Evolutionary engineering of industrial microorganisms-strategies and applications

CRISPR-Cas9 Cytidine-Base-Editor Mediated Continuous In Vivo Evolution in Aspergillus nidulans

Filamentous fungi are important cell factories for producing chemicals, organic acids, and enzymes. Although several genome editing tools are available for filamentous fungi, few effectively enable continuous evolution for rational engineering of complex phenotype. Here, we present CRISPR-Cas9 cytidine-base-editor (CBE) assisted in vivo evolution by continuously delivering a combinatorial sgRNA library to filamentous fungi. The method was validated by targeting core genes of 46 natural product biosynthetic gene clusters in Aspergillus nidulans NRRL 8112 to eliminate fungal toxins via six rounds of evolution. NGS analysis revealed the average C-to-T conversion rates in the first, third, and sixth rounds were 2.02%, 5.25%, and 9.34%, respectively. Metabolic profiles of the evolved mutants exhibited significant changes, allowing for the isolation of clean-background strains with enhanced production of an antifungal compound Echinocandin B. This study demonstrates that CBE-mediated in vivo evolution greatly facilitates the iterative refinement of complex morphogenetic traits in filamentous fungi.

Synthetic evolution of Saccharomyces cerevisiae for biomanufacturing: Approaches and applications

The yeast Saccharomyces cerevisiae is a well-studied unicellular eukaryote with a significant role in the biomanufacturing of natural products, biofuels, and bulk and value-added chemicals, as well as the principal model eukaryotic organism utilized for fundamental research. Robust tools for building and optimizing yeast chassis cells were made possible by the quick development of synthetic biology, especially in engineering evolution. In this review, we focused on methods and tools from synthetic biology that are used to design and engineer S. cerevisiae's evolution. A detailed discussion was held regarding transcriptional regulation, template-dependent and template-free approaches. Furthermore, the applications of evolved S. cerevisiae were comprehensively summarized. These included improving environmental stress tolerance and raising cell metabolic performance in the production of biofuels and bulk and value-added chemicals. Finally, the future considerations were briefly discussed.

Insights into the regulatory mechanisms and application prospects of the transcription factor Cra

Cra (catabolite repressor/activator) is a global transcription factor (TF) that plays a pleiotropic role in controlling the transcription of several genes involved in carbon utilization and energy metabolism. Multiple studies have investigated the regulatory mechanism of Cra and its rational use for metabolic regulation, but due to the complexity of its regulation, there remain challenges in the efficient use of Cra. Here, the structure, mechanism of action, and regulatory function of Cra in carbon and nitrogen flow are reviewed. In addition, this paper highlights the application of Cra in metabolic engineering, including the promotion of metabolite biosynthesis, the regulation of stress tolerance and virulence, the use of a Cra-based biosensor, and its coupling with other transcription factors. Finally, the prospects of Cra-related regulatory strategies are discussed. This review provides guidance for the rational design and construction of Cra-based metabolic regulation systems.

Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms

Metabolic burden is defined by the influence of genetic manipulation and environmental perturbations on the distribution of cellular resources. The rewiring of microbial metabolism for bio-based chemical production often leads to a metabolic burden, followed by adverse physiological effects, such as impaired cell growth and low product yields. Alleviating the burden imposed by undesirable metabolic changes has become an increasingly attractive approach for constructing robust microbial cell factories. In this review, we provide a brief overview of metabolic burden engineering, focusing specifically on recent developments and strategies for diminishing the burden while improving robustness and yield. A variety of examples are presented to showcase the promise of metabolic burden engineering in facilitating the design and construction of robust microbial cell factories. Finally, challenges and limitations encountered in metabolic burden engineering are discussed.

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.

Adaptive laboratory evolution of Naematelia aurantialba under high temperature for efficient production of exopolysaccharide

Liquid fermentation could revolutionize mushroom polysaccharide production, but the low temperature constraint hampers the process. This study implemented adaptive laboratory evolution (ALE) to enhance the thermotolerance of Naematelia aurantialba strains and increase expolysaccharide production. After 75 ALE cycles at 30 °C, the adaptive strain surpassed the wild-type strain by 5 °C. In a 7.5 L fermentor at 30 °C, the ALE strain yielded 17 % more exopolysaccharide than the wild type strain at 25 °C. Although the exopolysaccharide synthesized by both strains shares a consistent monosaccharide composition, infrared spectrum, and glycosidic bond composition, the ALE strain's exopolysaccharide has a larger molecular weight. Furthermore, the ALE strain's exopolysaccharide exhibits superior cryoprotection performance compared to that produced by the original strain. The adapted strain demonstrated lower ROS levels and increased activity of antioxidant enzymes, indicating improved performance. Fatty acid profiling and transcriptomics revealed reconfiguration of carbohydrate metabolism, amino acid metabolism, and membrane lipid synthesis in thermophilic strains, maintaining cellular homeostasis and productivity. This study provides efficient strains and fermentation methods for high-temperature mushroom polysaccharide production, reducing energy consumption and costs.

