Toward homosuccinate fermentation: metabolic engineering of Corynebacterium glutamicum for anaerobic production of succinate from glucose and formate

Prospects of formamide as nitrogen source in biotechnological production processes

This review presents an analysis of formamide, focussing on its occurrence in nature, its functional roles, and its promising applications in the context of the bioeconomy. We discuss the utilization of formamide as an innovative nitrogen source achieved through metabolic engineering. These approaches underscore formamide's potential in supporting growth and production in biotechnological processes. Furthermore, our review illuminates formamide's role as a nitrogen source capable of safeguarding cultivation systems against contamination in non-sterile conditions. This attribute adds an extra layer of practicality to its application, rendering it an attractive candidate for sustainable and resilient industrial practices. Additionally, the article unveils the versatility of formamide as a potential carbon source that could be combined with formate or CO2 assimilation pathways. However, its attributes, i.e., enriched nitrogen content and comparatively limited energy content, led to conclude that formamide is more suitable as a co-substrate and that its use as a sole source of carbon for biomass and bio-production is limited. Through our exploration of formamide's properties and its applications, this review underscores the significance of formamide as valuable resource for a large spectrum of industrial applications. KEY POINTS: • Formidases enable access to formamide as source of nitrogen, carbon, and energy • The formamide/formamidase system supports non-sterile fermentation • The nitrogen source formamide supports production of nitrogenous compounds.

An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis

Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34-90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids.

Metabolic engineering and fermentation optimization strategies for producing organic acids of the tricarboxylic acid cycle by microbial cell factories

The organic acids of the tricarboxylic acid (TCA) pathway are important platform compounds and are widely used in many areas. The high-productivity strains and high-efficient and low-cost fermentation are required to satisfy a huge market size. The high metabolic flux of the TCA pathway endows microorganisms potential to produce high titers of these organic acids. Coupled with metabolic engineering and fermentation optimization, the titer of the organic acids has been significantly improved in recent years. Herein, we discuss and compare the recent advances in synthetic pathway engineering, cofactor engineering, transporter engineering, and fermentation optimization strategies to maximize the biosynthesis of organic acids. Such engineering strategies were mainly based on the TCA pathway and glyoxylate pathway. Furthermore, organic-acid-secretion enhancement and renewable-substrate-based fermentation are often performed to assist the biosynthesis of organic acids. Further strategies are also discussed to construct high-productivity and acid-resistant strains for industrial large-scale production.

Recent advances in microbial production of diamines, aminocarboxylic acids, and diacids as potential platform chemicals and bio-based polyamides monomers

Recently, bio-based manufacturing processes of value-added platform chemicals and polymers in biorefineries using renewable resources have extensively been developed for sustainable and carbon dioxide (CO₂) neutral-based industry. Among them, bio-based diamines, aminocarboxylic acids, and diacids have been used as monomers for the synthesis of polyamides having different carbon numbers and ubiquitous and versatile industrial polymers and also as precursors for further chemical and biological processes to afford valuable chemicals. Until now, these platform bio-chemicals have successfully been produced by biorefinery processes employing enzymes and/or microbial host strains as main catalysts. In this review, we discuss recent advances in bio-based production of diamines, aminocarboxylic acids, and diacids, which has been developed and improved by systems metabolic engineering strategies of microbial consortia and optimization of microbial conversion processes including whole cell bioconversion and direct fermentative production.

High-Fidelity Cytosine Base Editing in a GC-Rich Corynebacterium glutamicum with Reduced DNA Off-Target Editing Effects

Genome editing technology is a powerful tool for programming microbial cell factories. However, rat APOBEC1-derived cytosine base editor (CBE) that converts C•G to T•A at target genes induced DNA off-targets, regardless of single-guide RNA (sgRNA) sequences. Although the high efficiencies of the bacterial CBEs have been developed, a risk of unidentified off-targets impeded genome editing for microbial cell factories. To address the issues, we demonstrate the genome engineering of Corynebacterium glutamicum as a GC-rich model industrial bacterium by generating premature termination codons (PTCs) in desired genes using high-fidelity cytosine base editors (CBEs). Through this CBE-STOP approach of introducing specific cytosine conversions, we constructed several single-gene-inactivated strains for three genes (ldh, idsA, and pyc) with high base editing efficiencies of average 95.6% (n = 45, C6 position) and the highest success rate of up to 100% for PTCs and ultimately developed a strain with five genes (ldh, actA, ackA, pqo, and pta) that were inactivated sequentially for enhancing succinate production. Although these mutant strains showed the desired phenotypes, whole-genome sequencing (WGS) data revealed that genome-wide point mutations occurred in each strain and further accumulated according to the duration of CBE plasmids. To lower the undesirable mutations, high-fidelity CBEs (pCoryne-YE1-BE3 and pCoryne-BE3-R132E) was employed for single or multiplexed genome editing in C. glutamicum, resulting in drastically reduced sgRNA-independent off-targets. Thus, we provide a CRISPR-assisted bacterial genome engineering tool with an average high efficiency of 90.5% (n = 76, C5 or C6 position) at the desired targets. IMPORTANCE Rat APOBEC1-derived cytosine base editor (CBE) that converts C•G to T•A at target genes induced DNA off-targets, regardless of single-guide RNA (sgRNA) sequences. Although the high efficiencies of bacterial CBEs have been developed, a risk of unidentified off-targets impeded genome editing for microbial cell factories. To address the issues, we identified the DNA off-targets for single and multiple genome engineering of the industrial bacterium Corynebacterium glutamicum using whole-genome sequencing. Further, we developed the high-fidelity (HF)-CBE with significantly reduced off-targets with comparable efficiency and precision. We believe that our DNA off-target analysis and the HF-CBE can promote CRISPR-assisted genome engineering over conventional gene manipulation tools by providing a markerless genetic tool without need for a foreign DNA donor.

