Production Of Value-added Compounds Research Articles

Two-domain GH30 xylanase from human gut microbiota as a tool for enzymatic production of xylooligosaccharides: Crystallographic structure and a synergy with GH11 xylosidase

Production of value-added compounds and sustainable materials from agro-industrial residues is essential for better waste management and building of circular economy. This includes valorization of hemicellulosic fraction of plant biomass, the second most abundant biopolymer from plant cell walls, aiming to produce prebiotic oligosaccharides, widely explored in food and feed industries. In this work, we conducted biochemical and biophysical characterization of a prokaryotic two-domain R. champanellensis xylanase from glycoside hydrolase (GH) family 30 (RcXyn30A), and evaluated its applicability for XOS production from glucuronoxylan in combination with two endo-xylanases from GH10 and GH11 families and a GH11 xylobiohydrolase. RcXyn30A liberates mainly long monoglucuronylated xylooligosaccharides and is inefficient in cleaving unbranched oligosaccharides. Crystallographic structure of RcXyn30A catalytic domain was solved and refined to 1.37 Å resolution. Structural analysis of the catalytic domain releveled that its high affinity for glucuronic acid substituted xylan is due to the coordination of the substrate decoration by several hydrogen bonds and ionic interactions in the subsite −2. Furthermore, the protein has a larger β5-α5 loop as compared to other GH30 xylanases, which might be crucial for creating an additional aglycone subsite (+3) of the catalytic site. Finally, RcXyn30A activity is synergic to that of GH11 xylobiohydrolase.

A sustainable and efficient strategy for bioconverting naringin to L-rhamnose, 2R-naringenin, and kaempferol

The development of a sustainable and efficient bioconversion strategy is crucial for the full-component utilization of naringin. In this study, an engineering Pichia pastoris co-culture system was developed to produce L-rhamnose and 2S/2R-naringenin. By optimizing transformation conditions, the co-culture system could completely convert naringin while fully consuming glucose. The production of 2S/2R-naringenin reached 59.5 mM with a molar conversion of 99.2%, and L-rhamnose reached 59.1 mM with a molar conversion of 98.5%. In addition, an engineering Escherichia coli co-culture system was developed to produce 2R-naringenin and kaempferol from 2S/2R-naringenin. Maximal kaempferol production reached 1050 mg/L with a corresponding molar conversion of 99.0%, and 996 mg/L 2R-naringenin was accumulated. Finally, a total of 17.4 g 2R-naringenin, 18.0 g kaempferol, and 26.1 g L-rhamnose were prepared from 100 g naringin. Thus, this study provides a novel strategy for the production of value-added compounds from naringin with an environmentally safe process.

Droplet microfluidic system for high throughput and passive selection of bacteria producing biosurfactants.

Traditional methods for the enrichment of microorganisms rely on growth in a selective liquid medium or on an agar plate, followed by tedious characterization. Droplet microfluidic techniques have been recently used to cultivate microorganisms and preserve enriched bacterial taxonomic diversity. However, new methods are needed to select droplets comprising not only growing microorganisms but also those exhibiting specific properties, such as the production of value-added compounds. We describe here a droplet microfluidic screening technique for the functional selection of biosurfactant-producing microorganisms, which are of great interest in the bioremediation and biotechnology industries. Single bacterial cells are first encapsulated into picoliter droplets for clonal cultivation and then passively sorted at high throughput based on changes in interfacial tension in individual droplets. Our method expands droplet-based microbial enrichment with a novel approach that reduces the time and resources needed for the selection of surfactant-producing bacteria.

