High-Yield Production of Catalytically Active Regulatory [NiFe]-Hydrogenase From Cupriavidus necator in Escherichia coli

Application of lactose based autoinduction for heterologous production of an active [NiFe] hydrogenase in E. coli

OBJECTIVES

This study aims to assess whether a fed-batch-based auto-induction method can enhance active hydrogenase production, encompassing cofactor formation and space-time yield.

RESULTS

The recombinant Escherichia coli strain BQF8RH8, possessing plasmids for assembly and proper maturation of Cupriavidus necator regulatory hydrogenase (RH), was cultivated in the fed-batch like EnPresso B medium with an autoinduction lactose-based system. In contrast to classical IPTG induction previously performed, we obtained active RH demonstrating the feasibility of the process for active hydrogenase production.

CONCLUSION

Our results affirm the viability of the previously developed auto-induction strategy also for a functional hydrogenase with the complex maturation process. This significantly accelerates the process and enhances hydrogenase productivity.

Co-expression of auxiliary genes enhances the activity of a heterologous O2-tolerant hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria bear great biotechnological potential as photosynthetic cell factories. In particular, hydrogenases are promising with respect to light-driven H2 production as well as H2-driven redox biocatalysis. Their utilization relies on effective strain design as well as a balanced synthesis and maturation of heterologous enzymes. In a previous study, the soluble O2-tolerant hydrogenase complex from Cupriavidus necator (CnSH) could be introduced into the model cyanobacterium Synechocystis sp. PCC 6803. Due to its O2-tolerance, it was indeed active under photoautotrophic growth conditions. However, the specific activity was rather low indicating that further engineering is required, for which we followed a two-step approach. First, we optimized the CnSH multigene expression in Synechocystis by applying different regulatory elements. Although corresponding protein levels and specific CnSH activity increased, the apparent rise in enzyme levels did not fully translate into activity increase. Second, the entire set of hyp genes, encoding CnSH maturases, was co-expressed in Synechocystis to investigate, if CnSH maturation was limiting. Indeed, the native CnSH maturation apparatus promoted functional CnSH synthesis, enabling a threefold higher H2 oxidation activity compared to the parental strain. Our results suggest that a fine balance between heterologous hydrogenase and maturase expression is required to ensure high specific activity over an extended time period.

Exploiting hydrogenases for biocatalytic hydrogenations

The ability of hydrogenase enzymes to activate H2 with excellent selectivity leads to many interesting possibilities for biotechnology driven by H2 as a clean reductant. Here, we review examples where hydrogenase enzymes have been used to drive native and non-native hydrogenation reactions in solution or as part of a redox cascade on a conductive support, with a focus on the developments we have contributed to this field. In all of the examples discussed, hydrogenation reactions are enabled by coupled redox reactions: the oxidation of H2 at a hydrogenase active site, linked electronically (via relay clusters in the enzyme and/or via conductive support) to the site of a reduction reaction, and we note how this parallels developments in site-separated reactivity in heterogeneous catalysis. We discuss the productivities achieved with biocatalytic hydrogenations, the scope for application of these approaches in industrial biotechnology, possibilities for scaling the production of hydrogenases, and future opportunities. Our focus is on NiFe hydrogenases, but we discuss briefly how FeFe hydrogenases might contribute to this field.

Developing high-affinity, oxygen-insensitive [NiFe]-hydrogenases as biocatalysts for energy conversion

The splitting of hydrogen (H2) is an energy-yielding process, which is important for both biological systems and as a means of providing green energy. In biology, this reaction is mediated by enzymes called hydrogenases, which utilise complex nickel and iron cofactors to split H2 and transfer the resulting electrons to an electron-acceptor. These [NiFe]-hydrogenases have received considerable attention as catalysts in fuel cells, which utilise H2 to produce electrical current. [NiFe]-hydrogenases are a promising alternative to the platinum-based catalysts that currently predominate in fuel cells due to the abundance of nickel and iron, and the resistance of some family members to inhibition by gases, including carbon monoxide, which rapidly poison platinum-based catalysts. However, the majority of characterised [NiFe]-hydrogenases are inhibited by oxygen (O2), limiting their activity and stability. We recently reported the isolation and characterisation of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis, which is insensitive to inhibition by O2 and has an extremely high affinity, making it capable of oxidising H2 in air to below atmospheric concentrations. These properties make Huc a promising candidate for the development of enzyme-based fuel cells (EBFCs), which utilise H2 at low concentrations and in impure gas mixtures. In this review, we aim to provide context for the use of Huc for this purpose by discussing the advantages of [NiFe]-hydrogenases as catalysts and their deployment in fuel cells. We also address the challenges associated with using [NiFe]-hydrogenases for this purpose, and how these might be overcome to develop EBFCs that can be deployed at scale.

Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site

BACKGROUND

Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production.

RESULTS

Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains.

CONCLUSION

The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.

Prospects for engineering Ralstonia eutropha and Zymomonas mobilis for the autotrophic production of 2,3-butanediol from CO2 and H2

The decarbonization of the chemical industry and a shift toward circular economies because of high global CO2 emissions make CO2 an attractive feedstock for manufacturing chemicals. Moreover, H2 is a low-cost and carbon-free reductant because technologies such as solar-driven electrolysis and supercritical water (scH2O) gasification enable sustainable production of molecular hydrogen (H2). We review the recent advances in engineering Ralstonia eutropha, the representative species of "Knallgas" bacteria, for utilizing CO2 and H2 to autotrophically produce 2,3-butanediol (2,3-BDO). This assessment is focused on state-of-the-art approaches for splitting H2 to supply energy in the form of ATP and NADH to power cellular reactions and employing the Calvin-Benson-Bassham cycle for CO2 fixation. Major challenges and opportunities for application and future perspectives are discussed in the context of developing other promising CO2 and H2-utilizing microorganisms, exemplified by Zymomonas mobilis.

Toward a synthetic hydrogen sensor in cyanobacteria: Functional production of an oxygen-tolerant regulatory hydrogenase in Synechocystis sp. PCC 6803

Cyanobacteria have raised great interest in biotechnology, e.g., for the sustainable production of molecular hydrogen (H₂) using electrons from water oxidation. However, this is hampered by various constraints. For example, H₂-producing enzymes compete with primary metabolism for electrons and are usually inhibited by molecular oxygen (O₂). In addition, there are a number of other constraints, some of which are unknown, requiring unbiased screening and systematic engineering approaches to improve the H₂ yield. Here, we introduced the regulatory [NiFe]-hydrogenase (RH) of Cupriavidus necator (formerly Ralstonia eutropha) H16 into the cyanobacterial model strain Synechocystis sp. PCC 6803. In its natural host, the RH serves as a molecular H₂ sensor initiating a signal cascade to express hydrogenase-related genes when no additional energy source other than H₂ is available. Unlike most hydrogenases, the C. necator enzymes are O₂-tolerant, allowing their efficient utilization in an oxygenic phototroph. Similar to C. necator, the RH produced in Synechocystis showed distinct H₂ oxidation activity, confirming that it can be properly matured and assembled under photoautotrophic, i.e., oxygen-evolving conditions. Although the functional H₂-sensing cascade has not yet been established in Synechocystis yet, we utilized the associated two-component system consisting of a histidine kinase and a response regulator to drive and modulate the expression of a superfolder gfp gene in Escherichia coli. This demonstrates that all components of the H₂-dependent signal cascade can be functionally implemented in heterologous hosts. Thus, this work provides the basis for the development of an intrinsic H₂ biosensor within a cyanobacterial cell that could be used to probe the effects of random mutagenesis and systematically identify promising genetic configurations to enable continuous and high-yield production of H₂ via oxygenic photosynthesis.

Implementation of a high cell density fed-batch for heterologous production of active [NiFe]-hydrogenase in Escherichia coli bioreactor cultivations

Background

O₂-tolerant [NiFe]-hydrogenases offer tremendous potential for applications in H₂-based technology. As these metalloenzymes undergo a complicated maturation process that requires a dedicated set of multiple accessory proteins, their heterologous production is challenging, thus hindering their fundamental understanding and the development of related applications. Taking these challenges into account, we selected the comparably simple regulatory [NiFe]-hydrogenase (RH) from Cupriavidus necator as a model for the development of bioprocesses for heterologous [NiFe]-hydrogenase production. We already reported recently on the high-yield production of catalytically active RH in Escherichia coli by optimizing the culture conditions in shake flasks.

Results

In this study, we further increase the RH yield and ensure consistent product quality by a rationally designed high cell density fed-batch cultivation process. Overall, the bioreactor cultivations resulted in ˃130 mg L⁻¹ of catalytically active RH which is a more than 100-fold increase compared to other RH laboratory bioreactor scale processes with C. necator. Furthermore, the process shows high reproducibility of the previously selected optimized conditions and high productivity.

Conclusions

This work provides a good opportunity to readily supply such difficult-to-express complex metalloproteins economically and at high concentrations to meet the demand in basic and applied studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01919-w.