Modular pathway engineering of Bacillus subtilis for improved N-acetylglucosamine production

A Review on the Extraction, Structural Characterization, Function, and Applications of Peptidoglycan

Peptidoglycan (PGN) is the primary component of bacterial cell walls, consisting of linear glycan chains formed by alternating linkages of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) through glycosidic bonds. It exhibits biological activity in various aspects, making it a biologically significant macromolecule with extensive industrial application. This review aims to explore the latest research advancements in the extraction techniques, structural characterization, functions, and applications of PGN. The review compares the advantages and limitations of traditional chemical lysis methods with modern mechanical-assisted and bio-assisted extraction techniques, discusses chemical composition analysis techniques and structural characterization methods of PGN. The review emphasizes the potential of PGN in immune modulation, specific recognition, and adsorption functions. Furthermore, the review examines potential applications of PGN in vaccine development, the livestock industry, the removal of harmful substances, and protein bioprocessing. In the end, based on the current development trend, future research directions for PGN are proposed, including in-depth studies on the mechanisms of PGN in different hosts and its immunomodulatory effects in various disease models. It is expected that a comprehensive reference framework for the research and application of PGN will be provided through this review, offering ideas and directions for further development and utilization.

Development of synthetic small regulatory RNA for Rhodococcus erythropolis

Rhodococci have been regarded as ideal chassis for biotransformation, biodegradation, and biosynthesis for their unique environmental persistence and robustness. However, most species of Rhodococcus are still difficult to metabolically engineer due to the lack of genetic tools and techniques. In this study, synthetic sRNA strategy was exploited for gene repression in R. erythropolis XP. The synthetic sRNA based on the RhlS scaffold from Pseudomonas aeruginosa functions better in repressing sfgfp expression than those based on E. coli MicC, SgrS, and P. aeruginosa PrrF1-2 scaffold. The RhlS-based sRNAs were applied to study the influence of sulfur metabolism on biodesulfurization (BDS) efficiency in R. erythropolis XP and successfully identified two genes involved in sulfur metabolism that affect the BDS efficiency significantly. The RhlS-based synthetic sRNAs show promise in the metabolic engineering of Rhodococcus and promote the industrial applications of Rhodococcus in environmental remediation and biosynthesis.

Microbial production of N-acetyl-D-glucosamine (GlcNAc) for versatile applications: Biotechnological strategies for green process development

N-acetyl-d-glucosamine (GlcNAc) is a commercially important amino sugar for its wide range of applications in pharmaceutical, food, cosmetics and biofuel industries. In nature, GlcNAc is polymerised into chitin biopolymer, which is one of the major constituents of fungal cell wall and outer shells of crustaceans. Sea food processing industries generate a large volume of chitin as biopolymeric waste. Because of its high abundance, chitinaceous shellfish wastes have been exploited as one of the major precursor substrates of GlcNAc production, both in chemical and enzymatic means. Nevertheless, the current process of GlcNAc extraction from shellfish wastes generates poor turnover and attracts environmental hazards. Moreover, GlcNAc isolated from shellfish could not be prescribed to certain groups of people because of the allergic nature of shell components. Therefore, an alternative route of GlcNAc production is advocated. With the advancement of metabolic construction and synthetic biology, microbial synthesis of GlcNAc is gaining much attention nowadays. Several new and cutting-edge technologies like substrate co-utilization strategy, promoter engineering, and CRISPR interference system were proposed in this fascinating area. The study would put forward the potential application of microbial engineering in the production of important pharmaceuticals. Very recently, autotrophic fermentation of GlcNAc synthesis has been proposed. The metabolic engineering approaches would offer great promise to mitigate the issues of low yield and high production cost, which are major challenges in microbial bio-processes industries. Further process optimization, optimising metabolic flux, and efficient recovery of GlcNAc from culture broth, should be investigated in order to achieve a high product titer. The current study presents a comprehensive review on microbe-based eco-friendly green methods that would pave the way towards the development of future research directions in this field for the designing of a cost-effective fermentation process on an industrial setup.

Bacillus genus industrial applications and innovation: First steps towards a circular bioeconomy

In recent decades, environmental concerns have directed several policies, investments, and production processes. The search for sustainable and eco-friendly strategies is constantly increasing to reduce petrochemical product utilization, fossil fuel pollution, waste generation, and other major ecological impacts. The concepts of circular economy, bioeconomy, and biorefinery are increasingly being applied to solve or reduce those problems, directing us towards a greener future. Within the biotechnology field, the Bacillus genus of bacteria presents extremely versatile microorganisms capable of producing a great variety of products with little to no dependency on petrochemicals. They are able to grow in different agro-industrial wastes and extreme conditions, resulting in healthy and environmentally friendly products, such as foods, feeds, probiotics, plant growth promoters, biocides, enzymes, and bioactive compounds. The objective of this review was to compile the variety of products that can be produced with Bacillus cells, using the concepts of biorefinery and circular economy as the scope to search for greener alternatives to each production method and providing market and bioeconomy ideas of global production. Although the genus is extensively used in industry, little information is available on its large-scale production, and there is little current data regarding bioeconomy and circular economy parameters for the bacteria. Therefore, as this work gathers several products' economic, production, and environmentally friendly use information, it can be addressed as one of the first steps towards those sustainable strategies. Additionally, an extensive patent search was conducted, focusing on products that contain or are produced by the Bacillus genus, providing an indication of global technology development and direction of the bacteria products. The Bacillus global market represented at least $18 billion in 2020, taking into account only the products addressed in this article, and at least 650 patent documents submitted per year since 2017, indicating this market's extreme importance. The data we provide in this article can be used as a base for further studies in bioeconomy and circular economy and show the genus is a promising candidate for a greener and more sustainable future.