Challenges and Advances in the Bioproduction of L-Cysteine

L-cysteine is a proteogenic amino acid with many applications in the pharmaceutical, food, animal feed, and cosmetic industries. Due to safety and environmental issues in extracting L-cysteine from animal hair and feathers, the fermentative production of L-cysteine offers an attractive alternative using renewable feedstocks. Strategies to improve microbial production hosts like Pantoea ananatis, Corynebacterium glutamicum, Pseudomonas sp., and Escherichia coli are summarized. Concerning the metabolic engineering strategies, the overexpression of feedback inhibition-insensitive L-serine O-acetyltransferase and weakening the degradation of L-cysteine through the removal of L-cysteine desulfhydrases are crucial adjustments. The overexpression of L-cysteine exporters is vital to overcome the toxicity caused by intracellular accumulating L-cysteine. In addition, we compiled the process engineering aspects for the bioproduction of L-cysteine. Utilizing the energy-efficient sulfur assimilation pathway via thiosulfate, fermenting cheap carbon sources, designing scalable, fed-batch processes with individual feedings of carbon and sulfur sources, and implementing efficient purification techniques are essential for the fermentative production of L-cysteine on an industrial scale.

Advances in the Discovery and Engineering of Gene Targets for Carotenoid Biosynthesis in Recombinant Strains

Carotenoids are naturally occurring pigments that are abundant in the natural world. Due to their excellent antioxidant attributes, carotenoids are widely utilized in various industries, including the food, pharmaceutical, cosmetic industries, and others. Plants, algae, and microorganisms are presently the main sources for acquiring natural carotenoids. However, due to the swift progress in metabolic engineering and synthetic biology, along with the continuous and thorough investigation of carotenoid biosynthetic pathways, recombinant strains have emerged as promising candidates to produce carotenoids. The identification and manipulation of gene targets that influence the accumulation of the desired products is a crucial challenge in the construction and metabolic regulation of recombinant strains. In this review, we provide an overview of the carotenoid biosynthetic pathway, followed by a summary of the methodologies employed in the discovery of gene targets associated with carotenoid production. Furthermore, we focus on discussing the gene targets that have shown potential to enhance carotenoid production. To facilitate future research, we categorize these gene targets based on their capacity to attain elevated levels of carotenoid production.

Microbial production of vitamin B5: current status and prospects

Vitamin B5, also called D-pantothenic acid (D-PA), is a necessary micronutrient that plays an essential role in maintaining the physiological function of an organism. It is widely used in: food, medicine, feed, cosmetics, and other fields. Currently, the production of D-PA in industry heavily relies on chemical processes and enzymatic catalysis. With an increasing demand on the market, replacing chemical-based production of D-PA with microbial fermentation utilizing renewable resources is necessary. In this review, the physiological role and applications of D-PA were firstly introduced, after which the biosynthesis pathways and enzymes will be summarized. Subsequently, a series of cell factory development strategies for excessive D-PA production are analyzed and discussed. Finally, the prospect of microbial production of D-PA production has been prospected.

Microbial production of L-methionine and its precursors using systems metabolic engineering

L-methionine is an essential amino acid with versatile applications in food, feed, cosmetics and pharmaceuticals. At present, the production of L-methionine mainly relies on chemical synthesis, which conflicts with the concern over serious environmental problems and sustainable development goals. In recent years, microbial production of natural products has been amply rewarded with the emergence and rapid development of system metabolic engineering. However, efficient L-methionine production by microbial fermentation remains a great challenge due to its complicated biosynthetic pathway and strict regulatory mechanism. Additionally, the engineered production of L-methionine precursors, L-homoserine, O-succinyl-L-homoserine (OSH) and O-acetyl-L-homoserine (OAH), has also received widespread attention because they can be catalyzed to L-methionine via a high-efficiently enzymatic reaction in vitro, which is also a promising alternative to chemical route. This review provides a comprehensive overview on the recent advances in the microbial production of L-methionine and its precursors, highlighting the challenges and potential solutions for developing L-methionine microbial cell factories from the perspective of systems metabolic engineering, aiming to offer guidance for future engineering.

Genetically Encoded Biosensor Engineering for Application in Directed Evolution

Although rational genetic engineering is nowadays the favored method for microbial strain improvement, building up mutant libraries based on directed evolution for improvement is still in many cases the better option. In this regard, the demand for precise and efficient screening methods for mutants with high performance has stimulated the development of biosensor-based high-throughput screening strategies. Genetically encoded biosensors provide powerful tools to couple the desired phenotype to a detectable signal, such as fluorescence and growth rate. Herein, we review recent advances in engineering several classes of biosensors and their applications in directed evolution. Furthermore, we compare and discuss the screening advantages and limitations of two-component biosensors, transcription-factor-based biosensors, and RNA-based biosensors. Engineering these biosensors has focused mainly on modifying the expression level or structure of the biosensor components to optimize the dynamic range, specificity, and detection range. Finally, the applications of biosensors in the evolution of proteins, metabolic pathways, and genome-scale metabolic networks are described. This review provides potential guidance in the design of biosensors and their applications in improving the bioproduction of microbial cell factories through directed evolution.

