Adaptive laboratory evolution boost Yarrowia lipolytica tolerance to vanillic acid

Hydroxybenzoic acids: Microbial metabolism, pathway engineering and products

Hydroxybenzoic acids (HBAs) are plant secondary metabolites exhibiting antioxidant, antiviral, anticancer and antibacterial activities. A high and constantly increasing demand for these compounds underlines the need for novel and efficient production methods, as commonly applied plant extraction and chemical synthesis approaches are susceptible to low yields and are environmentally hazardous. Switching to biotechnology and replacing petroleum-based chemicals has potential to improve eco-efficiency in sustainable bioeconomy. With the increased focus on the production of materials using renewable resources and bio-based feedstocks, microbial fermentation and engineering drives the development and optimization of sustainable bioproduction. This systematic review summarizes current knowledge of microbial HBAs metabolism and biosynthesis. Here, the existing challenges are highlighted and the potential strategies for improved microbial production of HBAs are identified. Key aspects of HBAs metabolism and complexity of the factors related to bacterial strain selection, titer, and bioprocess strategy are examined. The opportunities of HBAs bioproduction using engineered microbial cell factories are discussed in detail and insights for synthesis improvement are presented.

Mechanism and improvement of yeast tolerance to biomass-derived inhibitors: A review

Lignocellulosic biomass is regarded as a potentially valuable second-generation biorefinery feedstock. Yeast has the ability to metabolize this substrate and convert it into fuel ethanol and an array of other chemical products. Nevertheless, during the pretreatment of lignocellulosic biomass, inhibitors (furanaldehydes, carboxylic acids, phenolic compounds, etc.) are generated, which impede the growth and metabolic activities of yeast cells. Consequently, developing yeast strains with enhanced tolerance to these inhibitors is a crucial technological objective, as it can significantly enhance the efficiency of lignocellulosic biorefineries. This review provides a concise overview of the process of inhibitor generation and the detrimental effects of these inhibitors on yeast. It also summarizes the current state of research on the mechanisms of yeast tolerance to these inhibitors, focusing specifically on recent advances in enhancing yeast tolerance to these inhibitors by rational and non-rational strategies. Finally, it discusses the current challenges and future research directions.

Emerging biotechnological strategies advancing biological lignin valorization towards polyhydroxyalkanoates

Lignin is the largest renewable aromatic resource available for producing high-value products such as biomaterials, biofuels, and chemicals. Polyhydroxyalkanoate (PHA) is a biodegradable and biocompatible polymer synthesized by various microorganisms, offering broad application potential. Microbial conversion of lignin-derived aromatics into PHA promoted both lignin valorization and PHA biosynthesis. However, lignin's recalcitrance and heterogeneity pose significant challenges for its microbial degradation and value-added utilization. This review examines the entire pathway of lignin conversion into high-value products, highlighting the advantages of microbial processes for synthesizing PHA and promoting the biological upgrading of lignin. Additionally, synthetic biology techniques and metabolic regulation strategies can further enhance microbial PHA synthesis. Overall, integrating microbial PHA synthesis with lignin bioconversion not only facilitates lignin valorization but also supports the sustainable production of PHA, making a significant contribution to the utilization and sustainable development of biomass resources.

Enhanced tolerance of Clostridium tyrobutyricum to lignin-derived phenolic acids by overexpressing native reductases

Ferulic acid (Fer) and p-coumaric acid (Coum) are major phenolic inhibitors in lignocellulosic hydrolysates that severely hinder the growth and metabolism of Clostridia species. This study demonstrates that the reduction of Fer and Coum to dihydroferulic acid and phloretic acid by Clostridium tyrobutyricum significantly alleviates their toxicity. Overexpression of the dho1 and sdr1 genes, encoding Fer and Coum reductases, respectively, in C. tyrobutyricum can significantly enhance tolerance to these phenolic acids. As a result, the recombinant strain ATCC 25755/ds, which co-overexpresses dho1 and sdr1, exhibited a marked increase in butyrate production compared to the wild-type strain under phenolic acid stress. In fed-batch fermentation with a 1.0 g/L mixture of Fer and Coum (1:1, w/w), ATCC 25755/ds showed a 35.1 % increase in butyrate production and a 61.1 % higher productivity. These results indicate that enhancing phenolic acid reduction can significantly improve Clostridia's tolerance to phenolic acids, thereby strengthening the biotransformation of lignocellulose hydrolysates.