Production of N-acetylglucosamine with Vibrio alginolyticus FA2, an emerging platform for economical unsterile open fermentation

Members of the Vibrionaceae family are predominantly fast-growing and halophilic microorganisms that have captured the attention of researchers owing to their potential applications in rapid biotechnology. Among them, Vibrio alginolyticus FA2 is a particularly noteworthy halophilic bacterium that exhibits superior growth capability. It has the potential to serve as a biotechnological platform for sustainable and eco-friendly open fermentation with seawater. To evaluate this hypothesis, we integrated the N-acetylglucosamine (GlcNAc) pathway into V. alginolyticus FA2. Seven nag genes were knocked out to obstruct the utilization of GlcNAc, and then 16 exogenous gna1s co-expressing with EcglmS were introduced to strengthen the flux of GlcNAc pathway, respectively. To further enhance GlcNAc production, we fine-tuned promoter strength of the two genes and inactivated two genes alsS and alsD to prevent the production of acetoin. Furthermore, unsterile open fermentation was carried out using simulated seawater and a chemically defined medium, resulting in the production of 9.2 g/L GlcNAc in 14 h. This is the first report for de-novo synthesizing GlcNAc with a Vibrio strain, facilitated by an unsterile open fermentation process employing seawater as a substitute for fresh water. This development establishes a basis for production of diverse valuable chemicals using Vibrio strains and provides insights into biomanufacture.

Metabolic engineering of Bacillus amyloliquefaciens for efficient production of α-glucosidase inhibitor1-deoxynojirimycin

Owing to the feature of strong α-glucosidase inhibitory activity, 1-deoxynojirimycin (1-DNJ) has broad application prospects in areas of functional food, biomedicine, etc., and this research wants to construct an efficient strain for 1-DNJ production, basing on Bacillus amyloliquefaciens HZ-12. Firstly, using the temperature-sensitive shuttle plasmid T2 (2)-Ori, gene ptsG in phosphotransferase system (PTS) was weakened by homologous recombination, and non-PTS pathway was strengthened by deleting its repressor gene iolR, and 1-DNJ yield of resultant strain HZ-S2 was increased by 4.27-fold, reached 110.72 mg/L. Then, to increase precursor fructose-6-phosphate (F-6-P) supply, phosphofructokinase was weaken, fructose phosphatase GlpX and 6-phosphate glucose isomerase Pgi were strengthened by promoter replacement, moreover, regulator gene nanR was deleted, 1-DNJ yield was further increased to 267.37 mg/L by 2.41-fold. Subsequently, promoter of 1-DNJ synthetase cluster was optimized, as well as 5'-UTRs of downstream genes in synthetase cluster, and 1-DNJ produced by the final strain reached 478.62 mg/L. Last but not the least, 1-DNJ yield of 1632.50 mg/L was attained in 3 L fermenter, which was the highest yield of 1-DNJ reported to date. Taken together, our results demonstrated that metabolic engineering was an effective strategy for 1-DNJ synthesis, this research laid a foundation for industrialization of functional food and drugs based on 1-DNJ.

Aromatic natural products synthesis from aromatic lignin monomers using Acinetobacter baylyi ADP1

Achieving sustainable chemical synthesis and a circular economy will require process innovation to minimize or recover existing waste streams. Valorization of lignin biomass has the ability to advance this goal. While lignin has proved a recalcitrant feedstock for upgrading, biological approaches can leverage native microbial metabolism to simplify complex and heterogeneous feedstocks to tractable starting points for biochemical upgrading. Recently, we demonstrated that one microbe with lignin relevant metabolism, Acinetobacter baylyi ADP1, is both highly engineerable and capable of undergoing rapid design-build-test-learn cycles, making it an ideal candidate for these applications. Here, we utilize these genetic traits and ADP1's native β-ketoadipate metabolism to convert mock alkali pretreated liquor lignin (APL) to two valuable natural products, vanillin-glucoside and resveratrol. En route, we create strains with up to 22 genetic modifications, including up to 8 heterologously expressed enzymes. Our approach takes advantage of preexisting aromatic species in APL (vanillate, ferulate, and p-coumarate) to create shortened biochemical routes to end products. Together, this work demonstrates ADP1's potential as a platform for upgrading lignin waste streams and highlights the potential for biosynthetic methods to maximize the existing chemical potential of lignin aromatic monomers.

Modular Metabolic Engineering of Mortierella alpina by the 2A Peptide Platform to Improve Arachidonic Acid Production

Arachidonic acid (ARA) is an essential fatty acid in human nutrition. Mortierella alpina, a filamentous fungus, has been widely used for the production of ARA. Here, we report a modular engineering approach that systematically eliminates metabolic bottlenecks in the multigene elongase/desaturase pathway and has led to significant improvements of the ARA titer. The elongase/desaturase pathway in Mortierella alpina was recast into two modules, namely, push and pull modules, based on its function in the ARA synthesis. Combinatorial optimization of these two modules has balanced the production and consumption of intermediate metabolites. A 2A peptide-based facile assembly platform that can achieve multigene expression as a polycistron was first established. The platform was then applied to express the push and pull modules in Mortierella alpina. In the shake-flask fermentation, the lipid and ARA contents of the engineered strain MA5 were increased by 1.2-fold and 77.6%, respectively, resulting in about fivefold increase of the ARA yield. The final ARA titer reached 4.4 g L-1 in shake-flask fermentation. The modular engineering strategies presented in this study demonstrate a generalized approach for the engineering of cell factories in the production of valuable metabolites.

Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs

Synthetic sRNAs allow knockdown of target genes at translational level, but have been restricted to a limited number of bacteria. Here, we report the development of a broad-host-range synthetic sRNA (BHR-sRNA) platform employing the RoxS scaffold and the Hfq chaperone from Bacillus subtilis. BHR-sRNA is tested in 16 bacterial species including commensal, probiotic, pathogenic, and industrial bacteria, with >50% of target gene knockdown achieved in 12 bacterial species. For medical applications, virulence factors in Staphylococcus epidermidis and Klebsiella pneumoniae are knocked down to mitigate their virulence-associated phenotypes. For metabolic engineering applications, high performance Corynebacterium glutamicum strains capable of producing valerolactam (bulk chemical) and methyl anthranilate (fine chemical) are developed by combinatorial knockdown of target genes. A genome-scale sRNA library covering 2959 C. glutamicum genes is constructed for high-throughput colorimetric screening of indigoidine (natural colorant) overproducers. The BHR-sRNA platform will expedite engineering of diverse bacteria of both industrial and medical interest.

