb atom: the erythro forms and the b-phenyl substituent are preferred over the threo forms and the b-methyl substituent, respectively. Although several mechanisms have been proposed, what determines the substrate preference remains unclear. We first performed quantum mechanical calculations to assess the validity of the reaction mechanisms. The results indicate that the retro-aldol mechanism starting with abstraction of the proton from the b-hydroxyl group is plausible. This also suggests that Ca-Cb bond cleavage is the rate-limiting step. We next measured the dependence of the rate constants on temperature with four representative substrates and calculated the activation energies and pre-exponential factors from the Arrhenius plots. The activation energies of the erythro forms were lower than those of the threo forms. The b-phenyl substituent lowered the activation energy in the threo form, whereas it did not alter the activation energy but increased the pre-exponential factor in the erythro form. We present a unified model to explain the origin of the substituent and stereochemical preferences by combining the theoretical and experimental results. A possible biological role of the tetrahydrofolate-independent activity in thermophiles is also discussed.

Glutamate synthases are classified according to their specificities for electron donors. Ferredoxin-dependent glutamate synthases had been found only in plants and cyanobacteria, whereas many bacteria have NADPHdependent glutamate synthases. In this study, Hydrogenobacter thermophilus, a hydrogen-oxidizing chemoautotrophic bacterium, was shown to possess a ferredoxin-dependent glutamate synthase like those of phototrophs. This is the first observation, to our knowledge, of a ferredoxin-dependent glutamate synthase in a nonphotosynthetic organism. The purified enzyme from H. thermophilus was shown to be a monomer of a 168-kDa polypeptide homologous to ferredoxin-dependent glutamate synthases from phototrophs. In contrast to known ferredoxin-dependent glutamate synthases, the H. thermophilus glutamate synthase exhibited glutaminase activity. Furthermore, this glutamate synthase did not react with a plant-type ferredoxin (Fd3 from this bacterium) containing a [2Fe-2S] cluster but did react with bacterial ferredoxins (Fd1 and Fd2 from this bacterium) containing [4Fe-4S] clusters. Interestingly, the H. thermophilus glutamate synthase was activated by some of the organic acids in the reductive tricarboxylic acid cycle, the central carbon metabolic pathway of this organism. This type of activation has not been reported for any other glutamate synthases, and this property may enable the control of nitrogen assimilation by carbon metabolism.Glutamate synthase (glutamine:2-oxoglutarate amidotransferase [GOGAT]) is known to be one of the most important enzymes for ammonium assimilation. This enzyme synthesizes Glu from Gln and 2-oxoglutarate (2-OG) as follows: Gln ϩ 2-OG ϩ reduced electron carrier 3 2 Glu ϩ oxidized electron carrier.GOGAT couples with glutamine synthetase (GS) for ammonium assimilation, and their total reaction incorporates NH 3 into 2-OG at the expense of ATP and reducing power. This coupling reaction is called the GS/GOGAT pathway, a prevailing ammonium assimilatory pathway among many organisms (15,22).GOGATs are classified into several types according to their specificities for electron donors (27). The first type is ferredoxindependent GOGAT (Fd-GOGAT), which utilizes a reduced ferredoxin as an electron donor. Because Fd-GOGAT is found only in cyanobacteria and chloroplasts of plants and is not found in nonphotosynthetic organisms, it is often called "planttype GOGAT." Another type of GOGAT utilizes NADPH as an electron donor. NADPH-dependent GOGAT (NADPH-GOGAT) is common among most bacteria and is often referred to as "bacterial GOGAT."Fd-GOGAT is a monomeric protein with a molecular mass of Ϸ150 kDa, while NADPH-GOGAT forms an (␣␤) 4 heterooctamer with ␣ subunits of Ϸ150 kDa and ␤ subunits of Ϸ50 kDa. Fd-GOGAT and the ␣ subunit of NADPH-GOGAT are homologous to each other. There is an insertion of Ϸ18 amino acid residues conserved in Fd-GOGATs from phototrophs but not in reported NADPH-GOGATs. This insertion is called the Fd loop and is suspected to be involved in ferredoxin-Fd-GOGAT binding (26,27,28...

The reductive tricarboxylic acid (rTCA) cycle is among the most plausible candidates for the first autotrophic metabolism in the earliest life. Extant enzymes fixing CO2 in this cycle contain cofactors at the catalytic centers, but it is unlikely that the protein/cofactor system emerged at once in a prebiotic process. Here, we discuss the feasibility of non-enzymatic cofactor-assisted drive of the rTCA reactions in the primitive Earth environments, particularly focusing on the acetyl-CoA conversion to pyruvate. Based on the energetic and mechanistic aspects of this reaction, we propose that the deep-sea hydrothermal vent environments with active electricity generation in the presence of various sulfide catalysts are a promising setting for it to progress. Our view supports the theory of an autotrophic origin of life from primordial carbon assimilation within a sulfide-rich hydrothermal vent.