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

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

Production of chitosan from shrimp shell using ultrasound followed by subcritical water hydrolysis

The interest in shrimp shell valorization has been growing in line with sustainability goals. Therefore, the main objective of this study was to obtain chitosan from shrimp shell using ultrasound followed by subcritical water treatment. Ultrasonication of shells was performed at 600 and 1200 W for 5 min. Then, shells were hydrolyzed at 140–260 °C and 50 bar for 10–60 min followed by demineralization using citric acid, bleaching using hydrogen peroxide and deacetylation using sodium hydroxide solution. The highest deproteination (80.93 %) was obtained by ultrasonication at 1200 W/5 min followed by subcritical water hydrolysis at 260 °C/50 bar/60 min, where the residue with a yield of 10.56 %, whiteness index of 60.42, degree of deacetylation of 64.27 %, relative crystallinity of 32.66 % and similar functional groups to the commercial sample was obtained. These results indicated that the combination of ultrasound with subcritical water is promising to valorize shrimp shell towards production of value-added compounds.

Electrocatalytic Conversion of Glucose into Hydrogen and Value-Added Compounds on Gold and Nickel Catalysts

Fine chemistry historically relies on the fossil fuel industry, implying oil extraction and refining [1]. The rarefaction of this resource and adverse environmental consequences of its extraction motivate research for alternative sources of chemicals. Low carbon footprint chemicals can be synthesized from nonedible biomass waste [2]; cellulose extracted from biomass can therefore play an important role, being a clean and widely accessible carbon source. One can extract D-Glucose (units that constitute cellulose) from cellulose and obtain numerous chemicals of interest, such as sorbitol [3][4] or gluconic acid [5][6] (gluconate in alkaline media), respectively by selective reduction or oxidation.Searching for high-performance non-enzymatic catalysts to perform such reactions brought us to study the activity and selectivity of gold and nickel in alkaline media. At the anode, results from differential electrochemical mass spectrometry (DEMS) seem to indicate that the glucose oxidation on a gold surface initiates by its dissociative adsorption (dehydrogenation): the dihydrogen (H2) produced likely originates from the formation of metastable H adsorbates (Had) [7] that diffuse onto the surface [8] and recombine into H2. In parallel, the adsorbed glucose oxidizes into value-added products such as gluconic acid, through a mechanism proposed from in situ (Fourier Transform InfraRed spectroscopy, FTIR) and ex situ (products analysis by High Performance Liquid Chromatography, HPLC) observations, and on the evaluation of the number of exchanged electrons using the rotating ring disk electrode (RRDE). Confronting the experimental data to a microkinetics model enables to validate the proposed mechanism and to estimate the kinetics rate constants. At the cathode, the glucose reduction reaction (GRR) into sorbitol competes with the hydrogen evolution reaction (HER). The HER activity of nickel strongly depends on its surface oxidation state [9], which can be tuned to search the best selectivity towards sorbitol. Combining high value-added compounds production with H2 as by-product allows to improve the overall energy efficiency of this electrolysis.[1] P. G. Levi and J. M. Cullen, “Mapping global flows of chemicals: from fossil fuel feedstocks to chemical products,” Environ. Sci. Technol., vol. 52, no. 4, pp. 1725–1734, 2018, doi: 10.1021/acs.est.7b04573.[2] D. Saygin, D. J. Gielen, M. Draeck, E. Worrell, and M. K. Patel, “Assessment of the technical and economic potentials of biomass use for the production of steam, chemicals and polymers,” Renew. Sustain. Energy Rev., vol. 40, pp. 1153–1167, 2014, doi: 10.1016/j.rser.2014.07.114.[3] B. García, J. Moreno, G. Morales, J. A. Melero, and J. Iglesias, “Production of sorbitol via catalytic transfer hydrogenation of glucose,” Appl. Sci., vol. 10, no. 5, 2020, doi: 10.3390/app10051843.[4] X. Guo et al., “Selective hydrogenation of D-glucose to D-sorbitol over Ru/ZSM-5 catalysts,” Chinese J. Catal., vol. 35, no. 5, pp. 733–740, May 2014, doi: 10.1016/S1872-2067(14)60077-2.[5] H. S. Isbell, H. L. Frush, and F. J. Bates, “Manufacture of calcium gluconate by electrolytic oxidation of dextrose,” Ind. Eng. Chem., vol. 24, no. 4, pp. 375–378, 1932, doi: 10.1021/ie50268a003.[6] S. Anastassiadis and I. Morgunov, “Gluconic acid production,” Recent Pat. Biotechnol., vol. 1, no. 2, pp. 167–180, May 2007, doi: 10.2174/187220807780809472.[7] M. M. Jaksic, B. Johansen, and R. Tunold, “Electrochemical behaviour of gold in acidic and alkaline solutions of heavy and regular water,” Int. J. Hydrogen Energy, vol. 18, no. 2, pp. 91–110, Feb. 1993, doi: 10.1016/0360-3199(93)90196-H.[8] J. Cornejo-Romero, A. Solis-Garcia, S. M. Vega-Diaz, and J. C. Fierro-Gonzalez, “Reverse hydrogen spillover during ethanol dehydrogenation on TiO2-supported gold catalysts,” Mol. Catal., vol. 433, pp. 391–402, 2017, doi: 10.1016/j.mcat.2017.02.041.[9] A. G. Oshchepkov et al., “Nanostructured nickel nanoparticles supported on vulcan carbon as a highly active catalyst for the hydrogen oxidation reaction in alkaline media,” J. Power Sources, vol. 402, no. June, pp. 447–452, 2018, doi: 10.1016/j.jpowsour.2018.09.051. Figure 1

