Modular Metabolic Engineering for Biobased Chemical Production

Modular pathway engineering for enhanced production of para-aminobenzoic acid and 4-amino-phenylalanine in Escherichia coli via glucose/xylose co-utilization

The modularization of biosynthetic pathways is a promising approach for enhancing microbial chemical production. We have developed a co-utilization method with glucose and xylose substrates to divide metabolic pathways into distinct production and energy modules to enhance the biosynthesis of para-aminobenzoic acid (pABA) in Escherichia coli. Optimizing initial glucose/xylose concentrations and eliminating carbon leakage resulted in a pABA titer of 8.22 g/L (yield: 0.23 g/g glucose). This strategy was then applied to the biosynthesis of 4APhe, a compound synthesized from chorismate without pyruvate (PYR) release. Utilizing glucose and xylose as co-substrates resulted in the production of 4.90 g/L 4APhe. Although 4APhe production did not benefit from PYR-driven energy generation as pABA production did, high titer was still achieved. This study highlights the effectiveness of modular metabolic pathway division for enhancing the production of key aromatic compounds and provides valuable insight into microbial production of chemicals that require specific biosynthetic donors such as amino groups.

IMPORTANCE

Microbial biosynthesis of chemicals from renewable resources offers a sustainable alternative to fossil fuel-based production. However, inefficiencies due to substrate diversion into by-products and biomass hinder optimal yields. In this study, we employed a modular metabolic engineering approach, decoupling pathways for chemical production from cell growth. Using glucose and xylose as co-substrates, we achieved the enhancement of p-aminobenzoic acid production in Escherichia coli. Additionally, we demonstrated the versatility of this approach by applying it to the biosynthesis of 4-amino-phenylalanine production. This study highlights the potential of modular metabolic pathway division for increased production of target compounds and provides valuable insight into microbial production of chemicals that require specific biosynthetic donors such as amino groups.

Promoter Engineering and Two-Phase Whole-Cell Catalysis Improve the Biosynthesis of Naringenin in E. coli

Naringenin and its analogues are important flavonoids with various health benefits such as anti-inflammatory, antibacterial, and anticancer activities. Biosynthesis of naringenin using microbial cell factories is often hampered by the pool of intracellular malonyl-CoA and its inherent toxicity to host cells. Here, we investigated promoter engineering and two-phase whole-cell catalysis for improving the production of naringenin. A total of 357 T7-derived promoters were obtained and utilized to fine-tune acetyl-CoA carboxylase expression for enhanced intracellular malonyl-CoA in Escherichia coli, resulting in increased bioproduction by 62.0% compared to the original strain. Furthermore, through two-phase whole-cell catalysis using selected isopropyl myristate, the naringenin titer increased to 3001.7 mg L-1. Additionally, naringenin and its analogue homoeriodictyol showed significant anticancer activity against ID8, MC38, HepG2, B16-F10, and MDA-MB-231 cancer cells. This study provides an efficient strategy for naringenin biosynthesis and implies the potential of naringenin analogues for further drug development.

Efficient Biosynthesis of Furanocoumarin Intermediate Marmesin by Engineered Escherichia coli

Marmesin, a plant dihydrofuranocoumarin, is an important intermediate in the synthesis of linear furanocoumarins and exhibits a variety of pharmacological activities. However, due to the lack of efficient prenyltransferases, the incompatibility of redox partners for P450 enzymes, and the insufficient supply of precursor (DMAPP), the microbial synthesis of marmesin remained at an extremely low level. Here, we report the efficient biosynthesis of marmesin in Escherichia coli by screening the robust 6-prenyltransferase PpPT1 and marmesin synthase PpDCΔ2-29 from Peucedanum praeruptorum. Next, the activities of PpPT1 and PpDCΔ2-29 were enhanced using fusion protein tags and redox partner engineering, respectively. In addition, the synthesis of marmesin was further improved by strengthening the methylerythritol phosphate (MEP) pathway to increase the availability of DMAPP and by optimizing the modular pathway in the engineered strain. Finally, the titer of marmesin reached 203.69 mg L-1 in the fed-batch fermentation with a molar conversion rate of umbelliferone of 81.4%, which is the highest titer for marmesin production using engineered microorganisms. The applied strategy and marmesin-producing strain constructed in this study lay the foundation for the green production of valuable complex furanocoumarins.

Engineering microbial metabolic homeostasis for chemicals production

Microbial-based bio-refining promotes the development of a biotechnology revolution to encounter and tackle the enormous challenges in petroleum-based chemical production by biomanufacturing, biocomputing, and biosensing. Nevertheless, microbial metabolic homeostasis is often incompatible with the efficient synthesis of bioproducts mainly due to: inefficient metabolic flow, robust central metabolism, sophisticated metabolic network, and inevitable environmental perturbation. Therefore, this review systematically summarizes how to optimize microbial metabolic homeostasis by strengthening metabolic flux for improving biotransformation turnover, redirecting metabolic direction for rewiring bypass pathway, and reprogramming metabolic network for boosting substrate utilization. Future directions are also proposed for providing constructive guidance on the development of industrial biotechnology.

Assembly of functional microbial ecosystems: from molecular circuits to communities

Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate, or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. First, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn procedure including function specification, chassis selection, interaction design, system build, performance test, modeling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems.

Achievements and perspectives of synthetic biology in botanical insecticides

Botanical insecticides are the origin of all insecticidal compounds. They have been widely used to control pests in crops for a long time. Currently, the commercial production of botanical insecticides extracted from plants is limited because of insufficient raw material supply. Synthetic biology is a promising and effective approach for addressing the current problems of the production of botanical insecticides. It is an emerging biological research hotspot in the field of botanical insecticides. However, the biosynthetic pathways of many botanical insecticides are not completely elucidated. On the other hand, the cytotoxicity of botanical pesticides and low efficiency of these biosynthetic enzymes in new hosts make it still challenging for their heterologous production. In the present review, we summarized the recent developments in the heterologous production of botanical insecticides, analyzed the current challenges, and discussed the feasible production strategies, focusing on elucidating biosynthetic pathways, enzyme engineering, host engineering, and cytotoxicity engineering. Looking to the future, synthetic biology promises to further advance heterologous production of more botanical pesticides.

