Engineering nitrogen and carbon fixation for next-generation plants

Improving plant nitrogen (N) and carbon (C) acquisition and assimilation is a major challenge for global agriculture, food security, and ecological sustainability. Emerging synthetic biology techniques, including directed evolution, artificial intelligence (AI)-guided enzyme design, and metabolic engineering, have opened new avenues for optimizing nitrogenase to fix atmospheric N2 in plants, engineering Rhizobia or other nitrogen-fixing bacteria for symbiotic associations with both legume and nonlegume crops, and enhancing carbon fixation to improve photosynthetic efficiency and source-to-sink assimilate fluxes. Here, we discuss the potential for engineering nitrogen fixation and carbon fixation mechanisms in plants, from rational and AI-driven optimization of nitrogen and carbon fixation cycles. Furthermore, we discuss strategies for modifying source-to-sink relationships to promote robust growth in extreme conditions, such as arid deserts, saline-alkaline soils, or even extraterrestrial environments like Mars. The combined engineering of N and C pathways promises a new generation of crops with enhanced productivity, resource-use efficiency, and resilience. Finally, we explore future perspectives, focusing on the integration of enzyme engineering via directed evolution and computational design to accelerate metabolic innovation in plants.

The nitrogenase mechanism: new roles for the dangler?

Dangler sites protruding from a core metallocluster were introduced into the bioinorganic lexicon in 2000 by R.D. Britt and co-workers in an analysis of the tetramanganese oxygen-evolving cluster in photosystem II. In this perspective, we consider whether analogous dangler sites could participate in the mechanism of dinitrogen reduction by nitrogenase. Two possible roles for dynamic danglers in the active site FeMo cofactor are highlighted that might occur transiently during turnover. The first role for a dangler involves the S2B belt sulfur associated with displacement by carbon monoxide and other ligands, while the second dangler role could involve the entire cluster upon displacement of the His-  α  442 side chain to the molybdenum by a free carboxyl group of the homocitrate ligand. To assess whether waters might be able to interact with the cofactor, a survey of small ligands (water and alkali metal ions) contacting [4Fe4S] clusters in synthetic compounds and proteins was conducted. This survey reveals a preference for these sites to pack over the centers of 2Fe2S rhombs. Waters are excluded from the S2B site in the resting state of nitrogenase, suggesting it is unlikely that water molecules coordinate to the FeMo cofactor during catalysis. While alkali metal ions are found to generally influence the properties of catalysts for dinitrogen reduction, no convincing evidence was found that any of the waters near the FeMo cofactor could instead be sodium or potassium ions. Dangler sites, if they exist in the nitrogenase mechanism, are likely formed transiently by localized changes to the resting-state FeMo cofactor structure.

Improvement of the nitrogenase activity in Escherichia coli that expresses the nitrogen fixation-related genes from Azotobacter vinelandii

The transfer of nitrogen fixation (nif) genes from diazotrophs to non-diazotrophic hosts is of increasing interest for engineering biological nitrogen fixation. A recombinant Escherichia coli strain expressing Azotobacter vinelandii 18 nif genes (nifHDKBUSVQENXYWZMF, nifiscA, and nafU) were previously constructed and showed nitrogenase activity. In the present study, we constructed several E. coli strain derivatives in which all or some of the 18 nif genes were additionally integrated into the fliK locus of the chromosome in various combinations. E. coli derivatives with the chromosomal integration of nifiscA, nifU, and nifS, which are involved in the biosynthesis of the [4Fe-4S] cluster of dinitrogenase reductase, exhibited enhanced nitrogenase activity. We also revealed that overexpression of E. coli fldA and ydbK, which encode flavodoxin and flavodoxin-reducing enzyme, respectively, enhanced nitrogenase activity, likely by facilitating electron transfer to dinitrogenase reductase. The additional expression of nifM, putatively involved in maturation of dinitrogenase reductase, further enhanced nitrogenase activity and the amount of soluble NifH. By combining these factors, we successfully improved nitrogenase activity 10-fold.

Light-driven, bias-free nitrogenase-based bioelectrochemical cell for ammonia generation

Nitrogen fixation is a key process that sustains life on Earth. Nitrogenase is the sole enzyme capable of fixing nitrogen under ambient conditions. Extensive research efforts have been dedicated to elucidating the enzyme mechanism and its artificial activation through high applied voltage, photochemistry, or strong reducing agents. Harnessing light irradiation to minimize the required external bias can lower the process's high energy investment. Herein, we present the development of photo-bioelectrochemical cells (PBECs) utilizing BiVO4/CoP or CdS/NiO photoanodes for nitrogenase activation toward N2 fixation. The constructed PBEC based on BiVO4/CoP photoanode requires minimal external bias (200 mV) and suppresses O2 generation that allows efficient activation of the nitrogenase enzyme, using glucose as an electron donor. In a second developed PBEC configuration, CdS/NiO photoanode was used, enabling bias-free activation of the nitrogenase-based cathode to produce 100 μM of ammonia at a faradaic efficiency (FE) of 12%. The ammonia production was determined by a commonly used fluorescence probe and further validated using 1H-NMR spectroscopy. The presented PBECs lay the foundation for biotic-abiotic systems to directly activate enzymes toward value-added chemicals by light-driven reactions.