Screening of Saccharomyces cerevisiae metabolite transporters by 13C isotope substrate labeling.

The transportome of Saccharomyces cerevisiae comprises approximately 340 membrane-bound proteins, of which very few are well-characterized. Elucidating transporter proteins' function is essential not only for understanding central cellular processes in metabolite exchange with the external milieu but also for optimizing the production of value-added compounds in microbial cell factories. Here, we describe the application of 13C-labeled stable isotopes and detection by targeted LC-MS/MS as a screening tool for identifying Saccharomyces cerevisiae metabolite transporters. We compare the transport assay's sensitivity, reproducibility, and accuracy in yeast transporter mutant cell lines and Xenopus oocytes. As proof of principle, we analyzed the transport profiles of five yeast amino acid transporters. We first cultured yeast transporter deletion or overexpression mutants on uniformly labeled 13C-glucose and then screened their ability to facilitate the uptake or export of an unlabeled pool of amino acids. Individual transporters were further studied by heterologous expression in Xenopus oocytes, followed by an uptake assay with 13C labeled yeast extract. Uptake assays in Xenopus oocytes showed higher reproducibility and accuracy. Although having lower accuracy, the results from S. cerevisiae indicated the system's potential for initial high-throughput screening for native metabolite transporters. We partially confirmed previously reported substrates for all five amino acid transporters. In addition, we propose broader substrate specificity for two of the transporter proteins. The method presented here demonstrates the application of a comprehensive screening platform for the knowledge expansion of the transporter-substrate relationship for native metabolites in S. cerevisiae.

Transcription factor-based biosensors for detection of naturally occurring phenolic acids

Phenolic acids including hydroxybenzoic and hydroxycinnamic acids are secondary plant and fungal metabolites involved in many physiological processes offering health and dietary benefits. They are often utilised as precursors for production of value-added compounds. The limited availability of synthetic biology tools, such as whole-cell biosensors suitable for monitoring the dynamics of phenolic acids intracellularly and extracellularly, hinders the capabilities to develop high-throughput screens to study their metabolism and forward engineering. Here, by applying a multi-genome approach, we have identified phenolic acid-inducible gene expression systems composed of transcription factor-inducible promoter pairs responding to eleven different phenolic acids. Subsequently, they were used for the development of whole-cell biosensors based on model bacterial hosts, such as Escherichia coli, Cupriavidus necator and Pseudomonas putida. The dynamics and range of the biosensors were evaluated by establishing their response and sensitivity landscapes. The specificity and previously uncharacterised interactions between transcription factor and its effector(s) were identified by a screen of twenty major phenolic acids. To exemplify applicability, we utilise a protocatechuic acid-biosensor to identify enzymes with enhanced activity for conversion of p-hydroxybenzoate to protocatechuate. Transcription factor-based biosensors developed in this study will advance the analytics of phenolic acids and expedite research into their metabolism.

