Microbial Platform Research Articles

Microbial chassis design and engineering for production of gamma-aminobutyric acid.

Gamma-aminobutyric acid (GABA) is a non-protein amino acid which is widely applied in agriculture and pharmaceutical additive industries. GABA is synthesized from glutamate through irreversible α-decarboxylation by glutamate decarboxylase. Recently, microbial synthesis has become an inevitable trend to produce GABA due to its sustainable characteristics. Therefore, reasonable microbial platform design and metabolic engineering strategies for improving production of GABA are arousing a considerable attraction. The strategies concentrate on microbial platform optimization, fermentation process optimization, rational metabolic engineering as key metabolic pathway modification, promoter optimization, site-directed mutagenesis, modular transporter engineering, and dynamic switch systems application. In this review, the microbial producers for GABA were summarized, including lactic acid bacteria, Corynebacterium glutamicum, and Escherichia coli, as well as the efficient strategies for optimizing them to improve the production of GABA.

Insight into the autoproteolysis mechanism of the RsgI9 anti-σ factor from Clostridium thermocellum.

Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass-sensing RsgI-type anti-σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti-σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn-Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti-σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Pregnenolone and progesterone production from natural sterols using recombinant strain of Mycolicibacterium smegmatis mc2 155 expressing mammalian steroidogenesis system

BackgroundPregnenolone and progesterone are the life-important steroid hormones regulating essential vital functions in mammals, and widely used in different fields of medicine. Microbiological production of these compounds from sterols is based on the use of recombinant strains expressing the enzyme system cholesterol hydroxylase/C20-C22 lyase (CH/L) of mammalian steroidogenesis. However, the efficiency of the known recombinant strains is still low. New recombinant strains and combination approaches are now needed to produce these steroid hormones.ResultsBased on Mycolicibacterium smegmatis, a recombinant strain was created that expresses the steroidogenesis system (CYP11A1, adrenodoxin reductase, adrenodoxin) of the bovine adrenal cortex. The recombinant strain transformed cholesterol and phytosterol to form progesterone among the metabolites. When 3-methoxymethyl ethers of sterols were applied as bioconversion substrates, the corresponding 3-ethers of pregnenolone and dehydroepiandrosterone (DHEA) were identified as major metabolites. Under optimized conditions, the recombinant strain produced 85.2 ± 4.7 mol % 3-methoxymethyl-pregnenolone within 48 h, while production of 3-substituted DHEA was not detected. After the 3-methoxymethyl function was deprotected by acid hydrolysis, crystalline pregnenolone was isolated in high purity (over 98%, w/w). The structures of steroids were confirmed using TLC, HPLC, MS and 1H- and 13C-NMR analyses.ConclusionThe use of mycolicybacteria as a microbial platform for the expression of systems at the initial stage of mammalian steroidogenesis ensures the production of valuable steroid hormones—progesterone and pregnenolone from cholesterol. Selective production of pregnenolone from cholesterol is ensured by the use of 3-substituted cholesterol as a substrate and optimization of the conditions for its bioconversion. The results open the prospects for the generation of the new microbial biocatalysts capable of effectively producing value-added steroid hormones.

