Improving Microbial Cell Factory Performance by Engineering SAM Availability

NMR-based metabolomics of Burkholderia pseudomallei biofilms and extracellular polymeric substance cultured in LB and MVBM media

Burkholderia pseudomallei biofilms are resistant to antibiotics and immune responses, leading to persistent infections. This study aimed to investigate the metabolic profiles of B. pseudomallei in biofilms and the extracellular polymeric substances (EPS) produced during grown in LB or MVBM medium using Nuclear Magnetic Resonance (NMR) spectroscopy to identify key metabolites. The results revealed similar biofilm metabolites in both media. However, betaine was detected in LB, but not in the case of MVBM. Acetate was significantly higher in MVBM compared to that of LB. Pathway analysis revealed that betaine-producing B. pseudomallei biofilm in LB was associated with metabolism of glycine, serine, and threonine, while acetate in MVBM was associated with metabolism of taurine and hypotaurine, phosphonate and phosphinate, and glycolysis/gluconeogenesis. The NMR analysis of EPS disclosed shared metabolites including dimethylsulfide, 1-methyluric acid and oxypurinol. This study provides the first extensive investigation into B. pseudomallei biofilm and EPS metabolites, identifying pathways that offer potential targets for combating B. pseudomallei biofilm-associated infections.

Rewiring Escherichia coli to transform formate into methyl groups

BACKGROUND

Biotechnological applications are steadily growing and have become an important tool to reinvent the synthesis of chemicals and pharmaceuticals for lower dependence on fossil resources. In order to sustain this progression, new feedstocks for biotechnological hosts have to be explored. One-carbon (C1-)compounds, including formate, derived from CO2 or organic waste are accessible in large quantities with renewable energy, making them promising candidates. Previous studies showed that introducing the formate assimilation machinery from Methylorubrum extorquens into Escherichia coli allows assimilation of formate through the C1-tetrahydrofolate (C1-H4F) metabolism. Applying this route for formate assimilation, we here investigated utilisation of formate for the synthesis of value-added building blocks in E. coli using S-adenosylmethionine (SAM)-dependent methyltransferases (MT).

RESULTS

We first used a two-vector system to link formate assimilation and SAM-dependent methylation with three different MTs in E. coli BL21. By feeding isotopically labelled formate, methylated products with 51-81% 13C-labelling could be obtained without substantial changes in conversion rates. Focussing on improvement of product formation with one MT, we analysed the engineered C1-auxotrophic E. coli strain C1S. Screening of different formate concentrations allowed doubling of the conversion rate in comparison to the not formate-supplemented BL21 strain with a share of more than 70% formate-derived methyl groups.

CONCLUSIONS

Within this study transformation of formate into methyl groups is demonstrated in E. coli. Our findings support that feeding formate can improve the availability of usable C1-compounds and, as a result, increase whole-cell methylation with engineered E. coli. Using this as a starting point, the introduction of additional auxiliary enzymes and ideas to make the system more energy-efficient are discussed for future applications.

Construction of an Efficient O-Succinyl-L-homoserine Producing Cell Factory and Its Application for Coupling Production of L-Methionine and Succinic Acid

O-Succinyl-L-homoserine (OSH) is an important C4 platform compound with broad applications. Its green and efficient production is receiving increasing attention. Herein, the OSH producing chassic cell was constructed by deleting the transcriptional negative regulation factor, blocking the OSH consumption pathway, and inhibiting the competitive bypass pathways. The precursor synthesis pathways of aspartic acid and homoserine were further strengthened, and the pentose phosphate pathway and glycolysis pathway were modified to enhance the NADPH supply. Adaptive evolution was applied to improve the tolerance of the cell factory to the fermentation environment. With Raman online analysis, the metabolic process model was built to guide fermentation regulation. The final titer of OSH reached 121.7 g/L with conversion of 63% in a 50 L fermenter. Based on this, a coupling production route for L-methionine and succinic acid from OSH was established with good atomic economy and environmental friendliness.

Doping In Vivo Alkylation in E. coli by Introducing the Direct Sulfurylation Pathway of S. cerevisiae

Methylation and alkylation are important techniques used for the synthesis and derivatisation of small molecules and natural products. Application of S-adenosylmethionine (SAM)-dependent methyltransferases (MTs) in biotechnological hosts such as Escherichia coli lowers the environmental impact of alkylation compared to chemical synthesis and facilitates regio- and chemoselective alkyl chain transfer. Here, we address the limiting factor for SAM synthesis, methionine supply, to accelerate in vivo methylation activity. Introduction of the direct sulfurylation pathway, consisting of O-acetylhomoserine sulfhydrolase (ScOAHS) and O-acetyltransferase (ScMET2), from S. cerevisiae into E. coli and supplementation with methanethiol or the corresponding disulfide improves atom-economic methylation activity in three different MT reactions. Up to 17-fold increase of conversion compared to the sole expression of the MT and incorporation of up to 79 % of the thiol compound added were achieved. Promiscuity of ScOAHS allowed in vivo production of methionine analogues from organic thiols. Further co-overproduction of a methionine adenosyltransferase yielded SAM analogues which were further transferred by MTs onto different substrates. For methylation of non-physiological substrates, conversion rates up to 73 % were achieved, with an isolated yield of 41 % for N-methyl-2,5-aminonitrophenol. The here described technique enables E. coli to become a biotechnological host for improved methylation and selective alkylation reactions.

Enzymatic Reactions of S-Adenosyl-L-Methionine: Synthesis and Applications

S-adenosyl-L-methionine (SAM, AdoMet) is a ubiquitous biomolecule present in all living organisms, playing a central role in a wide array of biochemical reactions and intracellular regulatory pathways. It is the second most common participant in enzymatic reactions in living systems, following adenosine triphosphate (ATP). This review provides a comprehensive analysis of enzymatic reactions involving SAM, whether as a product, a reactant (cosubstrate), or as a non-consumable enzyme cofactor. The discussion encompasses various methods for SAM synthesis, including biotechnological, chemical, and enzymatic approaches. Particular emphasis is placed on the biochemical reactions where SAM functions as a cosubstrate, notably in trans-alkylation reactions, where it acts as a key methyl group donor. Beyond methylation, SAM also serves as a precursor for the synthesis of other molecular building blocks, which are explored in a dedicated section. The review also addresses the role of SAM as a non-consumable cofactor in enzymatic processes, highlighting its function as a prosthetic group for certain protein enzymes and its ability to form complexes with ribozymes. In addition, bioorthogonal systems involving SAM analogues are discussed. These systems employ engineered enzyme-cofactor pairs designed to enable highly selective interactions between target SAM analogues and specific enzymes, facilitating precise reactions even in the presence of other SAM-dependent enzymes. The concluding section explores practical applications of SAM analogues, including their use as selective inhibitors in clinical medicine and as components of reporter systems.