Four amino acids define the CO2 binding pocket of enoyl-CoA carboxylases/reductases

Biosystem-Inspired Engineering of Nanozymes for Biomedical Applications

Nanozymes with intrinsic enzyme-mimicking activities have shown great potential to become surrogates of natural enzymes in many fields by virtue of their advantages of high catalytic stability, ease of functionalization, and low cost. However, due to the lack of predictable descriptors, most of the nanozymes reported in the past have been obtained mainly through trial-and-error strategies, and the catalytic efficacy, substrate specificity, as well as practical application effect under physiological conditions, are far inferior to that of natural enzymes. To optimize the catalytic efficacies and functions of nanozymes in biomedical settings, recent studies have introduced biosystem-inspired strategies into nanozyme design. In this review, recent advances in the engineering of biosystem-inspired nanozymes by leveraging the refined catalytic structure of natural enzymes, simulating the behavior changes of natural enzymes in the catalytic process, and mimicking the specific biological processes or living organisms, are introduced. Furthermore, the currently involved biomedical applications of biosystem-inspired nanozymes are summarized. More importantly, the current opportunities and challenges of the design and application of biosystem-inspired nanozymes are discussed. It is hoped that the studies of nanozymes based on bioinspired strategies will be beneficial for constructing the new generation of nanozymes and broadening their biomedical applications.

Gas fermentation combined with water electrolysis for production of polyhydroxyalkanoate copolymer from carbon dioxide by engineered Ralstonia eutropha

A recycled-gas closed-circuit culture system was developed for safe autotrophic cultivation of a hydrogen-oxidizing, polyhydroxyalkanoate (PHA)-producing Ralstonia eutropha, using a non-combustible gas mixture with low-concentration of H2 supplied by water electrolysis. Automated feedback regulation of gas flow enabled input of H2, CO2, and O2 well balanced with the cellular demands, leading to constant gas composition throughout the cultivation. The engineered strain of R. eutropha produced 1.71 g/L of poly(3-hydroxybutyrate-co-12.5 mol% 3-hydroxyhexanoate) on a gas mixture of H2/CO2/O2/N2 = 4:12:7:77 vol% with a 69.2 wt% cellular content. Overexpression of can encoding cytosolic carbonic anhydrase increased the 3HHx fraction up to 19.6 mol%. The yields of biomass and PHA on input H2 were determined to be 72.9 % and 63.1 %, corresponding to 51.0 % and 44.2 % yield on electricity, respectively. The equivalent solar-to-biomass/PHA efficiencies were estimated to be 2.1-3.8 %, highlighting the high energy conversion capability of R. eutropha.

Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO2 Fixation

Crotonyl-CoA carboxylase/reductase (Ccr) is one of the fastest CO2 fixing enzymes and has become part of efficient artificial CO2-fixation pathways in vitro, paving the way for future applications. The underlying mechanism of its efficiency, however, is not yet completely understood. X-ray structures of different intermediates in the catalytic cycle reveal tetramers in a dimer of dimers configuration with two open and two closed active sites. Upon binding a substrate, this active site changes its conformation from the open state to the closed state. It is challenging to predict how these coupled conformational changes will alter the CO2 binding affinity to the reaction's active site. To determine whether the open or closed conformations of Ccr affect binding of CO2 to the active site, we performed all-atom molecular simulations of the various conformations of Ccr. The open conformation without a substrate showed the highest binding affinity. The CO2 binding sites are located near the catalytic relevant Asn81 and His365 residues and in an optimal position for CO2 fixation. Furthermore, they are unaffected by substrate binding, and CO2 molecules stay in these binding sites for a longer time. Longer times at these reactive binding sites facilitate CO2 fixation through the nucleophilic attack of the reactive enolate in the closed conformation. We previously demonstrated that the Asn81Leu variant cannot fix CO2. Simulations of the Asn81Leu variant explain the loss of activity through the removal of the Asn81 and His365 binding sites. Overall, our findings show that the conformational dynamics of the enzyme controls CO2 binding. Conformational changes in Ccr increase the level of CO2 in the open subunit before the substrate is bound, the active site closes, and the reaction starts. The full catalytic Ccr cycle alternates among CO2 addition, conformational change, and chemical reaction in the four subunits of the tetramer coordinated by communication between the two dimers.