Synthetic microbial communities: A gateway to understanding resistance, resilience, and functionality in spontaneously fermented food microbiomes

This review delves into the intricate traits of microbial communities encountered in spontaneously fermented foods (SFF), contributing to resistance, resilience, and functionality drivers. Traits of SFF microbiomes comprise of fluctuations in community composition, genetic stability, and condition-specific phenotypes. Synthetic microbial communities (SMCs) serve as a portal for mechanistic insights and strategic re-programming of microbial communities. Current literature underscores the pivotal role of microbiomes in SFF in shaping quality attributes and preserving the cultural heritage of their origin. In contrast to starter driven fermentations that tend to be more controlled but lacking the capacity to maintain or reproduce the complex flavors and intricacies found in SFF. SMCs, therefore, become indispensable tools, providing a nuanced understanding and control over fermented food microbiomes. They empower the prediction and engineering of microbial interactions and metabolic pathways with the aim of optimizing outcomes in food processing. Summarizing the current application of SMCs in fermented foods, there is still space for improvement. Challenges in achieving stability and reproducibility in SMCs are identified, stemming from non-standardized approaches. The future direction should involve embracing standardized protocols, advanced monitoring tools, and synthetic biology applications. A holistic, multi-disciplinary approach is paramount to unleashing the full potential of SMCs and fostering sustainable and innovative applications in fermented food systems.

Facilitating stable gene integration expression and copy number amplification in Bacillus subtilis through a reversible homologous recombination switch

Strengthening the expression level of integrated genes on the genome is crucial for consistently expressing key enzymes in microbial cell factories for efficient bioproduction in synthetic biology. In comparison to plasmid-based multi-copy expression, the utilization of chromosomal multi-copy genes offers increased stability of expression level, diminishes the metabolic burden on host cells, and enhances overall genetic stability. In this study, we developed the "BacAmp", a stabilized gene integration expression and copy number amplification system for high-level expression in Bacillus subtilis, which was achieved by employing a combination of repressor and non-natural amino acids (ncAA)-dependent expression system to create a reversible switch to control the key gene recA for homologous recombination. When the reversible switch is turned on, genome editing and gene amplification can be achieved. Subsequently, the reversible switch was turned off therefore stabilizing the gene copy number. The stabilized gene amplification system marked by green fluorescent protein, achieved a 3-fold increase in gene expression by gene amplification and maintained the average gene copy number at 10 after 110 generations. When we implemented the gene amplification system for the regulation of N-acetylneuraminic acid (NeuAc) synthesis, the copy number of the critical gene increased to an average of 7.7, which yielded a 1.3-fold NeuAc titer. Our research provides a new avenue for gene expression in synthetic biology and can be applied in metabolic engineering in B. subtilis.

Cell factories for biosynthesis of D-glucaric acid: a fusion of static and dynamic strategies

D-glucaric acid is an important organic acid with numerous applications in therapy, food, and materials, contributing significantly to its substantial market value. The biosynthesis of D-glucaric acid (GA) from renewable sources such as glucose has garnered significant attention due to its potential for sustainable and cost-effective production. This review summarizes the current understanding of the cell factories for GA production in different chassis strains, from static to dynamic control strategies for regulating their metabolic networks. We highlight recent advances in the optimization of D-glucaric acid biosynthesis, including metabolic dynamic control, alternative feedstocks, metabolic compartments, and so on. Additionally, we compare the differences between different chassis strains and discuss the challenges that each chassis strain must overcome to achieve highly efficient GA productions. In this review, the processes of engineering a desirable cell factory for highly efficient GA production are just like an epitome of metabolic engineering of strains for chemical biosynthesis, inferring general trends for industrial chassis strain developments.

Metabolic and enzymatic engineering approach for the production of 2-phenylethanol in engineered Escherichia coli

2-Phenylethanol, known for its rose-like odor and antibacterial activity, is synthesized via exogenous phenylpyruvate by the sequential reaction of phenylpyruvate decarboxylase (PDC) and aldehyde reductase. We first targeted ARO10, a phenylpyruvate decarboxylase gene from Saccharomyces cerevisiae, and identified a suitable aldehyde reductase gene. Co-expression of ARO10 and yahK in E. coli transformants yielded 1.1 g/L of 2-phenylethanol in batch culture. We hypothesized that there might be a bottleneck in PDC activity. The computer-based enzyme evolution was utilized to enhance production. The introduction of an amino acid substitution in ARO10 (ARO10 I544W) stabilized the aromatic ring of the phenylpyruvate substrate, increasing 2-phenylethanol yield 4.1-fold compared to wild-type ARO10. Cultivation of ARO10 I544W-expressing E. coli produced 2.5 g/L of 2-phenylethanol with a yield from glucose of 0.16 g/g after 72 h. This approach represents a significant advancement, achieving the highest yield of 2-phenylethanol from glucose using microbes to date.

Metabolic engineering for enhanced terpenoid production: Leveraging new horizons with an old technique

Terpenoids are a vast class of plant specialized metabolites (PSMs) manufactured by plants and are involved in their interactions with environment. In addition, they add health benefits to human nutrition and are widely used as pharmaceutically active compounds. However, native plants produce a limited amount of terpenes restricting metabolite yield of terpene-related metabolites. Exponential growth in the plant metabolome data and the requirement of alternative approaches for producing the desired amount of terpenoids, has redirected plant biotechnology research to plant metabolic engineering, which requires in-depth knowledge and precise expertise about dynamic plant metabolic pathways and cellular physiology. Metabolic engineering is an assuring tool for enhancing the concentration of terpenes by adopting specific strategies such as overexpression of the key genes associated with the biosynthesis of targeted metabolites, controlling the modulation of transcription factors, downregulation of competitive pathways (RNAi), co-expression of the biosynthetic pathway genes in heterologous system and other combinatorial approaches. Microorganisms, fast-growing host plants (such as Nicotiana benthamiana), and cell suspension/callus cultures have provided better means for producing valuable terpenoids. Manipulation in the biosynthetic pathways responsible for synthesis of terpenoids can provide opportunities to enhance the content of desired terpenoids and open up new avenues to enhance their production. This review deliberates the worth of metabolic engineering in medicinal plants to resolve issues associated with terpenoid production at a commercial scale. However, to bring the revolution through metabolic engineering, further implementation of genome editing, elucidation of metabolic pathways using omics approaches, system biology approaches, and synthetic biology tactics are essentially needed.