An update on the review of microbial synthesis of glucosamine and N-acetylglucosamine

Glucosamine (GlcN) is a natural amino monosaccharide in which a hydroxyl group of glucose is substituted by an amino group. It belongs to functional amino sugar compounds. In the traditional preparation process, GlcN and GlcNAc are obtained by hydrolyzing the cell wall of shrimp and crab. There are many potential problems with this method, such as geographical and seasonal restrictions on the supply of raw materials, serious environmental pollution and potential allergic reactions. Microbial fermentation has the advantages of mild conditions, low environmental pollution, high production intensity, and product safety. It can effectively solve the problem of shrimp and crab hydrolysis process, attracting many researchers to participate in the research of microbial fermentation production of GlcN. This paper mainly summarizes the research on strain construction method, metabolic pathway design and fermentation condition optimization in microbial fermentation, which has certain guiding significance for the further production, research and production of glucosamine.

Multifaceted production strategies and applications of glucosamine: a comprehensive review

Glucosamine (GlcN) and its derivatives are in high demand and used in various applications such as food, a precursor for the biochemical synthesis of fuels and chemicals, drug delivery, cosmetics, and supplements. The vast number of applications attributed to GlcN has raised its demand, and there is a growing emphasis on developing production methods that are sustainable and economical. Several: physical, chemical, enzymatic, microbial fermentation, recombinant processing methods, and their combinations have been reported to produce GlcN from chitin and chitosan available from different sources, such as animals, plants, and fungi. In addition, genetic manipulation of certain organisms has significantly improved the quality and yield of GlcN compared to conventional processing methods. This review will summarize the chitin and chitosan-degrading enzymes found in various organisms and the expression systems that are widely used to produce GlcN. Furthermore, new developments and methods, including genetic and metabolic engineering of Escherichia coli and Bacillus subtilis to produce high titers of GlcN and GlcNAc will be reviewed. Moreover, other sources of glucosamine production viz. starch and inorganic ammonia will also be discussed. Finally, the conversion of GlcN to fuels and chemicals using catalytic and biochemical conversion will be discussed.

Metabolic Engineering of Escherichia coli for Increased Bioproduction of N-Acetylneuraminic Acid

N-Acetylneuraminic acid (NeuAc) is widely used in the food and pharmaceutical industries. Therefore, it is important to develop an efficient and eco-friendly method for NeuAc production. Here, we achieved de novo biosynthesis of NeuAc in an engineered plasmid-free Escherichia coli strain, which efficiently synthesizes NeuAc using glycerol as the sole carbon source, via clustered regularly interspaced palindromic repeat (CRISPR)/CRISPR-associated protein 9-based genome editing. NeuAc key precursor, N-acetylmannosamine (ManNAc; 0.40 g/L), was produced by expressing UDP-N-acetylglucosamine-2-epimerase and glucosamine-6-phosphate synthase (GlmS) mutants and blocking the NeuAc catabolic pathway in E. coli BL21 (DE3). The expression levels of GlmM and GlmU-GlmS_A metabolic modules were optimized, significantly increasing the ManNAc titer to 8.95 g/L. Next, the expression levels of NeuAc synthase from different microorganisms were optimized, leading to the production of 6.27 g/L of NeuAc. Blocking the competing pathway of NeuAc biosynthesis increased the NeuAc titer to 9.65 g/L. In fed-batch culture in a 3 L fermenter, NeuAc titer reached 23.46 g/L with productivity of 0.69 g/L/h, which is the highest level achieved by microbial synthesis using glycerol as the sole carbon source in E. coli. The strategies used in our study can aid in the efficient bioproduction of NeuAc and its derivatives.

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

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

Engineering Halomonas bluephagenesis via small regulatory RNAs

Halomonas bluephagenesis, a robust and contamination-resistant microorganism has been developed as a chassis for "Next Generation Industrial Biotechnology". The non-model H. bluephagenesis requires efficient tools to fine-tune its metabolic fluxes for enhanced production phenotypes. Here we report a highly efficient gene expression regulation system (PrrF1-2-HfqPa) in H. bluephagenesis, small regulatory RNA (sRNA) PrrF1 scaffold from Pseudomonas aeruginosa and a target-binding sequence that downregulate gene expression, and its cognate P. aeruginosa Hfq (HfqPa), recruited by the scaffold to facilitate the hybridization of sRNA and the target mRNA. The PrrF1-2-HfqPa system targeting prpC in H. bluephagenesis helps increase 3-hydroxyvalerate fraction in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) to 21 mol% compared to 3.1 mol% of the control. This sRNA system repressed phaP1 and minD simultaneously, resulting in large polyhydroxybutyrate granules. Further, an sRNA library targeting 30 genes was employed for large-scale target identification to increase mevalonate production. This work expands the study on using an sRNA system not based on Escherichia coli MicC/SgrS-Hfq to repress gene expression, providing a framework to exploit new powerful genome engineering tools based on other sRNAs.

Post-transcriptional control of bacterial nitrogen metabolism by regulatory noncoding RNAs

Nitrogen metabolism is the most basic process of material and energy metabolism in living organisms, and processes involving the uptake and use of different nitrogen sources are usually tightly regulated at the transcriptional and post-transcriptional levels. Bacterial regulatory noncoding RNAs are novel post-transcriptional regulators that repress or activate the expression of target genes through complementarily pairing with target mRNAs; therefore, these noncoding RNAs play an important regulatory role in many physiological processes, such as bacterial substance metabolism and stress response. In recent years, a study found that noncoding RNAs play a vital role in the post-transcriptional regulation of nitrogen metabolism, which is currently a hot topic in the study of bacterial nitrogen metabolism regulation. In this review, we present an overview of recent advances that increase our understanding on the regulatory roles of bacterial noncoding RNAs and describe in detail how noncoding RNAs regulate biological nitrogen fixation and nitrogen metabolic engineering. Furthermore, our goal is to lay a theoretical foundation for better understanding the molecular mechanisms in bacteria that are involved in environmental adaptations and metabolically-engineered genetic modifications.

Recent advances in high-throughput metabolic engineering: Generation of oligonucleotide-mediated genetic libraries

The preparation of genetic libraries is an essential step to evolve microorganisms and study genotype-phenotype relationships by high-throughput screening/selection. As the large-scale synthesis of oligonucleotides becomes easy, cheap, and high-throughput, numerous novel strategies have been developed in recent years to construct high-quality oligo-mediated libraries, leveraging state-of-art molecular biology tools for genome editing and gene regulation. This review presents an overview of recent advances in creating and characterizing in vitro and in vivo genetic libraries, based on CRISPR/Cas, regulatory RNAs, and recombineering, primarily for Escherichia coli and Saccharomyces cerevisiae. These libraries' applications in high-throughput metabolic engineering, strain evolution and protein engineering are also discussed.

