Production of isopropyl and butyl esters by Clostridium mono-culture and co-culture

Deletion of atypical type II restriction genes in Clostridium cellulovorans using a Cas9-based gene editing system

The anaerobic bacterium Clostridium cellulovorans is a promising candidate for the sustainable production of biofuels and platform chemicals due to its cellulolytic properties. However, the genomic engineering of the species is hampered because of its poor genetic accessibility and the lack of genetic tools. To overcome this limitation, a protocol for triparental conjugation was established that enables the reliable transfer of vectors for markerless chromosomal modification into C. cellulovorans. The availability of reporter genes is another requirement for strain engineering and biotechnological applications. In this work, the oxygen-free fluorescence absorption-shift tag (FAST) system was used to characterize promoter strength in C. cellulovorans. Selected promoters were used to establish a CRISPR/Cas system for markerless chromosomal modifications. For stringent control of expression of Cas9, a theophylline-dependent riboswitch was used, and additionally, the anti-CRISPR protein AcrIIA4 was used to reduce the basal activity of the Cas9 in the off-state of the riboswitch. Finally, the newly established CRISPR/Cas system was used for the markerless deletion of the genes encoding two restriction endonucleases of a type II restriction-modification (RS) system from the chromosome of C. cellulovorans. In comparison to the WT, the conjugation efficiency when using the deletion mutant as the recipient strain was improved by about one order of magnitude, without the need for prior C. cellulovorans-specific in vivo methylation of the conjugative plasmid in the E. coli donor strain. KEY POINTS: • Quantification of heterologous promoters enables rational choice for genetic engineering. • CRISPR/Cas with riboswitch and anti-CRISPR allows efficient gene deletion in C. cellulovorans. • Conjugation protocol and type II REase deletion enhance genetic accessibility.

Carbon quantum dots in N,N'-Dicyclohexylcarbodiimide assisted cellulose: A fluorescence sensitive approach for ex vivo glucose monitoring in human serum

Bioactive functional materials have been focused recently because of their superior properties due to structural orientations. Herein, carbon quantum dots (CQDs) encapsulated chemically modified carboxymethyl cellulose (CMC) nanocomposites are designed for non-enzymatic ex vivo glucose sensing by a low-cost green technique. The N,N'-Dicyclohexylcarbodiimide (DCC) assisted Steglich esterification between CMC and glucose is responsible for the fluorescence "Turn ON-OFF" mechanism behind glucose detection. The in vitro sensing study derived a limit of detection (LOD) of 7 nM for glucose covering two linear ranges from 0 to 0.06 mM (R2 = 0.9346) and 1.28 to 61.44 mM (R2 = 0.9704). The sensing system maintained excellent stability under extreme ionic strength and pH conditions and the high selectivity is successfully studied against interferents such as homologous sugars, amino acids, cations, and anions. Clinical potential of the proposed sensor is validated through direct testing in human blood samples against commercial glucometer. The sensor proved its reliability with recovery rates of 100 ± 5 % confirming its promising application in glucose monitoring towards effective diabetes management.

Bioproduction of Geranyl Esters by Integrating Microbial Biosynthesis and Enzymatic Conversion

Geranyl esters (GEs) are valuable monoterpene esters derived from the esterification of geraniol and various carboxylic acids with a range of unique aromas and properties, making them valuable in perfumery, pharmaceutical, and cosmetic applications. Lipase-mediated esterification is considered to be a sustainable process but is challenged by the lack of a compatible catalytic method in conjunction with a customized microbial biosynthesis of geraniol. In this study, we developed an integrated process to convert glycerol and various carboxylates into GEs. The process includes microbial biosynthesis of geraniol using metabolically engineered Escherichia coli and enzymatic conversion of geraniol into GEs in a fermentation medium-organic biphasic system using an immobilized lipase. The enzymatic step for esterifying the target carboxylates with geraniol achieved >90% conversion under the optimized condition. Coupled with the geraniol from microbial fermentation, 0.59 g/L geranyl butyrate and 1.04 g/L geranyl hexanoate were produced subsequently, demonstrating the feasibility of converting renewable source into monoterpene esters through this integrated process, which bypassed feeding extra geraniol in the conventional lipase-mediated GE synthesis.