A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum

Corynebacterium glutamicum is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in C. glutamicum. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with C. glutamicum and contributes to a systemic understanding of this microbial cell factory.

Measurement(s)	Gene Expression Analysis
Technology Type(s)	Two Color Microarray
Factor Type(s)	WT condition A vs. WT condition B • Plasmid-based gene overexpression in parental strain vs. parental strain with empty vector control • Deletion mutant vs. parental strain
Sample Characteristic - Organism	Corynebacterium glutamicum
Sample Characteristic - Environment	laboratory environment
Sample Characteristic - Location	Germany

Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools

Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.

Modeling the Succinic Acid Bioprocess: A Review

Succinic acid has attracted much interest as a key platform chemical that can be obtained in high titers from biomass through sustainable fermentation processes, thus boosting the bioeconomy as a critical production strategy for the future. After several years of development of the production of succinic acid, many studies on lab or pilot scale production have been reported. The relevant experimental data reveal underlying physical and chemical dynamic phenomena. To take advantage of this vast, but disperse, kinetic information, a number of mathematical kinetic models of the unstructured non-segregated type have been proposed in the first place. These relatively simple models feature critical aspects of interest for the design, control, optimization and operation of this key bioprocess. This review includes a detailed description of the phenomena involved in the bioprocesses and how they reflect on the most important and recent models based on macroscopic and metabolic chemical kinetics, and in some cases even coupling mass transport.

A Review on the Production of C4 Platform Chemicals from Biochemical Conversion of Sugar Crop Processing Products and By-Products

The development and commercialization of sustainable chemicals from agricultural products and by-products is necessary for a circular economy built on renewable natural resources. Among the largest contributors to the final cost of a biomass conversion product is the cost of the initial biomass feedstock, representing a significant challenge in effective biomass utilization. Another major challenge is in identifying the correct products for development, which must be able to satisfy the need for both low-cost, drop-in fossil fuel replacements and novel, high-value fine chemicals (and/or commodity chemicals). Both challenges can be met by utilizing wastes or by-products from biomass processing, which have very limited starting cost, to yield platform chemicals. Specifically, sugar crop processing (e.g., sugarcane, sugar beet) is a mature industry that produces high volumes of by-products with significant potential for valorization. This review focuses specifically on the production of acetoin (3-hydroxybutanone), 2,3-butanediol, and C4 dicarboxylic (succinic, malic, and fumaric) acids with emphasis on biochemical conversion and targeted upgrading of sugar crop products/by-products. These C4 compounds are easily derived from fermentations and can be converted into many different final products, including food, fragrance, and cosmetic additives, as well as sustainable biofuels and other chemicals. State-of-the-art literature pertaining to optimization strategies for microbial conversion of sugar crop byproducts to C4 chemicals (e.g., bagasse, molasses) is reviewed, along with potential routes for upgrading and valorization. Directions and opportunities for future research and industrial biotechnology development are discussed.

Biosynthetic Pathway and Metabolic Engineering of Succinic Acid

Succinic acid, a dicarboxylic acid produced as an intermediate of the tricarboxylic acid (TCA) cycle, is one of the most important platform chemicals for the production of various high value-added derivatives. As traditional chemical synthesis processes suffer from nonrenewable resources and environment pollution, succinic acid biosynthesis has drawn increasing attention as a viable, more environmentally friendly alternative. To date, several metabolic engineering approaches have been utilized for constructing and optimizing succinic acid cell factories. In this review, different succinic acid biosynthesis pathways are summarized, with a focus on the key enzymes and metabolic engineering approaches, which mainly include redirecting carbon flux, balancing NADH/NAD⁺ ratios, and optimizing CO₂ supplementation. Finally, future perspectives on the microbial production of succinic acid are discussed.