Genomic Plasticity of Acid-Tolerant Phenotypic Evolution in Acetobacter pasteurianus

Acetic acid bacteria have a remarkable capacity to cope with elevated concentrations of cytotoxic acetic acid in their fermentation environment. In particular, the high-level acetate tolerance of Acetobacter pasteurianus that occurs in vinegar industrial settings must be constantly selected for. However, the improved acetic acid tolerance is rapidly lost without a selection pressure. To understand genetic and molecular biology of this acquired acetic acid tolerance in A. pasteurianus, we evolved three strains A. pasteurianus CICIM B7003, CICIM B7003-02, and ATCC 33,445 over 960 generations (4 months) in two initial acetic acids of 20 g·L-1 and 30 g·L-1, respectively. An acetic acid-adapted strain M20 with significantly improved specific growth rate of 0.159 h-1 and acid productivity of 1.61 g·L-1·h-1 was obtained. Comparative genome analysis of six evolved strains revealed that the genetic variations of adaptation were mainly focused on lactate metabolism, membrane proteins, transcriptional regulators, transposases, replication, and repair system. Among of these, lactate dehydrogenase, acetolactate synthase, glycosyltransferase, ABC transporter ATP-binding protein, two-component regulatory systems, the type II toxin-antitoxin system (RelE/RelB/StbE), exodeoxyribonuclease III, type I restriction endonuclease, tRNA-uridine 2-sulfurtransferase, and transposase might collaboratively contribute to the improved acetic acid tolerance in A. pasteurianus strains. The balance between repair factors and transposition variations might be the basis for genomic plasticity of A. pasteurianus strains, allowing the survival of populations and their offspring in acetic acid stress fluctuations. These observations provide important insights into the nature of acquired acetic acid tolerance phenotype and lay a foundation for future genetic manipulation of these strains.

DRAGON: Harnessing the power of DNA repair for accelerating genome evolution in Corynebacterium glutamicum

Hypermutation is a robust phenotype characterized by high elevation of spontaneous mutation rates, which has been shown to facilitate rapid adaptation to the stressful environments by hitchhiking with favorable mutations. Accumulating evidence argues that deficient DNA repair can give rise to hypermutation events in bacteria. Here, we provided a comprehensive survey of DNA repair systems to identify promising targets ensuring high DNA fidelity in Corynebacterium glutamicum. Four effective DNA repair factors, including nucS, tag, xpb, and dinP, were found to be strongly associated with the occurrence of hypermutable phenotypes, and these targets were then engineered to establish a CRISPRi-based all-in-one plasmid system for genome mutagenesis. On the basis of these findings, we presented a novel evolutionary engineering method named "DNA repair-assisted genome evolution (DRAGON)". As a proof-of-concept, DRAGON strategy was successfully applied to facilitate rapid acquisition of microbial robustness in C. glutamicum, such as increased tolerances towards kanamycin, acidic pH and high L-serine, showing its promise and potential for rapid strain improvement. Overall, our study will offer new insights into the understanding of DNA repair and evolutionary adaptation in C. glutamicum.

Microbial tolerance engineering for boosting lactic acid production from lignocellulose

Lignocellulosic biomass is an attractive non-food feedstock for lactic acid production via microbial conversion due to its abundance and low-price, which can alleviate the conflict with food supplies. However, a variety of inhibitors derived from the biomass pretreatment processes repress microbial growth, decrease feedstock conversion efficiency and increase lactic acid production costs. Microbial tolerance engineering strategies accelerate the conversion of carbohydrates by improving microbial tolerance to toxic inhibitors using pretreated lignocellulose hydrolysate as a feedstock. This review presents the recent significant progress in microbial tolerance engineering to develop robust microbial cell factories with inhibitor tolerance and their application for cellulosic lactic acid production. Moreover, microbial tolerance engineering crosslinking other efficient breeding tools and novel approaches are also deeply discussed, aiming to providing a practical guide for economically viable production of cellulosic lactic acid.

Improving Rhamnolipids Biosynthesis in Pseudomonas sp. L01 through Atmospheric and Room-Temperature Plasma (ARTP) Mutagenesis

Biosurfactants have significant applications in various industries, including microbial-enhanced oil recovery (MEOR). While the state-of-the-art genetic approaches can generate high-yield strains for biosurfactant production in fermenters, there remains a critical challenge in enhancing biosurfactant-producing strains for use in natural environments with minimal ecological risks. The objectives of this work are enhancing the strain's capacity for rhamnolipids production and exploring the genetic mechanisms for its improvement. In this study, we employed atmospheric and room-temperature plasma (ARTP) mutagenesis to enhance the biosynthesis of rhamnolipids in Pseudomonas sp. L01, a biosurfactant-producing strain isolated from petroleum-contaminated soil. Following ARTP treatment, we identified 13 high-yield mutants, with the highest yield of 3.45 ± 0.09 g/L, representing a 2.7-fold increase compared to the parent strain. To determine the genetic mechanisms behind the enhanced rhamnolipids biosynthesis, we sequenced the genomes of the strain L01 and five high-yield mutants. A comparative genomic analysis suggested that mutations in genes related to the synthesis of lipopolysaccharides (LPS) and the transport of rhamnolipids may contribute to the improved biosynthesis. To the best of our knowledge, this is the first instance of utilizing the ARTP approach to improve rhamnolipid production in Pseudomonas strains. Our study provides valuable insights into the enhancement of biosurfactant-producing strains and the regulatory mechanisms of rhamnolipids biosynthesis.

Application of Adaptive Laboratory Evolution in Lipid and Terpenoid Production in Yeast and Microalgae

Due to the complexity of metabolic and regulatory networks in microorganisms, it is difficult to obtain robust phenotypes through artificial rational design and genetic perturbation. Adaptive laboratory evolution (ALE) engineering plays an important role in the construction of stable microbial cell factories by simulating the natural evolution process and rapidly obtaining strains with stable traits through screening. This review summarizes the application of ALE technology in microbial breeding, describes the commonly used methods for ALE, and highlights the important applications of ALE technology in the production of lipids and terpenoids in yeast and microalgae. Overall, ALE technology provides a powerful tool for the construction of microbial cell factories, and it has been widely used in improving the level of target product synthesis, expanding the range of substrate utilization, and enhancing the tolerance of chassis cells. In addition, in order to improve the production of target compounds, ALE also employs environmental or nutritional stress strategies corresponding to the characteristics of different terpenoids, lipids, and strains.