Predicting the performance of chain elongating microbiomes through flow cytometric fingerprinting.

As part of the circular bio-economy paradigm shift, waste management and valorisation practices have moved away from sanitation and towards the production of added-value compounds. Recently, the development of mixed culture bioprocess for the conversion of waste(water) to platform chemicals, such as medium chain carboxylic acids, has attracted significant interest. Often, the microbiology of these novel bioprocesses is less diverse and more prone to disturbances, which can lead to process failure. This issue can be tackled by implementing an advanced monitoring strategy based on the microbiology of the process. In this study, flow cytometry was used to monitor the microbiology of lactic acid chain elongation for the production of caproic acid, and assess its performance both qualitatively and quantitatively. Two continuous stirred tank reactors for chain elongation were monitored flow cytometrically for over 336 days. Through community typing, four specific community types could be identified and correlated to both a specific functionality and genotypic diversity. Additionally, the machine-learning algorithms trained in this study demonstrated the ability to predict production rates of, amongst others, caproic acid with high accuracy in the present (R² > 0.87) and intermediate accuracy in the near future (R² > 0.63). The identification of specific community types and the development of predictive algorithms form the basis of advanced bioprocess monitoring based on flow cytometry, and have the potential to improve bioprocess control and optimization, leading to better product quality and yields.

Microbe-Anode Interactions: Comparing the impact of genetic and material engineering approaches to improve the performance of microbial electrochemical systems (MES).

Microbial electrochemical systems (MESs) are a highly versatile platform technology with a particular focus on power or energy production. Often, they are used in combination with substrate conversion (e.g., wastewater treatment) and production of value-added compounds via electrode-assisted fermentation. This rapidly evolving field has seen great improvements both technically and biologically, but this interdisciplinarity sometimes hampers overseeing strategies to increase process efficiency. In this review, we first briefly summarize the terminology of the technology and outline the biological background that is essential for understanding and thus improving MES technology. Thereafter, recent research on improvements at the biofilm-electrode interface will be summarized and discussed, distinguishing between biotic and abiotic approaches. The two approaches are then compared, and resulting future directions are discussed. This mini-review therefore provides basic knowledge of MES technology and the underlying microbiology in general and reviews recent improvements at the bacteria-electrode interface.

Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria.

Cyanobacteria are photosynthetic microorganisms capable of using solar energy to convert CO2 and H2O into O2 and energy-rich organic compounds, thus enabling sustainable production of a wide range of bio-products. More and more strains of cyanobacteria are identified that show great promise as cell platforms for the generation of bioproducts. However, strain development is still required to optimize their biosynthesis and increase titers for industrial applications. This review describes the most well-known, newest and most promising strains available to the community and gives an overview of current cyanobacterial biotechnology and the latest innovative strategies used for engineering cyanobacteria. We summarize advanced synthetic biology tools for modulating gene expression and their use in metabolic pathway engineering to increase the production of value-added compounds, such as terpenoids, fatty acids and sugars, to provide a go-to source for scientists starting research in cyanobacterial metabolic engineering.

Conversion of toxic chemicals into flammable gases through the thermolysis of polyurethane foam using CO2

Construction waste is considered an environmental problem because its landfilling/incineration treatment methods has noticeably increased the likelihood of releasing microplastics, leachates, air pollutants, and toxic gases into the environment. Nevertheless, an environmentally benign disposal protocol for building plastic waste has yet to be fully implemented. In this study, a cleaner and safer disposal platform for building plastic waste is suggested. Specifically, the thermo-chemical treatment of building insulator waste (BIW) was conducted using CO2 as a key detoxifying agent. The BIW used in this study was composed of polyurethane foam (PUF), according to instrumental analyses. The thermal degradation of the PUF resulted in the dominant production of hazardous chemicals such as 4,4′-methylenedianiline (MDA) and its derivatives. The toxic compounds were transformed/detoxified into syngas (H2/CO) through the catalytic pyrolysis of PUF over nickel-based catalysts. Using CO2 as a detoxifying agent, MDA and its derivatives were further transformed into CO due to the homogeneous chemical reaction between CO2 and toxic compounds. 78.4 wt% of toxic compounds were converted into syngas over the CO2-mediated catalytic pyrolysis. Simultaneous reduction of toxic chemicals and production of value-added compounds propose that CO2 has a great potential to be used as a reaction medium to suppress toxic chemical valorization. Thus, this study experimentally confirmed the technical viability of catalytic pyrolysis under CO2 as a promising disposal platform for BIW, effectively suppressing the fate of toxic compounds.