Production of Succinic Acid From Basfia succiniciproducens

Basfia succiniciproducens is a facultative anaerobic capnophilic bacterium, isolated from rumen, that naturally produces high amounts of succinic acid by fixing CO2 and using fumarate as final electron acceptor. This metabolic feature makes it one of the ideal candidates for developing biotechnological industrial routes that could eventually replace the polluting and environment unfriendly petrochemical ones that are still main sources for the production of this value-added compound. In fact, due to the large number of applications of succinic acid that range from the more traditional ones as food additive or pharmaceutical intermediate to the most recent as building block for biopolymers and bioplastic, increasing demand and market size growth are expected in the next years. In line with a “green revolution” needed to preserve our environment, the great challenge is the establishment of commercially viable production processes that exploit renewable materials and in particular preferably non-food lignocellulosic biomasses and waste products. In this review, we describe the currently available literature concerning B. succiniciproducens since the strain was first isolated, focusing on the different renewable materials and fermentation strategies used to improve succinic acid production titers to date. Moreover, an insight into the metabolic engineering approaches and the key physiological characteristics of B. succiniciproducens deduced from the different studies are presented.

Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress

Corynebacterium glutamicum is an ideal microbial chassis for production of valuable bioproducts including amino acids and next generation biofuels. Here we resequence engineered isopentenol (IP) producing C. glutamicum BRC-JBEI 1.1.2 strain and assess differential transcriptional profiles using RNA sequencing under industrially relevant conditions including scale transition and compare the presence vs absence of an ionic liquid, cholinium lysinate ([Ch][Lys]). Analysis of the scale transition from shake flask to bioreactor with transcriptomics identified a distinct pattern of metabolic and regulatory responses needed for growth in this industrial format. These differential changes in gene expression corroborate altered accumulation of organic acids and bioproducts, including succinate, acetate, and acetoin that occur when cells are grown in the presence of 50 mM [Ch][Lys] in the stirred-tank reactor. This new genome assembly and differential expression analysis of cells grown in a stirred tank bioreactor clarify the cell response of an C. glutamicum strain engineered to produce IP.

Metabolic engineering of Vibrio natriegens for anaerobic succinate production

The biotechnological production of succinate bears serious potential to fully replace existing petrochemical approaches in the future. In order to establish an economically viable bioprocess, obtaining high titre, yield and productivity is of central importance. In this study, we present a straightforward engineering approach for anaerobic succinate production with Vibrio natriegens, consisting of essential metabolic engineering and optimization of process conditions. The final producer strain V. natriegens Δlldh Δdldh Δpfl Δald Δdns::pyc_Cg (Succ1) yielded 1.46 mol of succinate per mol of glucose under anaerobic conditions (85% of the theoretical maximum) and revealed a particularly high biomass‐specific succinate production rate of 1.33 g_Succ g_CDW⁻¹ h⁻¹ compared with well‐established production systems. By applying carbon and redox balancing, we determined the intracellular flux distribution and show that under the tested conditions the reductive TCA as well as the oxidative TCA/glyoxylate pathway contributed to succinate formation. In a zero‐growth bioprocess using minimal medium devoid of complex additives and expensive supplements, we obtained a final titre of 60.4 g_Succ l⁻¹ with a maximum productivity of 20.8 g_Succ l⁻¹ h⁻¹ and an overall volumetric productivity of 8.6 g_Succ l⁻¹ h⁻¹ during the 7 h fermentation. The key performance indicators (titre, yield and productivity) of this first engineering approach in V. natriegens are encouraging and compete with costly tailored microbial production systems.

Application of Metabolomics in Diagnosis of Cow Mastitis: A Review

Cow mastitis, with high incidence rate and complex cause of disease, is one of the main diseases that affect the development of dairy industry in the world. Clinical mastitis and subclinical mastitis caused by Staphylococcus aureus, Escherichia coli, Streptococcus, and other pathogens have a huge potential safety hazard to food safety and the rapid development of animal husbandry. The economic loss caused by cow mastitis is billions of dollars every year in the world. In recent years, the omics technology has been widely used in animal husbandry with the continuous breakthrough of sequencing technology and the continuous reduction of sequencing cost. For dairy cow mastitis, the traditional diagnostic technique, such as histopathological screening, somatic cell count, milk pH test, milk conductivity test, enzyme activity test, and infrared thermography, are difficult to fully and comprehensively clarify its pathogenesis due to their own limitations. Metabolomics technology is an important part of system biology, which can simultaneously analyze all low molecular weight metabolites such as amino acids, lipids, carbohydrates under the action of complex factors including internal and external environment and in a specific physiological period accurately and efficiently, and then clarify the related metabolic pathways. Metabolomics, as the most downstream of gene expression, can amplify the small changes of gene and protein expression at the level of metabolites, which can more fully reflect the cell function. The application of metabolomics technology in cow mastitis can analyze the hetero metabolites, identify the related biomarkers, and reveal the physiological and pathological changes of cow mammary gland, so as to provide valuable reference for the prediction, diagnosis, and treatment of mastitis. The research progress of metabolomics technology in cow mastitis in recent years was reviewed, in order to provide guidance for the development of cow health and dairy industry safety in this manuscript.