Enhanced antimicrobial activity of lactic acid bacteria through genome shuffling and genetic variability among shuffled strains

In this investigation, lactic acid bacteria (LAB) isolated from milk were tested for their antibacterial properties and improved the antimicrobial activity of these isolates using genome shuffling. A total of sixty-one isolates were found in eleven samples, which were then tested using the agar diffusion method for their antibacterial activity against Staphylococcus aureus, Escherichia coli, Salmonella typhimurium, and Pseudomonas aeruginosa. Thirty-one strains exhibited antibacterial activity against at least one of the tested pathogens, with an inhibitory zone's diameter varying between 15.0 and 24.0 mm. Two isolates that showed the highest antimicrobial activity were identified as Lactobacillus plantarum CIP 103151 and Lactobacillus plantarum JCM 1149 according to 16S rRNA analysis. In the present study, applying genome shuffling approach significantly enhanced the antibacterial activity of L. plantarum. The initial populations were obtained via ultraviolet irradiation and were treated using the protoplast fusion method. The ideal condition for the production of protoplasts was 15 mg/ml of lysozyme and 10 μg/ml of mutanolysin. After two rounds of fusion, ten recombinants exhibited a significant increase in the inhibition zones versus S. aureus, S. typhimurium, P. aeruginosa, and E. coli, reaching up to 1.34, 1.31, 1.37, and 1.37-fold increase in inhibitory zone respectively. Random Amplified Polymorphic DNA results showed clear differences in DNA banding patterns among the wild strain of L. plantarum CIP 103151 and the three selected shuffled strains using primers 1283 & OPA09. On the other hand, no change was obtained using primers OPD03 neither among the wild strain and the three recombinant strains nor among the three shuffled strains.

Genome Shuffling Mutant of Streptomyces diastatochromogenes for Substantial Improvement of Toyocamycin Production

Toyocamycin, a nucleoside antibiotic, is a fungicide with the potential to control plant pathogens. In this study, three rounds of genome shuffling screening were applied to enhance the toyocamycin production in Streptomyces diastatochromogenes 1628. After three rounds of genome-shuffling screening, the toyocamycin production increased by 10.8-fold that of wild-type, and 2.64-fold of its parental strain. By optimization of its nutrition condition in medium, the highest production of toyocamycin reached 1173.6 mg/L in TY-producing medium. In addition, the mechanism for the improvement of shuffled strains was investigated. Recombinants with increased toyocamycin production exhibited higher transcriptional level of the toy cluster and product resistance. Furthermore, the rise of ATP hydrolysis rate indicated that intracellular ATP exhibit a significant role in tuning the toy cluster by an ATP-binding pathway-specific regulator. In all, we obtained S. diastatochromogenes mutants with enhanced toyocamycin production, and provided a valuable clue for the activation of secondary metabolites.

Comparative transcriptome analysis reveals the contribution of membrane transporters to acid tolerance in Lactococcus lactis

Acid stress caused by the accumulation of acidic metabolites severely affects the fermentation performance of lactic acid bacteria. In this study, to overcome the impact of acid stress during growth, nine membrane transporters were introduced in Lactococcus lactis NZ9000 to study their effects on acid tolerance. The engineered strains that overexpressed the metal ATP-binding cassette (ABC) transporters zitP (metal ABC transporter permease) and zitQ (metal ABC transporter ATP-binding protein) exhibited 14.5 and 9.5-fold higher survival rates, respectively, at pH 4.0 for 4 h than the control strain. During acid stress, the two recombinant strains maintained relatively higher ATP concentrations, i.e., 7.7- and 11.7-fold higher, respectively, than the control strain at pH 4.0 for 3 h. Subsequently, transcriptome analysis revealed that genes associated with ABC transporters, metal ion transport, transcriptional regulation, and stress response exhibited differentially expressed. The transcriptional level of ecfA2 gene (energy-coupling factor transporter ATPase) was substantially higher in L. lactis (ZitQ) during acid stress, and the ecfA2 gene was overexpressed in L. lactis. This recombinant strain L. lactis (EcfA2) exhibited a 598.7-fold higher survival rate than the control strain at pH 4.0 for 4 h. This study showed that the membrane transporters ZitP and ZitQ could increase acid tolerance and provided a strategy for constructing robust strains that can be used in food industry.

Rational Metabolic Engineering Combined with Biosensor-Mediated Adaptive Laboratory Evolution for l-Cysteine Overproduction from Glycerol in Escherichia coli

