Elimination of carbon catabolite repression in Clostridium tyrobutyricum for enhanced butyric acid production from lignocellulosic hydrolysates

Systems Metabolic Engineering of Clostridium tyrobutyricum for 1,3-Propanediol Production From Crude Glycerol

Clostridium tyrobutyricum has emerged as a non-pathogenic microbial cell factory capable of anaerobic production of various value-added products, such as butyrate, butanol, and butyl butyrate. This study reports the first systematic engineering of C. tyrobutyricum for the heterologous production of 1,3-propanediol (1,3-PDO) from industrial by-product crude glycerol. Initially, the glycerol reductive pathway for 1,3-PDO production was constructed, and the unique glycerol oxidation pathway in C. tyrobutyricum was elucidated. Subsequently, the glycerol metabolism and 1,3-PDO synthesis pathways were enhanced. Furthermore, the intracellular reducing power supply and the fermentation process were optimized to improve 1,3-PDO production. Consequently, 54.06 g/L 1,3-PDO with a yield of 0.64 mol/mol and a productivity of 1.13 g/L·h was obtained using crude glycerol and fish meal. The strategies described herein could facilitate the engineering of C. tyrobutyricum as a robust host for synthesizing valuable chemicals.

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.

Enhanced butanol production through intracellular NADH regeneration in CdSe-C. acetobutylicumg semi-photosynthetic biohybrid system

Current environmental challenges and energy crises highlight the urgent need for a transition in energy mix. In this study, an innovative semi-photosynthetic biohybrid system that combined light-activated cadmium selenide quantum dots (CdSe QDs) with engineered Gram-positive anaerobic bacteria, Clostridium acetobutylicumg (C. acetobutylicumg), was developed to enhance renewable butanol production. The results demonstrated that CdSe QDs could be biosynthesized intracellularly within C. acetobutylicumg through the introduction of glutathione pathway, without causing significant damage to bacteria. Furthermore, this system showed remarkable tolerance to butanol and weak acids. Under illumination, the biological synthesized CdSe QDs enabled C. acetobutylicumg to achieve a 45.5 % increase in NADH/NAD+ ratio compared to C. acetobutylicumg without CdSe QDs. When utilizing undetoxified rice straw hydrolysate in photo-fermentation, this system achieved a butanol titer of 14.82 g/L and a yield of 0.29 g/g. Overall, this work aims to effectively harness solar energy and biomass resources for sustainable clean biofuel production.

Co-utilization of carbon sources in microorganisms for the bioproduction of chemicals

Carbon source is crucial for the cell growth and metabolism in microorganisms, and its utilization significantly affects the synthesis efficiency of target products in microbial cell factories. Compared with a single carbon source, co-utilizing carbon sources provide an alternative approach to optimize the utilization of different carbon sources for efficient biosynthesis of many chemicals with higher titer/yield/productivity. However, the efficiency of bioproduction is significantly limited by the sequential utilization of a preferred carbon source and secondary carbon sources, attributed to carbon catabolite repression (CCR). This review aimed to introduce the mechanisms of CCR and further focus on the summary of the strategies for co-utilization of carbon sources, including alleviation of CCR, engineering of the transport and metabolism of secondary carbon sources, compulsive co-utilization in single culture, co-utilization of carbon sources via co-culture, and evolutionary approaches. The findings of representative studies with a significant improvement in the bioproduction of chemicals via the co-utilization of carbon sources were discussed in this review. It suggested that by combining rational metabolic engineering and irrational evolutionary approaches, co-utilizing carbon sources can significantly contribute to the bioproduction of chemicals.

Integration of food raw materials, food microbiology, and food additives: systematic research and comprehensive insights into sweet sorghum juice, Clostridium tyrobutyricum TGL-A236 and bio-butyric acid

Introduction

Sweet sorghum juice is a typical production feedstock for natural, eco-friendly sweeteners and beverages. Clostridium tyrobutyricum is one of the widely used microorganisms in the food industry, and its principal product, bio-butyric acid is an important food additive. There are no published reports of Clostridium tyrobutyricum producing butyric acid using SSJ as the sole substrate without adding exogenous substances, which could reach a food-additive grade. This study focuses on tailoring a cost-effective, safe, and sustainable process and strategy for their production and application.