Programming Dynamic Division of Labor Using Horizontal Gene Transfer

The metabolic engineering of microbes has broad applications, including biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multistep pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is the division of labor (DOL) in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted interstrain population dynamics. Through modeling, we show that dynamic division of labor (DDOL), which we define as the DOL between indiscrete populations capable of dynamic and reversible interchange, can overcome these limitations and enable the robust maintenance of burdensome, multistep pathways. We propose that DDOL can be mediated by horizontal gene transfer (HGT) and use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.

Catalytic Mechanism and Heterologous Biosynthesis Application of Sesquiterpene Synthases

Sesquiterpenes comprise a diverse group of natural products with a wide range of applications in cosmetics, food, medicine, agriculture, and biofuels. Heterologous biosynthesis is increasingly employed for sesquiterpene production, aiming to overcome the limitations associated with chemical synthesis and natural extraction. Sesquiterpene synthases (STSs) play a crucial role in the heterologous biosynthesis of sesquiterpene. Under the catalysis of STSs, over 300 skeletons are produced through various cyclization processes (C1-C10 closure, C1-C11 closure, C1-C6 closure, and C1-C7 closure), which are responsible for the diversity of sesquiterpenes. According to the cyclization types, we gave an overview of advances in understanding the mechanism of STSs cyclization from the aspects of protein crystal structures and site-directed mutagenesis. We also summarized the applications of engineering STSs in the heterologous biosynthesis of sesquiterpene. Finally, the bottlenecks and potential research directions related to the STSs cyclization mechanism and application of modified STSs were presented.

Enabling pathway design by multiplex experimentation and machine learning

The remarkable metabolic diversity observed in nature has provided a foundation for sustainable production of a wide array of valuable molecules. However, transferring the biosynthetic pathway to the desired host often runs into inherent failures that arise from intermediate accumulation and reduced flux resulting from competing pathways within the host cell. Moreover, the conventional trial and error methods utilized in pathway optimization struggle to fully grasp the intricacies of installed pathways, leading to time-consuming and labor-intensive experiments, ultimately resulting in suboptimal yields. Considering these obstacles, there is a pressing need to explore the enzyme expression landscape and identify the optimal pathway configuration for enhanced production of molecules. This review delves into recent advancements in pathway engineering, with a focus on multiplex experimentation and machine learning techniques. These approaches play a pivotal role in overcoming the limitations of traditional methods, enabling exploration of a broader design space and increasing the likelihood of discovering optimal pathway configurations for enhanced production of molecules. We discuss several tools and strategies for pathway design, construction, and optimization for sustainable and cost-effective microbial production of molecules ranging from bulk to fine chemicals. We also highlight major successes in academia and industry through compelling case studies.

The expanded CRISPR toolbox for constructing microbial cell factories

Microbial cell factories (MCFs) convert low-cost carbon sources into valuable compounds. The CRISPR/Cas9 system has revolutionized MCF construction as a remarkable genome editing tool with unprecedented programmability. Recently, the CRISPR toolbox has been significantly expanded through the exploration of new CRISPR systems, the engineering of Cas effectors, and the incorporation of other effectors, enabling multi-level regulation and gene editing free of double-strand breaks. This expanded CRISPR toolbox powerfully promotes MCF construction by facilitating pathway construction, enzyme engineering, flux redistribution, and metabolic burden control. In this article, we summarize different CRISPR tool designs and their applications in MCF construction for gene editing, transcriptional regulation, and enzyme modulation. Finally, we also discuss future perspectives for the development and application of the CRISPR toolbox.

Establishment of synthetic microbial consortia with Corynebacterium glutamicum and Pseudomonas putida: Design, construction, and application to production of γ-glutamylisopropylamide and l-theanine

Microbial synthetic consortia are a promising alternative to classical monoculture for biotechnological applications and fermentative processes. Their versatile use offers advantages in the degradation of complex substrates, the allocation of the metabolic burden between individual partners, or the division of labour in energy utilisation, substrate supply or product formation. Here, stable synthetic consortia between the two industrially relevant production hosts, Pseudomonas putida KT2440 and Corynebacterium glutamicum ATCC13032, were established for the first time. By applying arginine auxotrophy/overproduction and/or formamidase-based utilisation of the rare nitrogen source formamide, different types of interaction were realised, such as commensal relationships (+/0 and 0/+) and mutualistic cross-feeding (+/+). These consortia did not only show stable growth but could also be used for fermentative production of the γ-glutamylated amines theanine and γ-glutamyl-isopropylamide (GIPA). The consortia produced up to 2.8 g L-1 of GIPA and up to 2.6 g L-1 of theanine, a taste-enhancing constituent of green tea leaves. Thus, the advantageous approach of using synthetic microbial consortia for fermentative production of value-added compounds was successfully demonstrated.

Recent advances and prospects of Bacillus amyloliquefaciens as microbial cell factories: from rational design to industrial applications

Bacillus amyloliquefaciens is one of the most characterized Gram-positive bacteria. This species has unique characteristics that are beneficial for industrial applications, including its utilization of: cheap carbon as a substrate, a transparent genetic background, and large-scale robustness in fermentation. Indeed, the productivity characteristics of B. amyloliquefaciens have been thoroughly analyzed and further optimized through systems biology and synthetic biology techniques. Following the analysis of multiple engineering design strategies, B. amyloliquefaciens is now considered an efficient cell factory capable of producing large quantities of multiple products from various raw materials. In this review, we discuss the significant potential advantages offered by B. amyloliquefaciens as a platform for metabolic engineering and industrial applications. In addition, we systematically summarize the recent laboratory research and industrial application of B. amyloliquefaciens, including: relevant advances in systems and synthetic biology, various strategies adopted to improve the cellular performances of synthetic chemicals, as well as the latest progress in the synthesis of certain important products by B. amyloliquefaciens. Finally, we propose the current challenges and essential strategies to usher in an era of broader B. amyloliquefaciens use as microbial cell factories.