The potential of native and engineered Clostridia for biomass biorefining

Since their first industrial application in the acetone-butanol-ethanol (ABE) fermentation in the early 1900s, Clostridia have found large application in biomass biorefining. Overall, their fermentation products include organic acids (e.g., acetate, butyrate, lactate), short chain alcohols (e.g., ethanol, n-butanol, isobutanol), diols (e.g., 1,2-propanediol, 1,3-propanediol) and H2 which have several applications such as fuels, building block chemicals, solvents, food and cosmetic additives. Advantageously, several clostridial strains are able to use cheap feedstocks such as lignocellulosic biomass, food waste, glycerol or C1-gases (CO2, CO) which confer them additional potential as key players for the development of processes less dependent from fossil fuels and with reduced greenhouse gas emissions. The present review aims to provide a survey of research progress aimed at developing Clostridium-mediated biomass fermentation processes, especially as regards strain improvement by metabolic engineering.

Microbial cell factory for butyl butyrate production: Knowledges and perspectives

Butyl butyrate is a short-chain fatty acid ester (C8) with a fruity aroma. It has broad prospects in the fields of foods, cosmetics and biofuels. At present, butyl butyrate is produced by chemical synthesis in the industry, but it is highly dependent on petroleum-based products. The growing concerns regarding the future scarcity of fossil fuels have been strongly promoted the transition from traditional fossil fuels and products to renewable bioenergy and biochemicals. Therefore, it is necessary to develop a green biochemical technology to replace traditional petroleum-based materials. In recent years, microorganisms such as Escherichia coli and Clostridium have been engineered to serve as cell factories for the sustainable one-pot production of short-chain fatty acid esters, including butyl butyrate. This opinion highlights the recent development in the use of lipases and alcohol acyltransferases (AATs) for butyl butyrate production in microbial fermentation, as well as future perspectives.

Simultaneous fermentation and enzymatic biocatalysis-a useful process option?

Biotransformation with enzymes and de novo syntheses with whole-cell biocatalysts each have specific advantages. These can be combined to achieve processes with optimal performance. A recent approach is to perform bioconversion processes and enzymatic catalysis simultaneously in one-pot. This is a well-established process in the biorefinery, where starchy or cellulosic material is degraded enzymatically and simultaneously used as substrate for microbial cultivations. This procedure leads to a number of advantages like saving in time but also in the needed equipment (e.g., reaction vessels). In addition, the inhibition or side-reaction of high sugar concentrations can be overcome by combining the processes. These benefits of coupling microbial conversion and enzymatic biotransformation can also be transferred to other processes for example in the sector of biofuel production or in the food industry. However, finding a compromise between the different requirements of the two processes is challenging in some cases. This article summarises the latest developments and process variations.

Unravelling the hidden power of esterases for biomanufacturing of short-chain esters

Microbial production of esters has recently garnered wide attention, but the current production metrics are low. Evidently, the ester precursors (organic acids and alcohols) can be accumulated at higher titers by microbes like Escherichia coli. Hence, we hypothesized that their 'direct esterification' using esterases will be efficient. We engineered esterases from various microorganisms into E. coli, along with overexpression of ethanol and lactate pathway genes. High cell density fermentation exhibited the strains possessing esterase-A (SSL76) and carbohydrate esterase (SSL74) as the potent candidates. Fed-batch fermentation at pH 7 resulted in 80 mg/L of ethyl acetate and 10 mg/L of ethyl lactate accumulation by SSL76. At pH 6, the total ester titer improved by 2.5-fold, with SSL76 producing 225 mg/L of ethyl acetate, and 18.2 mg/L of ethyl lactate, the highest reported titer in E. coli. To our knowledge, this is the first successful demonstration of short-chain ester production by engineering 'esterases' in E. coli.