Methods

This study modeled the enzymolysis of non-reducing sugars via the first/second-order kinetics and added food-grade diatomite to the hydrolysate. Qualitative and quantitative analysis were performed using high-performance liquid chromatography, gas chromatography-mass spectrometer, full-scale laser diffraction method, ultra-performance liquid chromatography-tandem mass spectrometry, the cell double-staining assay, transmission electron microscopy, and Oxford nanopore technology sequencing. Quantitative real-time polymerase chain reaction, pathway and process enrichment analysis, and homology modeling were conducted for mutant genes.

Results

The treated sweet sorghum juice showed promising results, containing 70.60 g/L glucose and 63.09 g/L fructose, with a sucrose hydrolysis rate of 98.29% and a minimal sucrose loss rate of 0.87%. Furthermore, 99.62% of the colloidal particles and 82.13% of the starch particles were removed, and the concentrations of hazardous substances were effectively reduced. A food microorganism Clostridium tyrobutyricum TGL-A236 with deep utilization value was developed, which showed superior performance by converting 30.65% glucose and 37.22% fructose to 24.1364 g/L bio-butyric acid in a treated sweet sorghum juice (1:1 dilution) fermentation broth. This titer was 2.12 times higher than that of the original strain, with a butyric acid selectivity of 86.36%. Finally, the Genome atlas view, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and evolutionary genealogy of genes: Non-supervised Orthologous (eggNOG) functional annotations, three-dimensional structure and protein cavity prediction of five non-synonymous variant genes were obtained.

Conclusion

This study not only includes a systematic process flow and in-depth elucidation of relevant mechanisms but also provides a new strategy for green processing of food raw materials, improving food microbial performance, and ensuring the safe production of food additives.

ALACEN: A Holistic Herbaceous Biomass Fractionation Process Attaining a Xylose-Rich Stream for Direct Microbial Conversion to Bioplastics

Lignocellulose biorefining is a promising technology for the sustainable production of chemicals and biopolymers. Usually, when one component is focused on, the chemical nature and yield of the others are compromised. Thus, one of the bottlenecks in biomass biorefining is harnessing the maximum value from all of the lignocellulosic components. Here, we describe a mild stepwise process in a flow-through setup leading to separate flow-out streams containing cinnamic acid derivatives, glucose, xylose, and lignin as the main components from different herbaceous sources. The proposed process shows that minimal degradation of the individual components and conservation of their natural structure are possible. Under optimized conditions, the following fractions are produced from wheat straw based on their respective contents in the feed by the ALkaline ACid ENzyme process: (i) 78% ferulic acid from a mild ALkali step, (ii) 51% monomeric xylose free of fermentation inhibitors by mild ACidic treatment, (iii) 82% glucose from ENzymatic degradation of cellulose, and (iv) 55% native-like lignin. The benefits of using the flow-through setup are demonstrated. The retention of the lignin aryl ether structure was confirmed by HSQC NMR, and this allowed monomers to form from hydrogenolysis. More importantly, the crude xylose-rich fraction was shown to be suitable for producing polyhydroxybutyrate bioplastics. The direct use of the xylose-rich fraction by means of the thermophilic bacteria Schlegelella thermodepolymerans matched 91% of the PHA produced with commercial pure xylose, achieving 138.6 mgPHA/gxylose. Overall, the ALACEN fractionation method allows for a holistic valorization of the principal components of herbaceous biomasses.

Metabolic and Bioprocess Engineering of Clostridium tyrobutyricum for Butyl Butyrate Production on Xylose and Shrimp Shell Waste

Microbial conversion of agri-food waste to valuable compounds offers a sustainable route to develop the bioeconomy and contribute to sustainable biorefinery. Clostridium tyrobutyricum displays a series of native traits suitable for high productivity conversion of agri-food waste, which make it a promising host for the production of various compounds, such as the short-chain fatty acids and their derivative esters products. In this study, a butanol synthetic pathway was constructed in C. tyrobutyricum, and then efficient butyl butyrate production through in situ esterification was achieved by the supplementation of lipase into the fermentation. The butyryl-CoA/acyl-CoA transferase (cat1) was overexpressed to balance the ratio between precursors butyrate and butanol. Then, a suitable fermentation medium for butyl butyrate production was obtained with xylose as the sole carbon source and shrimp shell waste as the sole nitrogen source. Ultimately, 5.9 g/L of butyl butyrate with a selectivity of 100%, and a productivity of 0.03 g/L·h was achieved under xylose and shrimp shell waste with batch fermentation in a 5 L bioreactor. Transcriptome analyses exhibited an increase in the expression of genes related to the xylose metabolism, nitrogen metabolism, and amino acid metabolism and transport, which reveal the mechanism for the synergistic utilization of xylose and shrimp shell waste. This study presents a novel approach for utilizing xylose and shrimp shell waste to produce butyl butyrate by using an anaerobic fermentative platform based on C. tyrobutyricum. This innovative fermentation medium could save the cost of nitrogen sources (~97%) and open up possibilities for converting agri-food waste into other high-value products.