l-Cysteine is an important sulfur-containing amino acid with numerous applications in the pharmaceutical and cosmetic industries. The microbial production of l-cysteine has received substantial attention, and the supply of the precursor l-serine is important in l-cysteine biosynthesis. In this study, to achieve l-cysteine overproduction, we first increased l-serine production by deleting genes involved in the pathway of l-serine degradation to glycine (serine hydroxymethyl transferase, SHMT, encoded by glyA genes) in strain 4W (with l-serine titer of 1.1 g/L), thus resulting in strain 4WG with l-serine titer of 2.01 g/L. Second, the serine-biosensor based on the transcriptional regulator NCgl0581 of C. glutamicum was constructed in E. coli, and the validity and sensitivity of the biosensor were demonstrated in E. coli. Then 4WG was further evolved through adaptive laboratory evolution (ALE) combined with serine-biosensor, thus yielding the strain 4WGX with 4.13 g/L l-serine production. Moreover, the whole genome of the evolved strain 4WGX was sequenced, and ten non-synonymous mutations were found in the genome of strain 4WGX compared with strain 4W. Finally, 4WGX was used as the starting strain, and deletion of the l-cysteine desulfhydrases (encoded by tnaA), overexpression of serine acetyltransferase (encoded by cysE) and the key enzyme of transport pathway (encoded by ydeD) were performed in strain 4WGX. The recombinant strain 4WGX-∆tnaA-cysE-ydeD can produce 313.4 mg/L of l-cysteine using glycerol as the carbon source. This work provides an efficient method for the biosynthesis of value-added commodity products associated with glycerol conversion.

Past, Present, and Future Perspectives on Whey as a Promising Feedstock for Bioethanol Production by Yeast

Concerns about fossil fuel depletion and the environmental effects of greenhouse gas emissions have led to widespread fermentation-based production of bioethanol from corn starch or sugarcane. However, competition for arable land with food production has led to the extensive investigation of lignocellulosic sources and waste products of the food industry as alternative sources of fermentable sugars. In particular, whey, a lactose-rich, inexpensive byproduct of dairy production, is available in stable, high quantities worldwide. This review summarizes strategies and specific factors essential for efficient lactose/whey fermentation to ethanol. In particular, we cover the most commonly used strains and approaches for developing high-performance strains that tolerate fermentation conditions. The relevant genes and regulatory systems controlling lactose utilization and sources of new genes are also discussed in detail. Moreover, this review covers the optimal conditions, various feedstocks that can be coupled with whey substrates, and enzyme supplements for increasing efficiency and yield. In addition to the historical advances in bioethanol production from whey, this review explores the future of yeast-based fermentation of lactose or whey products for beverage or fuel ethanol as a fertile research area for advanced, environmentally friendly uses of industrial waste products.

Fermentation strategies to improve propionic acid production with propionibacterium ssp.: a review

Propionic acid (PA) is a carboxylic acid applied in a variety of processes, such as food and feed preservative, and as a chemical intermediate in the production of polymers, pesticides and drugs. PA production is predominantly performed by petrochemical routes, but environmental issues are making it necessary to use sustainable processes based on renewable materials. PA production by fermentation with the Propionibacterium genus is a promising option in this scenario, due to the ability of this genus to consume a variety of renewable carbon sources with higher productivity than other native microorganisms. However, Propionibacterium fermentation processes present important challenges that must be faced to make this route competitive, such as: a high fermentation time, product inhibition and low PA final titer, which increase the cost of product recovery. This article summarizes the state of the art regarding strategies to improve PA production by fermentation with the Propionibacterium genus. Firstly, strategies associated with environmental fermentation conditions and nutrition requirements are discussed. Subsequently, advantages and disadvantages of various strategies proposed to improve process performance (high cell concentration by immobilization or recycle, co-culture fermentation, genome shuffling, evolutive and metabolic engineering, and in situ recovery) are evaluated.

The challenges and prospects of Escherichia coli as an organic acid production host under acid stress

OBJECTIVE

Organic acids have a wide range of applications and have attracted the attention of many industries, and their large-scale applications have led fermentation production to low-cost development. Among them, the microbial fermentation method, especially using Escherichia coli as the production host, has the advantages of fast growth and low energy consumption, and has gradually shown better advantages and prospects in organic acid fermentation production.

IMPORTANCE

However, when the opportunity comes, the acidified environment caused by the acid products accumulated during the fermentation process also challenges E. coli. The acid sensitivity of E. coli is a core problem that needs to be solved urgently. The addition of neutralizers in traditional operations led to the emergence of osmotic stress inadvertently, the addition of strong acid substances to recover products in the salt state not only increases production costs, but the discharged sewage is also harmful to the environment.

ELABORATION

This article summarizes the current status of the application of E. coli in the production of organic acids, and based on the impact of acid stress on the physiological state of cells and the impact of industrial production profits, put forward some new conjectures that can make up for the deficiencies in existing research and application.

IMPLICATION

At this point, the diversified transformation of E. coli has become a chassis microbe that is more suitable for industrial fermentation, enhancing industrial application value.

KEY POINTS

• E. coli is a potential host for high value-added organic acids production. • Classify the damage mechanism and coping strategies of E. coli when stimulated by acid molecules. • Multi-dimensional expansion tools are needed to create acid-resistant E. coli chassis.

Rapid Enabling of Gluconobacter oxydans Resistance to High D-Sorbitol Concentration and High Temperature by Microdroplet-Aided Adaptive Evolution

Gluconobacter oxydans is important in the conversion of D-sorbitol into l-sorbose, which is an essential intermediate for industrial-scale production of vitamin C. In a previous study, the strain G. oxydans WSH-004 could directly produce 2-keto-l-gulonic acid (2-KLG). However, its D-sorbitol tolerance was poor compared with that of other common industrial G. oxydans strains, which grew well in the presence of more than 200 g/L of D-sorbitol. This study aimed to use the microbial microdroplet culture (MMC) system for the adaptive evolution of G. oxydans WSH-004 so as to improve its tolerance to high substrate concentration and high temperature. A series of adaptively evolved strains, G. oxydans MMC1-MMC10, were obtained within 90 days. The results showed that the best strain MMC10 grew in a 300 g/L of D-sorbitol medium at 40°C. The comparative genomic analysis revealed that genetic changes related to increased tolerance were mainly in protein translation genes. Compared with the traditional adaptive evolution method, the application of microdroplet-aided adaptive evolution could improve the efficiency in terms of reducing time and simplifying the procedure for strain evolution. This research indicated that the microdroplet-aided adaptive evolution was an effective tool for improving the phenotypes with undemonstrated genotypes in a short time.