Biosynthesis of fragrance 2-phenylethanol from sugars by Pseudomonasputida

BackgroundPetrochemicals contribute to environmental issues, with concerns ranging from energy consumption and carbon emission to pollution. In contrast, microbial biorefineries offer eco-friendly alternatives. The solvent-tolerant Pseudomonasputida DOT-T1E serves as a suitable host for producing aromatic compounds, specifically l-phenylalanine and its derivative, 2-phenylethanol (2-PE), which find widespread applications in various industries.ResultsThis study focuses on enhancing 2-PE production in two l-phenylalanine overproducing strains of DOT-T1E, namely CM12-5 and CM12-5Δgcd (xylABE), which grow with glucose and glucose-xylose, respectively. To synthesize 2-PE from l-phenylalanine, these strains were transformed with plasmid pPE-1, bearing the Ehrlich pathway genes, and it was found higher 2-PE production with glucose (about 50–60 ppm) than with xylose (< 3 ppm). To understand the limiting factors, we tested the addition of phenylalanine and intermediates from the Ehrlich and shikimate pathways. The results identified intracellular l-phenylalanine as a key limiting factor for 2-PE production. To overcame this limitation, a chorismate mutase/prephenate dehydratase variant—insentive to feedback inhibition by aromatic amino acids—was introduced in the producing strains. This led to increased l-phenylalanine production and subsequently produced more 2-PE (100 ppm). Random mutagenesis of the strains also produced strains with higher l-phenylalanine titers and increased 2-PE production (up to 120 ppm). The improvements resulted from preventing dead-end product accumulation from shikimate and limiting the catabolism of potential pathway intermediates in the Ehrlich pathway. The study explored agricultural waste substrates, such as corn stover, sugarcane straw and corn-syrup as potential C sources. The best results were obtained using 2G substrates at 3% (between 82 and 100 ppm 2-PE), with glucose being the preferred sugar for 2-PE production among the monomeric sugars in these substrates.ConclusionsThe findings of this study offer strategies to enhance phenylalanine production, a key substrate for the synthesis of aromatic compounds. The ability of P.putida DOT-T1E to thrive with various C-sources and its tolerance to substrates, products, and potential toxicants in industrial wastes, are highlighted. The study identified and overcome possible bottlenecks for 2-PE production. Ultimately, the strains have potential to become efficient microbial platforms for synthesizing 2-PE from agro-industrial waste materials.

Selective colonization of multifunctional microbes that facilitates caproate production in microbial electrosynthesis system

As promising and value-added platform chemicals, the biosynthesis of medium-chain fatty acids (MCFAs, C6-C12) via chain elongation (CE) in microbial electrosynthesis systems (MES) has recently garnered significant attentions due to the unique bioelectrocatalytic behaviors and the reduction of exogenous electron donors (EDs). Caproate-synthesizing bacteria (CSB) played a crucial role in the generation of acetyl-CoA, which subsequently underwent reverse β oxidation to synthesize MCFAs. However, the presence of electrochemically active bacteria (EAB) was also pivotal for MES as they generated hydrogen in the cathodic electron transfer pathways, the specific colonization patterns of key symbionts remained unknown. The aim of this study was to investigate the selective colonization of EAB and CSB on the performance of caproate production in MES. The reactors colonized EAB and CSB achieved the maximum caproate concentration of 5332.5 mg COD/L, which was 7.9 and 1.3 times higher compared to that inoculated with either sole EAB or CSB, respectively. Moreover, the reactors colonized with mixed culture exhibited a clear redox peak and preferable electron transfer efficiency. CSB and EAB mutually interacted in metabolic activities, thereby resulting in increased substrate utilization and caproate production. The findings of this study provide a new strategy and insights for value-added chemicals recovery in microbial electrosynthesis platform.

A CD25-biased interleukin-2 for autoimmune therapy engineered via a semi-synthetic organism

BackgroundNatural cytokines are poorly suited as therapeutics for systemic administration due to suboptimal pharmacological and pharmacokinetic (PK) properties. Recombinant human interleukin-2 (rhIL-2) has shown promise for treatment of autoimmune (AI) disorders yet exhibits short systemic half-life and opposing immune responses that negate an appropriate therapeutic index.MethodsA semi-synthetic microbial technology platform was used to engineer a site-specifically pegylated form of rhIL-2 with enhanced PK, specificity for induction of immune-suppressive regulatory CD4 + T cells (Tregs), and reduced stimulation of off-target effector T and NK cells. A library of rhIL-2 molecules was constructed with single site-specific, biorthogonal chemistry-compatible non-canonical amino acids installed near the interface where IL-2 engages its cognate receptor βγ (IL-2Rβγ) signaling complex. Biorthogonal site-specific pegylation and functional screening identified variants that retained engagement of the IL-2Rα chain with attenuated potency at the IL-2Rβγ complex.ResultsPhenotypic screening in mouse identifies SAR444336 (SAR’336; formerly known as THOR-809), rhIL-2 pegylated at H16, as a potential development candidate that specifically expands peripheral CD4+ Tregs with upregulation of markers that correlate with their suppressive function including FoxP3, ICOS and Helios, yet minimally expands CD8 + T or NK cells. In non-human primate, administration of SAR’336 also induces dose-dependent expansion of Tregs and upregulated suppressive markers without significant expansion of CD8 + T or NK cells. SAR’336 administration reduces inflammation in a delayed-type hypersensitivity mouse model, potently suppressing CD4+ and CD8 + T cell proliferation.ConclusionSAR’336 is a specific Treg activator, supporting its further development for the treatment of AI diseases.