Enzymatic Conversion of CO2: From Natural to Artificial Utilization

Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO₂, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO₂-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO₂-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO₂ fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO₂ derivates, such as formate or methanol, represents a suitable alternative to direct use of CO₂ and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO₂ fixation and its potential to reduce CO₂ emissions.

Challenges and opportunities in C1-based biomanufacturing

The intensifying impact of green-house gas (GHG) emission on environment and climate change has attracted increasing attention, and biorefinery represents one of the most effective routes for reducing GHG emissions from human activities. However, this requires a shift for microbial fermentation from the current use of sugars to the use of biomass, and even better to the primary fixation of single carbon (C1) compounds. Here how microorganisms can be engineered for fixation and conversion of C1 compounds into metabolites that can serve as fuels and platform chemicals are reviewed. Meanwhile, key factors for utilization of these different pathways are discussed, followed by challenges and barriers for the development of C1-based biorefinery.

Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases

Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient CO₂-fixing enzymes described to date. However, the molecular mechanisms underlying the extraordinary catalytic activity of ECRs on the level of the protein assembly remain elusive. Here we used a combination of ambient-temperature X-ray free electron laser (XFEL) and cryogenic synchrotron experiments to study the structural organization of the ECR from Kitasatospora setae. The K. setae ECR is a homotetramer that differentiates into a pair of dimers of open- and closed-form subunits in the catalytically active state. Using molecular dynamics simulations and structure-based mutagenesis, we show that catalysis is synchronized in the K. setae ECR across the pair of dimers. This conformational coupling of catalytic domains is conferred by individual amino acids to achieve high CO₂-fixation rates. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intrasubunit communications of this remarkably efficient CO₂-fixing enzyme during catalysis.

Biocatalytic One-Carbon Transfer – A Review

This review provides an overview of different C1 building blocks as substrates of enzymes, or part of their cofactors, and the resulting­ functionalized products. There is an emphasis on the broad range of possibilities of biocatalytic one-carbon extensions with C1 sources of different oxidation states. The identification of uncommon biosynthetic strategies, many of which might serve as templates for synthetic or biotechnological applications, towards one-carbon extensions is supported by recent genomic and metabolomic progress and hence we refer principally to literature spanning from 2014 to 2020.

1 Introduction

2 Methane, Methanol, and Methylamine

3 Glycine

4 Nitromethane

5 SAM and SAM Ylide

6 Other C1 Building Blocks

7 Formaldehyde and Glyoxylate as Formaldehyde Equivalents

8 Cyanide

9 Formic Acid

10 Formyl-CoA and Oxalyl-CoA

11 Carbon Monoxide

12 Carbon Dioxide

13 Conclusions

The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis

Enzymes possessing the nickel-pincer nucleotide (NPN) cofactor catalyze C2 racemization or epimerization reactions of α-hydroxyacid substrates. LarB initiates synthesis of the NPN cofactor from nicotinic acid adenine dinucleotide (NaAD) by performing dual reactions: pyridinium ring C5 carboxylation and phosphoanhydride hydrolysis. Here, we show that LarB uses carbon dioxide, not bicarbonate, as the substrate for carboxylation and activates water for hydrolytic attack on the AMP-associated phosphate of C5-carboxylated-NaAD. Structural investigations show that LarB has an N-terminal domain of unique fold and a C-terminal domain homologous to aminoimidazole ribonucleotide carboxylase/mutase (PurE). Like PurE, LarB is octameric with four active sites located at subunit interfaces. The complex of LarB with NAD⁺, an analog of NaAD, reveals the formation of a covalent adduct between the active site Cys221 and C4 of NAD⁺, resulting in a boat-shaped dearomatized pyridine ring. The formation of such an intermediate with NaAD would enhance the reactivity of C5 to facilitate carboxylation. Glu180 is well positioned to abstract the C5 proton, restoring aromaticity as Cys221 is expelled. The structure of as-isolated LarB and its complexes with NAD⁺ and the product AMP identify additional residues potentially important for substrate binding and catalysis. In combination with these findings, the results from structure-guided mutagenesis studies lead us to propose enzymatic mechanisms for both the carboxylation and hydrolysis reactions of LarB that are distinct from that of PurE.