Characterization and designing of an SAM riboswitch to establish a high-throughput screening platform for SAM overproduction in Saccharomyces cerevisiae

S-adenosyl- l-methionine (SAM) is a high-value compound widely used in the treatment of various diseases. SAM can be produced through fermentation, but further enhancing the microbial production of SAM requires novel high-throughput screening methods for rapid detection and screening of mutant libraries. In this work, an SAM-OFF riboswitch capable of responding to the SAM concentration was obtained and a high-throughput platform for screening SAM overproducers was established. SAM synthase was engineered by semirational design and directed evolution, which resulted in the SAM2S203F,W164R,T251S,Y285F,S365R mutant with almost twice higher catalytic activity than the parental enzyme. The best mutant was then introduced into Saccharomyces cerevisiae BY4741, and the resulting strain BSM8 produced a sevenfold higher SAM titer in shake-flask fermentation, reaching 1.25 g L-1 . This work provides a reference for designing biosensors to dynamically detect metabolite concentrations for high-throughput screening and the construction of effective microbial cell factories.

Photosynthetic Living Fiber Fabrication from Algal-Bacterial Consortia with Controlled Spatial Distribution

Living materials that combine living cells and synthetic matrix materials have become promising research fields in recent years. While multicellular systems present exclusive benefits in developing living materials over single-cell systems, creating artificial multicellular systems can be challenging due to the difficulty in controlling the multicellular assemblies and the complexity of cell-to-cell interactions. Here, we propose a coculture platform capable of isolating and controlling the spatial distribution of algal-bacterial consortia, which can be utilized to construct photosynthetic living fibers. Through coaxial extrusion-based 3D printing, hydrogel fibers containing bacteria or algae can be deposited into designated structures and further processed into materials with precise geometries. In addition, the photosynthetic living fibers demonstrate a significant synergistic catalytic effect resulting from the immobilization of both bacteria and algae, which effectively optimizes sewage treatment for bioremediation purposes. The integration of microbial consortia and 3D printing yields functional living materials with promising applications in biocatalysis, biosensing, and biomedicine. Our approach provides an optimized solution for constructing efficient multicellular systems and opens a new avenue for the development of advanced materials.

Construction of Coculture System Containing Escherichia coli with Different Microbial Species for Biochemical Production

Microbial synthesis of target chemicals usually involves multienzymatic reactions in vivo, especially for compounds with a long metabolic pathway. However, when various genes are introduced into one single strain, it leads to a heavy metabolic burden. In contrast, the microbial coculture system can allocate metabolic pathways into different hosts, which will relieve the metabolic burdens. Escherichia coli is the most used chassis to synthesize biofuels and chemicals owing to its well-known genetics, high transformation efficiency, and easy cultivation. Accordingly, cocultures containing the cooperative E. coli with other microbial species have received great attention. In this review, the individual applications and boundedness of different combinations will be summarized. Additionally, the strategies for the self-regulation of population composition, which can help enhance the stability of a coculture system, will also be discussed. Finally, perspectives for the cocultures will be proposed.

Leveraging interactions in microfluidic droplets for enhanced biotechnology screens

Microfluidic droplet screens serve as an innovative platform for high-throughput biotechnology, enabling significant advancements in discovery, product optimization, and analysis. This review sheds light on the emerging trends of interaction assays in microfluidic droplets, underscoring the unique suitability of droplets for these applications. Encompassing a diverse range of biological entities such as antibodies, enzymes, DNA, RNA, various microbial and mammalian cell types, drugs, and other molecules, these assays demonstrate their versatility and scope. Recent methodological breakthroughs have escalated these screens to novel scales of bioanalysis and biotechnological product design. Moreover, we highlight pioneering advancements that extend droplet-based screens into new domains: cargo delivery within human bodies, application of synthetic gene circuits in natural environments, 3D printing, and the development of droplet structures responsive to environmental signals. The potential of this field is profound and only set to increase.

Modular Metabolic Engineering and Synthetic Coculture Strategies for the Production of Aromatic Compounds in Yeast

Microbial-derived aromatics provide a sustainable and renewable alternative to petroleum-derived chemicals. In this study, we used the model yeast Saccharomyces cerevisiae to produce aromatic molecules by exploiting the concept of modularity in synthetic biology. Three different modular approaches were investigated for the production of the valuable fragrance raspberry ketone (RK), found in raspberry fruits and mostly produced from petrochemicals. The first strategy used was modular cloning, which enabled the generation of combinatorial libraries of promoters to optimize the expression level of the genes involved in the synthesis pathway of RK. The second strategy was modular pathway engineering and involved the creation of four modules, one for product formation: RK synthesis module (Mod. RK); and three for precursor synthesis: aromatic amino acid synthesis module (Mod. Aro), p-coumaric acid synthesis module (Mod. p-CA), and malonyl-CoA synthesis module (Mod. M-CoA). The production of RK by combinations of the expression of these modules was studied, and the best engineered strain produced 63.5 mg/L RK from glucose, which is the highest production described in yeast, and 2.1 mg RK/g glucose, which is the highest yield reported in any organism without p-coumaric acid supplementation. The third strategy was the use of modular cocultures to explore the effects of division of labor on RK production. Two two-member communities and one three-member community were created, and their production capacity was highly dependent on the structure of the synthetic community, the inoculation ratio, and the culture media. In certain conditions, the cocultures outperformed their monoculture controls for RK production, although this was not the norm. Interestingly, the cocultures showed up to 7.5-fold increase and 308.4 mg/L of 4-hydroxy benzalacetone, the direct precursor of RK, which can be used for the semi-synthesis of RK. This study illustrates the utility of modularity in synthetic biology tools and their applications to the synthesis of products of industrial interest.