Engineering of Synthetic Multiplexed Pathways for High-Level N-Acetylneuraminic Acid Bioproduction

N-Acetylneuraminic acid (NeuAc) is widely used as a supplement to promote brain health and enhance immunity. However, the low efficiency of de novo NeuAc synthesis limits its cost-efficient bioproduction. Herein, a synthetic multiplexed pathway engineering (SMPE) strategy is proposed to improve NeuAc synthesis. First, we compare the key enzyme sources and optimize the expression levels of three NeuAc synthesis pathways in Bacillus subtilis; the AGE, NeuC, and NanE pathways, for which NeuAc production reached 3.94, 5.67, and 0.19 g/L, respectively. Next, these synthesis pathways were combined and modularly optimized via the SMPE strategy, with production reaching 7.87 g/L. Finally, fed-batch fermentation in a 5 L fermenter reached 30.10 g/L NeuAc production, the highest reported production using glucose as the sole carbon source. Using a generally regarded as safe strain as a production host, the developed NeuAc-producing approach should be favorable for efficient bioproduction, without the need for plasmids, antibiotics, or chemical inducers.

Targeting riboswitches with synthetic small RNAs for metabolic engineering

Our growing knowledge of the diversity of non-coding RNAs in natural systems and our deepening knowledge of RNA folding and function have fomented the rational design of RNA regulators. Based on that knowledge, we designed and implemented a small RNA tool to target bacterial riboswitches and activate gene expression (rtRNA). The synthetic rtRNA is suitable for regulation of gene expression both in cell-free and in cellular systems. It targets riboswitches to promote the antitermination folding regardless the cognate metabolite concentration. Therefore, it prevents transcription termination increasing gene expression up to 103-fold. We successfully used small RNA arrays for multiplex targeting of riboswitches. Finally, we used the synthetic rtRNAs to engineer an improved riboflavin producer strain. The easiness to design and construct, and the fact that the rtRNA works as a single genome copy, make it an attractive tool for engineering industrial metabolite-producing strains.

Function Enhancement of a Metabolic Module via Endogenous Promoter Replacement for Pseudomonas sp. JY-Q to Degrade Nicotine in Tobacco Waste Treatment

Nicotine-degrading Pseudomonas sp. JY-Q is a preferred strain utilized in reconstituted tobacco process for tobacco waste treatment. However, its efficiency of nicotine metabolism still requires to be improved via genomic technology such as promoter engineering based on genomic information. Concerning upstream module of nicotine metabolic pathway, we found that two homologous genes of nicotine dehydrogenase (nicA2 and nox) coexisted in strain JY-Q. However, the transcriptional amount of nox was 20-fold higher than that of nicA2. Thus, the nicA2 expression required improvement. Combinatorial displacement was accomplished for two predicted endogenous promoters, named as PnicA2 and Pnox for nicA2 and nox, respectively. The mutant with Pnox as the promoters for both nicA2 and nox exhibited the best nicotine metabolic capacity which increased by 66% compared to the wild type. These results suggested that endogenous promoter replacement is also feasible for function improvement of metabolic modules and strain enhancement of biodegradation capacity to meet real environment demand.

Genetic strategies for improving hyaluronic acid production in recombinant bacterial culture

Hyaluronic acid (HA) is a biopolymer of repeating units of glucuronic acid and N-acetylglucosamine. Its market was valued at USD 8.9 billion in 2019. Traditionally, HA has been obtained from rooster comb-like animal tissues and fermentative cultures of attenuated pathogenic streptococci. Various attempts have been made to engineer a safe micro-organism for HA synthesis; however, the HA titres obtained from these attempts are in general still lower than those achieved by natural, pathogenic producers. In this scenario, ways to increase HA molecule length and titres in already constructed strains are gaining attention in the last years, but no recent publication has reviewed the main genetic strategies applied to improve HA production on heterologous hosts. In light of that, we hereby compile the advances made in the engineering of micro-organisms to improve HA synthesis.

Modular optimization in metabolic engineering

There is an increasing demand for bioproducts produced by metabolically engineered microbes, such as pharmaceuticals, biofuels, biochemicals and other high value compounds. In order to meet this demand, modular optimization, the optimizing of subsections instead of the whole system, has been adopted to engineer cells to overproduce products. Research into modularity has focused on traditional approaches such as DNA, RNA, and protein-level modularity of intercellular machinery, by optimizing metabolic pathways for enhanced production. While research into these traditional approaches continues, limitations such as scale-up and time cost hold them back from wider use, while at the same time there is a shift to more novel methods, such as moving from episomal expression to chromosomal integration. Recently, nontraditional approaches such as co-culture systems and cell-free metabolic engineering (CFME) are being investigated for modular optimization. Co-culture modularity looks to optimally divide the metabolic burden between different hosts. CFME seeks to modularly optimize metabolic pathways in vitro, both speeding up the design of such systems and eliminating the issues associated with live hosts. In this review we will examine both traditional and nontraditional approaches for modular optimization, examining recent developments and discussing issues and emerging solutions for future research in metabolic engineering.

Highly Efficient Production of N-Acetyl-glucosamine in Escherichia coli by Appropriate Catabolic Division of Labor in the Utilization of Mixed Glycerol/Glucose Carbon Sources

Currently, microbial production is becoming a competitive method for N-acetyl-glucosamine production. As the biosynthesis of N-acetyl-glucosamine originating from fructose-6-P directly competes with central carbon metabolism for precursor supply, the consumption of glucose for cell growth and cellular metabolism severely limits the yield of N-acetyl-glucosamine. In this study, appropriate catabolic division of labor in the utilization of mixed carbon sources was achieved by deleting the pfkA gene and enhancing the utilization of glycerol by introducing the glpK mutant. Glycerol thus mainly contributed to cell growth and cellular metabolism, and more glucose was saved for efficient N-acetyl-glucosamine synthesis. By optimizing the ratio of glycerol to glucose, the balancing of cell growth/cellular metabolism and N-acetyl-glucosamine synthesis was achieved. The resulting strain GLALD-7 produced 179.7 g/L N-acetyl-glucosamine using mixed glycerol/glucose (1:8, m/m) carbon sources in a 5 L bioreactor, with a yield of 0.458 g/g total carbon sources (0.529 g/g glucose) and a productivity of 2.57 g/L/h. Coherent high titer/yield/productivity was obtained, with the highest values ever reported, suggesting that an appropriate catabolic division of labor using mixed glycerol/glucose carbon sources is a useful strategy for facilitating the microbial production of chemicals originating from glucose or metabolites upstream of glycolysis.