Efficient production of butyl butyrate from mannitol by engineered Clostridium tyrobutyricum

Butyl butyrate has a wide range of applications as flavors, solvents, and biofuels. Green production of butyl butyrate by microorganism fermentation in an industry level attracts great attention on the basis of bio-refinery. In this study, a dark horse Clostridium tyrobutyricum was employed for de novo production of butyl butyrate. Herein, reinforcement of EMP and butyl butyrate fermentation pathways (e.g., pfkA, pykA, crt-hbd-bcd/etfAB, adhE2 and VAAT) and regulation of carbon distribution towards butyl butyrate (e.g., CAT1 inactivation or overexpression of NADPH-dependent hbd1) were conducted in C. tyrobutyricum (MUV3) to enhance butyl butyrate production. The outstanding strain MV12 generated 1.8-fold butyl butyrate production compared to the initial strain MUV3. Subsequently, organic nitrogen source concentration was optimized, 21.1 g/L and 30.1 g/L butyl butyrate were obtained in 37 °C and 25 °C, respectively. Ultimately, fed-batch with two-stage temperature shift fermentation was performed for high titer and yield of butyl butyrate production (142.6 g/L titer and 0.28 mol/mol yield) from mannitol. Hence this study presented a microbial fermentation platform for butyl butyrate or other value-added chemicals production from renewable resources.

Development of a co-culture system for green production of caffeic acid from sugarcane bagasse hydrolysate.

Caffeic acid (CA) is a phenolic acid compound widely used in pharmaceutical and food applications. However, the efficient synthesis of CA is usually limited by the resources of individual microbial platforms. Here, a cross-kingdom microbial consortium was developed to synthesize CA from sugarcane bagasse hydrolysate using Escherichia coli and Candida glycerinogenes as chassis. In the upstream E. coli module, shikimate accumulation was improved by intensifying the shikimate synthesis pathway and blocking shikimate metabolism to provide precursors for the downstream CA synthesis module. In the downstream C. glycerinogenes module, conversion of p-coumaric acid to CA was improved by increasing the supply of the cytoplasmic cofactor FAD(H2). Further, overexpression of ABC transporter-related genes promoted efflux of CA and enhanced strain resistance to CA, significantly increasing CA titer from 103.8 mg/L to 346.5 mg/L. Subsequently, optimization of the inoculation ratio of strains SA-Ec4 and CA-Cg27 in this cross-kingdom microbial consortium resulted in an increase in CA titer to 871.9 mg/L, which was 151.6% higher compared to the monoculture strain CA-Cg27. Ultimately, 2311.6 and 1943.2 mg/L of CA were obtained by optimization of the co-culture system in a 5 L bioreactor using mixed sugar and sugarcane bagasse hydrolysate, respectively, with 17.2-fold and 14.6-fold enhancement compared to the starting strain. The cross-kingdom microbial consortium developed in this study provides a reference for the production of other aromatic compounds from inexpensive raw materials.

Pseudomonas putida as a platform for medium-chain length α,ω-diol production: Opportunities and challenges.

Medium-chain-length α,ω-diols (mcl-diols) play an important role in polymer production, traditionally depending on energy-intensive chemical processes. Microbial cell factories offer an alternative, but conventional strains like Escherichia coli and Saccharomyces cerevisiae face challenges in mcl-diol production due to the toxicity of intermediates such as alcohols and acids. Metabolic engineering and synthetic biology enable the engineering of non-model strains for such purposes with P. putida emerging as a promising microbial platform. This study reviews the advancement in diol production using P. putida and proposes a four-module approach for the sustainable production of diols. Despite progress, challenges persist, and this study discusses current obstacles and future opportunities for leveraging P. putida as a microbial cell factory for mcl-diol production. Furthermore, this study highlights the potential of using P. putida as an efficient chassis for diol synthesis.