Physiological characteristics of Corynebacterium glutamicum as a cell factory under anaerobic conditions

Corynebacterium glutamicum, a gram-positive and facultative anaerobic bacterium, is widely used for the industrial production of amino acids, such as L-glutamate and L-lysine. C. glutamicum grows and produces amino acids under aerobic conditions. When restricted under anaerobic conditions, it produces organic acids, such as L-lactate and succinate, through metabolic shift. With the increasing threat of global warming, these organic acids have drawn considerable attention as bio-based plastic monomers. In addition to the organic acids, the anaerobic bioprocess is also used to produce other value-added compounds, including isobutanol, ethanol, 3-methyl-1-butanol, 2,3-butanediol, L-alanine, and L-valine. Therefore, C. glutamicum is now a versatile cell factory for producing a wide variety of useful chemicals under both aerobic and anaerobic conditions. The growth and metabolism of the bacterium depend on the oxygen levels, which modulate the rearrangement of the carbon flux by reprogramming gene expression patterns and intracellular redox states. Anaerobic cell growth and L-lysine production as well as aerobic succinate production have been demonstrated by engineering the metabolic pathways or supplying a terminal electron acceptor instead of oxygen. In this review, we discuss the physiological and metabolic changes in C. glutamicum associated with its application as a cell factory under different oxygen states. Physiological switching in bacteria is initiated with the sensing of oxygen availability. While such a sensor has not been identified in C. glutamicum yet, the molecular mechanism for oxygen sensing in related bacteria is also discussed. KEY POINTS: • C. glutamicum produces a wide variety of useful compounds under anaerobic conditions. • C. glutamicum is a versatile cell factory under both aerobic and anaerobic conditions. • Metabolic fate can be overcome by engineering metabolic pathways.

Advances in metabolic engineering of Corynebacterium glutamicum to produce high-value active ingredients for food, feed, human health, and well-being

The soil microbe Corynebacterium glutamicum is a leading workhorse in industrial biotechnology and has become famous for its power to synthetise amino acids and a range of bulk chemicals at high titre and yield. The product portfolio of the microbe is continuously expanding. Moreover, metabolically engineered strains of C. glutamicum produce more than 30 high value active ingredients, including signature molecules of raspberry, savoury, and orange flavours, sun blockers, anti-ageing sugars, and polymers for regenerative medicine. Herein, we highlight recent advances in engineering of the microbe into novel cell factories that overproduce these precious molecules from pioneering proofs-of-concept up to industrial productivity.

A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria

Many bacteria and other organisms carry out fermentations forming acetate. These fermentations have broad importance for foods, agriculture, and industry. They also are important for bacteria themselves because they often generate ATP. Here, we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in fermentative bacteria. We found that the bacterium Cutibacterium granulosum formed acetate during fermentation of glucose. It did not use phosphotransacetylase or acetate kinase, enzymes found in nearly all acetate-forming bacteria. Instead, it used a pathway involving two different enzymes. The first enzyme, succinyl coenzyme A (succinyl-CoA):acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. We identified the genes encoding these enzymes, and they were homologs of SCACT and SCS genes found in other bacteria. The pathway resembles one described in eukaryotes, but it uses bacterial, not eukaryotic, gene homologs. To find other instances of the pathway, we analyzed sequences of all biochemically characterized homologs of SCACT and SCS (103 enzymes from 64 publications). Homologs with similar enzymatic activity had similar sequences, enabling a large-scale search for them in genomes. We searched nearly 600 genomes of bacteria known to form acetate, and we found that 6% encoded homologs with SCACT and SCS activity. This included >30 species belonging to 5 different phyla, showing that a diverse range of bacteria encode the SCACT/SCS pathway. This work suggests the SCACT/SCS pathway is important for acetate formation in many branches of the tree of life. IMPORTANCE Pathways for forming acetate during fermentation have been studied for over 80 years. In that time, several pathways in a range of organisms, from bacteria to animals, have been described. However, one pathway (involving succinyl-CoA:acetate CoA-transferase and succinyl-CoA synthetase) has not been reported in prokaryotes. Here, we discovered enzymes for this pathway in the fermentative bacterium Cutibacterium granulosum. We also found >30 other fermentative bacteria that encode this pathway, demonstrating that it could be common. This pathway represents a new way for bacteria to form acetate from acetyl-CoA and synthesize ATP via substrate-level phosphorylation. It could be a target for controlling yield of acetate during fermentation, with relevance for foods, agriculture, and industry.

Microaerobic growth-decoupled production of α-ketoglutarate and succinate from xylose in a one-pot process using Corynebacterium glutamicum

BACKGROUND

Lignocellulosic biomass is the most abundant raw material on earth. Its efficient use for novel bio-based materials is essential for an emerging bioeconomy. Possible building blocks for such materials are the key TCA-cycle intermediates α-ketoglutarate and succinate. These organic acids have a wide range of potential applications, particularly in use as monomers for established or novel biopolymers. Recently, Corynebacterium glutamicum was successfully engineered and evolved towards an improved utilization of d-xylose via the Weimberg pathway, yielding the strain WMB2_evo . The Weimberg pathway enables a carbon-efficient C5-to-C5 conversion of d-xylose to α-ketoglutarate and a shortcut route to succinate as co-product in a one-pot process.