Predicting partner fitness based on spatial structuring in a light-driven microbial community

Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology (e.g., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.

Spatial organization of pathway enzymes via self-assembly to improve 2'-fucosyllactose biosynthesis in engineered Escherichia coli

As one of the most abundant components in human milk oligosaccharides, 2'-fucosyllactose (2'-FL) possesses versatile beneficial health effects. Although most studies focused on overexpressing or fine-tuning the expression of pathway enzymes and achieved a striking increase of 2'-FL production, directly facilitating the metabolic flux toward the key intermediate GDP-l-fucose seems to be ignored. Here, multienzyme complexes consisting of sequential pathway enzymes were constructed by using specific peptide interaction motifs in recombinant Escherichia coli to achieve a higher titer of 2'-FL. Specifically, we first fine-tuned the expression level of pathway enzymes and balanced the metabolic flux toward 2'-FL synthesis. Then, two key enzymes (GDP-mannose 4,6-dehydratase and GDP- l-fucose synthase) were self-assembled into enzyme complexes in vivo via a short peptide interaction pair RIAD-RIDD (RI anchoring disruptor-RI dimer D/D domains), resulting in noticeable improvement of 2'-FL production. Next, to further strengthen the metabolic flux toward 2'-FL, three pathway enzymes were further aggregated into multienzyme assemblies by using another orthogonal protein interaction motif (Spycatcher-SpyTag or PDZ-PDZlig). Intracellular multienzyme assemblies remarkably enlarged the flux toward 2'-FL biosynthesis and showed a 2.1-fold increase of 2'-FL production compared with a strain expressing free-floating and unassembled enzymes. The optimally engineered strain EZJ23 accumulated 4.8 g/L 2'-FL in shake flask fermentation and was capable of producing 25.1 g/L 2'-FL by fed-batch cultivation. This work provides novel approaches for further improvement and large-scale production of 2'-FL and demonstrates the effectiveness of spatial assembly of pathway enzymes to improve the production of valuable products in the engineered host strain.

Synthetic mutualism in engineered E. coli mutant strains as functional basis for microbial production consortia

In nature, microorganisms often reside in symbiotic co-existence providing nutrition, stability, and protection for each partner by applying "division of labor." This principle may also be used for the overproduction of targeted compounds in bioprocesses. It requires the engineering of a synthetic co-culture with distributed tasks for each partner. Thereby, the competition on precursors, redox cofactors, and energy-which occurs in a single host-is prevented. Current applications often focus on unidirectional interactions, that is, the product of partner A is used for the completion of biosynthesis by partner B. Here, we present a synthetically engineered Escherichia coli co-culture of two engineered mutant strains marked by the essential interaction of the partners which is achieved by implemented auxotrophies. The tryptophan auxotrophic strain E. coli ANT-3, only requiring small amounts of the aromatic amino acid, provides the auxotrophic anthranilate for the tryptophan producer E. coli TRP-3. The latter produces a surplus of tryptophan which is used to showcase the suitability of the co-culture to access related products in future applications. Co-culture characterization revealed that the microbial consortium is remarkably functionally stable for a broad range of inoculation ratios. The range of robust and functional interaction may even be extended by proper glucose feeding which was shown in a two-compartment bioreactor setting with filtrate exchange. This system even enables the use of the co-culture in a parallel two-level temperature setting which opens the door to access temperature sensitive products via heterologous production in E. coli in a continuous manner.

Construction of microbial consortia for microbial degradation of complex compounds

Increasingly complex synthetic environmental pollutants are prompting further research into bioremediation, which is one of the most economical and safest means of environmental restoration. From the current research, using microbial consortia to degrade complex compounds is more advantageous compared to using isolated bacteria, as the former is more adaptable and stable within the growth environment and can provide a suitable catalytic environment for each enzyme required by the biodegradation pathway. With the development of synthetic biology and gene-editing tools, artificial microbial consortia systems can be designed to be more efficient, stable, and robust, and they can be used to produce high-value-added products with their strong degradation ability. Furthermore, microbial consortia systems are shown to be promising in the degradation of complex compounds. In this review, the strategies for constructing stable and robust microbial consortia are discussed. The current advances in the degradation of complex compounds by microbial consortia are also classified and detailed, including plastics, petroleum, antibiotics, azo dyes, and some pollutants present in sewage. Thus, this paper aims to support some helps to those who focus on the degradation of complex compounds by microbial consortia.

The bright frontiers of microbial metabolic optogenetics

In recent years, light-responsive systems from the field of optogenetics have been applied to several areas of metabolic engineering with remarkable success. By taking advantage of light's high tunability, reversibility, and orthogonality to host endogenous processes, optogenetic systems have enabled unprecedented dynamical controls of microbial fermentations for chemical production, metabolic flux analysis, and population compositions in co-cultures. In this article, we share our opinions on the current state of this new field of metabolic optogenetics.We make the case that it will continue to impact metabolic engineering in increasingly new directions, with the potential to challenge existing paradigms for metabolic pathway and strain optimization as well as bioreactor operation.

Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production

Microbial consortia have been considered potential platforms for bioprocessing applications. However, the complexity in process control owing to the use of multiple strains necessitates the use of an efficient population control strategy. Herein, we report circuit-guided synthetic acclimation as a strategy to improve biochemical production by a microbial consortium. We designed a consortium comprising alginate-utilizing Vibrio sp. dhg and 3-hydroxypropionic acid (3-HP)-producing Escherichia coli strains for the direct conversion of alginate to 3-HP. We introduced a genetic circuit, named "Population guider", in the E. coli strain, which degrades ampicillin only when 3-HP is produced. In the presence of ampicillin as a selection pressure, the consortium was successfully acclimated for increased 3-HP production by 4.3-fold compared to that by a simple co-culturing consortium during a 48-h fermentation. We believe this concept is a useful strategy for the development of robust consortium-based bioprocesses.

