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

Methanotrophs mediated biogas valorization: Sustainable route to polyhydroxybutyrate production

This study explores the ability of methanotrophs to convert biogas into biopolymers, addressing H2S as a limitation in the utilization of biogas as a carbon source for bioconversion. Transcriptomic analysis was conducted to understand the growth and changes in the expression patterns of Type I and II methanotrophs under varying H2S concentrations. Results suggested that Type II methanotrophs can possess a native H2S utilization pathway. Both Type I and II methanotrophs were evaluated for their growth and polyhydroxybutyrate (PHB) production from biogas. Methylocystis sp. MJC1 and Methylocystis sp. OK1 exhibited a maximum biomass production of 4.0 and 4.5 gDCW/L, respectively, in fed-batch culture, aligning with the transcriptome data. Furthermore, Methylocystis sp. MJC1 produced 2.9 g PHB/L from biogas through gas fermentation. These findings underscore biogas-based biotechnology as an innovative solution for environmental and industrial challenges with further optimization and productivity enhancement research expected to broaden the potential in this field.

Comparative phenotype and transcriptome analysis revealed the role of ferric uptake regulator (Fur) in the virulence of Vibrio harveyi isolated from diseased American eel (Anguilla rostrata)

Vibrio harveyi is commonly found in salt and brackish water and is recognized as a serious bacterial pathogen in aquaculture worldwide. In this study, we cloned the ferric uptake regulator (fur) gene from V. harveyi wild-type strain HA_1, which was isolated from diseased American eels (Anguilla rostrata) and has a length of 450 bp, encoding 149 amino acids. Then, a mutant strain, HA_1-Δfur, was constructed through homologous recombination of a suicide plasmid (pCVD442). The HA_1-Δfur mutant exhibited weaker biofilm formation and swarming motility, and 18-fold decrease (5.5%) in virulence to the American eels; compared to the wild-type strain, the mutant strain showed time and diameter differences in growth and haemolysis, respectively. Additionally, the adhesion ability of the mutant strain was significantly decreased. Moreover, there were 15 different biochemical indicators observed between the two strains. Transcriptome analysis revealed that 875 genes were differentially expressed in the Δfur mutant, with 385 up-regulated and 490 down-regulated DEGs. GO and KEGG enrichment analysis revealed that, compared to the wild-type strain, the type II and type VI secretion systems (T2SS and T6SS), amino acid synthesis and transport and energy metabolism pathways were significantly down-regulated, but the ABC transporters and biosynthesis of siderophore group non-ribosomal peptides pathways were up-regulated in the Δfur strain. The qRT-PCR results further confirmed that DEGs responsible for amino acid transport and energy metabolism were positively regulated, but DEGs involved in iron acquisition were negatively regulated in the Δfur strain. These findings suggest that the virulence of the Δfur strain was significantly decreased, which is closely related to phenotype changing and gene transcript regulation.

Leveraging genome-scale metabolic models to understand aerobic methanotrophs

Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.

Engineering type I methanotrophic bacteria as novel platform for sustainable production of 3-hydroxybutyrate and biodegradable polyhydroxybutyrate from methane and xylose

Methylotuvimicrobium alcaliphilum20Z recombinant strain co-utilizing methane and xylose from anthropogenic activities and lignocellulose biomassis a promising cell factory platform. In this study, the production of (R)-3-hydroxybutyrate and poly (3-hydroxybutyrate) inM. alcaliphilum20Z was demonstrated. The production of (R)-3-hydroxybutyrate was optimized by introducing additional thioesterase, and a tunable genetic module. The final recombinant strain produced the highest titer of 334.52 ± 2 mg/L (R)-3-hydroxybutyrate (yield of 1,853 ± 429 mg/g dry cell weight). The poly (3-hydroxybutyrate) yielded 1.29 ± 0.08% (w/w) from methane and xylose in one-stage cultivation. Moreover, the study demonstrated the importance of pathway reversibility as an effective design strategy for balancing the driving force and intermediate accumulation. This is the first demonstration of the production ofbiodegradablepoly (3-hydroxybutyrate) from methane in type I methanotrophs, which is a key step toward sustainable biomanufacturing and carbon-neutral society.