A comparative screening of laccase-mediator systems by white-rot fungi laccases for biocatalytic benzyl alcohol oxidation

Production of value-added compounds from waste materials is of utmost importance for the development of a sustainable society especially regarding their use as catalysts in industrially relevant synthetic reactions. Herein, we show the production of laccases from four white-rot fungi, which were grown on agricultural residues, specifically Trametes versicolor 11269, Pleurotus ostreatus 1020, Panus tigrinus 707 and Lentinula edodes SC-495. The produced laccases were tested on a laccase-mediator system (LMS) for the biocatalytic oxidation of the model substrate benzyl alcohol into benzaldehyde. The LMS was carried out in the presence both of tetrahydrofuran as co-solvent and of the mediator 2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO) due to its high redox potential and its ability to perform the oxidation. Tolerance studies showed that the dialyzed solutions were able to tolerate 1% (99:1 v/v) of co-solvent, whereas a concentration of 10% v/v had a detrimental activity. Performances in the biocatalytic oxidation of laccase solutions from different purification steps were compared. Similar conversion was observed for laccase in dialysis (raw) and gel filtration (GF) product versus commercial T. versicolor laccase. The latter oxidized almost 99% of substrate while the other laccase solutions were able to reach a conversion from 91% for the laccase solution from P. tigrinus 707 after dialysis, to 50% for the laccase solution from P. ostreatus 1020 after gel filtration. This work highlights the potential of unpurified laccase solutions to be used as catalysts in synthetic reactions.

Characterization of a Novel Cytochrome Involved in Geobacter sulfurreducens' Electron Harvesting Pathways.

Electron harvesting bacteria are key targets to develop microbial electrosynthesis technologies, which are valid alternatives for the production of value-added compounds without utilization of fossil fuels. Geobacter sulfurreducens, that is capable of donating and accepting electrons from electrodes, is one of the most promising electroactive bacteria. Its electron transfer mechanisms to electrodes have been progressively elucidated, however the electron harvesting pathways are still poorly understood. Previous studies showed that the periplasmic cytochromes PccH and GSU2515 are overexpressed in current-consuming G. sulfurreducens biofilms. PccH was characterized, though no putative partners have been identified. In this work, GSU2515 was characterized by complementary biophysical techniques and in silico simulations using the AlphaFold neural network. GSU2515 is a low-spin monoheme cytochrome with a disordered N-terminal region and an α-helical C-terminal domain harboring the heme group. The cytochrome undergoes a redox-linked heme axial ligand switch, with Met91 and His94 as distal axial ligands in the reduced and oxidized states, respectively. The reduction potential of the cytochrome is negative and modulated by the pH in the physiological range: -78 mV at pH 6 and -113 mV at pH 7. Such pH-dependence coupled to the redox-linked switch of the axial ligand allows the cytochrome to drive a proton-coupled electron transfer step that is crucial to confer directionality to the respiratory chain. Biomolecular interactions and electron transfer experiments indicated that GSU2515 and PccH form a redox complex. Overall, the data obtained highlight for the first time how periplasmic proteins bridge the electron transfer between the outer and inner membrane in the electron harvesting pathways of G. sulfurreducens.