Tailored polyhydroxyalkanoate production from renewable non-fatty acid carbon sources using engineered Cupriavidus necator H16

As thermoplastic, nontoxic, and biocompatible polyesters, polyhydroxyalkanoates (PHAs) are considered promising biodegradable plastic candidates for diverse applications. Short-chain-length/medium-chain-length (SCL/MCL) PHA copolymers are flexible and versatile PHAs that are typically produced from fatty acids, which are expensive and toxic. Therefore, to achieve the sustainable biosynthesis of SCL/MCL-PHAs from renewable non-fatty acid carbon sources (e.g., sugar or CO2), we used the lithoautotrophic bacterium Cupriavidus necator H16 as a microbial platform. Specifically, we synthesized tailored PHA copolymers with varying MCL-3-hydroxyalkanoate (3HA) compositions (10–70 mol%) from fructose by rewiring the MCL-3HA biosynthetic pathways, including (i) the thioesterase-mediated free fatty acid biosynthetic pathway coupled with the beta-oxidation cycle and (ii) the hydroxyacyl transferase-mediated fatty acid de novo biosynthetic pathway. In addition to sugar-based feedstocks, engineered strains are also promising platforms for the lithoautotrophic production of SCL/MCL-PHAs from CO2. The set of engineered C. necator strains developed in this study provides greater opportunities to produce customized polymers with controllable monomer compositions from renewable resources.

Establishing CRISPRi for Programmable Gene Repression and Genome Evolution in Cupriavidus necator.

Cupriavidus necator H16 is a "Knallgas" bacterium with the ability to utilize various carbon sources and has been employed as a versatile microbial cell factory to produce a wide range of value-added compounds. However, limited genome engineering, especially gene regulation methods, has constrained its full potential as a microbial production platform. The advent of CRISPR/Cas9 technology has shown promise in addressing this limitation. Here, we developed an optimized CRISPR interference (CRISPRi) system for gene repression in C. necator by expressing a codon-optimized deactivated Cas9 (dCas9) and appropriate single guide RNAs (sgRNAs). CRISPRi was proven to be a programmable and controllable tool and could successfully repress both exogenous and endogenous genes. As a case study, we decreased the accumulation of polyhydroxyalkanoate (PHB) via CRISPRi and rewired the carbon fluxes to the synthesis of lycopene. Additionally, by disturbing the expression of DNA mismatch repair gene mutS with CRISPRi, we established CRISPRi-Mutator for genome evolution, rapidly generating mutant strains with enhanced hydrogen peroxide tolerance and robustness in microbial electrosynthesis (MES) system. Our work provides an efficient CRISPRi toolkit for advanced genetic manipulation and optimization of C. necator cell factories for diverse biotechnology applications.

De Novo Synthesis of Dihydro-β-ionone through Metabolic Engineering and Bacterium-Yeast Coculture.

Dihydro-β-ionone is a common type of ionone used in the flavor and fragrance industries because of its characteristic scent. The production of flavors in microbial cell factories offers a sustainable and environmentally friendly approach to accessing them, independent of extraction from natural sources. However, the native pathway of dihydro-β-ionone remains unclear, hindering heterologous biosynthesis in microbial hosts. Herein, we devised a microbial platform for de novo syntheses of dihydro-β-ionone from a simple carbon source with glycerol. The complete dihydro-β-ionone pathway was reconstructed in Escherichia coli with multiple metabolic engineering strategies to generate a strain capable of producing 8 mg/L of dihydro-β-ionone, although this was accompanied by a surplus precursor β-ionone in culture. To overcome this issue, Saccharomyces cerevisiae was identified as having a conversion rate for transforming β-ionone to dihydro-β-ionone that was higher than that of E. coli via whole-cell catalysis. Consequently, the titer of dihydro-β-ionone was increased using the E. coli-S. cerevisiae coculture to 27 mg/L. Our study offers an efficient platform for biobased dihydro-β-ionone production and extends coculture engineering to overproducing target molecules in extended metabolic pathways.

Overview of the research work of Dr. Hui-Ping Chuang

Dr Hui-Ping Chuang, Sustainable Environment Research Laboratories, National Cheng Kung University, Taiwan, is investigating the ability of different environmental microorganisms to degrade pollutants and produce sustainable resources. A particular focus is on the microbes involved in the nitrogen cycle. She collaborates with Japanese researchers at DHS Technology, Hiroshima University and Tohoku University, among others, as well as communicating with Taiwan researchers based at National Taiwan University and National Chiayi University. Chuang is currently involved in five studies: exploring different types of sponge media for cultivating slow-growing functional microbes; investigating aerobic autotrophic microbes for the conversion of greenhouse potential (GHP) gases such as N2O and CO2 to mitigate global warming; investigating the application of different functional microbes for treating different types of wastewaters containing nitrogenous compounds or alkylphenol compounds or long-term alkanes; cultivating a chloroethane-degrading community used for remediation of soil and groundwater pollution; exploring the use of an anaerobic microbial community for the treatment of biological waste to produce the green energy as methane (CH4) and nitrogen fertiliser as resources; and developing a microbial monitoring platform integrating chemical and molecular analyses. This microbial monitoring platform can be used to detect and quantify nitrogen oxidising or reducing microorganisms, as well as other groups with some modifications and it has now been used in various fields to understand important relationships.

