Adaptive laboratory evolution of Bacillus subtilis to overcome toxicity of lignocellulosic hydrolysate derived from Distiller's dried grains with solubles (DDGS)

Valorization of brewing by-products as protein resources: Extraction, structural insights, functional properties, and value-added applications

Distiller's grains (DGS), a rich protein byproduct of brewing, is mainly used as animal feed due to the challenges in protein extraction techniques and the lack of clarity regarding the potential applications. The insufficient development of DGS limits its high-value utilization. Therefore, this work aims to comprehensively review the latest progress in DGS protein separation, elaborate on their structural and functional characteristics, and emphasize potential applications and future research directions. The extraction and application of DGS proteins mainly focus on the total protein as well as specific fractions such as prolamins and glutelins. DGS proteins can be extracted through a series of techniques, including conventional chemical, enzymatic, and physical-assisted methods, which have a significant impact on their structural and functional properties. Their unique functional characteristics have made DGS proteins key components in the fields of bulk food ingredients, drug delivery systems, and bioactive peptide research. In addition, based on their excellent hydrophobicity and assembly properties, the potential of DGS proteins as biodegradable food-grade films is attracting increasing research attention. Future research should innovate extraction methods and identify influential applications to address the problem of protein scarcity in food processing and enhance the value of proteins.

Upgrading Pseudomonas sp. toward Tolerance to a Synthetic Biomass Hydrolysate Enriched with Furfural and 5-Hydroxymethylfurfural

Several Pseudomonas species, including Pseudomonas putida KT2440, have a broad metabolic repertoire to assimilate biomass monomers such as lignin-derived compounds but struggle to tolerate biomass hydrolysates. Here, we examined the furan derivatives tolerance in a novel and nonpathogenic Pseudomonas species (strain BJa5) and in P. putida KT2440 using tolerance adaptive laboratory evolution (TALE) to enhance growth performance in a synthetic straw sugar cane hydrolysate enriched with furfural and 5-hydroxymethylfurfural (5-HMF). Initially, wild-type strains showed prolonged lag phases and low tolerance in the synthetic hydrolysate, but tolerance was improved after 90 days of sequential batch growth. Post-TALE, BJa5 and KT2440 end strains grew in synthetic hydrolysate containing 2 g/L furfural and 1 g/L 5-HMF at 48 and 24 h, respectively. Moreover, the KT2440 end strain notably grew in 2 g/L furfural and ≥1.7 g/L 5-HMF. Genome sequencing of end strains revealed mutations in genes and intergenic regions associated with transcriptional factors, acetate metabolism enzymes, environmental response proteins, and transposases. In a proof-of-concept experiment, the BJa5 end strain demonstrated the potential to detoxify synthetic hydrolysate by reducing the titers of acetate and furfural. This ability could enable industrial microorganisms, which are typically nontolerant to toxic hydrolysates, to be used for producing value-added compounds from biodetoxified hydrolysates.

The 6-phosphofructokinase reaction in Acetivibrio thermocellus is both ATP- and pyrophosphate-dependent

Acetivibrio thermocellus (formerly Clostridium thermocellum) is a potential platform for lignocellulosic ethanol production. Its industrial application is hampered by low product titres, resulting from a low thermodynamic driving force of its central metabolism. It possesses both a functional ATP- and a functional PPi-dependent 6-phosphofructokinase (PPi-Pfk), of which only the latter is held responsible for the low driving force. Here we show that, following the replacement of PPi-Pfk by cytosolic pyrophosphatase and transaldolase, the native ATP-Pfk is able to carry the full glycolytic flux. Interestingly, the barely-detectable in vitro ATP-Pfk activities are only a fraction of what would be required, indicating its contribution to glycolysis has consistently been underestimated. A kinetic model demonstrated that the strong inhibition of ATP-Pfk by PPi can prevent futile cycling that would arise when both enzymes are active simultaneously. As such, there seems to be no need for a long-sought-after PPi-generating mechanism to drive glycolysis, as PPi-Pfk can simply use whatever PPi is available, and ATP-Pfk complements the rest of the PFK-flux. Laboratory evolution of the ΔPPi-Pfk strain, unable to valorize PPi, resulted in a mutation in the GreA transcription elongation factor. This mutation likely results in reduced RNA-turnover, hinting at transcription as a significant (and underestimated) source of anabolic PPi. Together with other mutations, this resulted in an A. thermocellus strain with the hitherto highest biomass-specific cellobiose uptake rate of 2.2 g/gx/h. These findings are both relevant for fundamental insight into dual ATP/PPi Pfk-nodes, which are not uncommon in other microorganisms, as well as for further engineering of A. thermocellus for consolidated bioprocessing.

Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration

The field of hybrid engineered living materials seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. Engineered living materials have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication is demonstrated in which spores from polymer-degrading bacteria are incorporated into a thermoplastic polyurethane using high-temperature melt extrusion. Bacteria are engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 °C. Furthermore, the overall tensile properties of spore-filled thermoplastic polyurethanes are substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitate disintegration in compost in the absence of a microbe-rich environment. Finally, embedded spores demonstrate a rationally programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.

Engineering Bacillus subtilis J46 for efficient utilization of galactose through adaptive laboratory evolution

Efficient utilization of galactose by microorganisms can lead to the production of valuable bio-products and improved metabolic processes. While Bacillus subtilis has inherent pathways for galactose metabolism, there is potential for enhancement via evolutionary strategies. This study aimed to boost galactose utilization in B. subtilis using adaptive laboratory evolution (ALE) and to elucidate the genetic and metabolic changes underlying the observed enhancements. The strains of B. subtilis underwent multiple rounds of adaptive laboratory evolution (approximately 5000 generations) in an environment that favored the use of galactose. This process resulted in an enhanced specific growth rate of 0.319 ± 0.005 h-1, a significant increase from the 0.03 ± 0.008 h-1 observed in the wild-type strains. Upon selecting the evolved strain BSGA14, a comprehensive whole-genome sequencing revealed the presence of 63 single nucleotide polymorphisms (SNPs). Two of them, located in the coding sequences of the genes araR and glcR, were found to be the advantageous mutations after reverse engineering. The strain with these two accumulated mutations, BSGALE4, exhibited similar specific growth rate on galactose to the evolved strain BSGA14 (0.296 ± 0.01 h-1). Furthermore, evolved strain showed higher productivity of protease and β-galactosidase in mock soybean biomass medium. ALE proved to be a potent tool for enhancing galactose metabolism in B. subtilis. The findings offer valuable insights into the potential of evolutionary strategies in microbial engineering and pave the way for industrial applications harnessing enhanced galactose conversion.