Improving riboflavin production by knocking down ribF, purA and guaC genes using synthetic regulatory small RNA

Riboflavin is a commercially important compound in the food, pharmaceutical, chemical, and cosmetic industries. The down-regulation of expression levels of ribF, purA and guaC genes involved in the downstream or branch reactions of riboflavin biosynthesis pathway could direct more carbon flux to riboflavin accumulation. In this study, we made an attempt to fine-tune the expression levels of the 3 genes by using synthetic regulatory small RNA to enhance riboflavin production in Escherichia coli. Firstly, each of the 3 genes was knocking down by using 5 different sRNAs, respectively, and a highest increase of 50.2 % in riboflavin titer was achieved by using anti-ribF₅ sRNA. Then this sRNA was further co-expressed with 5 anti-purA and 5 anti-guaC sRNAs to simultaneously knocking down 2 or 3 genes. Co-expression of anti-ribF₅ and anti-guaC₃ led to the highest riboflavin production of 1091.3 mg/L, which was further increased by 97.6 % compared to the base strain. Finally, the expression levels of anti-ribF₅ and anti-guaC₃ were further fine-tuned by using 4 different promoters. The best strain WY40, in which the two sRNAs were respectively expressed by P_J23100 and P_J23107 promoter, produced 1454.5 mg/L riboflavin with an increase of 163.4 % compared to the base strain. To our knowledge, it's the first study to enhance riboflavin synthesis by simultaneously regulating the expression levels of ribF, purA and guaC genes, which led to a highest yield of 0.147 g/g glucose among all reported riboflavin-producing strains.

Production of proteins and commodity chemicals using engineered Bacillus subtilis platform strain

Currently, increasing demand of biochemicals produced from renewable resources has motivated researchers to seek microbial production strategies instead of traditional chemical methods. As a microbial platform, Bacillus subtilis possesses many advantages including the generally recognized safe status, clear metabolic networks, short growth cycle, mature genetic editing methods and efficient protein secretion systems. Engineered B. subtilis strains are being increasingly used in laboratory research and in industry for the production of valuable proteins and other chemicals. In this review, we first describe the recent advances of bioinformatics strategies during the research and applications of B. subtilis. Secondly, the applications of B. subtilis in enzymes and recombinant proteins production are summarized. Further, the recent progress in employing metabolic engineering and synthetic biology strategies in B. subtilis platform strain to produce commodity chemicals is systematically introduced and compared. Finally, the major limitations for the further development of B. subtilis platform strain and possible future directions for its research are also discussed.

Gene repression using synthetic small regulatory RNA in Methylorubrum extorquens

AIM

Genetic tools are a prerequisite for engineering cell factories for synthetic biology and biotechnology. Methylorubrum extorquens is an important platform for a future one-carbon (C1) bioeconomy, but its application is currently limited by the availability of genetic tools. Small regulatory RNA (sRNA) is an important regulatory factor in bacteria and has been applied for gene repression in several strains. This study aimed to construct a synthetic sRNA system based on the MicC scaffold and the chaperone Hfq to control gene expression in M. extorquens.

METHODS AND RESULTS

Initially, the exogenous lacZ gene was transposed into the M. extorquens chromosome as a reporter, and corresponding β-galactosidase was measured to assess the knockdown efficiency of lacZ. A synthetic sRNA containing a 24-nt antisense RNA targeting lacZ and an Escherichia coli MicC scaffold were constructed, and different Hfqs from E. coli, M. extorquens AM1 and PA1 were further identified. The results showed that the expression of endogenous hfqs from the chromosome in M. extorquens strains was inadequate, and only when it was overexpressed via the plasmid did the colonies show a colour change and a corresponding decrease in β-galactosidase expression. More specifically, M. extorquens strains with overexpressing their own Hfq showed the best gene repression efficiency. Furthermore, this E. coli MicC scaffold and AM1 Hfq system were combined to knock down crtI gene expression in AM1, leading to an 86% decrease in carotenoid production (0·09 mg g^-1 ) compared to that (0·65 mg g^-1 ) in the wild-type strain.

CONCLUSION

A functional synthetic sRNA system combined with E. coli MicC and endogenous Hfq was constructed in M. extorquens strains, which was able to interfere with the target crtI gene and reduce carotenoid production.

SIGNIFICANCE AND IMPACT OF THE STUDY

The synthetic sRNA system reported in this study provides a genetic tool for the manipulation of M. extorquens. The present findings might be helpful for achieving high-throughput gene knockdown expression.

Recent Research Advances in Small Regulatory RNAs in Streptococcus

Small non-coding RNAs (sRNAs) are a class of regulatory RNAs 20-500 nucleotides in length, which have recently been discovered in prokaryotic organisms. sRNAs are key regulators in many biological processes, such as sensing various environmental changes and regulating intracellular gene expression through binding target mRNAs or proteins. Bacterial sRNAs have recently been rapidly mined, thus providing new insights into the regulatory network of biological functions in prokaryotes. Although most bacterial sRNAs have been discovered and studied in Escherichia coli and other Gram-negative bacteria, sRNAs have increasingly been predicted and verified in Gram-positive bacteria in the past decade. The genus Streptococcus includes many commensal and pathogenic Gram-positive bacteria. However, current understanding of sRNA-mediated regulation in Streptococcus is limited. Most known sRNAs in Streptococcus are associated with the regulation of virulence. In this review, we summarize recent advances in understanding of the functions and mechanisms of sRNAs in Streptococcus, and we discuss the RNA chaperone protein and synthetic sRNA-mediated gene regulation, with the aim of providing a reference for the study of microbial sRNAs.

