Cyanobacterial aldehyde deformylating oxygenase: Structure, function, and potential in biofuels production

Pathway elucidation and heterologous reconstitution of the long-chain alkane pentadecane biosynthesis from Pogostemon cablin

Very-long-chain (VLC) alkanes are major components of hydrophobic cuticular waxes that cover the aerial epidermis of land plants, serving as a waterproofing barrier to protect the plant against environmental stresses. The mechanism of VLC-alkane biosynthesis has been extensively elucidated in plants. However, little is known about the biosynthesis of long-chain alkanes (LC, C13 ~ C19) such as pentadecane in plants. Alkanes with different chain lengths are also major constituents of fossil fuels and thus the discovery of the alkane biosynthetic machinery in plants would provide a toolbox of enzymes for the production of renewable hydrocarbon sources and next generations of biofuels. The top leaves of Pogostemon cablin at young stage accumulate large amounts of LC-alkane pentadecane, making this plant an excellent system for the elucidation of LC-alkane biosynthetic machinery in plant. We show here that LC-alkane pentadecane biosynthesis in P. cablin involves an endoplasmic reticulum (ER)-localized complex made of PcCER1-LIKE3 and PcCER3, homologues of Arabidopsis ECERIFERUM1 (AtCER1) and AtCER3 proteins that are involved in Arabidopsis VLC-alkane biosynthesis. We reconstitute the biosynthesis of pentadecane in Nicotiana benthamiana by co-expression of PcCER1-LIKE3 and PcCER3 and further improve its production by silencing multifunctional acetyl-CoA carboxylases involved in fatty acid elongation pathway. Taken together, we uncovered the key biosynthetic machinery of LC-alkane pentadecane in P. cablin and demonstrated that using these newly identified enzymes to engineer this LC-alkane for liquid biofuel production in a heterologous plant host is possible.

Upper limit efficiency estimates for electromicrobial production of drop-in jet fuels

Microbes which participate in extracellular electron uptake (EEU) or H2 oxidation have the ability to manufacture organic compounds using electricity as the primary source of metabolic energy. So-called electromicrobial production could be valuable to efficiently synthesize drop-in jet fuels using renewable energy. Here, we calculate the upper limit electrical-to-fuel conversion efficiency for a model jet fuel blend containing 85% straight-chain alkanes and 15% terpenoids. When using the Calvin cycle for carbon-fixation, the energy conversion efficiency is 37.8-4.3+1.8% when using EEU for electron delivery and 40.1-4.6+0.7% when using H2 oxidation. The production efficiency can be raised to 44.2-3.7+0.5% when using the Formolase formate-assimilation pathway, and to 49.2-2.1+0.3% with the Wood-Ljungdahl pathway. This efficiency can be further raised by swapping the well-known Aldehyde Deformolating Oxygenase (ADO) termination pathway with the recently discovered Fatty Acid Photodecarboxylase (FAP) pathway. If these systems were supplied with electricity from a maximally-efficient silicon solar photovoltaic, even the least efficient pathway exceeds the maximum solar-to-fuel efficiency of all known forms of photosynthesis.

Systematic Electronic Tuning on the Property and Reactivity of Cobalt-(Hydro)peroxo Intermediates

A series of cobalt(III)-peroxo complexes, [Co^III(R₂-TBDAP)(O₂)]⁺ (1^R2; R₂ = Cl, H, and OMe), and cobalt(III)-hydroperoxo complexes, [Co^III(R₂-TBDAP)(O₂H)(CH₃CN)]²⁺ (2^R2), bearing electronically tuned tetraazamacrocyclic ligands (R₂-TBDAP = N,N'-di-tert-butyl-2,11-diaza[3.3](2,6)-p-R₂-pyridinophane) were prepared from their cobalt(II) precursors and characterized by various physicochemical methods. The X-ray diffraction and spectroscopic analyses unambiguously showed that all 1^R2 compounds have similar octahedral geometry with a side-on peroxocobalt(III) moiety, but the O-O bond lengths of 1^Cl [1.398(3) Å] and 1^OMe [1.401(4) Å] were shorter than that of 1^H [1.456(3) Å] due to the different spin states. For 2^R2, the O-O bond vibration energies of 2^Cl and 2^OMe were identical at 853 cm^-1 (856 cm^-1 for 2^H), but their Co-O bond vibration frequencies were observed at 572 cm^-1 for 2^Cl and 550 cm^-1 for 2^OMe, respectively, by resonance Raman spectroscopy (560 cm^-1 for 2^H). Interestingly, the redox potentials (E_1/2) of 2^R2 increased in the order of 2^OMe (0.19 V) < 2^H (0.24 V) < 2^Cl (0.34 V) according to the electron richness of the R₂-TBDAP ligands, but the oxygen-atom-transfer reactivities of 2^R2 showed a reverse trend (k₂: 2^Cl < 2^H < 2^OMe) with a 13-fold rate enhancement at 2^OMe over 2^Cl in a sulfoxidation reaction with thioanisole. Although the reactivity trend contradicts the general consideration that electron-rich metal-oxygen species with low E_1/2 values have sluggish electrophilic reactivity, this could be explained by a weak Co-O bond vibration of 2^OMe in the unusual reaction pathway. These results provide considerable insight into the electronic nature-reactivity relationship of metal-oxygen species.