METHODS AND RESULTS

C. glutamicum WMB2_evo was grown under dynamic microaerobic conditions on d-xylose, leading to the formation of comparably high amounts of succinate and only small amounts of α-ketoglutarate. Subsequent carbon isotope labeling experiments verified the targeted production route for both products in C. glutamicum WMB2_evo . Fed-batch process development was initiated and the effect of oxygen supply and feeding strategy for a growth-decoupled co-production of α-ketoglutarate and succinate were studied in detail. The finally established fed-batch production process resulted in the formation of 78.4 mmol L^-1 (11.45 g L^-1 ) α-ketoglutarate and 96.2 mmol L^-1 (11.36 g L^-1 ) succinate.

CONCLUSION

The developed one-pot process represents a promising approach for the combined supply of bio-based α-ketoglutarate and succinate. Future work will focus on tailor-made down-stream processing of both organic acids from the fermentation broth to enable their application as building blocks in chemical syntheses. Alternatively, direct conversion of one or both acids via whole-cell or cell-free enzymatic approaches can be envisioned; thus, extending the network of value chains starting from cheap and renewable d-xylose.

Impact of nitrogen deficiency on succinic acid production by engineered strains of Yarrowia lipolytica

Yarrowia lipolytica strains PGC01003 and PGC202 engineered for succinic acid production were studied and compared to the wild type strain W29. For the first time, these two strains were characterized in a chemically defined medium. Strain growth and organic acid production were investigated in fed-batch mode with glycerol as carbon and energy source. This study evaluated the impact of nitrogen deficiency strategy to redirect carbon flux toward succinic acid synthesis. Strain PGC01003 produced 19 g L^-1 succinic acid with an overall yield of 0.23 g g^-1 and an overall productivity of 0.23 g L^-1 h^-1, while strain PGC202 produced 33 g L^-1 succinic acid with an overall yield of 0.12 g g^-1 and a productivity of 0.57 g L^-1 h^-1. Nitrogen limitation effectively stopped biomass growth and increased succinic acid yield of PGC01003 and PGC202 by 18 % and 62 %, respectively. However, the specific succinic acid production rate was reduced by 77 % and 66 %, respectively.

Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens

BACKGROUND

Feed contributes most to livestock production costs. Improving feed efficiency is crucial to increase profitability and sustainability for animal production. Host genetics and the gut microbiota can both influence the host phenotype. However, the association between the gut microbiota and host genetics and their joint contribution to feed efficiency in chickens is largely unclear.

RESULTS

Here, we examined microbial data from the duodenum, jejunum, ileum, cecum, and feces in 206 chickens and their host genotypes and confirmed that the microbial phenotypes and co-occurrence networks exhibited dramatic spatial heterogeneity along the digestive tract. The correlations between host genetic kinship and gut microbial similarities within different sampling sites were weak, with coefficients ranging from - 0.07 to 0.08. However, microbial genome-wide analysis revealed that genetic markers near or inside the genes MTHFD1L and LARGE1 were associated with the abundances of cecal Megasphaera and Parabacteroides, respectively. The effect of host genetics on residual feed intake (RFI) was 39%. We further identified three independent genetic variations that were related to feed efficiency and had a modest effect on the gut microbiota. The contributions of the gut microbiota from the different parts of the intestinal tract on RFI were distinct. The cecal microbiota accounted for 28% of the RFI variance, a value higher than that explained by the duodenal, jejunal, ileal, and fecal microbiota. Additionally, six bacteria exhibited significant associations with RFI. Specifically, lower abundances of duodenal Akkermansia muciniphila and cecal Parabacteroides and higher abundances of cecal Lactobacillus, Corynebacterium, Coprobacillus, and Slackia were related to better feed efficiency.

CONCLUSIONS

Our findings solidified the notion that both host genetics and the gut microbiota, especially the cecal microbiota, can drive the variation in feed efficiency. Although host genetics has a limited effect on the entire microbial community, a small fraction of gut microorganisms tends to interact with host genes, jointly contributing to feed efficiency. Therefore, the gut microbiota and host genetic variations can be simultaneously targeted by favoring more-efficient taxa and selective breeding to improve feed efficiency in chickens. Video abstract.

A staged representation electrochemical stimulated strategy to regulate intracellular reducing power for improving succinate production by Escherichia coli AFP111

BACKGROUND

Escherichia coli AFP111 was previously engineered for succinate production by eliminating byproducts of synthesis pathways. Still, the succinate yield is limited due to the insufficient NADH supplement, when fed with glucose. Microbial electrolysis cell (MEC) allows microorganisms to perform unbalanced fermentation by establishing polarized cathode interaction.

