Metabolic engineering of Escherichia coli to utilize methanol as a co-substrate for the production of (R)-1,3-butanediol

Biosensor-Assisted Evolution of a β-Glucosidase for Enzymatic Robustness and In Vivo Cellobiose Metabolism in Escherichia coli

β-Glucosidase is one of the essential components of the enzyme cocktail required for the degradation of lignocellulose, which catalyzes the conversion of cellobiose into glucose both in vitro and in vivo. For the in vivo utilization of cellobiose in Escherichia coli, it is crucial to express and regulate a BGL optimally with enhanced enzymatic properties. This study characterizes the enzymatic properties of a BGL named AtBgl1, derived from Alteromonadales bacterium TW-7. A cellobiose biosensor, Cbio3-R-R3, was constructed and optimized, showing a 2.27-fold increase in sensitivity compared to Cbio1. A mutant library was constructed through two rounds of error-prone mutagenesis. Using cellobiose-based screening plates and a biosensor, we identified the BGL mutant strain M5, which showed a 2.13-fold increase in kcat/Km compared to AtBgl1. Structural analysis and molecular dynamics simulations provided insights into the molecular mechanisms underlying this enhanced performance. Finally, E. coli was given the ability to metabolize cellobiose, and the E. coli BL21-M5 showed remarkable improvements in metabolic efficiency, achieving an 88.4% cellobiose utilization rate within 48 h. This study provides valuable strategies and insights for the biosensor-assisted directed evolution of BGL, enhancing its enzymatic robustness and facilitating in vivo cellobiose metabolism in E. coli metabolic engineering.

Thermodynamic tools for more efficient biotechnological processes: an example in poly-(3-hydroxybutyrate) production from carbon monoxide

Modern biotechnology requires the integration of several disciplines, with thermodynamics being a crucial one. Experimental approaches frequently used in biotechnology, such as rewiring of metabolic networks or culturing of micro-organisms in engineered environments, can benefit from the application of thermodynamic tools. In this paper, we provide an overview of several thermodynamic tools that are useful for the design and optimization of biotechnological processes, and we demonstrate their potential application in the production of poly-(3-hydroxybutyrate) (PHB) from carbon monoxide (CO). We discuss how these tools can aid in the design of metabolic engineering strategies, the calculation of expected yields, the assessment of the thermodynamic feasibility of the targeted conversions, the identification of potential thermodynamic bottlenecks, and the selection of genetic engineering targets. Although we illustrate these tools using the specific example of PHB production from CO, they can be applied to other substrates and products.

Evaluation of Cellular Responses of Heterotrophic Escherichia coli Cultured with Autotrophic Chlamydomonas reinhardtii as a Nutrient Source by Analyses Based on Microbiology and Transcriptome

Heterotrophic microorganism Escherichia coli LS5218 was cultured with flesh green alga Chlamydomonas reinhardtii C-9: NIES-2235 as a nutrient supplier. In order to evaluate the cell response of Escherichia coli with Chlamydomonas reinhardtii, Escherichia coli was evaluated with microbial methods and comprehensive gene transcriptional analyses. Escherichia coli with Chlamydomonas reinhardtii showed a specific growth rate (µmax) of 1.04 ± 0.27, which was similar to that for cells growing in Luria-Bertani medium (µmax = 1.20 ± 0.40 h-1). Furthermore, comparing the cellular responses of Escherichia coli in a green-algae-containing medium with those in the Luria-Bertani medium, transcriptomic analysis showed that Escherichia coli upregulated gene transcription levels related to glycolysis, 5-phospho-d-ribosyl-1-diphosphate, and lipid synthesis; on the other hand, it decreased the levels related to lipid degradation. In particular, the transcription levels were increased by 103.7 times on pgm (p * < 0.05 (p = 0.015)) in glycolysis, and decreased by 0.247 times on fadE (p * < 0.05 (p = 0.041)) in lipolysis. These genes are unique and could regulate the direction of metabolism; these responses possibly indicate carbon source assimilation as a cellular response in Escherichia coli. This paper is the first report to clarify that Escherichia coli, a substance-producing strain, directly uses Chlamydomonas reinhardtii as a nutrient supplier by evaluation of the cellular responses analyzed with microbial methods and transcriptome analysis.