Biological production of 2-propanol from propane using a metabolically engineered type I methanotrophic bacterium

2-Propanol is a widely used industrial solvents. Herein, we employed a unique feature of type I methanotrophic bacterium Methylotuvimicrobium alcaliphilum 20Z possessing only particulate methane monooxygenase (pMMO) for one-step direct production of pure 2-propanol from propane. By maintaining cell growth on glycerol, and after deletion of both Ca²⁺-dependent and La³⁺-dependent methanol dehydrogenases, propane was converted to 2-propanol by pMMO. Although most of the 2-propanol produced was further oxidized to acetone, deletion of active alcohol dehydrogenase, concomitant with synchronous overexpression of secondary alcohol dehydrogenase, significantly inhibited such undesirable oxidation. As a result, a remarkable enhancement (263 mg/L) of 2-propanol was achieved for 120 h by increasing cell growth with a supply of 50% (v/v) propane in headspace. This is the first demonstration to develop an engineered methanotrophic strain for the one-step direct production of pure 2-propanol from propane using one-phase cultivation without the supply of chemical inhibitors or additional reducing-power sources.

Development of Methylorubrum extorquens AM1 as a promising platform strain for enhanced violacein production from co-utilization of methanol and acetate

Violacein, a blue-violet compound with a wide range of beneficial bioactivities, is an attractive product for microbial production. Currently, violacein production has been demonstrated in several sugar heterotrophs through metabolic engineering; however, the cost of production remains an obstacle for business ventures. To address this issue, the development of host strains that can utilize inexpensive alternative substrates to reduce production costs would enable the commercialization of violacein. In this study, we engineered a facultative methylotroph, Methylorubrum extorquens AM1, to develop a methanol-based platform for violacein production. By optimizing expression vectors as well as inducer concentrations, 11.7 mg/L violacein production was first demonstrated using methanol as the sole substrate. Considering that unidentified bottlenecks for violacein biosynthesis in the shikimate pathway of M. extorquens AM1 would be difficult to address using generic metabolic engineering approaches, random mutagenesis and site-directed mutagenesis were implemented, and a 2-fold improvement in violacein production was achieved. Finally, by co-utilization of methanol and acetate, a remarkable enhancement of violacein production to 118 mg/L was achieved. Our results establish a platform strain for violacein production from non-sugar feedstocks, which may contribute to the development of an economically efficient large-scale fermentation system for violacein production.

Essential role of pyrophosphate homeostasis mediated by the pyrophosphate-dependent phosphofructokinase in Toxoplasma gondii

Many biosynthetic pathways produce pyrophosphate (PPi) as a by-product, which is cytotoxic if accumulated at high levels. Pyrophosphatases play pivotal roles in PPi detoxification by converting PPi to inorganic phosphate. A number of apicomplexan parasites, including Toxoplasma gondii and Cryptosporidium parvum, express a PPi-dependent phosphofructokinase (PPi-PFK) that consumes PPi to power the phosphorylation of fructose-6-phosphate. However, the physiological roles of PPi-PFKs in these organisms are not known. Here, we report that Toxoplasma expresses both ATP- and PPi-dependent phosphofructokinases in the cytoplasm. Nonetheless, only PPi-PFK was indispensable for parasite growth, whereas the deletion of ATP-PFK did not affect parasite proliferation or virulence. The conditional depletion of PPi-PFK completely arrested parasite growth, but it did not affect the ATP level and only modestly reduced the flux of central carbon metabolism. However, PPi-PFK depletion caused a significant increase in cellular PPi and decreased the rates of nascent protein synthesis. The expression of a cytosolic pyrophosphatase in the PPi-PFK depletion mutant reduced its PPi level and increased the protein synthesis rate, therefore partially rescuing its growth. These results suggest that PPi-PFK has a major role in maintaining pyrophosphate homeostasis in T. gondii. This role may allow PPi-PFK to fine-tune the balance of catabolism and anabolism and maximize the utilization efficiency for carbon nutrients derived from host cells, increasing the success of parasitism. Moreover, PPi-PFK is essential for parasite propagation and virulence in vivo but it is not present in human hosts, making it a potential drug target to combat toxoplasmosis.