Electron inventory of the iron-sulfur scaffold complex HypCD essential in [NiFe]-hydrogenase cofactor assembly

The [4Fe-4S] cluster containing scaffold complex HypCD is the central construction site for the assembly of the [Fe](CN)2CO cofactor precursor of [NiFe]-hydrogenase. While the importance of the HypCD complex is well established, not much is known about the mechanism by which the CN- and CO ligands are transferred and attached to the iron ion. We report an efficient expression and purification system producing the HypCD complex from E. coli with complete metal content. This enabled in-depth spectroscopic characterizations. The results obtained by EPR and Mössbauer spectroscopy demonstrate that the [Fe](CN)2CO cofactor and the [4Fe-4S] cluster of the HypCD complex are redox active. The data indicate a potential-dependent interconversion of the [Fe]2+/3+ and [4Fe-4S]2+/+ couple, respectively. Moreover, ATR FTIR spectroscopy reveals potential-dependent disulfide formation, which hints at an electron confurcation step between the metal centers. MicroScale thermophoresis indicates preferable binding between the HypCD complex and its in vivo interaction partner HypE under reducing conditions. Together, these results provide comprehensive evidence for an electron inventory fit to drive multi-electron redox reactions required for the assembly of the CN- and CO ligands on the scaffold complex HypCD.

In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways

In the recent years, engineering new-to-nature CO2- and C1-fixing metabolic pathways made a leap forward. New, artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham (CBB) cycle. The question remains how to best predict their in vivo performance and what actually makes one pathway "better" than another. In this context, we explore aerobic carbon fixation pathways by a computational approach and compare them based on their specific activity and yield on methanol, formate, and CO2/H2 considering the kinetics and thermodynamics of the reactions. Besides pathways found in nature or implemented in the laboratory, this included two completely new cycles with favorable features: the reductive citramalyl-CoA cycle and the 2-hydroxyglutarate-reverse tricarboxylic acid cycle. A comprehensive kinetic data set was collected for all enzymes of all pathways, and missing kinetic data were sampled with the Parameter Balancing algorithm. Kinetic and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway-specific activities. The specific activities of the reductive glycine pathway, the CETCH cycle, and the new reductive citramalyl-CoA cycle were predicted to match the best natural cycles with superior product-substrate yield. However, the CBB cycle performed better in terms of activity compared to the alternative pathways than previously thought. We make an argument that stoichiometric yield is likely not the most important design criterion of the CBB cycle. Still, alternative carbon fixation pathways were paretooptimal for specific activity and product-substrate yield in simulations with C1 substrates and CO2/H2 and therefore hold great potential for future applications in Industrial Biotechnology and Synthetic Biology.

The impact of photorespiration on plant primary metabolism through metabolic and redox regulation

Photorespiration is an inevitable trait of all oxygenic phototrophs, being the only known metabolic route that converts the inhibitory side-product of Rubisco's oxygenase activity 2-phosphoglycolate (2PG) back into the Calvin-Benson (CB) cycle's intermediate 3-phosphoglycerate (3PGA). Through this function of metabolite repair, photorespiration is able to protect photosynthetic carbon assimilation from the metabolite intoxication that would occur in the present-day oxygen-rich atmosphere. In recent years, much plant research has provided compelling evidence that photorespiration safeguards photosynthesis and engages in cross-talk with a number of subcellular processes. Moreover, the potential of manipulating photorespiration to increase the photosynthetic yield potential has been demonstrated in several plant species. Considering this multifaceted role, it is tempting to presume photorespiration itself is subject to a suite of regulation mechanisms to eventually exert a regulatory impact on other processes, and vice versa. The identification of potential pathway interactions and underlying regulatory aspects has been facilitated via analysis of the photorespiratory mutant phenotype, accompanied by the emergence of advanced omics' techniques and biochemical approaches. In this mini-review, I focus on the identification of enzymatic steps which control the photorespiratory flux, as well as levels of transcriptional, posttranslational, and metabolic regulation. Most importantly, glycine decarboxylase (GDC) and 2PG are identified as being key photorespiratory determinants capable of controlling photorespiratory flux and communicating with other branches of plant primary metabolism.