The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes

Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".

Recent Advances in Lactic Acid Production by Lactic Acid Bacteria

Lactic acid can synthesize high value-added chemicals such as poly lactic acid. In order to further minimize the cost of lactic acid production, some effective strategies (e.g., effective mutagenesis and metabolic engineering) have been applied to increase productive capacity of lactic acid bacteria. In addition, low-cost cheap raw materials (e.g., cheap carbon source and cheap nitrogen source) are also used to reduce the cost of lactic acid production. In this review, we summarized the recent developments in lactic acid production, including efficient strain modification technology (high-efficiency mutagenesis means, adaptive laboratory evolution, and metabolic engineering), the use of low-cost cheap raw materials, and also discussed the future prospects of this field, which could promote the development of lactic acid industry.

Dynamic regulation of membrane integrity to enhance l-malate stress tolerance in Candida glabrata

Microbial cell factories provide a sustainable and economical way to produce chemicals from renewable feedstocks. However, the accumulation of targeted chemicals can reduce the robustness of the industrial strains and affect the production performance. Here, the physiological functions of Mediator tail subunit CgMed16 at l-malate stress were investigated. Deletion of CgMed16 decreased the survival, biomass, and half-maximal inhibitory concentration (IC₅₀ ) by 40.4%, 34.0%, and 30.6%, respectively, at 25 g/L l-malate stress. Transcriptome analysis showed that this growth defect was attributable to changes in the expression of genes involved in lipid metabolism. In addition, tolerance transcription factors CgUSV1 and CgYAP3 were found to interact with CgMed16 to regulate sterol biosynthesis and glycerophospholipid metabolism, respectively, ultimately endowing strains with excellent membrane integrity to resist l-malate stress. Furthermore, a dynamic tolerance system (DTS) was constructed based on CgUSV1, CgYAP3, and an l-malate-driven promoter P_cgr-10 to improve the robustness and productive capacity of Candida glabrata. As a result, the biomass, survival, and membrane integrity of C. glabrata 012 (with DTS) increased by 22.6%, 31.3%, and 53.8%, respectively, compared with those of strain 011 (without DTS). Therefore, at shake-flask scale, strain 012 accumulated 35.5 g/L l-malate, and the titer and productivity of l-malate increased by 32.5% and 32.1%, respectively, compared with those of strain 011. This study provides a novel strategy for the rational design and construction of DTS for dynamically enhancing the robustness of industrial strains.

Adaptive laboratory evolution principles and applications in industrial biotechnology

Adaptive laboratory evolution (ALE) is an innovative approach for the generation of evolved microbial strains with desired characteristics, by implementing the rules of natural selection as presented in the Darwinian Theory, on the laboratory bench. New as it might be, it has already been used by several researchers for the amelioration of a variety of characteristics of widely used microorganisms in biotechnology. ALE is used as a tool for the deeper understanding of the genetic and/or metabolic pathways of evolution. Another important field targeted by ALE is the manufacturing of products of (high) added value, such as ethanol, butanol and lipids. In the current review, we discuss the basic principles and techniques of ALE, and then we focus on studies where it has been applied to bacteria, fungi and microalgae, aiming to improve their performance to biotechnological procedures and/or inspect the genetic background of evolution. We conclude that ALE is a promising and efficacious method that has already led to the acquisition of useful new microbiological strains in biotechnology and could possibly offer even more interesting results in the future.

Identification of a novel metabolic engineering target for carotenoid production in Saccharomyces cerevisiae via ethanol-induced adaptive laboratory evolution

Carotenoids are a large family of health-beneficial compounds that have been widely used in the food and nutraceutical industries. There have been extensive studies to engineer Saccharomyces cerevisiae for the production of carotenoids, which already gained high level. However, it was difficult to discover new targets that were relevant to the accumulation of carotenoids. Herein, a new, ethanol-induced adaptive laboratory evolution was applied to boost carotenoid accumulation in a carotenoid producer BL03-D-4, subsequently, an evolved strain M3 was obtained with a 5.1-fold increase in carotenoid yield. Through whole-genome resequencing and reverse engineering, loss-of-function mutation of phosphofructokinase 1 (PFK1) was revealed as the major cause of increased carotenoid yield. Transcriptome analysis was conducted to reveal the potential mechanisms for improved yield, and strengthening of gluconeogenesis and downregulation of cell wall-related genes were observed in M3. This study provided a classic case where the appropriate selective pressure could be employed to improve carotenoid yield using adaptive evolution and elucidated the causal mutation of evolved strain.

Genome comparison of three lager yeasts reveals key genes affecting yeast flocculation during beer fermentation

Yeast flocculation plays an essential role in industrial application. Appropriate flocculation of yeast cells at the end of fermentation benefits the cell separation in production, which is an important characteristic of lager yeast for beer production. Due to the complex fermentation environment and diverse genetic background of yeast strains, it is difficult to explain the flocculation mechanism and find key genes that affect yeast flocculation during beer brewing. By analyzing the genomic mutation of two natural mutant yeasts with stronger flocculation ability compared to the parental strain, it was found that the mutated genes common in both mutants were enriched in protein processing in endoplasmic reticulum, membrane lipid metabolism and other pathways or biological processes involved in stress responses. Further functional verification of genes revealed that regulation of RIM101 and VPS36 played a role in lager yeast flocculation under the brewing condition. This work provided new clues for improving yeast flocculation in beer brewing.