Carboxylic acid reductases: Structure, catalytic requirements, and applications in biotechnology

Biocatalysts have been gaining extra attention in recent decades due to their industrial-relevance properties, which may hasten the transition to a cleaner environment. Carboxylic acid reductases (CARs) are large, multi-domain proteins that can catalyze the reduction of carboxylic acids to corresponding aldehydes, with the presence of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH). This biocatalytic reaction is of great interest due to the abundance of carboxylic acids in nature and the ability of CAR to convert carboxylic acids to a wide range of aldehydes essentially needed as end products such as vanillin or reaction intermediates for several compounds production such as alcohols, alkanes, and amines. This modular enzyme, found in bacteria and fungi, demands an activation via post-translational modification by the phosphopantetheinyl transferase (PPTase). Recent advances in the characterization and structural studies of CARs revealed valuable information about the enzymes' dynamics, mechanisms, and unique features. In this comprehensive review, we summarize the previous findings on the phylogeny, structural and mechanistic insight of the domains, post-translational modification requirement, strategies for the cofactors regeneration, the extensively broad aldehyde-related industrial application properties of CARs, as well as their recent immobilization approaches.

Production of Fatty Acids and Derivatives Using Cyanobacteria

Fatty acids and their derivatives are highly valuable chemicals that can be produced through chemical or enzymatic processes using plant lipids. This may compete with human food sources. Therefore, there has been an urge to create a new method for synthesizing these chemicals. One approach is to use microbial cells, specifically cyanobacteria, as a factory platform. Engineering may need to be implemented in order to allow a cost-competitive production and to enable a production of a variety of different fatty acids and derivatives. In this chapter, we explain in details the importance of fatty acids and their derivatives, including fatty aldehydes, fatty alcohols, hydrocarbons, fatty acid methyl esters, and hydroxy fatty acids. The production of these chemicals using cyanobacterial native metabolisms together with strategies to engineer them are also explained. Moreover, recent examples of fatty acid and fatty acid derivative production from engineered cyanobacteria are gathered and reported. Commercial opportunities to manufacture fatty acids and derivatives are also discussed in this chapter. Altogether, it is clear that fatty acids and their derivatives are important chemicals, and with recent advancements in genetic engineering, a cyanobacterial platform for bio-based production is feasible. However, there are regulations and guidelines in place for the use of genetically modified organisms (GMOs) and some further developments are still needed before commercialization can be reached.

Recent advances in the improvement of cyanobacterial enzymes for bioalkane production

The use of biologically produced alkanes has attracted considerable attention as an alternative energy source to petroleum. In 2010, the alkane synthesis pathway in cyanobacteria was found to include two small globular proteins, acyl-(acyl carrier protein [ACP]) reductase (AAR) and aldehyde deformylating oxygenase (ADO). AAR produces fatty aldehydes from acyl-ACPs/CoAs, which are then converted by ADO to alkanes/alkenes equivalent to diesel oil. This discovery has paved the way for alkane production by genetically modified organisms. Since then, many studies have investigated the reactions catalyzed by AAR and ADO. In this review, we first summarize recent findings on structures and catalytic mechanisms of AAR and ADO. We then outline the mechanism by which AAR and ADO form a complex and efficiently transfer the insoluble aldehyde produced by AAR to ADO. Furthermore, we describe recent advances in protein engineering studies on AAR and ADO to improve the efficiency of alkane production in genetically engineered microorganisms such as Escherichia coli and cyanobacteria. Finally, the role of alkanes in cyanobacteria and future perspectives for bioalkane production using AAR and ADO are discussed. This review provides strategies for improving the production of bioalkanes using AAR and ADO in cyanobacteria for enabling the production of carbon-neutral fuels.