Biocatalytic C-C Bond Formation for One Carbon Resource Utilization

The carbon-carbon bond formation has always been one of the most important reactions in C1 resource utilization. Compared to traditional organic synthesis methods, biocatalytic C-C bond formation offers a green and potent alternative for C1 transformation. In recent years, with the development of synthetic biology, more and more carboxylases and C-C ligases have been mined and designed for the C1 transformation in vitro and C1 assimilation in vivo. This article presents an overview of C-C bond formation in biocatalytic C1 resource utilization is first provided. Sets of newly mined and designed carboxylases and ligases capable of catalyzing C-C bond formation for the transformation of CO₂, formaldehyde, CO, and formate are then reviewed, and their catalytic mechanisms are discussed. Finally, the current advances and the future perspectives for the development of catalysts for C1 resource utilization are provided.

The activity of RubisCO and energy demands for its biosynthesis. Comparative studies with CO2-reductases

Most CO₂ on Earth is fixed into organic matter via reactions catalysed by enzymes called carboxylases. CO₂-fixation via carboxylases occurs in the Calvin-Benson-Bassham (CBB) cycle, and the crucial role in this cycle is played by RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase). CO₂ can also be fixed by pathways, where a reduction of CO₂ to formate or carbon monoxide (CO) occurs. The latter reactions are performed by so-called CO₂-reductases e.g. formate dehydrogenase (FDH), carbon-monooxide (CO) dehydrogenase (CODH), and crotonyl-CoA reductase/carboxylase (CCR). In general, a simple model of enzymatic activity based only on a turnover rate of an enzyme for an appropriate substrate (k_cat) is insufficient. Based on estimated metabolic costs of each amino acid, the average energetic costs of amino acid biosynthesis (E_aa), and the total costs (E_T) for selected CO₂-fixing enzymes were analyzed concerning 1) k_cat for CO₂ (k_C), and 2) specificity factor (S_rel) for RubisCO. A comparison of E_aa and E_T to their k_C showed that CODH and FDHs do not need to be more efficient enzymes in CO₂ capturing pathways than some forms of RubisCO. CCR was the only both low-cost and highly active CO₂-fixing enzyme. The obtained results showed also that there exists an evolutionarily conserved trade-off between S_rel of RubisCOs and the energetic demands needed for their biosynthesis. Phylogenetic analysis demonstrated that RubisCO, CODH, FDH, and CCR are enzymes formed as a result of parallel evolution. Moreover, the kinetic parameters (k_C) of CO₂-fixing enzymes were plausibly optimized already at the early stages of life evolution on Earth.

CO2-converting enzymes for sustainable biotechnology: from mechanisms to application

To realize a circular, carbon-neutral economy, it will become important to utilize the greenhouse gas CO₂ as a sustainable carbon source. Carboxylases, the enzymes that capture and convert gaseous CO₂ are the prime candidates to pave the way towards realizing this vision of a CO₂-based bio-economy. In the last couple of years, the interest in using and engineering carboxylases has been steadily growing. Here, we discuss how basic research on the mechanism of CO₂ binding and activation by carboxylases opened the way to develop new-to-nature CO₂-fixing enzymes that found application in the development of synthetic CO₂-fixation pathways and their further realization in vitro and in vivo. These pioneering efforts in the field pave the way to realize a diverse CO₂-fixation biochemistry that can find application in biocatalysis, biotechnology, and artificial photosynthesis.