Enhanced production of nonanedioic acid from nonanoic acid by engineered Escherichia coli

In this study, whole-cell biotransformation was conducted to produce nonanedioic acid from nonanoic acid by expressing the alkane hydroxylating system (AlkBGT) from Pseudomonas putida GPo1 in Escherichia coli. Following adaptive laboratory evolution, an efficient E. coli mutant strain, designated as MRE, was successfully obtained, demonstrating the fastest growth (27-fold higher) on nonanoic acid as the sole carbon source compared to the wild-type strain. Additionally, the MRE strain was engineered to block nonanoic acid degradation by deleting fadE. The resulting strain exhibited a 12.8-fold increase in nonanedioic acid production compared to the wild-type strain. Six mutations in acrR, P_crp , dppA, P_fadD , e14, and yeaR were identified in the mutant MRE strain, which was characterized using genomic modifications and RNA-sequencing. The acquired mutations were found to be beneficial for rapid growth and nonanedioic acid production.

Advanced strategies and tools to facilitate and streamline microbial adaptive laboratory evolution

Adaptive laboratory evolution (ALE) has served as a historic microbial engineering method that mimics natural selection to obtain desired microbes. The past decade has witnessed improvements in all aspects of ALE workflow, in terms of growth coupling, genotypic diversification, phenotypic selection, and genotype-phenotype mapping. The developing growth-coupling strategies facilitate ALE to a wider range of appealing traits. In vivo mutagenesis methods and multiplexed automated culture platforms open new gates to streamline its execution. Meanwhile, the application of multi-omics analyses and multiplexed genetic engineering promote efficient knowledge mining. This article provides a comprehensive and updated review of these advances, highlights newest significant applications, and discusses future improvements, aiming to provide a practical guide for implementation of novel, effective, and efficient ALE experiments.

Applications and research advance of genome shuffling for industrial microbial strains improvement

Genome shuffling, an efficient and practical strain improvement technology via recursive protoplasts fusion, can break through the limits of species even genus to accelerate the directed evolution of microbial strains, without requiring the comprehensively cognized genetic background and operable genetic system. Hence this technology has been widely used for many important strains to obtain the desirable industrial phenotypes. In this review, we introduce the procedure of genome shuffling, discuss the new aid strategies of genome shuffling, summarize the applications of genome shuffling for increasing metabolite yield, improving strain tolerance, enhancing substrate utilization, and put forward the outlook to the future development of this technology.

A CRISPR activation and interference toolkit for industrial Saccharomyces cerevisiae strain KE6-12

Recent advances in CRISPR/Cas9 based genome editing have considerably advanced genetic engineering of industrial yeast strains. In this study, we report the construction and characterization of a toolkit for CRISPR activation and interference (CRISPRa/i) for a polyploid industrial yeast strain. In the CRISPRa/i plasmids that are available in high and low copy variants, dCas9 is expressed alone, or as a fusion with an activation or repression domain; VP64, VPR or Mxi1. The sgRNA is introduced to the CRISPRa/i plasmids from a double stranded oligonucleotide by in vivo homology-directed repair, allowing rapid transcriptional modulation of new target genes without cloning. The CRISPRa/i toolkit was characterized by alteration of expression of fluorescent protein-encoding genes under two different promoters allowing expression alterations up to ~ 2.5-fold. Furthermore, we demonstrated the usability of the CRISPRa/i toolkit by improving the tolerance towards wheat straw hydrolysate of our industrial production strain. We anticipate that our CRISPRa/i toolkit can be widely used to assess novel targets for strain improvement and thus accelerate the design-build-test cycle for developing various industrial production strains.

Enhancement of Acid Protease Activity of Aspergillus oryzae Using Atmospheric and Room Temperature Plasma

Atmospheric and room temperature plasma (ARTP) system is a novel and efficient mutagenesis protocol for microbial breeding. In this study, ARTP was employed to treat spores of Aspergillus oryzae strain 3.042 for selection of high acid protease producers. With an irradiation time of 150 s at the lethal rate of 90%, 19 mutants with higher acid protease activity were initially selected based on different mutant colony morphology and ratio of the clarification halo of protease activity to the colony diameter. Measurements of the acid protease activity revealed that mutant strain B-2 is characterized by a steady hereditary stability with increased acid protease, neutral protease and total protease activities of 54.7, 17.3, and 8.5%, respectively, and decreased alkaline protease activity of 8.1%. In summary, the identified mutant strain B-2 exhibits great potential for the enhancement of the insufficient acid protease activity during the middle and later stages of soy sauce fermentation.