Identifying and charactering a 4-aminobutyryl-CoA ligase for the production of butyrolactam

Butyrolactam, a crucial four-carbon molecule, serves as building block in synthesis of polyamides. While biosynthesis of butyrolactam from renewable carbon sources offers a more sustainable approach, it has faced challenges in achieving high product titer and yield. Here, an efficient microbial platform for butyrolactam production was constructed by elimination of rate-limiting step and systematic pathway optimization. Initially, a superior 4-aminobutyryl-CoA ligase was discovered and characterized among six acyl-CoA ligases from different sources, which greatly improved the pathway efficiency. Subsequent optimizations were implemented to further enhance butyrolactam production, including promoter engineering, the elimination of competing pathways, transporter engineering and improving the availability of precursors. There efforts resulted in achieving approximately 2 g/L butyrolactam in shake flask experiments. Finally, the biosynthesis of butyrolactam was scaled up in a 3-L bioreactor in 84 hours, resulting in a significantly increased production of 45.2 g/L, with a carbon yield of 0.34 g/g glucose. This study highlights the construction of a microbial platform with the capability to achieve elevated levels of butyrolactam production and unlocks its potential in sustainable manufacturing processes.

Influence of acetate concentration on acetone production by a modified Acetobacterium woodii

Global warming is the driving force for developing production processes of chemical compounds based on CO2 reduction technologies. Bacteria can act as biological catalysts that reduce this gaseous substrate in added-value compounds. Acetobacterium woodii is one of the best-performing strains on H2–CO2 blends and naturally produces acetate. Acetone is a raw material deeply used in the chemical industry, and its global demand is increasing. Acetone-butanol-ethanol (ABE) fermentation is the oldest microbial production platform for acetone synthesis from organic substrates, and Clostridium acetobutylicum is the model strain for its production. In various wild-type acetogens and ABE-producing Clostridium species, acetate positively influences the synthesis of reduced products. In this work, a modified A. woodii strain expressing the enzymes of the acetone pathway from C. acetobutylicum was used to convert H2–CO2 streams into acetone. This study aims to assess the impact of acetate on acetone production catalyzed by such a modified A. woodii. Tests were carried out in serum bottles and a continuous stirred tank reactor up to a pressure of 10 bar, in gas-batch or in continuous gassing, providing different gas mixes. Outcomes indicated that acetone synthesis was stimulated when acetate concentration in the medium exceeded the threshold of 100–120 mM. Thus, acetic acid can affect acetone productivity in the modified A. woodii strain. This outcome should be considered in the design of fermentation processes, especially in setting up fermentations with the liquid continuous operative mode.

Direct and robust citramalate production from brown macroalgae using fast-growing Vibrio sp. dhg

Brown macroalgae is a promising feedstock for biorefinery owing to its high biomass productivity and contents of carbohydrates such as alginate and mannitol. However, the limited availability of microbial platforms efficiently catabolizing the brown macroalgae sugars has restricted its utilization. In this study, the direct production of citramalate, an important industrial compound, was demonstrated from brown macroalgae by utilizing Vibrio sp. dhg, which has a remarkably efficient catabolism of alginate and mannitol. Specifically, citramalate synthase from Methanocaldococcus jannaschii was synthetically expressed, and competing pathways were removed to maximally redirect the carbon flux toward citramalate production. Notably, a resulting strain, VXHC, produced citramalate up to 9.8 g/L from a 20 g/L mixture of alginate and mannitol regardless of their ratios. Citramalate was robustly produced even when diverse brown macroalgae were provided directly. Collectively, this study showcased the high potential of brown macroalgae biorefinery using Vibrio sp. dhg.

Scalable and Consolidated Microbial Platform for Rare Earth Element Leaching and Recovery from Waste Sources.