De novo biosynthesis of butyl butyrate in engineered Clostridium tyrobutyricum

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

Construction of a Microbial Consortium for the De Novo Synthesis of Butyl Butyrate from Renewable Resources

Butyl butyrate has shown wide applications in food, cosmetic, and biofuel sectors. Currently, biosynthesis of butyl butyrate still requires exogenous addition of precursors and lipase, which increases the production cost and limits further large-scale development. In this study, a microbial consortium was first designed to realize direct butyl butyrate production from lignocellulose. The highest butyl butyrate concentration of 34.42 g/L was detected in the solvent phase from 60 g/L glucose using a microbial coculture system composed of Clostridium acetobutylicum NJ4 and Clostridium tyrobutyricum LD with the elimination of butyric acid supplementation. Meanwhile, 13.52 g/L butyl butyrate was synthesized from 60 g/L glucose using a microbial consortium composed of three strains including strain NJ4, strain LD, and Escherichia coli BL21- pET-29a(+)-LE without the addition of any exogenous precursors and lipase. In addition, 2.94 g/L butyl butyrate could be directly produced from 60 g/L microcrystalline cellulose when Trichoderma asperellum was added to the above-mentioned three-strain microbial consortium. This four-strain microbial consortium represents the first study regarding the direct butyl butyrate production from lignocellulose without the supplementation of exogenous precursors and lipase, which may be extended to the biosynthesis of other short-chain esters, such as ethyl acetate and butyl lactate.

Current progress on engineering microbial strains and consortia for production of cellulosic butanol through consolidated bioprocessing

In the last decades, fermentative production of n-butanol has regained substantial interest mainly owing to its use as drop-in-fuel. The use of lignocellulose as an alternative to traditional acetone-butanol-ethanol fermentation feedstocks (starchy biomass and molasses) can significantly increase the economic competitiveness of biobutanol over production from non-renewable sources (petroleum). However, the low cost of lignocellulose is offset by its high recalcitrance to biodegradation which generally requires chemical-physical pre-treatment and multiple bioreactor-based processes. The development of consolidated processing (i.e., single-pot fermentation) can dramatically reduce lignocellulose fermentation costs and promote its industrial application. Here, strategies for developing microbial strains and consortia that feature both efficient (hemi)cellulose depolymerization and butanol production will be depicted, that is, rational metabolic engineering of native (hemi)cellulolytic or native butanol-producing or other suitable microorganisms; protoplast fusion of (hemi)cellulolytic and butanol-producing strains; and co-culture of (hemi)cellulolytic and butanol-producing microbes. Irrespective of the fermentation feedstock, biobutanol production is inherently limited by the severe toxicity of this solvent that challenges process economic viability. Hence, an overview of strategies for developing butanol hypertolerant strains will be provided.

Recent advances in microbial co-culture for production of value-added compounds

Micro-organisms have often been used to produce bioactive compounds as antibiotics, antifungals, and anti-tumors, etc. due to their easy and applicable culture, genetic manipulation, and extraction, etc. Mainly, microbial mono-cultures have been applied to produce value-added compounds and gotten numerous valuable results. However, mono-culture also has several complicated problems, such as metabolic burdens affecting the growth and development of the host, leading to a decrease in titer of the target compound. To circumvent those limitations, microbial co-culture has been technically developed and gained much interest compared to mono-culture. For example, co-culture simplifies the design of artificial biosynthetic pathways and restricts the recombinant host's metabolic burden, causing increased titer of desired compounds. This paper summarizes the recent advanced progress in applying microbial platform co-culture to produce natural products, such as flavonoid, terpenoid, alkaloid, etc. Furthermore, importantly different strategies for enhancing production, overcoming the metabolic burdens, building autonomous modulation of cell growth rate and culture composition in response to a quorum-sensing signal, etc., were also described in detail.

Next-Generation Genetic and Fermentation Technologies for Safe and Sustainable Production of Food Ingredients: Colors and Flavorings

A growing human population is a significant issue in food security owing to the limited land and resources available for agricultural food production. To solve these problems, sustainable food manufacturing processes and the development of alternative foods and ingredients are needed. Metabolic engineering and synthetic biology can help solve the food security issue and satisfy the demand for alternative food production. Bioproduction of food ingredients by microbial fermentation is a promising method to replace current manufacturing processes, such as extraction from natural materials and chemical synthesis, with more ecofriendly and sustainable operations. This review highlights successful examples of bioproduction for food additives by engineered microorganisms, with an emphasis on colorants and flavors that are extensively used in the food industry. Recent strain engineering developments and fermentation strategies for producing selected food colorants and flavors are introduced with discussions on the current status and future perspectives.

Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Comprehensive evaluation for the one-pot biosynthesis of butyl acetate by using microbial mono- and co-cultures

BACKGROUND

Butyl acetate has shown wide applications in food, cosmetics, medicine, and biofuel sectors. These short-chain fatty acid esters can be produced by either chemical or biological synthetic process with corresponding alcohols and acids. Currently, biosynthesis of short chain fatty acid esters, such as butyl butyrate, through microbial fermentation systems has been achieved; however, few studies regarding biosynthesis of butyl acetate were reported.

RESULTS

In this study, three proof-of-principle strategies for the one-pot butyl acetate production from glucose through microbial fermentation were designed and evaluated. (1) 7.3 g/L of butyl acetate was synthesized by butanol-producing Clostridium acetobutylicum NJ4 with the supplementation of exogenous acetic acid; (2) With the addition of butanol, 5.76 g/L of butyl acetate can be synthesized by acetate-producing Actinobacillus succinogenes130z (ΔpflA); (3) Microbial co-culture of C. acetobutylicum NJ4 and A. succinogenes130z (ΔpflA) can directly produce 2.2 g/L of butyl acetate from glucose by using microbial co-culture system with the elimination of precursors. Through the further immobilization of A. succinogenes130z (ΔpflA), butyl acetate production was improved to 2.86 g/L.

CONCLUSION

Different microbial mono- and co-culture systems for butyl acetate biosynthesis were successfully constructed. These strategies may be extended to the biosynthesis of a wide range of esters, especially to some longer chain ones.

Microbial production of butyl butyrate: from single strain to cognate consortium

Butyl butyrate (BB) is an important chemical with versatile applications in beverage, food and cosmetics industries. Since chemical synthesis of BB may cause adverse impacts on the environment, biotechnology is an emerging alternative approach for microbial esters biosynthesis. BB can be synthesized by using a single Clostridium strain natively producing butanol or butyrate, with exogenously supplemented butyrate or butanol, in the presence of lipase. Recently, E. coli strains have been engineered to produce BB, but the titer and yield remained very low. This review highlighted a new trend of developing cognate microbial consortium for BB production and associated challenges, and end up with new prospects for further improvement for microbial BB biosynthesis.

Developing Clostridia as Cell Factories for Short- and Medium-Chain Ester Production

Short- and medium-chain volatile esters with flavors and fruity fragrances, such as ethyl acetate, butyl acetate, and butyl butyrate, are usually value-added in brewing, food, and pharmacy. The esters can be naturally produced by some microorganisms. As ester-forming reactions are increasingly deeply understood, it is possible to produce esters in non-natural but more potential hosts. Clostridia are a group of important industrial microorganisms since they can produce a variety of volatile organic acids and alcohols with high titers, especially butanol and butyric acid through the CoA-dependent carbon chain elongation pathway. This implies sufficient supplies of acyl-CoA, organic acids, and alcohols in cells, which are precursors for ester production. Besides, some Clostridia could utilize lignocellulosic biomass, industrial off-gas, or crude glycerol to produce other branched or straight-chain alcohols and acids. Therefore, Clostridia offer great potential to be engineered to produce short- and medium-chain volatile esters. In the review, the efforts to produce esters from Clostridia via in vitro lipase-mediated catalysis and in vivo alcohol acyltransferase (AAT)-mediated reaction are comprehensively revisited. Besides, the advantageous characteristics of several Clostridia and clostridial consortia for bio-ester production and the driving force of synthetic biology to clostridial chassis development are also discussed. It is believed that synthetic biotechnology should enable the future development of more effective Clostridia for ester production.