High-level de novo biosynthesis of cordycepin by systems metabolic engineering in Yarrowia lipolytica

Cordycepin is a nucleoside antibiotic with various biological activities, which has wide applications in the area of cosmetic and medicine industries. However, the current production of cordycepin is costly and time-consuming. To construct the promising cell factory for high-level cordycepin production, firstly, the design and construction of cordycepin biosynthetic pathway were performed in Yarrowia lipolytica. Secondly, the adaptivity between cordycepin biosynthetic pathway and Y. lipolytica was enhanced by enzyme fusion and integration site engineering. Then, the production of cordycepin was improved by the enhancement of adenosine supply. Furthermore, through modular engineering, the production of cordycepin was achieved at 3588.59 mg/L from glucose. Finally, 3249.58 mg/L cordycepin with a yield of 76.46 mg/g total sugar was produced by the engineered strain from the mixtures of glucose and molasses. This research is the first report on the de novo high-level production of cordycepin in the engineered Y. lipolytica.

Multivariate modular metabolic engineering for enhanced gibberellic acid biosynthesis in Fusarium fujikuroi

Gibberellic acid (GA3) is one of natural phytohormones, widely used in agriculture and downstream fields. Qualified for the nature productivity, Fusarium fujikuroi was currently employed for the industrial biotransformation from agriculture residues into GA3. Herein, Multivariate modular metabolic engineering (MMME) was assigned to reconstitute the metabolic balance in F. fujikuroi for enhancing GA3 production. Three modules including precursor pool, cluster-specific channel and P450-mediated oxidation in GA3 biosynthetic pathway were defined and optimized separately. The enhancement of both precursor pool and cluster-specific channel pushed metabolic flux transfer into the GA3-specific pathway. Moreover, both introduction of Vitreoscilla hemoglobin and reinforcement of NADPH-dependent cytochrome P450 reductase facilitated oxidation cofactor transfer and subsequently boosted mycelium growth and GA3 biosynthesis. Integration of three modules in the engineered strain accumulated 2.89 g/L GA3 in shake flask via submerged fermentation, presenting a promising modular metabolic engineering model for efficient microbial transformation in agro-industrial application.

Functional diversity and metabolic engineering of plant-specialized metabolites

Plants are talented biochemists that produce a broad diversity of small molecules. These so-called specialized metabolites (SMs) play critical roles in the adaptive evolution of plants to defend against biotic and abiotic stresses, attract pollinators, and modulate soil microbiota for their own benefits. Many plant SMs have been used as nutrition and flavor compounds in our daily food, as well as drugs for treatment of human diseases. Current multi-omics tools have significantly accelerated the process of biosynthetic pathway elucidation in plants through correlation analyses, genetic mapping, and de novo biosynthetic gene cluster predictions. Understanding the biosynthesis of plant SMs has enabled reconstitution of naturally occurring specialized metabolic pathways in microbial hosts, providing a sustainable supply of these high-value molecules. In this review, we illustrate the general functions of several typical plant SMs in natural ecosystems and for human societies. We then provide an overview of current methods elucidating the biosynthetic pathways of plant SMs, and synthetic biology strategies that optimize the efficiency of heterologous biosynthetic pathways in microbial hosts. Moving forward, dissection of the functions and application of plant SMs by using current multidiscipline approaches would be greatly benefit to the scientific community and human societies.

Effects of different carbon sources on metabolic profiles of carbohydrates in Streptococcus thermophilus during fermentation

BACKGROUND

Streptococcus thermophilus is a major starter used in the dairy industry and it could improve the flavor of fermented products. It is necessary to improve biomass of S. thermophilus for its application and industrialization. The utilization of carbon sources directly affects the biomass of S. thermophilus. Therefore, the carbohydrate metabolism of S. thermophilus should be investigated.

RESULTS

In the present study, metabolic parameters and gene expression of S. thermophilus S-3 with different carbon sources were investigated. The physicochemical results showed that S. thermophilus S-3 had high lactose utilization. Transcriptome analysis found that approximately 104 genes were annotated onto 15 carbohydrate metabolic pathways, of which 15 unigenes were involved in the phosphotransferase system and 75 were involved in the ATP-binding cassette transporter system. In addition, 171 differentially expressed genes related to carbohydrate metabolism were identified. Expression of the galactose metabolism genes lacSZ and galKTEM increased significantly from the lag phase to the mid-exponential growth phase as a result of the global regulator protein, catabolite control protein A (CcpA). The high expression of galK in the mid- to late- phases indicated that the metabolite galactose is re-transported for intracellular utilization. CcpA regulation may also induce high expressions of glycolytic pathway regulated-genes related to lactose utilization, including ldh, fba, eno, pfkA, bglA, pgi, pgm and pyk, producing optimal glycolytic flux and S. thermophilus S-3 growth.

CONCLUSION

The present study provides new insights into the carbon metabolism regulation and provide theoretical support for high-density fermentation of S. thermophilus S-3. © 2022 Society of Chemical Industry.

Establishing Komagataella phaffii as a Cell Factory for Efficient Production of Sesquiterpenoid α-Santalene

Santalene, a major component of the sandalwood essential oil, is a typical representative of sesquiterpenes and has important applications in medicine, food, flavors, and other fields. Due to the limited supply of natural sandalwood resources, there is a growing interest in engineering microbial cell factories for the mass production of santalene. In the present study, Komagataella phaffii (also known as Pichia pastoris) was established as a cell factory for high-level production of α-santalene for the first time. The metabolic fluxes were rewired toward α-santalene biosynthesis through the optimization of promoters to drive the expression of the α-santalene synthase (SAS) gene, overexpression of the key mevalonate pathway genes (i.e., tHMG1, IDI1, and ERG20), and multi-copy integration of the SAS expression cassette. In combination with medium optimization and bioprocess engineering, the optimal strain (STE-9) was able to produce α-santalene with a titer as high as 829.8 ± 70.6 mg/L, 4.4 ± 0.3 g/L, and 21.5 ± 1.6 g/L in a shake flask, batch fermenter, and fed-batch fermenter, respectively. These represented the highest production of α-santalene ever reported, highlighting the advantages of K. phaffii cell factories for the production of terpenoids and other natural products.