Fusing an exonuclease with Cas9 enhances homologous recombination in Pichia pastoris

BackgroundThe methylotrophic yeast Pichia pastoris is considered as an ideal host for the production of recombinant proteins and chemicals. However, low homologous recombination (HR) efficiency hinders its precise and extensive genetic manipulation. To enhance the homology-directed repair over non-homologous end joining (NHEJ), we expressed five exonucleases that were fused with the Cas9 for enhancing end resection of double strand breaks (DSBs) of DNA cuts.ResultsThe endogenous exonuclease Mre11 and Exo1 showed the highest positive rates in seamless deletion of FAA1, and fusing the MRE11 to the C-terminal of CAS9 had the highest positive rate and relatively high number of clones. We observed that expression of CAS9-MRE11 significantly improved positive rates when simultaneously seamless deletion of double genes (from 76.7 to 86.7%) and three genes (from 10.8 to 16.7%) when overexpressing RAD52. Furthermore, MRE11 overexpression significantly improved the genomic integration of multi-fragments with higher positive rate and clone number.ConclusionsFusion expression of the endogenous exonuclease Mre11 with Cas9 enhances homologous recombination efficiency in P. pastoris. The strategy described here should facilitate the metabolic engineering of P. pastoris toward high-level production of value-added compounds.

Design of a genetically encoded biosensor to establish a high-throughput screening platform for L-cysteine overproduction

Metabolic engineering seeks to rewire the metabolic network of cells for the efficient production of value-added compounds from renewable substrates. However, it remains challenging to evaluate and identify strains with the desired phenotype from the vast rational or random mutagenesis library. One effective approach to resolve this bottleneck is to design an efficient high-throughput screening (HTS) method to rapidly detect and analyze target candidates. L-cysteine is an important sulfur-containing amino acid and has been widely used in agriculture, pharmaceuticals, cosmetics, and food additive industries. However, HTS methods that enable monitoring of L-cysteine levels and screening of the enzyme variants and strains to confer superior L-cysteine biosynthesis remain unavailable, greatly limiting the development of efficient microbial cell factories for L-cysteine production at the industrial scale. Here, we took advantage of the L-cysteine-responsive transcriptional regulator CcdR to develop a genetically encoded biosensor for engineering and screening the L-cysteine overproducer. The in vivo L-cysteine-responsive assays and in vitro electrophoretic mobility shift assay (EMSA) and DNase I footprint analysis indicated that CcdR is a transcriptional activator that specifically interacts with L-cysteine and binds to its regulatory region to induce the expression of target genes. To improve the response performance of the L-cysteine biosensor, multilevel optimization strategies were performed, including regulator engineering by semi-rational design and systematic optimization of the genetic elements by modulating the promoter and RBS combination. As a result, the dynamic range and sensitivity of the biosensor were significantly improved. Using this the excellent L-cysteine biosensor, a HTS platform was established by coupling with fluorescence-activated cell sorting (FACS) and was successfully applied to achieve direct evolution of the key enzyme in the L-cysteine biosynthetic pathway to increase its catalytic performance and to screen the high L-cysteine-producing strains from the random mutagenesis library. These results presented a paradigm of design and optimization of biosensors to dynamically detect metabolite concentrations and provided a promising tool enabling HTS and metabolic regulation to construct L-cysteine hyperproducing strains to satisfy industrial demand.

Trends on CO2 Capture with Microalgae: A Bibliometric Analysis.

The alarming levels of carbon dioxide (CO2) are an environmental problem that affects the economic growth of the world. CO2 emissions represent penalties and restrictions due to the high carbon footprint. Therefore, sustainable strategies are required to reduce the negative impact that occurs. Among the potential systems for CO2 capture are microalgae. These are defined as photosynthetic microorganisms that use CO2 and sunlight to obtain oxygen (O2) and generate value-added products such as biofuels, among others. Despite the advantages that microalgae may present, there are still technical–economic challenges that limit industrial-scale commercialization and the use of biomass in the production of added-value compounds. Therefore, this study reviews the current state of research on CO2 capture with microalgae, for which bibliometric analysis was used to establish the trends of the subject in terms of scientometric parameters. Technological advances in the use of microalgal biomass were also identified. Additionally, it was possible to establish the different cooperation networks between countries, which showed interactions in the search to reduce CO2 concentrations through microalgae.

