In Vivo Genome Editing in Type I and II Methanotrophs Using a CRISPR/Cas9 System

Effects of impurities on the syngas fermentation: Mechanism and future perspectives

In the process of syngas bioconversion into high value-added chemicals, the presence and impact of impurities must be acknowledged. The present review aims to summarize the progress regarding the effects of various impurities on the syngas fermentation, with the focus on impurity formation in gasification, its inhibition on syngas conversion and influential mechanism. The production of impurities is influenced by various parameters in the gasification process, but substance characteristics is the most relevant factor on impurities composition and concentration. The inhibitory threshold of H2S, NH3 and CN- on syngas bioconversion was 108 ppm, 1520 ppm and 0.025 mM, respectively. In the response to impurities, functional microorganisms related to syngas bioconversion were normally inhibited. Furthermore, the inhibitory mechanisms in aspect of electron transfer and energy synthesis were revealed via the analysis of syngas and impurities metabolic pathway. To alleviate the impurity inhibition, the potential solutions are proposed.

Enhancing D-lactic acid production from methane through metabolic engineering of Methylomonas sp. DH-1

BACKGROUND

Methane is an abundant and low-cost carbon source with great potential for conversion into value-added chemicals. Methanotrophs, microorganisms that utilize methane as their sole carbon and energy source, present a promising platform for biotechnological applications. This study aimed to engineer Methylomonas sp. DH-1 to enhance D-LA production through metabolic pathway optimization during large-scale cultivation.

RESULTS

In this study, we regulated the expression of D-lactate dehydrogenase (D-LDH) using a Ptac promoter with IPTG induction to mitigate the toxic effects of lactate accumulation. To further optimize carbon flow away from glycogen, the glgA gene was deleted. However, this modification led to growth inhibition, especially during scale-up, likely due to the accumulation of ADP-glucose caused by the rewired carbon flux under carbon-excess conditions. Deleting the glgC gene, which encodes glucose 1-phosphate adenylyltransferase, alleviated this issue. The final optimized strain, JHM805, achieved a D-LA production of 6.17 g/L in a 5-L bioreactor, with a productivity of 0.057 g/L/h, marking a significant improvement in D-LA production from methane.

CONCLUSIONS

The metabolic engineering strategies employed in this study, including the use of an inducible promoter and alleviation of ADP-glucose accumulation toxicity, successfully enhanced the ability of the strain to produce D-LA from methane. Furthermore, optimizing the bioreactor fermentation process through methane and nitrate supplementation resulted in a significant increase in both the titer and productivity, exceeding previously reported values.

Advancements in the production of value-added products via methane biotransformation by methanotrophs: Current status and future perspectives

Methane gas is recognized as a promising carbon substrate for the biosynthesis of value-added products due to its abundance and low price. Methanotrophs utilized methane as their sole source of carbon and energy, thus they can serve as efficient biocatalysts for methane bioconversion. Methanotrophs-catalyzed microbial bioconversion offer numerous advantages, compared to chemical processes. Current indirect chemical conversions of methane suffer from their energy-intensive processes and high capital expenditure. Methanotrophs can be cell factories capable of synthesizing various value-added products from methane such as methanol, organic acids, ectoine, polyhydroxyalkanoates, etc. However, the large-scale commercial implementation using methanotrophs remains a formidable challenge, primarily due to limitations in gas-liquid mass transfer and low metabolic capacity. This review explores recent advancements in methanotroph research, providing insights into their potential for enabling methane bioconversion.

A Patent Landscape on Methane Oxidizing Bacteria (MOB) or Methanotrophs

Methane-oxidizing bacteria (MOB) or methanotrophs are a category of bacteria that rely on methane as their primary carbon and energy source. Methane is the second most abundant greenhouse gas after carbon dioxide and is comparatively far more potent in trapping heat in the atmosphere. MOBs are important microorganisms in the global carbon cycle where they play a crucial role in the oxidation of methane. The present review provides a comprehensive patent landscape on technology development using MOB. The first patent in this technology domain was recorded in 1971, with a notable surge in activity observed in 2020. A detailed patent analysis revealed that the early inventions were mainly focused on the production of various metabolites and bioremediation using MOB. In the later years, patents were filed in the area of identification of various species of MOB and their large-scale production. From 2010 onwards, consistent patent filing was observed in the genetic engineering of MOB to enhance their methane oxidizing capacity. The United States and China have emerged as the global leaders in terms of patent filing in this technology space. Precigen Inc. and Exxon Research Engineering Co., US were the top patent assignees followed by the University of Tsinghua and Calysta Inc. The Highest number of patent applications have claimed metabolite production by using MOB followed by their use in bioremediation. Methylosinus has emerged as the predominant microorganism of choice for methane oxidation applications.