DFT Mechanistic Insights into Aldehyde Deformylations with Biomimetic Metal-Dioxygen Complexes: Distinct Mechanisms and Reaction Rules

Aldehyde deformylations occurring in organisms are catalyzed by metalloenzymes through metal-dioxygen active cores, attracting great interest to study small-molecule metal-dioxygen complexes for understanding relevant biological processes and developing biomimetic catalysts for aerobic transformations. As the known deformylation mechanisms, including nucleophilic attack, aldehyde α-H-atom abstraction, and aldehyde hydrogen atom abstraction, undergo outer-sphere pathways, we herein report a distinct inner-sphere mechanism based on density functional theory (DFT) mechanistic studies of aldehyde deformylations with a copper (II)-superoxo complex. The inner-sphere mechanism proceeds via a sequence mainly including aldehyde end-on coordination, homolytic aldehyde C-C bond cleavage, and dioxygen O-O bond cleavage, among which the C-C bond cleavage is the rate-determining step with a barrier substantially lower than those of outer-sphere pathways. The aldehyde C-C bond cleavage, enabled through the activation of the dioxygen ligand radical in a second-order nucleophilic substitution (S_N2)-like fashion, leads to an alkyl radical and facilitates the subsequent dioxygen O-O bond cleavage. Furthermore, we deduced the rules for the reactions of metal-dioxygen complexes with aldehydes and nitriles via the inner-sphere mechanism. Expectedly, our proposed inner-sphere mechanisms and the reaction rules offer another perspective to understand relevant biological processes involving metal-dioxygen cores and to discover metal-dioxygen catalysts for aerobic transformations.

Metalloenzymes for Fatty Acid-Derived Hydrocarbon Biosynthesis: Nature's Cryptic Catalysts

Waning resources, massive energy consumption, everdeepening global warming crisis, and climate change have raised grave concerns regarding continued dependence on fossil fuels as the predominant source of energy and generated tremendous interest for developing biofuels, which are renewable. Hydrocarbon-based 'drop-in' biofuels can be a proper substitute for fossil fuels such as gasoline or jet fuel. In Nature, hydrocarbons are produced by diverse organisms such as insects, plants, bacteria, and cyanobacteria. Metalloenzymes play a crucial role in hydrocarbons biosynthesis, and the past decade has witnessed discoveries of a number of metalloenzymes catalyzing hydrocarbon biosynthesis from fatty acids and their derivatives employing unprecedented mechanisms. These discoveries elucidated the enigma related to the divergent chemistries involved in the catalytic mechanisms of these metalloenzymes. There is substantial diversity in the structure, mode of action, cofactor requirement, and substrate scope among these metalloenzymes. Detailed structural analysis along with mutational studies of some of these enzymes have contributed significantly to identifying the key amino acid residues that dictate substrate specificity and catalytic intricacy. In this Review, we discuss the metalloenzymes that catalyze fatty acid-derived hydrocarbon biosynthesis in various organisms, emphasizing the active site architecture, catalytic mechanism, cofactor requirements, and substrate specificity of these enzymes. Understanding such details is essential for successfully implementing these enzymes in emergent biofuel research through protein engineering and synthetic biology approaches.

Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes

Ferritin-like proteins share a common fold, a four α-helix bundle core, often coordinating a pair of metal ions. Although conserved, the ferritin fold permits a diverse set of reactions, and is central in a multitude of macromolecular enzyme complexes. Here, we emphasize this diversity through three members of the ferritin-like superfamily: the soluble methane monooxygenase, the class I ribonucleotide reductase and the aldehyde deformylating oxygenase. They all rely on dinuclear metal cofactors to catalyze different challenging oxygen-dependent reactions through the formation of multi-protein complexes. Recent studies using cryo-electron microscopy, serial femtosecond crystallography at an X-ray free electron laser source, or single-crystal X-ray diffraction, have reported the structures of the active protein complexes, and revealed unprecedented insights into the molecular mechanisms of these three enzymes.