Communities of Niche-optimized Strains (CoNoS) – Design and creation of stable, genome-reduced co-cultures

Current bioprocesses for production of value-added compounds are mainly based on pure cultures that are composed of rationally engineered strains of model organisms with versatile metabolic capacities. However, in the comparably well-defined environment of a bioreactor, metabolic flexibility provided by various highly abundant biosynthetic enzymes is much less required and results in suboptimal use of carbon and energy sources for compound production. In nature, non-model organisms have frequently evolved in communities where genome-reduced, auxotrophic strains cross-feed each other, suggesting that there must be a significant advantage compared to growth without cooperation. To prove this, we started to create and study synthetic communities of niche-optimized strains (CoNoS) that consists of two strains of the same species Corynebacterium glutamicum that are mutually dependent on one amino acid. We used both the wild-type and the genome-reduced C1* chassis for introducing selected amino acid auxotrophies, each based on complete deletion of all required biosynthetic genes. The best candidate strains were used to establish several stably growing CoNoS that were further characterized and optimized by metabolic modelling, microfluidic experiments and rational metabolic engineering to improve amino acid production and exchange. Finally, the engineered CoNoS consisting of an l-leucine and l-arginine auxotroph showed a specific growth rate equivalent to 83% of the wild type in monoculture, making it the fastest co-culture of two auxotrophic C. glutamicum strains to date. Overall, our results are a first promising step towards establishing improved biobased production of value-added compounds using the CoNoS approach.

Biosynthesis of microalgal lipids, proteins, lutein, and carbohydrates using fish farming wastewater and forest biomass under photoautotrophic and heterotrophic cultivation

Biorefineries enable the circular, sustainable, and economic use of waste resources if value-added products can be recovered from all the generated fractions at a large-scale. In the present studies the comparison and assessment for the production of value-added compounds (e.g., proteins, lutein, and lipids) by the microalga Chlorella sorokiniana grown under photoautotrophic or heterotrophic conditions was performed. Photoautotrophic cultivation generated little biomass and lipids, but abundant proteins (416.66 mg/gCDW) and lutein (6.40 mg/gCDW). Heterotrophic conditions using spruce hydrolysate as a carbon source favored biomass (8.71 g/L at C/N 20 and 8.28 g/L at C/N 60) and lipid synthesis (2.79 g/L at C/N 20 and 3.61 g/L at C/N 60) after 72 h of cultivation. Therefore, heterotrophic cultivation of microalgae using spruce hydrolysate instead of glucose offers a suitable biorefinery concept at large-scale for biodiesel-grade lipids production, whereas photoautotrophic bioreactors are recommended for sustainable protein and lutein biosynthesis.

Underground metabolism as a rich reservoir for pathway engineering.

MotivationBioproduction of value-added compounds is frequently achieved by utilizing enzymes from other species. However, expression of such heterologous enzymes can be detrimental due to unexpected interactions within the host cell. Recently, an alternative strategy emerged, which relies on recruiting side activities of host enzymes to establish new biosynthetic pathways. Although such low-level ‘underground’ enzyme activities are prevalent, it remains poorly explored whether they may serve as an important reservoir for pathway engineering.ResultsHere, we use genome-scale modeling to estimate the theoretical potential of underground reactions for engineering novel biosynthetic pathways in Escherichia coli. We found that biochemical reactions contributed by underground enzyme activities often enhance the in silico production of compounds with industrial importance, including several cases where underground activities are indispensable for production. Most of these new capabilities can be achieved by the addition of one or two underground reactions to the native network, suggesting that only a few side activities need to be enhanced during implementation. Remarkably, we find that the contribution of underground reactions to the production of value-added compounds is comparable to that of heterologous reactions, underscoring their biotechnological potential. Taken together, our genome-wide study demonstrates that exploiting underground enzyme activities could be a promising addition to the toolbox of industrial strain development.Availability and implementationThe data and scripts underlying this article are available on GitHub at https://github.com/pappb/Kovacs-et-al-Underground-metabolism.Supplementary information Supplementary data are available at Bioinformatics online.