Awakening a latent carbon fixation cycle in Escherichia coli

Carbon fixation is one of the most important biochemical processes. Most natural carbon fixation pathways are thought to have emerged from enzymes that originally performed other metabolic tasks. Can we recreate the emergence of a carbon fixation pathway in a heterotrophic host by recruiting only endogenous enzymes? In this study, we address this question by systematically analyzing possible carbon fixation pathways composed only of Escherichia coli native enzymes. We identify the GED (Gnd-Entner-Doudoroff) cycle as the simplest pathway that can operate with high thermodynamic driving force. This autocatalytic route is based on reductive carboxylation of ribulose 5-phosphate (Ru5P) by 6-phosphogluconate dehydrogenase (Gnd), followed by reactions of the Entner-Doudoroff pathway, gluconeogenesis, and the pentose phosphate pathway. We demonstrate the in vivo feasibility of this new-to-nature pathway by constructing E. coli gene deletion strains whose growth on pentose sugars depends on the GED shunt, a linear variant of the GED cycle which does not require the regeneration of Ru5P. Several metabolic adaptations, most importantly the increased production of NADPH, assist in establishing sufficiently high flux to sustain this growth. Our study exemplifies a trajectory for the emergence of carbon fixation in a heterotrophic organism and demonstrates a synthetic pathway of biotechnological interest.

CO2 -Folded Single-Chain Nanoparticles as Recyclable, Improved Carboxylase Mimics

Emulating the function of natural carboxylases to convert CO₂ under atmospheric condition is a great challenge. Herein we report a class of CO₂ -folded single-chain nanoparticles (SCNPs) that can function as recyclable, function-intensified carboxylase mimics. Lewis pair polymers containing bulky Lewis acidic and basic groups as the precursor, can bind CO₂ to drive an intramolecular folding into SCNPs, in which CO₂ as the folded nodes can form gas-bridged bonds. Such bridging linkages highly activate CO₂ , which endows the SCNPs with extraordinary catalytic ability that can not only catalyze CO₂ -insertion of C(sp³ )-H for imitating the natural enzyme's function, it can also act on non-natural carboxylation pathways for C(sp² and sp)-H substrates. The nanocatalysts are of highly catalytic efficiency and recyclability, and can work at room temperature and near ambient CO₂ condition, inspiring a new approach to sustainable C₁ utilization.

Coenzyme A thioester-mediated carbon chain elongation as a paintbrush to draw colorful chemical compounds

The biosynthesis of various useful chemicals from simple substrates using industrial microorganisms is becoming increasingly crucial to address the challenge of dwindling non-renewable resources. As the most common intermediate substrates in organisms, Coenzyme A (CoA) thioesters play a central role in the carbon chain elongation process of their products. As a result, numerous of chemicals can be synthesized by the iterative addition of various CoA thioester extender units at a given CoA thioester primer backbone. However, these elongation reactions and the product yields are still restricted due to the low enzymatic performance and supply of CoA thioesters. This review highlights the current protein and metabolic engineering strategies used to enhance the diversity and product yield by coupling different primers, extender units, enzymes, and termination pathways, in an attempt to provide a road map for producing a more diverse range of industrial chemicals.

Atom-Condensed Fukui Function in Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

Local reactivity descriptors such as atom-condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here we propose to combine quantum mechanics/molecular mechanics Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann-weighted atom-condensed local reactivity descriptors based on conceptual density functional theory. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account, allowing us to analyze the effect of the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared with an aqueous solution. Our main result is that the protein environment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α,β-unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.

Awakening the Sleeping Carboxylase Function of Enzymes: Engineering the Natural CO2-Binding Potential of Reductases

Developing new carbon dioxide (CO₂) fixing enzymes is a prerequisite to create new biocatalysts for diverse applications in chemistry, biotechnology and synthetic biology. Here we used bioinformatics to identify a “sleeping carboxylase function” in the superfamily of medium-chain dehydrogenases/reductases (MDR), i.e. enzymes that possess a low carboxylation side activity next to their original enzyme reaction. We show that propionyl-CoA synthase from Erythrobacter sp. NAP1, as well as an acrylyl-CoA reductase from Nitrosopumilus maritimus possess carboxylation yields of 3 ± 1 and 4.5 ± 0.9%. We use rational design to engineer these enzymes further into carboxylases by increasing interactions of the proteins with CO₂ and suppressing diffusion of water to the active site. The engineered carboxylases show improved CO₂-binding and kinetic parameters comparable to naturally existing CO₂-fixing enzymes. Our results provide a strategy to develop novel CO₂-fixing enzymes and shed light on the emergence of natural carboxylases during evolution.