Implications of carbon catabolite repression for Aspergillus-based cell factories: A review

Carbon catabolite repression (CCR) is a global regulatory mechanism that allows organisms to preferentially utilize a preferred carbon source (usually glucose) by suppressing the expression of genes associated with the utilization of nonpreferred carbon sources. Aspergillus is a large genus of filamentous fungi, some species of which have been used as microbial cell factories for the production of organic acids, industrial enzymes, pharmaceuticals, and other fermented products due to their safety, substrate convenience, and well-established post-translational modifications. Many recent studies have verified that CCR-related genetic alterations can boost the yield of various carbohydrate-active enzymes (CAZymes), even under CCR conditions. Based on these findings, we emphasize that appropriate regulation of the CCR pathway, especially the expression of the key transcription factor CreA gene, has great potential for further expanding the application of Aspergillus cell factories to develop strains for industrial CAZymes production. Further, the genetically modified CCR strains (chassis hosts) can also be used for the production of other useful natural products and recombinant proteins, among others. We here review the regulatory mechanisms of CCR in Aspergillus and its direct application in enzyme production, as well as its potential application in organic acid and pharmaceutical production to illustrate the effects of CCR on Aspergillus cell factories.

Identification of a Novel Lactose-Specific PTS Operon in Bacillus licheniformis and Development of Derivative Artificial Operon Modules

Bacillus licheniformis plays a crucial role as a microbial host in the food industry and shows promising potential as a probiotic for human intestinal regulation. It exhibits a remarkable ability to utilize lactose as its sole carbon source. Despite its significance, the lactose-related metabolic pathway in this strain remains unclear. In this study, we identified a novel lactose-specific operon (lacDCAB) in B. licheniformis, consisting of the lacD gene that encodes a unique 6-phospho-β-galactosidase belonging to the GH4 family, and the lacCAB genes encoding a lactose-specific PTS1 system. Notably, we constructed and assessed an array library of transport and catabolic modules specifically for lactose utilization. Among these modules, PDS-lacD-P2-pts1 demonstrated the highest specific lactose consumption rate of 0.64 g/(L·h·OD), which was 8 times higher than that of the control strain. Furthermore, we developed a dual carbon source transport model based on the PDS-lacD-P2-pts1 assembly module, which highlighted efficient coutilization of glucose/sucrose, lactose/sucrose, lactose/galactose, and lactose/2,3-butanediol. This study provides insight into the lactose-specific metabolic pathway of B. licheniformis and presents a promising strategy for enhancing lactose utilization efficiency and mixed carbon source coutilization.

De novo biosynthesis of butyl butyrate in engineered Clostridium tyrobutyricum

Butyl butyrate has broad applications in foods, cosmetics, solvents, and biofuels. Microbial synthesis of bio-based butyl butyrate has been regarded as a promising approach recently. Herein, we engineered Clostridium tyrobutyricum ATCC 25755 to achieve de novo biosynthesis of butyl butyrate from fermentable sugars. Through introducing the butanol synthetic pathway (enzyme AdhE2), screening alcohol acyltransferases (AATs), adjusting transcription of VAAT and adhE2 (i.e., optimizing promoter), and efficient supplying butyryl-CoA, an excellent engineered strain, named MUV3, was obtained with ability to produce 4.58 g/L butyl butyrate at 25 °C with glucose in serum bottles. More NADH is needed for butyl butyrate synthesis, thus mannitol (the more reduced substrate) was employed to produce butyl butyrate. Ultimately, 62.59 g/L butyl butyrate with a selectivity of 95.97%, and a yield of 0.21 mol/mol was obtained under mannitol with fed-batch fermentation in a 5 L bioreactor, which is the highest butyl butyrate titer reported so far. Altogether, this study presents an anaerobic fermentative platform for de novo biosynthesis of butyl butyrate in one step, which lays the foundation for butyl butyrate biosynthesis from renewable biomass feedstocks.