Chemical methods for the extraction and refinement of technologically critical rare earth elements (REEs) are energy-intensive, hazardous, and environmentally destructive. Current biobased extraction systems rely on extremophilic organisms and generate many of the same detrimental effects as chemical methodologies. The mesophilic methylotrophic bacterium Methylobacterium extorquens AM1 was previously shown to grow using electronic waste by naturally acquiring REEs to power methanol metabolism. Here we show that growth using electronic waste as a sole REE source is scalable up to 10 L with consistent metal yields without the use of harsh acids or high temperatures. The addition of organic acids increases REE leaching in a nonspecific manner. REE-specific bioleaching can be engineered through the overproduction of REE-binding ligands (called lanthanophores) and pyrroloquinoline quinone. REE bioaccumulation increases with the leachate concentration and is highly specific. REEs are stored intracellularly in polyphosphate granules, and genetic engineering to eliminate exopolyphosphatase activity increases metal accumulation, confirming the link between phosphate metabolism and biological REE use. Finally, we report the innate ability of M. extorquens to grow using other complex REE sources, including pulverized smartphones, demonstrating the flexibility and potential for use as a recovery platform for these critical metals.

Xylose and shikimate transporters facilitates microbial consortium as a chassis for benzylisoquinoline alkaloid production

Plant-sourced aromatic amino acid (AAA) derivatives are a vast group of compounds with broad applications. Here, we present the development of a yeast consortium for efficient production of (S)-norcoclaurine, the key precursor for benzylisoquinoline alkaloid biosynthesis. A xylose transporter enables the concurrent mixed-sugar utilization in Scheffersomyces stipitis, which plays a crucial role in enhancing the flux entering the highly regulated shikimate pathway located upstream of AAA biosynthesis. Two quinate permeases isolated from Aspergillus niger facilitates shikimate translocation to the co-cultured Saccharomyces cerevisiae that converts shikimate to (S)-norcoclaurine, resulting in the maximal titer (11.5 mg/L), nearly 110-fold higher than the titer reported for an S. cerevisiae monoculture. Our findings magnify the potential of microbial consortium platforms for the economical de novo synthesis of complex compounds, where pathway modularization and compartmentalization in distinct specialty strains enable effective fine-tuning of long biosynthetic pathways and diminish intermediate buildup, thereby leading to increases in production.

Production of carotenoids from aromatics and pretreated lignocellulosic biomass by Novosphingobium aromaticivorans.

There is economic and environmental interest in generating commodity chemicals from renewable resources, such as lignocellulosic biomass, that can substitute for chemicals derived from fossil fuels. The bacterium Novosphingobium aromaticivorans is a promising microbial platform for producing commodity chemicals from lignocellulosic biomass because it can produce these from compounds in pretreated lignocellulosic biomass, which many industrial microbial catalysts cannot metabolize. Here, we show that N. aromaticivorans can be engineered to produce several valuable carotenoids. We also show that engineered N. aromaticivorans strains can produce these lipophilic chemicals concurrently with the extracellular commodity chemical 2-pyrone-4,6-dicarboxylic acid when grown in a complex liquor obtained from alkaline pretreated lignocellulosic biomass. Concurrent microbial production of valuable intra- and extracellular products can increase the economic value generated from the conversion of lignocellulosic biomass-derived compounds into commodity chemicals and facilitate the separation of water- and membrane-soluble products.

Discovery and remodeling of Vibrio natriegens as a microbial platform for efficient formic acid biorefinery

Formic acid (FA) has emerged as a promising one-carbon feedstock for biorefinery. However, developing efficient microbial hosts for economically competitive FA utilization remains a grand challenge. Here, we discover that the bacterium Vibrio natriegens has exceptional FA tolerance and metabolic capacity natively. This bacterium is remodeled by rewiring the serine cycle and the TCA cycle, resulting in a non-native closed loop (S-TCA) which as a powerful metabolic sink, in combination with laboratory evolution, enables rapid emergence of synthetic strains with significantly improved FA-utilizing ability. Further introduction of a foreign indigoidine-forming pathway into the synthetic V. natriegens strain leads to the production of 29.0 g · L−1 indigoidine and consumption of 165.3 g · L−1 formate within 72 h, achieving a formate consumption rate of 2.3 g · L−1 · h−1. This work provides an important microbial chassis as well as design rules to develop industrially viable microorganisms for FA biorefinery.