The properties and potential metabolic role of glucokinase in halotolerant obligate methanotroph Methylomicrobium alcaliphilum 20Z

Systematic Engineering of Eriodictyol-7-O-glucoside Biosynthetic Pathway through Enzyme Screening and Gene Regulation

The natural product eriodictyol-7-O-glucoside is more water-soluble and stable than eriodictyol and also exhibits novel biological activities and functions. However, its biosynthesis is hindered by the limited catalytic efficiency of key enzymes. Furthermore, the intricate interplay between cell growth and UDP-glucose supply adds another layer of complexity, rendering the engineering of productive strains challenging. To address this challenge, we introduced a novel "top-down" strategy in which bioinformatics analysis was initially used to identify six specific flavonoid 7-O-glucosyltransferases uniquely capable of converting eriodictyol into its 7-O-glucoside derivative. By manipulation of the plasmid copy number and promoter strength, the expression levels of the most promising flavonoid 7-O-glucosyltransferases from Arabidopsis thaliana were precisely fine-tuned, resulting in a remarkable 66.16% increase in eriodictyol-7-O-glucoside production. To improve the enhancement process, we focused on the overexpression of two pivotal enzymes: phosphoglucose mutase (encoded by the pgm gene) and UDP-glucose pyrophosphorylase (encoded by the galU gene). This strategic step was implemented to significantly increase the availability of glycosylation donors. Moreover, the eriodictyol concentration was increased to ensure ample feedstock. Finally, through comprehensive optimization of the fermentation conditions, eriodictyol-7-O-glucoside production was substantially enhanced, with a staggering 1187.36 mg L-1 obtained (molar conversion rate: 94.99%) at a substrate titer of 800 mg L-1 eriodictyol after 48 h of fermentation. The best engineered strain produced 2.70 g L-1 of eriodictyol-7-O-glucoside in a 5 L bioreactor. This study provides an effective and sustainable method for the high-yield production of flavonoid glycoside derivatives.

Methanotrophs: Metabolic versatility from utilization of methane to multi-carbon sources and perspectives on current and future applications

The development of biorefineries for a sustainable bioeconomy has been driven by the concept of utilizing environmentally friendly and cost-effective renewable energy sources. Methanotrophic bacteria with a unique capacity to utilize methane as a carbon and energy source can serve as outstanding biocatalysts to develop C1 bioconversion technology. By establishing the utilization of diverse multi-carbon sources, integrated biorefinery platforms can be created for the concept of the circular bioeconomy. An understanding of physiology and metabolism could help to overcome challenges for biomanufacturing. This review summaries fundamental gaps for methane oxidation and the capability to utilize multi-carbon sources in methanotrophic bacteria. Subsequently, breakthroughs and challenges in harnessing methanotrophs as robust microbial chassis for industrial biotechnology were compiled and overviewed. Finally, capabilities to exploit the inherent advantages of methanotrophs to synthesize various target products in higher titers are proposed.

Enzymes of an alternative pathway of glucose metabolism in obligate methanotrophs

Aerobic methanotrophic bacteria utilize methane as a growth substrate but are unable to grow on any sugars. In this study we have shown that two obligate methanotrophs, Methylotuvimicrobium alcaliphilum 20Z and Methylobacter luteus IMV-B-3098, possess functional glucose dehydrogenase (GDH) and gluconate kinase (GntK). The recombinant GDHs from both methanotrophs were homotetrameric and strongly specific for glucose preferring NAD⁺ over NADP⁺. GDH from Mtm. alcaliphilum was most active at pH 10 (V_max = 95 U/mg protein) and demonstrated very high K_m for glucose (91.8 ± 3.8 mM). GDH from Mb. luteus was most active at pH 8.5 (V_max = 43 U/mg protein) and had lower K_m for glucose (16 ± 0.6 mM). The cells of two Mtm. alcaliphilum double mutants with deletions either of the genes encoding GDH and glucokinase (gdh^─/glk^─) or of the genes encoding gluconate kinase and glucokinase (gntk^─/glk^─) had the lower glycogen level and the higher contents of intracellular glucose and trehalose compared to the wild type strain. The gntk^─/glk^─ knockout mutant additionally accumulated gluconic acid. These data, along with bioinformatics analysis, demonstrate that glycogen derived free glucose can enter the Entner–Doudoroff pathway or the pentose phosphate cycle in methanotrophs, bypassing glycolysis via the gluconate shunt.

ATP- and Polyphosphate-Dependent Glucokinases from Aerobic Methanotrophs

The genes encoding adenosine triphosphate (ATP)- and polyphosphate (polyP)-dependent glucokinases (Glk) were identified in the aerobic obligate methanotroph Methylomonas sp. 12. The recombinant proteins were obtained by the heterologous expression of the glk genes in Esherichia coli. ATP-Glk behaved as a multimeric protein consisting of di-, tri-, tetra-, penta- and hexamers with a subunit molecular mass of 35.5 kDa. ATP-Glk phosphorylated glucose and glucosamine using ATP (100% activity), uridine triphosphate (UTP) (85%) or guanosine triphosphate (GTP) (71%) as a phosphoryl donor and exhibited the highest activity in the presence of 5 mM Mg²⁺ at pH 7.5 and 65 °C but was fully inactivated after a short-term incubation at this temperature. According to a gel filtration in the presence of polyP, the polyP-dependent Glk was a dimeric protein (2 × 28 kDa). PolyP-Glk phosphorylated glucose, mannose, 2-deoxy-D-glucose, glucosamine and N-acetylglucosamine using polyP as the phosphoryl donor but not using nucleoside triphosphates. The K_m values of ATP-Glk for glucose and ATP were about 78 μM, and the K_m values of polyP-Glk for glucose and polyP_(n=45) were 450 and 21 μM, respectively. The genomic analysis of methanotrophs showed that ATP-dependent glucokinase is present in all sequenced methanotrophs, with the exception of the genera Methylosinus and Methylocystis, whereas polyP-Glks were found in all species of the genus Methylomonas and in Methylomarinum vadi only. This work presents the first characterization of polyphosphate specific glucokinase in a methanotrophic bacterium.

Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach

Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, ¹³C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20Z^R an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20Z^R. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confirmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. The computational framework of C₁-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.