Time-course transcriptome analysis reveals the mechanisms of Burkholderia sp. adaptation to high phenol concentrations

Microbial tolerance to phenolic pollutants is the key to their efficient biodegradation. However, the metabolic mechanisms that allow some microorganisms to adapt to high phenol concentrations remain unclear. In this study, to reveal the underlying mechanisms of how Burkholderia sp. adapt to high phenol concentrations, the strain's tolerance ability and time-course transcriptome in combination with cell phenotype were evaluated. Surprisingly, Burkholderia sp. still grew normally after a long adaptation to a relatively high phenol concentration (1500 mg/L) and exhibited some time-dependent changes compared to unstressed cells prior to the phenol addition. Time-course transcriptome analysis results revealed that the mechanism of adaptations to phenol was an evolutionary process that transitioned from tolerance to positive degradation through precise gene regulation at appropriate times. Specifically, basal stress gene expression was upregulated and contributed to phenol tolerance, which involved stress, DNA repair, membrane, efflux pump and antioxidant protein-coding genes, while a phenol degradation gene cluster was specifically induced. Interestingly, both the catechol and protocatechuate branches of the β-ketoadipate pathway contributed to the early stage of phenol degradation, but only the catechol branch was used in the late stage. In addition, pathways involving flagella, chemotaxis, ATP-binding cassette transporters and two-component systems were positively associated with strain survival under phenolic stress. This study provides the first insights into the specific response of Burkholderia sp. to high phenol stress and shows potential for application in remediation of polluted environments. KEY POINTS: • Shock, DNA repair and antioxidant-related genes contributed to phenol tolerance. • β-Ketoadipate pathway branches differed at different stages of phenol degradation. • Adaptation mechanisms transitioned from negative tolerance to positive degradation.

Systemic understanding of Lactococcus lactis response to acid stress using transcriptomics approaches

During fermentation, acid stress caused by the accumulation of acidic metabolites seriously affects the metabolic activity and production capacity of microbial cells. To elucidate the acid stress-tolerance mechanisms of microbial cells, we performed genome mutagenesis combined with high-throughput technologies to screen acid stress-tolerant strains. Mutant strain Lactococcus lactis WH101 showed a 16,000-fold higher survival rate than that of the parent strain after 5 h of acid shock at pH 4.0 and maintained higher ATP, NH₄⁺, and intracellular pH (pH_i) levels during acid stress. Additionally, comparative transcriptomics analysis revealed enhanced regulation of carbohydrate metabolism and sugar transport to provide additional energy, amino acid metabolism and transport to maintain pH_i homeostasis and ATP generation, and fatty acid metabolism to enhance cellular acid tolerance. Moreover, overexpression of identified components resulted in 12.6- and 12.9-fold higher survival rates after acid shock for 3 h at pH 4.0 in L. lactis (ArcB) and L. lactis (MalQ) compared to the control strain, respectively. These findings provide valuable insight into the acid stress-response mechanisms of L. lactis and promote the further development of robust industrial strains.

Enhanced acid-stress tolerance in Lactococcus lactis NZ9000 by overexpression of ABC transporters

Background

Microbial cell factories are widely used in the production of acidic products such as organic acids and amino acids. However, the metabolic activity of microbial cells and their production efficiency are severely inhibited with the accumulation of intracellular acidic metabolites. Therefore, it remains a key issue to enhance the acid tolerance of microbial cells. In this study, we investigated the effects of four ATP-binding cassette (ABC) transporters on acid stress tolerance in Lactococcus lactis.

Results

Overexpressing the rbsA, rbsB, msmK, and dppA genes exhibited 5.8-, 12.2-, 213.7-, and 5.2-fold higher survival rates than the control strain, respectively, after acid shock for 3 h at pH 4.0. Subsequently, transcriptional profile alterations in recombinant strains were analyzed during acid stress. The differentially expressed genes associated with cold-shock proteins (csp), fatty acid biosynthesis (fabH), and coenzyme A biosynthesis (coaD) were up-regulated in the four recombinant strains during acid stress. Additionally, some genes were differentially expressed in specific recombinant strains. For example, in L. lactis (RbsB), genes involved in the pyrimidine biosynthetic pathway (pyrCBDEK) and glycine or betaine transport process (busAA and busAB) were up-regulated during acid stress, and the argG genes showed up-regulations in L. lactis (MsmK). Finally, we found that overexpression of the ABC transporters RbsB and MsmK increased intracellular ATP concentrations to protect cells against acidic damage in the initial stage of acid stress. Furthermore, L. lactis (MsmK) consistently maintained elevated ATP concentrations under acid stress.

Conclusions

This study elucidates the common and specific mechanisms underlying improved acid tolerance by manipulating ABC transporters and provides a further understanding of the role of ABC transporters in acid-stress tolerance.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1188-8) contains supplementary material, which is available to authorized users.

Improved acid-stress tolerance of Lactococcus lactis NZ9000 and Escherichia coli BL21 by overexpression of the anti-acid component recT

Acid accumulation caused by carbon metabolism severely affects the fermentation performance of microbial cells. Here, different sources of the recT gene involved in homologous recombination were functionally overexpressed in Lactococcus lactis NZ9000 and Escherichia coli BL21, and their acid-stress tolerances were investigated. Our results showed that L. lactis NZ9000 (ERecT and LRecT) strains showed 1.4- and 10.4-fold higher survival rates against lactic acid (pH 4.0), respectively, and that E. coli BL21 (ERecT) showed 16.7- and 9.4-fold higher survival rates than the control strain against lactic acid (pH 3.8) for 40 and 60 min, respectively. Additionally, we found that recT overexpression in L. lactis NZ9000 improved their growth under acid-stress conditions, as well as increased salt- and ethanol-stress tolerance and intracellular ATP concentrations in L. lactis NZ9000. These findings demonstrated the efficacy of recT overexpression for enhancing acid-stress tolerance and provided a promising strategy for insertion of anti-acid components in different hosts.