Elimination of carbon catabolite repression through gene-modifying a solventogenic Clostridium sp. strain WK to enhance butanol production from the galactose-rich red seaweed

With the determination of the Leloir pathway in a solventogenic wild-type strain WK through the transcriptional analysis, two pivotal genes (galK and galT) were systematically co-expressed to demonstrate a significantly enhanced galactose utilization for butanol production with the elimination of carbon catabolite repression (CCR). The gene-modified strain WK-Gal-4 could effectively co-utilize galactose and glucose by directly using an ultrasonication-assisted butyric acid-pretreated Gelidium amansii hydrolysate (BAU) as the substrate, exhibiting the optimal sugar consumption and butanol production from BAU of 20.31 g/L and 7.8 g/L with an increment by 62.35 % and 61.49 % over that by strain WK, respectively. This work for the first time develops a feasible approach to utilizing red algal biomass for butanol fermentation through exploring the metabolic regulation of carbohydrate catabolism, also offering a novel route to develop the future biorefinery using the cost-effective and sustainable marine feedstocks.

Deciphering of the Mannitol Metabolism Pathway in Clostridium tyrobutyricum ATCC 25755 by Comparative Transcriptome Analysis

Clostridium tyrobutyricum has great potential for bio-based chemicals and biofuel production from mannitol; however, the mannitol metabolic pathway and its metabolic regulatory mechanism have not been elucidated. To this end, the RNA-seq analysis on the mid-log growth phase of C. tyrobutyricum grown on mannitol or xylose was performed. Comparative transcriptome analysis and co-transcription experiment indicated that mtlARFD, which encodes the mannitol-specific IIA component, transcription activator, mannitol-specific IIBC components, and mannitol-1-phosphate 5-dehydrogenase, respectively, formed a polycistronic operon and could be responsible for mannitol uptake and metabolism. In addition, comparative genomic analysis of the mtlARFD organization and the MtlR protein structural domain among various Firmicutes strains identified the putative cre (catabolite-responsive element) sites and conserved phosphorylation sites, but whether the expression of mannitol operon was affected by CcpA- and MtlR-mediated metabolic regulation during mixed substrate fermentation needs to be further verified experimentally. Based on the gene knockout and complementation results, the predicted mannitol operon mtlARFD was confirmed to be responsible for mannitol utilization in C. tyrobutyricum. The results of this study could be used to enhance the mannitol metabolic pathway and explore the potential metabolic regulation mechanism of mannitol during mixed substrate fermentation.

Engineering of global transcription factors in Bacillus, a genetic tool for increasing product yields: a bioprocess overview

Transcriptional factors are well studied in bacteria for their global interactions and the effects they produce at the phenotypic level. Particularly, Bacillus subtilis has been widely employed as a model Gram-positive microorganism used to characterize these network interactions. Bacillus species are currently used as efficient commercial microbial platforms to produce diverse metabolites such as extracellular enzymes, antibiotics, surfactants, industrial chemicals, heterologous proteins, among others. However, the pleiotropic effects caused by the genetic modification of specific genes that codify for global regulators (transcription factors) have not been implicated commonly from a bioprocess point of view. Recently, these strategies have attracted the attention in Bacillus species because they can have an application to increase production efficiency of certain commercial interest metabolites. In this review, we update the recent advances that involve this trend in the use of genetic engineering (mutations, deletion, or overexpression) performed to global regulators such as Spo0A, CcpA, CodY and AbrB, which can provide an advantage for the development or improvement of bioprocesses that involve Bacillus species as production platforms. Genetic networks, regulation pathways and their relationship to the development of growth stages are also discussed to correlate the interactions that occur between these regulators, which are important to consider for application in the improvement of commercial-interest metabolites. Reported yields from these products currently produced mostly under laboratory conditions and, in a lesser extent at bioreactor level, are also discussed to give valuable perspectives about their potential use and developmental level directed to process optimization at large-scale.

Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks

The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.

A consolidated review of commercial-scale high-value products from lignocellulosic biomass

For decades, lignocellulosic biomass has been introduced to the public as the most important raw material for the environmentally and economically sustainable production of high-valued bioproducts by microorganisms. However, due to the strong recalcitrant structure, the lignocellulosic materials have major limitations to obtain fermentable sugars for transformation into value-added products, e.g., bioethanol, biobutanol, biohydrogen, etc. In this review, we analyzed the recent trends in bioenergy production from pretreated lignocellulose, with special attention to the new strategies for overcoming pretreatment barriers. In addition, persistent challenges in developing for low-cost advanced processing technologies are also pointed out, illustrating new approaches to addressing the global energy crisis and climate change caused by the use of fossil fuels. The insights given in this study will enable a better understanding of current processes and facilitate further development on lignocellulosic bioenergy production.