Metabolic Engineering of Saccharomyces cerevisiae for Ethyl Acetate Biosynthesis

Ethyl acetate can be synthesized from acetyl-CoA and ethanol via a reaction by alcohol acetyltransferases (AATase) in yeast. In order to increase the yield of acetyl-CoA, different terminators were used to optimize the expressions of acetyl-CoA synthetase (ACS1/2) and aldehyde dehydrogenase (ALD6) to increase the contents of acetyl-CoA in Saccharomyces cerevisiae. ATF1 coding AATase was coexpressed in expression cassettes of ACS1/ACS2 and ALD6 to promote the carbon flux toward ethyl acetate from acetyl-CoA. Further to improve ethyl acetate production, four heterologous AATase including HuvEAT1 (Hanseniaspora uvarum), KamEAT1 (Kluyveromyces marxianus), VAAT (wild strawberry), and AeAT9 (kiwifruit) were introduced. Subsequently mitochondrial transport and utilization of pyruvate and acetyl-CoA were impeded to increase the ethyl acetate accumulation in cytoplasm. Under the optimal fermentation conditions, the engineered strain of PGAeΔPOR2 produced 1.69 g/L ethyl acetate, which was the highest value reported to date by metabolic engineering methods.

Bacillus subtilis as a robust host for biochemical production utilizing biomass

Bacillus subtilis is regarded as a suitable host for biochemical production owing to its excellent growth and bioresource utilization characteristics. In addition, the distinct endogenous metabolic pathways and the suitability of the heterologous pathways have made B. subtilis a robust and promising host for producing biochemicals, such as: bioalcohols; bioorganic acids (lactic acids, α-ketoglutaric acid, and γ-aminobutyric acid); biopolymers (poly(γ-glutamic acid, polyhydroxyalkanoates (PHA), and polysaccharides and monosaccharides (N-acetylglucosamine, xylooligosaccharides, and hyaluronic acid)); and bioflocculants. Also for producing oligopeptides and functional peptides, owing to its efficient protein secretion system. Several metabolic and genetic engineering techniques, such as target gene overexpression and inactivation of bypass pathways, have led to the improvement in production titers and product selectivity. In this review article, recent progress in the utilization of robust B. subtilis-based host systems for biomass conversion and biochemical production has been highlighted, and the prospects of such host systems are suggested.

Synthetic small regulatory RNAs in microbial metabolic engineering

Small regulatory RNAs (sRNAs) finely control gene expression in prokaryotes and synthetic sRNA has become a useful high-throughput approach to tackle current challenges in metabolic engineering because of its many advantages compared to conventional gene knockouts. In this review, we first focus on the modular structures of sRNAs and rational design strategies of synthetic sRNAs on the basis of their modular structures. The wide applications of synthetic sRNAs in bacterial metabolic engineering, with or without the aid of heterogeneously expressed Hfq protein, were also covered. In addition, we give attention to the improvements in implementing synthetic sRNAs, which make the synthetic sRNA strategy universally applicable in metabolic engineering and synthetic biology. KEY POINTS: • Synthetic sRNAs can be rationally designed based on modular structures of natural sRNAs. • Synthetic sRNAs were widely used for metabolic engineering in various microorganisms. • Several technological improvements made the synthetic sRNA strategy more applicable.

The elucidation of phosphosugar stress response in Bacillus subtilis guides strain engineering for high N-acetylglucosamine production

Bacillus subtilis is a preferred microbial host for the industrial production of nutraceuticals and a promising candidate for the synthesis of functional sugars, such as N-acetylglucosamine (GlcNAc). Previously, a GlcNAc-overproducer B. subtilis SFMI was constructed using glmS ribozyme dual-regulatory tool. Herein, we further engineered to enhance carbon flux from glucose towards GlcNAc synthesis. As a result, the increased flux towards GlcNAc synthesis triggered phosphosugar stress response, which caused abnormal cell growth. Unfortunately, the mechanism of phosphosugar stress response had not been elucidated in B. subtilis. To reveal the stress mechanism and overcome its negative effect in bioproduction, we performed comparative transcriptome analysis. The results indicate that cells slow glucose utilization by repression of glucose import and accelerate catabolic reactions of phosphosugar. To verify these results, we overexpressed the phosphatase YwpJ, which relieved phosphosugar stress and allowed us to identify the enzyme responsible for GlcNAc synthesis from GlcNAc 6-phosphate. In addition, the deletion of nagBB and murQ, responsible for GlcNAc precursor degradation, further improved GlcNAc synthesis. The best engineered strain, B. subtilis FMIP34, increased GlcNAc titer from 11.5 to 26.1 g/L in shake flasks and produced 87.5 g/L GlcNAc in 30-L fed-batch bioreactor. Our results not only elucidate, for the first time, the phosphosugar stress response mechanism in B. subtilis, but also demonstrate how the combination of rational metabolic engineering with novel insights into physiology and metabolism allows the construction of highly efficient microbial cell factories for the production of high-value chemicals.

Bacillus subtilis: a universal cell factory for industry, agriculture, biomaterials and medicine

Due to its clear inherited backgrounds as well as simple and diverse genetic manipulation systems, Bacillus subtilis is the key Gram-positive model bacterium for studies on physiology and metabolism. Furthermore, due to its highly efficient protein secretion system and adaptable metabolism, it has been widely used as a cell factory for microbial production of chemicals, enzymes, and antimicrobial materials for industry, agriculture, and medicine. In this mini-review, we first summarize the basic genetic manipulation tools and expression systems for this bacterium, including traditional methods and novel engineering systems. Secondly, we briefly introduce its applications in the production of chemicals and enzymes, and summarize its advantages, mainly focusing on some noteworthy products and recent progress in the engineering of B. subtilis. Finally, this review also covers applications such as microbial additives and antimicrobials, as well as biofilm systems and spore formation. We hope to provide an overview for novice researchers in this area, offering them a better understanding of B. subtilis and its applications.