Expanding the Boundary of Biorefinery: Organonitrogen Chemicals from Biomass

Organonitrogen chemicals are essential in many aspects of modern life. Over 80% of the top 200 prescribed pharmaceutical products contain at least one nitrogen atom in the molecule, while all top 10 agrochemicals contain nitrogen, just to name a few. At present, the prevailing industrial processes for manufacturing organonitrogen chemicals start from nonrenewable fossil resources, but eventually we have to make these chemicals in a more sustainable manner. Biomass represents the largest renewable carbon resource on earth, which is inexpensive and widely available. Integrating biomass into the organonitrogen chemical supply chain will mitigate the carbon footprint, diversify the product stream, and enhance the economic competitiveness of biorefinery. Short-cut synthesis routes can be created for oxygen-containing organonitrogen compounds by exploiting the inherent oxygen functionalities in the biomass resources. Moreover, for nitrogen-containing biomass components such as chitin, a unique opportunity to make organonitrogen chemicals bypassing the energy-intensive Haber-Bosch ammonia synthesis process arises. Estimated at 100 billion tons of annual production in the world, chitin captures more nitrogen than the Haber-Bosch process in the form of amide functional groups in its polymer side chain.In this Account, we intend to summarize our efforts to establish new reaction routes to synthesize valuable organonitrogen chemicals from renewable resources. Enabled by tailor-designed catalytic systems, diverse nitrogen-containing products including amines, amino acids, nitriles, and N-heterocycles have been obtained from a range of biomass feedstock either directly or via intermediate platform compounds. Two strategies to produce organonitrogen chemicals are presented. For platform chemicals derived from cellulose, hemicellulose, lignin, and lipids, which are enriched with oxygen functionalities, in particular, hydroxyl groups, the key chemistry to be developed is the catalytic transformation of hydroxyl groups into nitrogen-containing groups using NH₃ as the nitrogen source. Along this line, Ru- and Ni-based heterogeneous catalysts are developed to convert alcohols to amines and/or nitriles via a thermal catalytic pathway, while CdS nanomaterials are explored to promote -OH to -NH₂ conversion under visible-light irradiation. Metal-zeolite multifunctional systems are further established to enable the synthesis of N-heterocycles from O-heterocycles. The second strategy involves the use of chitin and chitin derivatives as the starting materials. Under the concept of shell biorefinery, distinctive protocols have been established to chemically transform chitin as the sole feedstock to amino sugars, amino alcohols, furanic amides, and N-heterocycles. By combining mechanochemistry with biotransformation, an integrated process to convert shrimp shell waste to complex, high-value, chiral compounds including tyrosine and l-DOPA is also demonstrated.

One-pot production of butyl butyrate from glucose using a cognate "diamond-shaped" E. coli consortium

Esters are widely used in plastics, textile fibers, and general petrochemicals. Usually, esters are produced via chemical synthesis or enzymatic processes from the corresponding alcohols and acids. However, the fermentative production of esters from alcohols and/or acids has recently also become feasible. Here we report a cognate microbial consortium capable of producing butyl butyrate. This microbial consortium consists of two engineered butyrate- and butanol-producing E. coli strains with nearly identical genetic background. The pathways for the synthesis of butyrate and butanol from butyryl-CoA in the respective E. coli strains, together with a lipase-catalyzed esterification reaction, created a "diamond-shaped" consortium. The concentration of butyrate and butanol in the fermentation vessel could be altered by adjusting the inoculation ratios of each E. coli strain in the consortium. After optimization, the consortium produced 7.2 g/L butyl butyrate with a yield of 0.12 g/g glucose without the exogenous addition of butanol or butyrate. To our best knowledge, this is the highest titer and yield of butyl butyrate produced by E. coli reported to date. This study thus provides a new way for the biotechnological production of esters.

Using Co-Culture to Functionalize Clostridium Fermentation

Clostridium fermentations have been developed for producing butanol and other value-added chemicals, but their development is constrained by some limitations, such as relatively high substrate cost and the need to maintain an anaerobic condition. Recently, co-culture is emerging as a popular way to address these limitations by introducing a partner strain with Clostridium. Generally speaking, the co-culture strategy enables the use of a cheaper substrate, maintains the growth of Clostridium without any anaerobic treatment, improves product yields, and/or widens the product spectrum. Herein, we review recent developments of co-culture strategies involving Clostridium species according to their partner stains' functions with representative examples. We also discuss research challenges that need to be addressed for the future development of Clostridium co-cultures.