Different from classic ATP-dependent phosphofructokinases, PPi-PFKs use pyrophosphate consumption to power the conversion of fructose-6-phosphate to fructose-1,6-bisphosphate, the committed step of glycolysis. PPi-PFK is found in diverse organisms including archaea, bacteria, protists and plants. However, half a century after its first discovery, the physiological functions of PPi-PFK are still not well defined. Using the Toxoplasma gondii parasite as a model, here we show that PPi-PFK has a coordinator function to assure matched activities of anabolism and catabolism. This is achieved by maintaining the homeostasis of PPi, which is a byproduct, as well as an inhibitor of many biosynthetic reactions. PPi-PFK hydrolyzes PPi to promote anabolism, meanwhile being a glycolytic enzyme involved in catabolism. As such, it gauges the anabolic and catabolic activities in parasites to maximize the utilization efficiency of acquired nutrients. This work provides important insights to understand the physiological significance of PPi-PFK in Toxoplasma and other organisms.

Boosting the acetol production in methanotrophic biocatalyst Methylomonas sp. DH-1 by the coupling activity of heteroexpressed novel protein PmoD with endogenous particulate methane monooxygenase

BACKGROUND

Methylacidiphilum sp. IT6 has been validated its C3 substrate assimilation pathway via acetol as a key intermediate using the PmoCAB3, a homolog of the particulate methane monooxygenase (pMMO). From the transcriptomic data, the contribution of PmoD of strain IT6 in acetone oxidation was questioned. Methylomonas sp. DH-1, a type I methanotroph containing pmo operon without the existence of its pmoD, has been deployed as a biocatalyst for the gas-to-liquid bioconversion of methane and propane to methanol and acetone. Thus, Methylomonas sp. DH-1 is a suitable host for investigation. The PmoD-expressed Methylomonas sp. DH-1 can also be deployed for acetol production, a well-known intermediate for various industrial applications. Microbial production of acetol is a sustainable approach attracted attention so far.

RESULTS

In this study, bioinformatics analyses elucidated that novel protein PmoD is a C-terminal transmembrane-helix membrane with the proposed function as a transport protein. Furthermore, the whole-cell biocatalyst was constructed in Methylomonas sp. DH-1 by co-expression the PmoD of Methylacidiphilum sp. IT6 with the endogenous pMMO to enable acetone oxidation. Under optimal conditions, the maximum accumulation, and specific productivity of acetol were 18.291 mM (1.35 g/L) and 0.317 mmol/g cell/h, respectively. The results showed the first coupling activity of pMMO with a heterologous protein PmoD, validated the involvement of PmoD in acetone oxidation, and demonstrated an unprecedented production of acetol from acetone in type I methanotrophic biocatalyst. From the data achieved in batch cultivation conditions, an assimilation pathway of acetone via acetol as the key intermediate was also proposed.

CONCLUSION

Using bioinformatics tools, the protein PmoD has been elucidated as the membrane protein with the proposed function as a transport protein. Furthermore, results from the assays of PmoD-heteroexpressed Methylomonas sp. DH-1 as a whole-cell biocatalyst validated the coupling activity of PmoD with pMMO to convert acetone to acetol, which also unlocks the potential of this recombinant biocatalyst for acetol production. The proposed acetone-assimilated pathway in the recombinant Methylomonas sp. DH-1, once validated, can extend the metabolic flexibility of Methylomonas sp. DH-1.

Sustainable biosynthesis of chemicals from methane and glycerol via reconstruction of multi-carbon utilizing pathway in obligate methanotrophic bacteria

Obligate methanotrophic bacteria can utilize methane, an inexpensive carbon feedstock, as a sole energy and carbon substrate, thus are considered as the only nature-provided biocatalyst for sustainable biomanufacturing of fuels and chemicals from methane. To address the limitation of native C1 metabolism of obligate type I methanotrophs, we proposed a novel platform strain that can utilize methane and multi-carbon substrates, such as glycerol, simultaneously to boost growth rates and chemical production in Methylotuvimicrobium alcaliphilum 20Z. To demonstrate the uses of this concept, we reconstructed a 2,3-butanediol biosynthetic pathway and achieved a fourfold higher titer of 2,3-butanediol production by co-utilizing methane and glycerol compared with that of methanotrophic growth. In addition, we reported the creation of a methanotrophic biocatalyst for one-step bioconversion of methane to methanol in which glycerol was used for cell growth, and methane was mainly used for methanol production. After the deletion of genes encoding methanol dehydrogenase (MDH), 11.6 mM methanol was obtained after 72 h using living cells in the absence of any chemical inhibitors of MDH and exogenous NADH source. A further improvement of this bioconversion was attained by using resting cells with a significantly increased titre of 76 mM methanol after 3.5 h with the supply of 40 mM formate. The work presented here provides a novel framework for a variety of approaches in methane-based biomanufacturing.