Synthetic biology approaches to improve tolerance of inhibitors in lignocellulosic hydrolysates

Increasing attention is being focused on using lignocellulose for valuable products. Microbial decomposition can convert lignocellulose into renewable biofuels and other high-value bioproducts, contributing to sustainable development. However, the presence of inhibitors in lignocellulosic hydrolysates can negatively affect microorganisms during fermentation. Improving microbial tolerance to these hydrolysates is a major focus in metabolic engineering. Traditional detoxification methods increase costs, so there is a need for cheap and efficient cell-based detoxification strategies. Synthetic biology approaches offer several strategies for improving microbial tolerance, including redox balancing, membrane engineering, omics-guided technologies, expression of protectants and transcription factors, irrational engineering, cell flocculation, and other novel technologies. Advances in molecular biology, high-throughput sequencing, and artificial intelligence (AI) allow for precise strain modification and efficient industrial production. Developing AI-based computational models to guide synthetic biology efforts and creating large-scale heterologous libraries with automation and high-throughput technologies will be important for future research.

Rational and Semirational Approaches for Engineering Salicylate Production in Escherichia coli

Salicylate plays a pivotal role as a pharmaceutical intermediate in drugs, such as aspirin and lamivudine. The low catalytic efficiency of key enzymes and the inherent toxicity of salicylates to cells pose significant challenges to large-scale microbial production. In this study, we introduced the salicylate synthase Irp9 into an l-phenylalanine-producing Escherichia coli, constructing the shortest salicylate biosynthetic pathway. Subsequent protein engineering increased the catalytic efficiency of Irp9 by 33.5%. Furthermore, by integrating adaptive evolution with transcriptome analysis, we elucidated the crucial mechanism of efflux proteins in salicylate tolerance. The elucidation of this mechanism guided us in the targeted modification of these transport proteins, achieving a reported maximum level of 3.72 g/L of salicylate in a shake flask. This study highlights the importance of efflux proteins for enhancing the productivity of microbial cell factories in salicylate production, which also holds potential for application in the green synthesis of other phenolic acids.

Adaptive evolution of Paecilomyces variotii enhanced the biodetoxification of high-titer inhibitors in pretreated lignocellulosic feedstock

High inhibitor concentrations in lignocellulose feedstock negatively affect the degradation rate of biodetoxification strains. This study designed two adaptive laboratory evolutions in solid substrate and liquid medium to boost the biodetoxification capacity of P. variotii to high titers of lignocellulose-derived inhibitors, resulting in two evolved strains AC70 and ZW70. The results showed that the evolutionary adaptation in liquid medium could better boost the acetic acid assimilation compared to that on solid substrate. Transcriptional analysis revealed that the evolved strains exhibited a significant upregulation of adh, acs, ach1, and ackA directly related to the initial steps of acetate and furan aldehydes metabolisms. ZW70 strain can effectively remove the high concentration inhibitors cocktail from the hydrolysates derived from pretreated wheat straw and furfural residues. The biodetoxified hydrolysates by ZW70 were successfully used for cellulose chiral L-lactic acid production with the titers of ∼110 g/L, which were over 20 % higher than that detoxified by parental strain.

General mechanisms of weak acid-tolerance and current strategies for the development of tolerant yeasts

Yeast cells are often subjected to various types of weak acid stress in the process of industrial production, food processing, and preservation, resulting in growth inhibition and reduced fermentation performance. Under acidic conditions, weak acids enter the near-neutral yeast cytoplasm and dissociate into protons and anions, leading to cytoplasmic acidification and cell damage. Although some yeast strains have developed the ability to survive weak acids, the complexity and diversity of stresses during industrial production still require the application of appropriate strategies for phenotypes improvement. In this review, we summarized current knowledge concerning weak acid stress response and resistance, which may suggest important targets for further construction of more robust strains. We also highlight current feasible strategies for improving the weak acid resistance of yeasts, such as adaptive laboratory evolution, transcription factors engineering, and cell membrane/wall engineering. Moreover, the challenges and perspectives associated with improving the competitiveness of industrial strains are also discussed. This review provides effective strategies for improving the industrial phenotypes of yeast from multiple dimensions in future studies.