Engineering for life in toxicity: Key to industrializing microbial synthesis of high energy density fuels

With the growing demand for air transportation combined with global concerns about environmental issues and the instability and lack of renewability of the oil market, microbial production of high energy density fuels for jets (bio-jet fuels) has received more attention in recent years. Bio-jet fuels can be derived from both isoprenoids and fatty acids, and, additionally, aromatic hydrocarbons derived from expanded shikimate pathways are also candidates for jet fuels. Compared to fatty acid derivatives, most of isoprenoids and aromatic hydrocarbons used for jet fuels have higher density energies. However, they are also highly toxic to host microbes. The cytotoxicity induced during the synthesis of isoprenoid or shikimate pathway-derived biofuels remains one of the major obstacles for industrial production even though synthetic and systems biology approaches have reconstructed and optimized metabolic pathways for production of these bio-jet fuels. Here, we review recent developments in the production of known and potential jet fuels by microorganisms, with a focus on alleviating cytotoxicity caused by the final products, intermediates, and metabolic pathways.

Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges

In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.

Metabolic engineering of Oryza sativa for complete biodegradation of thiocyanate

Industrial thiocyanate (SCN^-) waste streams from gold mining and coal coking have caused serious environmental pollution worldwide. Phytoremediation is an efficient technology in treating hazardous wastes from the environment. However, the phytoremediation efficiency of thiocyanate is very low due to the fact that plants lack thiocyanate degradation enzymes. In this study, the thiocyanate hydrolase module was assembled correctly in rice seedlings and showed thiocyanate hydrolase activity. Rice seedlings engineered to express thiocyanate degrading activity were able to completely remove thiocyanate from coking wastewater. Our findings suggest that transforming the thiocyanate hydrolase module into plants is an efficient strategy for rapid phytoremediation of thiocyanate in the environment. Moreover, the rice seedlings expressing apoplastic or cytoplasmic targeted thiocyanate hydrolase module were constructed to compare the phytoremediation efficiency of secretory/intracellular recombinant thiocyanate hydrolase. The most obvious finding from this study is that the apoplastic expression system is more efficient than the cytoplasm expression system in the phytoremediation of thiocyanate. At last, this research also shows that the secreted thiocyanate hydrolase from engineered rice plants does not influence rhizosphere bacterial community composition.

Real-Time Monitoring of Dynamic Microbial Fe(III) Respiration Metabolism with a Living Cell-Compatible Electron-Sensing Probe

Monitoring microbial metabolism is vital for biomanufacturing processes optimization. However, it remains a grand challenge to offer insight into microbial metabolism due to particularly complex and dynamic processes. Here, we report an electron-sensing probe Zn₂ GeO₄ :Mn@Fe³⁺ for real-time and dynamic monitoring of Fe(III) respiration metabolism. The quenched persistent luminescence of Zn₂ GeO4:Mn@Fe³⁺ is recovered when Fe³⁺ accepted electrons from the dynamic Fe(III) respiration metabolism, enabling the real-time monitoring of microbial metabolism. The probe shows the capability to verify the role of related biomolecules in microbial Fe(III) respiration metabolism, to track the dynamic Fe(III) respiration metabolic response to environmental stress and microbial co-culture interactions. Furthermore, the Zn₂ GeO₄ :Mn@Fe³⁺ probe provides guidance for improving biosynthesis efficiency by monitoring Fe redox recycling in microbial co-culture.

Enhancing biofuels production by engineering the actin cytoskeleton in Saccharomyces cerevisiae

Saccharomyces cerevisiae is widely employed as a cell factory for the production of biofuels. However, product toxicity has hindered improvements in biofuel production. Here, we engineer the actin cytoskeleton in S. cerevisiae to increase both the cell growth and production of n-butanol and medium-chain fatty acids. Actin cable tortuosity is regulated using an n-butanol responsive promoter-based autonomous bidirectional signal conditioner in S. cerevisiae. The budding index is increased by 14.0%, resulting in the highest n-butanol titer of 1674.3 mg L-1. Moreover, actin patch density is fine-tuned using a medium-chain fatty acid responsive promoter-based autonomous bidirectional signal conditioner. The intracellular pH is stabilized at 6.4, yielding the highest medium-chain fatty acids titer of 692.3 mg L-1 in yeast extract peptone dextrose medium. Engineering the actin cytoskeleton in S. cerevisiae can efficiently alleviate biofuels toxicity and enhance biofuels production.

Engineering microbial consortia of Elizabethkingia meningoseptica and Escherichia coli strains for the biosynthesis of vitamin K2

BACKGROUND

The study and application of microbial consortia are topics of interest in the fields of metabolic engineering and synthetic biology. In this study, we report the design and optimisation of Elizabethkingia meningoseptica and Escherichia coli co-culture, which bypass certain limitations found during the molecular modification of E. meningoseptica, such as resistance to many antibiotics and fewer available molecular tools.

RESULTS

The octaprenyl pyrophosphate synthase from E. meningoseptica sp. F2 (EmOPPS) was expressed, purified, and identified in the present study. Then, owing to the low vitamin K2 production by E. coli or E. meningoseptica sp. F2 monoculture, we introduced the E. meningoseptica and E. coli co-culture strategy to improve vitamin K2 biosynthesis. We achieved production titres of 32 mg/L by introducing vitamin K2 synthesis-related genes from E. meningoseptica sp. F2 into E. coli, which were approximately three-fold more than the titre achieved with E. meningoseptica sp. F2 monoculture. This study establishes a foundation for further engineering of MK-n (n = 4, 5, 6, 7, 8) in a co-cultivation system of E. meningoseptica and E. coli. Finally, we analysed the surface morphology, esterase activity, and membrane permeability of these microbial consortia using scanning electron microscopy, confocal laser scanning microscopy, and flow cytometry, respectively. The results showed that the co-cultured bacteria were closely linked and that lipase activity and membrane permeability improved, which may be conducive to the exchange of substances between bacteria.

CONCLUSIONS

Our results demonstrated that co-culture engineering can be a useful method in the broad field of metabolic engineering of strains with restricted molecular modifications.