Hole-scavenging in photo-driven N2 reduction catalyzed by a CdS-nitrogenase MoFe protein biohybrid system

The light-driven reduction of dinitrogen (N2) to ammonia (NH3) catalyzed by a cadmium sulfide (CdS) nanocrystal‑nitrogenase MoFe protein biohybrid is dependent on a range of different factors, including an appropriate hole-scavenging sacrificial electron donor (SED). Here, the impact of different SEDs on the overall rate of N2 reduction catalyzed by a CdS quantum dot (QD)-MoFe protein system was determined. The selection of SED was guided by several goals: (i) molecules with standard reduction potentials sufficient to reduce the oxidized CdS QD, (ii) molecules that do not absorb the excitation wavelength of the CdS QD, and (iii) molecules that could be readily reduced by sustainable processes. Earlier studies utilized buffer molecules or ascorbic acid as the SED. The effectiveness of ascorbic acid as SED was compared to dithionite (DT), triethanolamine (TEOA), and hydroquinone (HQ) across a range of concentrations in supporting N2 reduction to NH3 in a CdS QD-MoFe protein photocatalytic system. It was found that TEOA supported N2 reduction rates comparable to those observed for dithionite and ascorbic acid. HQ was found to support significantly higher rates of N2 reduction compared to the other SEDs at a concentration of 50 mM. A comparison of the rates of N2 reduction by the biohybrid complex to the standard reduction potential (Eo) of the SEDs reveals that Eo is not the only factor impacting the efficiency of hole-scavenging. These findings reveal the importance of the SED properties for improving the efficiency of hole-scavenging in the light-driven N2 reduction reaction catalyzed by a CdS QD-MoFe protein hybrid.

A. Hochberg G, Rebelein JG. Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase in Rhodobacter capsulatus

Nitrogenases are the only enzymes able to fix gaseous nitrogen into bioavailable ammonia and hence are essential for sustaining life. Catalysis by nitrogenases requires both a large amount of ATP and electrons donated by strongly reducing ferredoxins or flavodoxins. Our knowledge about the mechanisms of electron transfer to nitrogenase enzymes is limited: The electron transport to the iron (Fe)-nitrogenase has hardly been investigated. Here, we characterized the electron transfer pathway to the Fe-nitrogenase in Rhodobacter capsulatus via proteome analyses, genetic deletions, complementation studies, and phylogenetics. Proteome analyses revealed an upregulation of four ferredoxins under nitrogen-fixing conditions reliant on the Fe-nitrogenase in a molybdenum nitrogenase knockout strain, compared to non-nitrogen-fixing conditions. Based on these findings, R. capsulatus strains with deletions of ferredoxin (fdx) and flavodoxin (fld, nifF) genes were constructed to investigate their roles in nitrogen fixation by the Fe-nitrogenase. R. capsulatus deletion strains were characterized by monitoring diazotrophic growth and Fe-nitrogenase activity in vivo. Only deletions of fdxC or fdxN resulted in slower growth and reduced Fe-nitrogenase activity, whereas the double deletion of both fdxC and fdxN abolished diazotrophic growth. Differences in the proteomes of ∆fdxC and ∆fdxN strains, in conjunction with differing plasmid complementation behaviors of fdxC and fdxN, indicate that the two Fds likely possess different roles and functions. These findings will guide future engineering of the electron transport systems to nitrogenase enzymes, with the aim of increased electron flux and product formation.IMPORTANCENitrogenases are essential for biological nitrogen fixation, converting atmospheric nitrogen gas to bioavailable ammonia. The production of ammonia by diazotrophic organisms, harboring nitrogenases, is essential for sustaining plant growth. Hence, there is a large scientific interest in understanding the cellular mechanisms for nitrogen fixation via nitrogenases. Nitrogenases rely on highly reduced electrons to power catalysis, although we lack knowledge as to which proteins shuttle the electrons to nitrogenases within cells. Here, we characterized the electron transport to the iron (Fe)-nitrogenase in the model diazotroph Rhodobacter capsulatus, showing that two distinct ferredoxins are very important for nitrogen fixation despite having different redox centers. In addition, our research expands upon the debate on whether ferredoxins have functional redundancy or perform distinct roles within cells. Here, we observe that both essential ferredoxins likely have distinct roles based on differential proteome shifts of deletion strains and different complementation behaviors.