METHODS AND RESULTS

In this study, a cathode electrode was used as an additional electron donor to improve succinate synthesis by E. coli AFP111. In MEC with -0.65 V (vs. Ag/AgCl) poised on cathode electrode, 95.72% electrons were transferred into cells via neutral red (NR), and the ratio of NADH/NAD⁺ increased by 2.5-fold. Meanwhile, compared with the control experiment, the value of oxidation-reduction potential (ORP) changed from -240 to -265 mV in MEC, which was beneficial for NADH generation. During two-stage fermentation (no potential growth stage followed by electric stimulation) in MEC, succinate yield was increased by 29.09% (the final yield was 0.71 g g^-1 ), and glucose consumption rate was enhanced by 36.22%. In addition, the carbon flux was pumped to succinate and pyruvate metabolism was enhanced.

CONCLUSION AND IMPLICATIONS

Staged representation of electrochemical stimulated strategy is effective for succinate producing in engineered E. coli by regulating intracellular reducing power, which provides a new concept for producing reduced metabolite in unbalanced fermentation.

An energetic profile of Corynebacterium glutamicum underpinned by measured biomass yield on ATP

The supply and usage of energetic cofactors in metabolism is a central concern for systems metabolic engineering, particularly in case of energy intensive products. One of the most important parameters for systems wide balancing of energetic cofactors is the ATP requirement for biomass formation Y_ATP/Biomass. Despite its fundamental importance, Y_ATP/Biomass values for non-fermentative organisms are still rough estimates deduced from theoretical considerations. For the first time, we present an approach for the experimental determination of Y_ATP/Biomass using comparative ¹³C metabolic flux analysis (¹³C MFA) of a wild type strain and an ATP synthase knockout mutant. We show that the energetic profile of a cell can then be deduced from a genome wide stoichiometric model and experimental maintenance data. Particularly, the contributions of substrate level phosphorylation (SLP) and electron transport phosphorylation (ETP) to ATP generation become available which enables the overall energetic efficiency of a cell to be characterized. As a model organism, the industrial platform organism Corynebacterium glutamicum is used. C. glutamicum uses a respiratory type of energy metabolism, implying that ATP can be synthesized either by SLP or by ETP with the membrane-bound F₁F_O-ATP synthase using the proton motive force (pmf) as driving force. The presence of two terminal oxidases, which differ in their proton translocation efficiency by a factor of three, further complicates energy balancing for this organism. By integration of experimental data and network models, we show that in the wild type SLP and ETP contribute equally to ATP generation. Thus, the role of ETP in respiring bacteria may have been overrated in the past. Remarkably, in the genome wide setting 65% of the pmf is actually not used for ATP synthesis. However, it turns out that, compared to other organisms C. glutamicum still uses its energy budget rather efficiently.

Metabolic engineering of Saccharomyces cerevisiae for the production of top value chemicals from biorefinery carbohydrates

The implementation of biorefineries for a cost-effective and sustainable production of energy and chemicals from renewable carbon sources plays a fundamental role in the transition to a circular economy. The US Department of Energy identified a group of key target compounds that can be produced from biorefinery carbohydrates. In 2010, this list was revised and included organic acids (lactic, succinic, levulinic and 3-hydroxypropionic acids), sugar alcohols (xylitol and sorbitol), furans and derivatives (hydroxymethylfurfural, furfural and furandicarboxylic acid), biohydrocarbons (isoprene), and glycerol and its derivatives. The use of substrates like lignocellulosic biomass that impose harsh culture conditions drives the quest for the selection of suitable robust microorganisms. The yeast Saccharomyces cerevisiae, widely utilized in industrial processes, has been extensively engineered to produce high-value chemicals. For its robustness, ease of handling, genetic toolbox and fitness in an industrial context, S. cerevisiae is an ideal platform for the founding of sustainable bioprocesses. Taking these into account, this review focuses on metabolic engineering strategies that have been applied to S. cerevisiae for converting renewable resources into the previously identified chemical targets. The heterogeneity of each chemical and its manufacturing process leads to inevitable differences between the development stages of each process. Currently, 8 of 11 of these top value chemicals have been already reported to be produced by recombinant S. cerevisiae. While some of them are still in an early proof-of-concept stage, others, like xylitol or lactic acid, are already being produced from lignocellulosic biomass. Furthermore, the constant advances in genome-editing tools, e.g. CRISPR/Cas9, coupled with the application of innovative process concepts such as consolidated bioprocessing, will contribute for the establishment of S. cerevisiae-based biorefineries.