Cell-free synthesis system-assisted pathway bottleneck diagnosis and engineering in Bacillus subtilis

Metabolic engineering is a key technology for cell factories construction by rewiring cellular resources to achieve efficient production of target chemicals. However, the existence of bottlenecks in synthetic pathway can seriously affect production efficiency, which is also one of the core issues for metabolic engineers to solve. Therefore, developing an approach for diagnosing potential metabolic bottlenecks in a faster and simpler manner is of great significance to accelerate cell factories construction. The cell-free reaction system based on cell lysates can transfer metabolic reactions from in vivo to in vitro, providing a flexible access to directly change protein and metabolite variables, thus provides a potential solution for rapid identification of bottlenecks. Here, bottleneck diagnosis of the N-acetylneuraminic acid (NeuAc) biosynthesis pathway in industrially important chassis microorganism Bacillus subtilis was performed using cell-free synthesis system. Specifically, a highly efficient B. subtilis cell-free system for NeuAc de novo synthesis was firstly constructed, which had a 305-fold NeuAc synthesis rate than that in vivo and enabled fast pathway dynamics analysis. Next, through the addition of all potential key intermediates in combination with substrate glucose respectively, it was found that insufficient phosphoenolpyruvate supply was one of the NeuAc pathway bottlenecks. Rational in vivo metabolic engineering of NeuAc-producing B. subtilis was further performed to eliminate the bottleneck. By down-regulating the expression level of pyruvate kinase throughout the growth phase or only in the stationary phase using inhibitory N-terminal coding sequences (NCSs) and growth-dependent regulatory NCSs respectively, the maximal NeuAc titer increased 2.0-fold. Our study provides a rapid method for bottleneck diagnosis, which may help to accelerate the cycle of design, build, test and learn cycle for metabolic engineering.

Enhancement of Production of D-Glucosamine in Escherichia coli by Blocking Three Pathways Involved in the Consumption of GlcN and GlcNAc

D-Glucosamine is a commonly used dietary supplement that promotes cartilage health in humans. Metabolic flux analysis showed that D-glucosamine production could be increased by blocking three pathways involved in the consumption of glucosamine-6-phosphate and acetylglucosamine-6-phosphate. By homologous single-exchange, two key genes (nanE and murQ) of Escherichia coli BL21 were knocked out, respectively. The D-glucosamine yields of the engineered strains E. coli BL21ΔmurQ and E. coli BL21ΔnanE represented increases by factors of 2.14 and 1.79, respectively. Meanwhile, for bifunctional gene glmU, we only knocked out its glucosamine-1-phosphate acetyltransferase domain by 3D structural analysis to keep the engineered strain E. coli BL21glmU-Δgpa survival, which resulted in an increase in the production of D-glucosamine by a factor of 2.16. Moreover, for further increasing D-glucosamine production, two genes encoding rate-limiting enzymes, named glmS and gna1, were coexpressed by an RBS sequence in those engineered strains. The total concentrations of D-glucosamine in E. coli BL21 glmU-Δgpa', E. coli BL21ΔmurQ', and E. coli BL21ΔnanE' were 2.65 g/L, 1.73 g/L, and 1.38 g/L, which represented increases by factors of 8.83, 5.76, and 3.3, respectively.

Microbial Engineering for Production of N-Functionalized Amino Acids and Amines

N-functionalized amines play important roles in nature and occur, for example, in the antibiotic vancomycin, the immunosuppressant cyclosporine, the cytostatic actinomycin, the siderophore aerobactin, the cyanogenic glucoside linamarin, and the polyamine spermidine. In the pharmaceutical and fine-chemical industries N-functionalized amines are used as building blocks for the preparation of bioactive molecules. Processes based on fermentation and on enzyme catalysis have been developed to provide sustainable manufacturing routes to N-alkylated, N-hydroxylated, N-acylated, or other N-functionalized amines including polyamines. Metabolic engineering for provision of precursor metabolites is combined with heterologous N-functionalizing enzymes such as imine or ketimine reductases, opine or amino acid dehydrogenases, N-hydroxylases, N-acyltransferase, or polyamine synthetases. Recent progress and applications of fermentative processes using metabolically engineered bacteria and yeasts along with the employed enzymes are reviewed and the perspectives on developing new fermentative processes based on insight from enzyme catalysis are discussed.

CRISPRi-Based Dynamic Control of Carbon Flow for Efficient N-Acetyl Glucosamine Production and Its Metabolomic Effects in Escherichia coli

Carbon competition between cell growth and product synthesis is the bottleneck in efficient N-acetyl glucosamine (GlcNAc) production in microbial cell factories. In this study, a xylose-induced T7 RNA polymerase-P_T7 promoter system was introduced in Escherichia coli W3110 to control the GlcNAc synthesis. Meanwhile, an arabinose-induced CRISPR interference (CRISPRi) system was applied to adjust cell growth by attenuating the transcription of key growth-related genes. By designing proper sgRNAs, followed by elaborate adjustment of the addition time and concentration of the two inducers, the carbon flux between cell growth and GlcNAc synthesis was precisely redistributed. Comparative metabolomics analysis results confirmed that the repression of pfkA and zwf significantly attenuated the TCA cycle and the synthesis of related amino acids, saving more carbon for the GlcNAc synthesis. Finally, the simultaneous repression of pfkA and zwf in strain GLA-14 increased the GlcNAc titer by 47.6% compared with that in E. coli without the CRISPRi system in a shake flask. GLA-14 could produce 90.9 g/L GlcNAc within 40 h in a 5 L bioreactor, with a high productivity of 2.27 g/L/h. This dynamic strategy for rebalancing cell growth and product synthesis could be applied in the fermentative production of other chemicals derived from precursors synthesized via central carbon metabolism.

Enzyme assembly guided by SPFH-induced functional inclusion bodies for enhanced cascade biocatalysis

Enzyme clustering into compact agglomerates could accelerate the processing of intermediates to enhance metabolic pathway flux. However, enzyme clustering is still a challenging task due to the lack of universal assembly strategy applicable to all enzymes. Therefore, we proposed an alternative enzyme assembly strategy based on functional inclusion bodies. First, functional inclusion bodies in cells were formed by the fusion expression of stomatin/prohibitin/flotillin/HflK/C (SPFH) domain and enhanced green fluorescent protein, as observed visually and by transmission electron microscopy. The formation of SPFH-induced functional inclusion bodies enhanced intermolecular polymerization as revealed by further analysis combined with Förster resonance energy transfer and bimolecular fluorescent complimentary. Finally, the functional inclusion bodies significantly improved the enzymatic catalysis in living cells, as proven by the examples with whole-cell biocatalysis of phenyllactic acid by Escherichia coli, and the production of N-acetylglucosamine by Bacillus subtilis. Our findings suggest that SPFH-induced functional inclusion bodies can enhance the cascade reaction of enzymes, to serve as a potential universal strategy for the construction of efficient microbial cell factories.