Photoinduced Charge Transfer from Quantum Dots Measured by Cyclic Voltammetry

Measuring and modulating charge-transfer processes at quantum dot interfaces are crucial steps in developing quantum dots as photocatalysts. In this work, cyclic voltammetry under illumination is demonstrated to measure the rate of photoinduced charge transfer from CdS quantum dots by directly probing the changing oxidation states of a library of molecular charge acceptors, including both hole and electron acceptors. The voltammetry data demonstrate the presence of long-lived charge donor states generated by native photodoping of the quantum dots as well as a positive correlation between driving force and rate of charge transfer. Changes to the voltammograms under illumination follow mechanistic predictions from the E_rC_i' zone diagram, and electrochemical modeling allows for measurement of the rate of productive electron transfer. Observed rates for photoinduced charge transfer are on the order of 0.1 s^-1, which are distinct from the picosecond dynamics measured by conventional transient optical spectroscopy methods and are more closely connected to the quantum yield of light-mediated chemical transformations.

Tailoring Quantum Dot Sizes for Optimal Photoinduced Catalytic Activation of Nitrogenase

Many efforts have been directed towards elucidating the nitrogenase structure, its biocatalytic activity, and methods to artificially activate it by external stimuli. Here, we investigated how semiconductor nanoparticles (NPs) with sizes ranging between 2.3-3.5 nm form nano-biohybrids with the nitrogenase enzyme and enable its photoinduced biocatalytic activity. We examined two homogenously synthesized quantum dots (QDs), CdS, CdSe, and two nitrogenase variants, the wild-type and a cysteine-mutated. We show that the cysteine-mutated variant does not enhance the hydrogen generation amounts, as compared with the wild type. Nevertheless, we show that the 2.3 nm-sized CdSe NPs facilitate an eightfold increase compared with larger CdSe NPs. The obtained results were investigated using electrochemical techniques, transmission electron microscopy, and further confirmed by time-resolved spectroscopic measurements, which allow us to determine the electron tranfer rate constant (k_ET ) of the different configurations.

Molecular mechanisms of electron transfer employed by native proteins and biological-inorganic hybrid systems

Recent advances in enzymatic electrosynthesis of desired chemicals in biological-inorganic hybrid systems has generated interest because it can use renewable energy inputs and employs highly specific catalysts that are active at ambient conditions. However, the development of such innovative processes is currently limited by a deficient understanding of the molecular mechanisms involved in electrode-based electron transfer and biocatalysis. Mechanistic studies of non-electrosynthetic electron transferring proteins have provided a fundamental understanding of the processes that take place during enzymatic electrosynthesis. Thus, they may help explain how redox proteins stringently control the reduction potential of the transferred electron and efficiently transfer it to a specific electron acceptor. The redox sites at which electron donor oxidation and electron acceptor reduction take place are typically located in distant regions of the redox protein complex and are electrically connected by an array of closely spaced cofactors. These groups function as electron relay centers and are shielded from the surrounding environment by the electrically insulating apoporotein. In this matrix, electrons travel via electron tunneling, i.e. hopping between neighboring cofactors, over impressive distances of upto several nanometers and, as in the case of the Shewanella oneidensis Mtr electron conduit, traverse the bacterial cell wall to extracellular electron acceptors such as solid ferrihydrite. Here, the biochemical strategies of protein-based electron transfer are presented in order to provide a basis for future studies on the basis of which a more comprehensive understanding of the structural biology of enzymatic electrosynthesis may be attained.

Artificial, Photoinduced Activation of Nitrogenase Using Directed and Mediated Electron Transfer Processes

Nitrogenase, a bacteria-based enzyme, is the sole enzyme that is able to generate ammonia by atmospheric nitrogen fixation. Thus, improved understanding of its utilization and developing methods to artificially activate it may contribute to basic research, as well as to the design of future artificial systems. Here, we present methods to artificially activate nitrogenase using photoinduced reactions. Two nitrogenase variants originating from Azotobacter vinelandii were examined using photoactivated CdS nanoparticles (NPs) capped with thioglycolic acid (TGA) or 2-mercaptoethanol (ME) ligands. The effect of methyl viologen (MV) as a redox mediator of hydrogen and ammonia generation was tested and analyzed. We further determined the NPs conductive band edges and their effect on the nitrogenase photoactivation. The nano-biohybrid systems comprising CdS NPs and nitrogenase were further imaged by transmission electron microscopy, visualizing their formation for the first time. Our results show that the ME-capped CdS NPs–nitrogenase enzyme biohybrid system with added MV as a redox mediator leads to a five-fold increase in the production of ammonia compared with the non-mediated biohybrid system; nevertheless, it stills lag behind the natural process rate. On the contrary, a maximal hydrogen generation amount was achieved by the αL158C MoFe-P and the ME-capped CdS NPs.