Reconstruction of methanol and formate metabolic pathway in non-native host for biosynthesis of chemicals and biofuels

Methanol-based biomanufacturing of fuels and chemicals using native and synthetic methylotrophs

Methanol has recently gained significant attention as a potential carbon substrate for the production of fuels and chemicals, owing to its high degree of reduction, abundance, and low price. Native methylotrophic yeasts and bacteria have been investigated for the production of fuels and chemicals. Alternatively, synthetic methylotrophic strains are also being developed by reconstructing methanol utilization pathways in model microorganisms, such as Escherichia coli. Owing to the complex metabolic pathways, limited availability of genetic tools, and methanol/formaldehyde toxicity, the high-level production of target products for industrial applications are still under development to satisfy commercial feasibility. This article reviews the production of biofuels and chemicals by native and synthetic methylotrophic microorganisms. It also highlights the advantages and limitations of both types of methylotrophs and provides an overview of ways to improve their efficiency for the production of fuels and chemicals from methanol.

Constructing a methanol-dependent Bacillus subtilis by engineering the methanol metabolism

Methanol is a promising green feedstock for producing fuels and chemicals because it is inexpensive, clean, environmentally friendly, and easily prepared. Thus, many studies have been devoted to engineering non-native methylotrophic platform microorganisms to utilize methanol. This study adopted a series of strategies to develop a synthetic methylotrophic Bacillus subtilis that can use methanol as the carbon source, including the heterologous expression of methanol dehydrogenase (Mdh), enhancement of the expressions of 3-hexulose-6-phosphate synthase (Hps) and 6-phospho-3-hexuloisomerase (Phi), regulation of the expressions of key enzymes at both the translational and transcriptional levels, stabilization of the key enzyme expression through a dual-system for expressing the target genes on both the plasmid and genome, and improvement of the catalytic activity of Mdh with a recycling strategy for NAD⁺. As a result, the methanol consumption of the synthetic methylotrophic B. subtilis reached 4.09 g/L, with the maximum OD₆₀₀ showing a 2.21-fold increase compared with the wild-type B. subtilis, which cannot use methanol. We further deleted the phosphoglucose isomerase (Pgi) and added co-substrates to increase the supply of ribulose-5-phosphate (Ru-5-P), and the specific methanol consumption rate increased by an additional 27.54%. Finally, we successfully constructed two strains that cannot grow in M9 medium with xylose or ribose unless methanol is utilized. The strategies used in this study are generally applicable to other studies on synthetic methylotrophy.

Engineered Methanotrophy: A Sustainable Solution for Methane-Based Industrial Biomanufacturing

Methane is a promising feedstock with high abundance and low cost for the sustainable production of biochemicals and biofuels. Methanotrophic bacteria are particularly interesting platforms for methane bioconversion as they can utilize methane as a carbon substrate. Recently, breakthroughs in the understanding of methane metabolism in methanotrophs as well as critical advances in systems metabolic engineering of methanotrophic bacteria have been reported. Here, we discuss the important gaps in the understanding of methanotrophic metabolism that have been uncovered recently and the current trends in systems metabolic engineering in both methanotrophic bacteria and non-native hosts to advance the potential of methane-based biomanufacturing.

Empowering a Methanol-Dependent Escherichia coli via Adaptive Evolution Using a High-Throughput Microbial Microdroplet Culture System

Recently, a methanol-essential Escherichia coli was constructed; this strain is highly dependent on a supply of gluconate as a co-substrate for growth. Adaptive laboratory evolution is commonly applied to obtain mutants with specific phenotypes under certain selected pressure. However, conventional adaptive evolution approaches are not only laborious and time consuming, but they also come with lower throughput and inefficiency. In order to empower the aforementioned E. coli with reduced gluconate usage and enhanced growth rate, an irrational strategy based on a microbial microdroplet culture (MMC) platform was developed in this study. Given the automatic high-throughput selection of the MMC, a three-stage regime of an adaptive evolution experiment via gradually decreasing the availability of gluconate during the cultivation was performed for 50 days continuously in order to obtain the mutations. Finally, a candidate mutant was obtained with a 3-fold faster growth rate, a 43% shorter lag phase, and 40% less gluconate usage compared with the starting strain. Moreover, the gene mutations of gntU, idnT, edd, and pckA were identified by analyzing the whole-genome sequencing of mutants, which are strongly associated with the efficiency of gluconate uptake and cell growth. In conclusion, we have successfully demonstrated the feasibility of using MMC platform to empower the target strain with specific requirements in a manner of labor, time efficiency, and directed evolution.

Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z

BACKGROUND

Methanotrophs is a promising biocatalyst in biotechnological applications with their ability to utilize single carbon (C1) feedstock to produce high-value compounds. Understanding the behavior of biological networks of methanotrophic bacteria in different parameters is vital to systems biology and metabolic engineering. Interestingly, methanotrophic bacteria possess the pyrophosphate-dependent 6-phosphofructokinase (PPi-PFK) instead of the ATP-dependent 6-phosphofructokinase, indicating their potentials to serve as promising model for investigation the role of inorganic pyrophosphate (PPi) and PPi-dependent glycolysis in bacteria. Gene knockout experiments along with global-omics approaches can be used for studying gene functions as well as unraveling regulatory networks that rely on the gene product.

RESULTS

In this study, we performed gene knockout and RNA-seq experiments in Methylotuvimicrobium alcaliphilum 20Z to investigate the functional roles of PPi-PFK in C1 metabolism when cells were grown on methane and methanol, highlighting its metabolic importance in C1 assimilation in M. alcaliphilum 20Z. We further conducted adaptive laboratory evolution (ALE) to investigate regulatory architecture in pfk knockout strain. Whole-genome resequencing and RNA-seq approaches were performed to characterize the genetic and metabolic responses of adaptation to pfk knockout. A number of mutations, as well as gene expression profiles, were identified in pfk ALE strain to overcome insufficient C1 assimilation pathway which limits the growth in the unevolved strain.

CONCLUSIONS

This study first revealed the regulatory roles of PPi-PFK on C1 metabolism and then provided novel insights into mechanism of adaptation to the loss of this major metabolic enzyme as well as an improved basis for future strain design in type I methanotrophs.

Discovery and Biochemical Characterization of a Methanol Dehydrogenase From Lysinibacillus xylanilyticus

Bioconversion of C1 chemicals such as methane and methanol into higher carbon-chain chemicals has been widely studied. Methanol oxidation catalyzed by methanol dehydrogenase (Mdh) is one of the key steps in methanol utilization in bacterial methylotrophy. In bacteria, few NAD⁺-dependent Mdhs have been reported that convert methanol to formaldehyde. In this study, an uncharacterized Mdh gene from Lysinibacillus xylanilyticus (Lxmdh) was cloned and expressed in Escherichia coli. The maximum alcohol oxidation activity of the recombinant enzyme was observed at pH 9.5 and 55°C in the presence of 10 mM Mg²⁺. To improve oxidation activity, rational approach-based, site-directed mutagenesis of 16 residues in the putative active site and NAD⁺-binding region was performed. The mutations S101V, T141S, and A164F improved the enzyme’s specific activity toward methanol compared to that of the wild-type enzyme. These mutants show a slightly higher turnover rate than that of wild-type, although their K_M values were increased compared to that of wild-type. Consequently, according the kinetic results, S101, T141, and A164 positions may related to the catalytic activity in the active site for methanol dehydrogenation. It should be further studied other mutant variants with high activity for methanol. In conclusion, we characterized a new Lxmdh and its variants that may be potentially useful for the development of synthetic methylotrophy in the future.

Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol

Methylotuvimicrobium alcaliphilum 20Z is a promising platform strain for bioconversion of one-carbon (C1) substrates into value-added products. To carry out robust metabolic engineering with methylotrophic bacteria and to implement C1 conversion machinery in non-native hosts, systems-level evaluation and understanding of central C1 metabolism in methanotrophs under various conditions is pivotal but yet elusive. In this study, a genome-scale integrated approach was used to provide in-depth knowledge on the metabolic pathways of M. alcaliphilum 20Z grown on methane and methanol. Systems assessment of core carbon metabolism indicated the methanol assimilation pathway is mostly coupled with the efficient Embden-Meyerhof-Parnas (EMP) pathway along with the serine cycle. In addition, an incomplete TCA cycle operated in M. alcaliphilum 20Z on methanol, which might only supply precursors for de novo synthesis but not reducing powers. Instead, it appears that the direct formaldehyde oxidation pathway supply energy for the whole metabolic system. Additionally, a comparative transcriptomic analysis in multiple gammaproteobacterial methanotrophs also revealed the transcriptional responses of central metabolism on carbon substrate change. These findings provided a systems-level understanding of carbon metabolism and new opportunities for strain design to produce relevant products from different C1-feedstocks.

Methanol-essential growth of Escherichia coli

Methanol represents an attractive substrate for biotechnological applications. Utilization of reduced one-carbon compounds for growth is currently limited to methylotrophic organisms, and engineering synthetic methylotrophy remains a major challenge. Here we apply an in silico-guided multiple knockout approach to engineer a methanol-essential Escherichia coli strain, which contains the ribulose monophosphate cycle for methanol assimilation. Methanol conversion to biomass was stoichiometrically coupled to the metabolization of gluconate and the designed strain was subjected to laboratory evolution experiments. Evolved strains incorporate up to 24% methanol into core metabolites under a co-consumption regime and utilize methanol at rates comparable to natural methylotrophs. Genome sequencing reveals mutations in genes coding for glutathione-dependent formaldehyde oxidation (frmA), NAD(H) homeostasis/biosynthesis (nadR), phosphopentomutase (deoB), and gluconate metabolism (gntR). This study demonstrates a successful metabolic re-routing linked to a heterologous pathway to achieve methanol-dependent growth and represents a crucial step in generating a fully synthetic methylotrophic organism.

Engineering synthetic methylotrophy remains challenging. Here, the authors engineer a methanol-essential E. coli by an in silico-guided multiple knockout approach and show a laboratory evolved strain can incorporate up to 24% methanol into core metabolites during growth.

Biological conversion of methane to chemicals and fuels: technical challenges and issues

Methane is a promising next-generation carbon feedstock for industrial biotechnology due to its low price and huge availability. Biological conversion of methane to valuable products can mitigate methane-induced global warming as greenhouse gas. There have been challenges for the conversion of methane into various chemicals and fuels using engineered non-native hosts with synthetic methanotrophy or methanotrophs with the reconstruction of synthetic pathways for target products. Herein, we analyze the technical challenges and issues of potent methane bioconversion technology. Pros and cons of metabolic engineering of methanotrophs for methane bioconversion, and perspectives on the bioconversion of methane to chemicals and liquid fuels are discussed.

Fine-tuning the P. pastoris iMT1026 genome-scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources

The methylotrophic yeast Pichia pastoris (Komagataella spp.) is widely used as cell factory for recombinant protein production. In the past recent years, important breakthroughs in the systems-level quantitative analysis of its physiology have been achieved. This wealth of information has allowed the development of genome-scale metabolic models, which make new approaches possible for host cell and bioprocess engineering. Nevertheless, the predictive accuracy of the previous consensus model required to be upgraded and validated with new experimental data sets for P. pastoris growing on glycerol or methanol as sole carbon sources, two of the most relevant substrates for this cell factory. In this study, we have characterized P. pastoris growing in chemostat cultures using glycerol or methanol as sole carbon sources over a wide range of growth rates, thereby providing physiological data on the effect of growth rate and culture conditions on biomass macromolecular and elemental composition. In addition, these data sets were used to improve the performance of the P. pastoris consensus genomic-scale metabolic model iMT1026. Thereupon, new experimentally determined bounds, including the representation of biomass composition for these growth conditions, have been incorporated. As a result, here, we present version 3 (v3.0) of the consensus P. pastoris genome-scale metabolic model as an update of the iMT1026 model. The v3.0 model was validated for growth on glycerol and methanol as sole carbon sources, demonstrating improved prediction capabilities over an extended substrate range including two biotechnologically relevant carbon sources.