Methane to bioproducts: unraveling the potential of methanotrophs for biomanufacturing

With the continuous increase in the world population, anthropogenic activities will generate more waste and create greenhouse gases such as methane, amplifying global warming. The biological conversion of methane into biochemicals is a sustainable solution to sequester and convert this greenhouse gas. Methanotrophic bacteria fulfill this role by utilizing methane as a feedstock while manufacturing various bioproducts. Recently, methanotrophs have made their mark in industrial biomanufacturing. However, unlike glucose-utilizing model organisms such as Escherichia coli and Saccharomyces cerevisiae, methanotrophs do not have established transformation methods and genetic tools, making these organisms challenging to engineer. Despite these challenges, recent advancements in methanotroph engineering demonstrate great promise, showcasing these C1-carbon-utilizing microbes as prospective hosts for bioproduction. This review discusses the recent developments and challenges in strain engineering, biomolecule production, and process development methodologies in the methanotroph field.

Biosynthesis of polyhydroxybutyrate from methane and carbon dioxide using type II methanotrophs

Methane (CH4) and carbon dioxide (CO2) are the dominant greenhouse gases (GHGs) that are increasing at an alarming rate. Methanotrophs have emerged as potential CH4 and CO2 biorefineries. This study demonstrated the synchronous incorporation of CH4 and CO2 into polyhydroxybutyrate (PHB) for the first time using 13C-labeling experiments in methanotrophs. By supplying substantial amounts of CO2, PHB content was enhanced in all investigated type II methanotrophic strains by 140 %, 146 %, and 162 %. The highest content of PHB from CH4 and CO2 in flask-scale cultivation reached 38 % dry cell weight in Methylocystis sp. MJC1, in which carbon percentage in PHB from CO2 was 45 %. Flux balance analysis predicted the critical roles of crotonyl-CoA carboxylase/reductase and phosphoenolpyruvate carboxylase in CO2 recycling. This study provided proof of the conversion of GHGs into a valuable and practical product using methanotrophic bacteria, contributing to addressing GHG emissions.

Construction of a broad-host-range Anderson promoter series and particulate methane monooxygenase promoter variants expand the methanotroph genetic toolbox

Methanotrophic bacteria are currently used industrially for the bioconversion of methane-rich natural gas and anaerobic digestion-derived biogas to valuable products. These bacteria may also serve to mitigate the negative effects of climate change by capturing atmospheric greenhouse gases. Several genetic tools have previously been developed for genetic and metabolic engineering of methanotrophs. However, the available tools for use in methanotrophs are significantly underdeveloped compared to many other industrially relevant bacteria, which hinders genetic and metabolic engineering of these biocatalysts. As such, expansion of the methanotroph genetic toolbox is needed to further our understanding of methanotrophy and develop biotechnologies that leverage these unique microbes for mitigation and conversion of methane to valuable products. Here, we determined the copy number of three broad-host-range plasmids in Methylococcus capsulatus Bath and Methylosinus trichosporium OB3b, representing phylogenetically diverse Gammaproteobacterial and Alphaproteobacterial methanotrophs, respectively. Further, we show that the commonly used synthetic Anderson series promoters are functional and exhibit similar relative activity in M. capsulatus and M. trichosporium OB3b, but the synthetic series had limited range. Thus, we mutagenized the native M. capsulatus particulate methane monooxygenase promoter and identified variants with activity that expand the activity range of synthetic, constitutive promoters functional not only in M. capsulatus, but also in Escherichia coli. Collectively, the tools developed here advance the methanotroph genetic engineering toolbox and represent additional synthetic genetic parts that may have broad applicability in Pseudomonadota bacteria.

Modular and Flexible Molecular Device for Simultaneous Cytosine and Adenine Base Editing at Random Genomic Loci in Filamentous Fungi

Random base editing is regarded as a fundamental method for accelerating the genomic evolution in both scientific research and industrial applications. In this study, we designed a modular interaction-based dual base editor (MIDBE) that assembled a DNA helicase and various base editors through dockerin/cohesin-mediated protein-protein interactions, resulting in a self-assembled MIDBE complex capable of editing bases at any locus in the genome. The base editing type of MIDBE can be readily controlled by the induction of cytidine or/and adenine deaminase gene expression. MIDBE exhibited the highest editing efficiency 2.3 × 10³ times greater than the native genomic mutation rate. To evaluate the potential of MIDBE in genomic evolution, we developed a removable plasmid-based MIDBE tool, which led to a remarkable 977.1% increase of lovastatin production in Monascus purpureus HJ11. MIDBE represents the first biological tool for generating and accumulating base mutations in Monascus chromosome and also offers a bottom-up strategy for designing the base editor.