Relevance of NADH Dehydrogenase and Alternative Two-Enzyme Systems for Growth of Corynebacterium glutamicum With Glucose, Lactate, and Acetate

The oxidation of NADH with the concomitant reduction of a quinone is a crucial step in the metabolism of respiring cells. In this study, we analyzed the relevance of three different NADH oxidation systems in the actinobacterial model organism Corynebacterium glutamicum by characterizing defined mutants lacking the non-proton-pumping NADH dehydrogenase Ndh (Δndh) and/or one of the alternative NADH-oxidizing enzymes, L-lactate dehydrogenase LdhA (ΔldhA) and malate dehydrogenase Mdh (Δmdh). Together with the menaquinone-dependent L-lactate dehydrogenase LldD and malate:quinone oxidoreductase Mqo, the LdhA-LldD and Mdh-Mqo couples can functionally replace Ndh activity. In glucose minimal medium the Δndh mutant, but not the ΔldhA and Δmdh strains, showed reduced growth and a lowered NAD+/NADH ratio, in line with Ndh being the major enzyme for NADH oxidation. Growth of the double mutants ΔndhΔmdh and ΔndhΔldhA, but not of strain ΔmdhΔldhA, in glucose medium was stronger impaired than that of the Δndh mutant, supporting an active role of the alternative Mdh-Mqo and LdhA-LldD systems in NADH oxidation and menaquinone reduction. In L-lactate minimal medium the Δndh mutant grew better than the wild type, probably due to a higher activity of the menaquinone-dependent L-lactate dehydrogenase LldD. The ΔndhΔmdh mutant failed to grow in L-lactate medium and acetate medium. Growth with L-lactate could be restored by additional deletion of sugR, suggesting that ldhA repression by the transcriptional regulator SugR prevented growth on L-lactate medium. Attempts to construct a ΔndhΔmdhΔldhA triple mutant were not successful, suggesting that Ndh, Mdh and LdhA cannot be replaced by other NADH-oxidizing enzymes in C. glutamicum.

Elevated, non-proliferative temperatures change the profile of fermentation products in Corynebacterium glutamicum

Although temperature is a crucial factor affecting enzymatic activity on biochemical and biofuel production, the reaction temperature for the generation of these products is usually set at the optimal growth temperature of the host strain, even under non-proliferative conditions. Given that the production of fermentation products only requires a fraction of the cell's metabolic pathways, the optimal temperatures for microbial growth and the fermentative production of a target compound may be different. Here, we investigated the effect of temperature on lactic and succinic acids production, and related enzymatic activities, in wild-type and succinic acid-overproducing strains of Corynebacterium glutamicum. Interestingly, fermentative production of lactic acid increased with the temperature in wild-type: production was 69% higher at 42.5 °C, a temperature that exceeded the upper limit for growth, than that at the optimal growth temperature (30 °C). Conversely, succinic acid production was decreased by 13% under the same conditions in wild-type. The specific activity of phosphoenolpyruvate carboxylase decreased with the increase in temperature. In contrast, the other glycolytic and reductive TCA cycle enzymes demonstrated increased or constant activity as the temperature was increased. When using a succinic acid over-producing strain, succinic acid production was increased by 34% at 42.5 °C. Our findings demonstrate that the profile of fermentation products is dependent upon temperature, which could be caused by the modulation of enzymatic activities. Moreover, we report that elevated temperatures, exceeding the upper limit for cell growth, can be used to increase the production of target compounds in C. glutamicum. KEY POINTS: • Lactate productivity was increased by temperature elevation. • Succinate productivity was increased by temperature elevation when lactate pathway was deleted. • Specific activity of phosphoenolpyruvate carboxylase was decreased by temperature elevation.

Increasement of O-acetylhomoserine production in Escherichia coli by modification of glycerol-oxidative pathway coupled with optimization of fermentation

OBJECTIVE

O-acetylhomoserine (OAH) is an important platform chemical to produce high-valuable chemicals. To improve the production of O-acetylhomoserine from glycerol, the glycerol-oxidative pathway was investigated and the optimization of fermentation with crude glycerol was carried out.

RESULTS

The glycerol-uptake system and glycerol-oxidative pathway were modified and O-acetyltransferase from Corynebacterium glutamicum was introduced into the engineered strain to produce O-acetylhomoserine. It was found that overexpression of glycerol 3-phosphate dehydrogenase improved the OAH production to 6.79 and 4.21 g/L from pure and crude glycerol, respectively. And the higher OAH production depending on higher level of transcription of glpD. Two-step statistical approach was employed to optimize the fermentation conditions. The significant effects of glycerol, ammonium chloride and yeast extract were screened applying Plackett-Burman design and were optimized further by employing the Response Surface Methodology. Under optimized conditions, the OAH production was up to 9.42 and 7.01 g/L when pure and crude glycerol were used in shake flask cultivations, respectively.

CONCLUSIONS

The enzymatic step catalyzing the oxidation of glycerol through GlpD was the key step for OAH production, which served the foundation for realization of a consistent OAH production from crude glycerol in the future.

