Characterization of [FeFe] Hydrogenase O2 Sensitivity Using a New, Physiological Approach

Cell-Free Protein Synthesis of Metalloproteins

Metalloproteins, proteins containing metal atoms or clusters within their structures, are critical for various biological functions across all domains of life. More than hundreds of different types have been discovered, which conduct various roles such as transportation of O2, catalyzing chemical reactions, sensing environmental changes, and relaying electrons. Metalloprotein molecules incorporate a variety of metal atoms, coordinated to specific amino acid residues that affect their conformation and functionality. The process of metal incorporation typically occurs during or post-protein folding, often requiring chaperones for metal ion delivery and quality control. Progress in understanding metal incorporation and metalloprotein functionality has been enhanced by cell-free protein synthesis (CFPS) methods that offer direct control over the synthesis environment. This chapter reviews the diverse applications of CFPS methods in metalloprotein research, encompassing structure-function studies, protein engineering, and creation of artificial metalloproteins. Examples demonstrating the utility and advances brought about by CFPS in synthetic biology, electrochemistry, and drug discovery are highlighted. Despite remarkable progress, challenges remain in optimizing and advancing the CFPS methods, underscoring the need for future explorations in this transformative approach to metalloprotein study and engineering.

The response of Naegleria gruberi to oxidative stress

Aerobic organisms require oxygen for respiration but must simultaneously cope with oxidative damages inherently linked with this molecule. Unicellular amoeboflagellates of the genus Naegleria, containing both free-living species and opportunistic parasite, thrive in aerobic environments. However, they are also known to maintain typical features of anaerobic organisms. Here, we describe the mechanisms of oxidative damage mitigation in Naegleria gruberi and focus on the molecular characteristics of three noncanonical proteins interacting with oxygen and its derived reactive forms. We show that this protist expresses hemerythrin, protoglobin and an aerobic-type rubrerythrin, with spectral properties characteristic of the cofactors they bind. We provide evidence that protoglobin and hemerythrin interact with oxygen in vitro and confirm the mitochondrial localization of rubrerythrin by immunolabeling. Our proteomic analysis and immunoblotting following heavy metal treatment revealed upregulation of hemerythrin, while rotenone treatment resulted in an increase in rubrerythrin protein levels together with vast upregulation of alternative oxidase. Our study provided new insights into the mechanisms employed by N. gruberi to cope with different types of oxidative stress and allowed us to propose specific roles for three unique and understudied proteins: hemerythrin, protoglobin and rubrerythrin.

Investigation of the Ferredoxin's Influence on the Anaerobic and Aerobic, Enzymatic H2 Production

Ferredoxins are metalloproteins that deliver electrons to several redox partners, including [FeFe] hydrogenases that are potentially a component of biological H₂ production technologies. Reduced ferredoxins can also lose electrons to molecular oxygen, which may lower the availability of electrons for cellular or synthetic reactions. Ferredoxins thus play a key role in diverse kinds of redox biochemistry, especially the enzymatic H₂ production catalyzed by [FeFe] hydrogenases. We investigated how the yield of anaerobic and aerobic H₂ production vary among the four different types of ferredoxins that are used to deliver electrons extracted from NADPH within the synthetic, fermentative pathway. We also assessed the electron loss due to O₂ reduction by reduced ferredoxins within the pathway, for which the difference was as high as five-fold. Our findings provide valuable insights for further improving biological H₂ production technologies and can also facilitate elucidation of mechanisms governing interactions between Fe–S cluster(s) and molecular oxygen.

Remodeling of photosynthetic electron transport in Synechocystis sp. PCC 6803 for future hydrogen production from water

Photosynthetic microorganisms such as the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis) can be exploited for the light-driven synthesis of valuable compounds. Thermodynamically, it is most beneficial to branch-off photosynthetic electrons at ferredoxin (Fd), which provides electrons for a variety of fundamental metabolic pathways in the cell, with the ferredoxin-NADP⁺ Oxido-Reductase (FNR, PetH) being the main target. In order to re-direct electrons from Fd to another consumer, the high electron transport rate between Fd and FNR has to be reduced. Based on our previous in vitro experiments, corresponding FNR-mutants at position FNR_K190 (Wiegand, K., et al.: "Rational redesign of the ferredoxin-NADP-oxido-reductase/ferredoxin-interaction for photosynthesis-dependent H₂-production". Biochim Biophys Acta, 2018) have been generated in Synechocystis cells to study their impact on the cellular metabolism and their potential for a future hydrogen-producing design cell. Out of two promising candidates, mutation FNR_K190D proved to be lethal due to oxidative stress, while FNR_K190A was successfully generated and characterized: The light induced NADPH formation is clearly impaired in this mutant and it shows also major metabolic adaptations like a higher glucose metabolism as evidenced by quantitative mass spectrometric analysis. These results indicate a high potential for the future use of photosynthetic electrons in engineered design cells - for instance for hydrogen production. They also show substantial differences of interacting proteins in an in vitro environment vs. physiological conditions in whole cells.

Opportunities toward hydrogen production biotechnologies

Hydrogen is already a major commodity and process intermediate for fertilizer production, petroleum processing, and chemical synthesis. It also offers unrealized potential for energy storage. While biological production offers an expandable and sustainable source, enthusiasm has been dampened by slow research progress. Also, the very low cost of natural gas (the major current hydrogen source) imposes severe economic challenges. This discussion describes process, metabolic, and protein engineering opportunities toward cost-effective biohydrogen production. Recent progress in hydrogenase engineering and photosynthetic bacterial research now suggests a favorable risk versus reward opportunity. Although the risks are still significant, successful technologies would provide important components in an integrated energy portfolio that enables global sustainability.

O2 sensitivity and H2 production activity of hydrogenases-A review

Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H₂ production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O₂ sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O₂ but proficient in H₂ production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O₂ tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O₂ sensitivity of the enzyme while it catalyzes H₂ production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H₂ production and other industrial processes, as well as our own perspective on future applications.

Clostridial whole cell and enzyme systems for hydrogen production: current state and perspectives

Strictly anaerobic bacteria of the Clostridium genus have attracted great interest as potential cell factories for molecular hydrogen production purposes. In addition to being a useful approach to this process, dark fermentation has the advantage of using the degradation of cheap agricultural residues and industrial wastes for molecular hydrogen production. However, many improvements are still required before large-scale hydrogen production from clostridial metabolism is possible. Here we review the literature on the basic biological processes involved in clostridial hydrogen production, and present the main advances obtained so far in order to enhance the hydrogen productivity, as well as suggesting some possible future prospects.