Synergetic utilization of glucose and glycerol for efficient myo-inositol biosynthesis

myo-Inositol (MI) as a dietary supplement can provide various health benefits. One major challenge to its efficient biosynthesis is to achieve proper distribution of carbon flux between growth and production. Herein, this challenge was overcome by synergetic utilization of glucose and glycerol. Specifically, glycerol was catabolized to support cell growth while glucose was conserved as the building block for MI production. Growth and production were coupled via the phosphotransferase system, and both modules were optimized to achieve efficient production. First, the optimal enzyme combination was established for the production module. It was observed that enhancing the production module resulted in both increased MI production and better cell growth. In addition, glucose was shown to inhibit glycerol utilization via carbon catabolite repression and the inhibition was released by over-expressing glycerol kinase. Furthermore, the inducible promoter was replaced by strong constitutive promoters to avoid inducer use. With these efforts, the final strain produced MI with both high titer and yield. In fed-batch cultivation, 76 g/L of MI was produced, showing scale-up potential. This study provides a promising strategy to achieve rational distribution of carbon flux.

Metabolic engineering of Bacillus amyloliquefaciens for enhanced production of S-adenosylmethionine by coupling of an engineered S-adenosylmethionine pathway and the tricarboxylic acid cycle

BACKGROUND

S-Adenosylmethionine (SAM) is a critical cofactor involved in many biochemical reactions. However, the low fermentation titer of SAM in methionine-free medium hampers commercial-scale production. The SAM synthesis pathway is specially related to the tricarboxylic acid (TCA) cycle in Bacillus amyloliquefaciens. Therefore, the SAM synthesis pathway was engineered and coupled with the TCA cycle in B. amyloliquefaciens to improve SAM production in methionine-free medium.

RESULTS

Four genes were found to significantly affect SAM production, including SAM2 from Saccharomyces cerevisiae, metA and metB from Escherichia coli, and native mccA. These four genes were combined to engineer the SAM pathway, resulting in a 1.42-fold increase in SAM titer using recombinant strain HSAM1. The engineered SAM pathway was subsequently coupled with the TCA cycle through deletion of succinyl-CoA synthetase gene sucC, and the resulted HSAM2 mutant produced a maximum SAM titer of 107.47 mg/L, representing a 0.59-fold increase over HSAM1. Expression of SAM2 in this strain via a recombinant plasmid resulted in strain HSAM3 that produced 648.99 mg/L SAM following semi-continuous flask batch fermentation, a much higher yield than previously reported for methionine-free medium.

CONCLUSIONS

This study reports an efficient strategy for improving SAM production that can also be applied for generation of SAM cofactors supporting group transfer reactions, which could benefit metabolic engineering, chemical biology and synthetic biology.

Metabolic engineering of Bacillus amyloliquefaciens LL3 for enhanced poly-γ-glutamic acid synthesis

Poly-γ-glutamic acid (γ-PGA) is a biocompatible and biodegradable polypeptide with wide-ranging applications in foods, cosmetics, medicine, agriculture and wastewater treatment. Bacillus amyloliquefaciens LL3 can produce γ-PGA from sucrose that can be obtained easily from sugarcane and sugar beet. In our previous work, it was found that low intracellular glutamate concentration was the limiting factor for γ-PGA production by LL3. In this study, the γ-PGA synthesis by strain LL3 was enhanced by chromosomally engineering its glutamate metabolism-relevant networks. First, the downstream metabolic pathways were partly blocked by deleting fadR, lysC, aspB, pckA, proAB, rocG and gudB. The resulting strain NK-A6 synthesized 4.84 g l-1 γ-PGA, with a 31.5% increase compared with strain LL3. Second, a strong promoter PC 2up was inserted into the upstream of icd gene, to generate strain NK-A7, which further led to a 33.5% improvement in the γ-PGA titre, achieving 6.46 g l-1 . The NADPH level was improved by regulating the expression of pgi and gndA. Third, metabolic evolution was carried out to generate strain NK-A9E, which showed a comparable γ-PGA titre with strain NK-A7. Finally, the srf and itu operons were deleted respectively, from the original strains NK-A7 and NK-A9E. The resulting strain NK-A11 exhibited the highest γ-PGA titre (7.53 g l-1 ), with a 2.05-fold improvement compared with LL3. The results demonstrated that the approaches described here efficiently enhanced γ-PGA production in B. amyloliquefaciens fermentation.

Creating an in vivo bifunctional gene expression circuit through an aptamer-based regulatory mechanism for dynamic metabolic engineering in Bacillus subtilis

Aptamer-based regulatory biosensors can dynamically regulate the expression of target genes in response to ligands and could be used in dynamic metabolic engineering for pathway optimization. However, the existing aptamer-ligand biosensors can only function with non-complementary DNA elements that cannot replicate in growing cells. Here, we construct an aptamer-based synthetic regulatory circuit that can dynamically upregulate and downregulate the expression of target genes in response to the ligand thrombin at transcriptional and translational levels, respectively, and further used this system to dynamically engineer the synthesis of 2'-fucosyllactose (2'-FL) in Bacillus subtilis. First, we demonstrated the binding of ligand molecule thrombin with the aptamer can induce the unwinding of fully complementary double-stranded DNA. Based on this finding, we constructed a bifunctional gene expression regulatory circuit using ligand thrombin-bound aptamers. The expression of the reporter gene ranged from 0.084- to 48.1-fold. Finally, by using the bifunctional regulatory circuit, we dynamically upregulated the expression of key genes fkp and futC and downregulated the expression of gene purR, resulting in the significant increase of 2'-FL titer from 24.7 to 674 mg/L. Compared with the other pathway-specific dynamic engineering systems, here the constructed aptamer-based regulatory circuit is independent of pathways, and can be generally used to fine-tune gene expression in other microbes.