Integrative Genome-Scale Metabolic Modeling Reveals Versatile Metabolic Strategies for Methane Utilization in Methylomicrobium album BG8

Methylomicrobium album BG8 is an aerobic methanotrophic bacterium with promising features as a microbial cell factory for the conversion of methane to value-added chemicals. However, the lack of a genome-scale metabolic model (GEM) of M. album BG8 has hindered the development of systems biology and metabolic engineering of this methanotroph. To fill this gap, a high-quality GEM was constructed to facilitate a system-level understanding of the biochemistry of M. album BG8. Flux balance analysis, constrained with time-series data derived from experiments with various levels of methane, oxygen, and biomass, was used to investigate the metabolic states that promote the production of biomass and the excretion of carbon dioxide, formate, and acetate. The experimental and modeling results indicated that M. album BG8 requires a ratio of ∼1.5:1 between the oxygen- and methane-specific uptake rates for optimal growth. Integrative modeling revealed that at ratios of  >2:1 oxygen-to-methane uptake flux, carbon dioxide and formate were the preferred excreted compounds, while at ratios of <1.5:1 acetate accounted for a larger fraction of the total excreted flux. Our results showed a coupling between biomass production and the excretion of carbon dioxide that was linked to the ratio between the oxygen- and methane-specific uptake rates. In contrast, acetate excretion was experimentally detected during exponential growth only when the initial biomass concentration was increased. A relatively lower growth rate was also observed when acetate was produced in the exponential phase, suggesting a trade-off between biomass and acetate production.

IMPORTANCE A genome-scale metabolic model (GEM) is an integrative platform that enables the incorporation of a wide range of experimental data. It is used to reveal system-level metabolism and, thus, clarify the link between the genotype and phenotype. The lack of a GEM for Methylomicrobium album BG8, an aerobic methane-oxidizing bacterium, has hindered its use in environmental and industrial biotechnology applications. The diverse metabolic states indicated by the GEM developed in this study demonstrate the versatility in the methane metabolic processes used by this strain. The integrative GEM presented here will aid the implementation of the design-build-test-learn paradigm in the metabolic engineering of M. album BG8. This advance will facilitate the development of a robust methane bioconversion platform and help to mitigate methane emissions from environmental systems.

Natural 5-Aminolevulinic Acid: Sources, Biosynthesis, Detection and Applications

5-Aminolevulinic acid (5-ALA) is the key precursor for the biosynthesis of tetrapyrrole compounds, with wide applications in medicine, agriculture and other burgeoning fields. Because of its potential applications and disadvantages of chemical synthesis, alternative biotechnological methods have drawn increasing attention. In this review, the recent progress in biosynthetic pathways and regulatory mechanisms of 5-ALA synthesis in biological hosts are summarized. The research progress on 5-ALA biosynthesis via the C4/C5 pathway in microbial cells is emphasized, and the corresponding biotechnological design strategies are highlighted and discussed in detail. In addition, the detection methods and applications of 5-ALA are also reviewed. Finally, perspectives on potential strategies for improving the biosynthesis of 5-ALA and understanding the related mechanisms to further promote its industrial application are conceived and proposed.

Metabolic engineering for valorization of macroalgae biomass

Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate change and environmental destruction linked to use of fossil fuels. Microorganisms play pivotal roles in converting macroalgae into valuable products, and metabolic engineering technologies have been developed to extend their native capabilities. This review showcases current achievements in engineering the metabolisms of various microbial chassis to convert red, green, and brown macroalgae into bioproducts. Unique features of macroalgae, such as seasonal variation in carbohydrate content and salinity, provide the next challenges to advancing macroalgae-based biorefineries. Three emerging engineering strategies are discussed here: (1) designing dynamic control of metabolic pathways, (2) engineering strains of halophilic (salt-tolerant) microbes, and (3) developing microbial consortia for conversion. This review illuminates opportunities for future research communities by elucidating current approaches to engineering microbes so they can become cell factories for the utilization of macroalgae feedstocks.

Fourth generation biofuel from genetically modified algal biomass: Challenges and future directions

Genetic engineering applications in the field of biofuel are rapidly expanding due to their potential to boost biomass productivity while lowering its cost and enhancing its quality. Recently, fourth-generation biofuel (FGB), which is biofuel obtained from genetically modified (GM) algae biomass, has gained considerable attention from academic and industrial communities. However, replacing fossil resources with FGB is still beset with many challenges. Most notably, technical aspects of genetic modification operations need to be more fully articulated and elaborated. However, relatively little attention has been paid to GM algal biomass. There is a limited number of reviews on the progress and challenges faced in the algal genetics of FGB. Therefore, the present review aims to fill this gap in the literature by recapitulating the findings of recent studies and achievements on safe and efficient genetic manipulation in the production of FGB. Then, the essential issues and parameters related to genome editing in algal strains are highlighted. Finally, the main challenges to FGB pertaining to the diffusion risk and regulatory frameworks are addressed. This review concluded that the technical and biosafety aspects of FGB, as well as the complexity and diversity of the related regulations, legitimacy concerns, and health and environmental risks, are among the most important challenges that require a strong commitment at the national/international levels to reach a global consensus.

Reprogramming microbial populations using a programmed lysis system to improve chemical production

Microbial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.

Marine drugs: Biology, pipelines, current and future prospects for production

The marine environment is a huge reservoir of biodiversity and represents an excellent source of chemical compounds, some of which have large economical values. In the urgent quest for new pharmaceuticals, marine-based drug discovery has progressed significantly over the past several decades and we now benefit from a series of approved marine natural products (MNPs) to treat cancer and pain while an additional collection of promising leads are in clinical trials. However, the discovery and supply of MNPs has always been challenging given their low bioavailability and structural complexity. Their manufacture for pre-clinical and clinical development but also commercialization mainly relies upon marine source extraction and chemical synthesis, which are associated with high costs, unsustainability and severe environmental problems. In this review, we discuss how metabolic engineering now raises reasonable expectations for the implementation of microbial cell factories, which may provide a sustainable approach for MNP-based drug supply in the near future.