Enzymatic regeneration and conservation of ATP: challenges and opportunities

Adenosine triphosphate (ATP), the universal energy currency of life, has a central role in numerous biochemical reactions with potential for the synthesis of numerous high-value products. ATP can be regenerated by three types of mechanisms: substrate level phosphorylation, oxidative phosphorylation, and photophosphorylation. Current ATP regeneration methods are mainly based on substrate level phosphorylation catalyzed by one enzyme, several cascade enzymes, or in vitro synthetic enzymatic pathways. Among them, polyphosphate kinases and acetate kinase, along with their respective phosphate donors, are the most popular approaches for in vitro ATP regeneration. For in vitro artificial pathways, either ATP-free or ATP-balancing strategies can be implemented via smart pathway design by choosing ATP-independent enzymes. Also, we discuss some remaining challenges and suggest perspectives, especially for industrial biomanufacturing. Development of ATP regeneration systems featuring low cost, high volumetric productivity, long lifetime, flexible compatibility, and great robustness could be one of the bottom-up strategies for cascade biocatalysis and in vitro synthetic biology.

Multiplex Design of the Metabolic Network for Production of l-Homoserine in Escherichia coli

In this study, the bottlenecks that sequentially limit l-homoserine biosynthesis were identified and resolved, based on rational and efficient metabolic-engineering strategies, coupled with CRISPR interference (CRISPRi)-based systematic analysis. The metabolomics data largely expanded our understanding of metabolic effects and revealed relevant targets for further modification to achieve better performance. The systematic analysis strategy, as well as metabolomics analysis, can be used to rationally design cell factories for the production of highly valuable chemicals.

l-Homoserine, which is one of the few amino acids that is not produced on a large scale by microbial fermentation, plays a significant role in the synthesis of a series of valuable chemicals. In this study, systematic metabolic engineering was applied to target Escherichia coli W3110 for the production of l-homoserine. Initially, a basic l-homoserine producer was engineered through the strategies of overexpressing thrA (encoding homoserine dehydrogenase), removing the degradative and competitive pathways by knocking out metA (encoding homoserine O-succinyltransferase) and thrB (encoding homoserine kinase), reinforcing the transport system, and redirecting the carbon flux by deleting iclR (encoding the isocitrate lyase regulator). The resulting strain constructed by these strategies yielded 3.21 g/liter of l-homoserine in batch cultures. Moreover, based on CRISPR-Cas9/dCas9 (nuclease-dead Cas9)-mediated gene repression for 50 genes, the iterative genetic modifications of biosynthesis pathways improved the l-homoserine yield in a stepwise manner. The rational integration of glucose uptake and recovery of l-glutamate increased l-homoserine production to 7.25 g/liter in shake flask cultivation. Furthermore, the intracellular metabolic analysis further provided targets for strain modification by introducing the anaplerotic route afforded by pyruvate carboxylase to oxaloacetate formation, which resulted in accumulating 8.54 g/liter l-homoserine (0.33 g/g glucose, 62.4% of the maximum theoretical yield) in shake flask cultivation. Finally, a rationally designed strain gave 37.57 g/liter l-homoserine under fed-batch fermentation, with a yield of 0.31 g/g glucose.

IMPORTANCE In this study, the bottlenecks that sequentially limit l-homoserine biosynthesis were identified and resolved, based on rational and efficient metabolic-engineering strategies, coupled with CRISPR interference (CRISPRi)-based systematic analysis. The metabolomics data largely expanded our understanding of metabolic effects and revealed relevant targets for further modification to achieve better performance. The systematic analysis strategy, as well as metabolomics analysis, can be used to rationally design cell factories for the production of highly valuable chemicals.

Anaerobic glucose consumption is accelerated at non-proliferating elevated temperatures through upregulation of a glucose transporter gene in Corynebacterium glutamicum

Cell proliferation is achieved through numerous enzyme reactions. Temperature governs the activity of each enzyme, ultimately determining the optimal growth temperature. The synthesis of useful chemicals and fuels utilizes a fraction of available metabolic pathways, primarily central metabolic pathways including glycolysis and the tricarboxylic acid cycle. However, it remains unclear whether the optimal temperature for these pathways is correlated with that for cell proliferation. Here, we found that wild-type Corynebacterium glutamicum displayed increased glycolytic activity under non-growing anaerobic conditions at 42.5 °C, at which cells do not proliferate under aerobic conditions. At this temperature, glucose consumption was not inhibited and increased by 28% compared with that at the optimal growth temperature of 30 °C. Transcriptional analysis revealed that a gene encoding glucose transporter (iolT2) was upregulated by 12.3-fold compared with that at 30 °C, with concomitant upregulation of NCgl2954 encoding the iolT2-regulating transcription factor. Deletion of iolT2 decreased glucose consumption rate at 42.5 °C by 28%. Complementation of iolT2 restored glucose consumption rate, highlighting the involvement of iolT2 in the accelerating glucose consumption at an elevated temperature. This study shows that the optimal temperature for glucose metabolism in C. glutamicum under anaerobic conditions differs greatly from that for cell growth under aerobic conditions, being beyond the upper limit of the growth temperature. This is beneficial for fuel and chemical production not only in terms of increasing productivity but also for saving cooling costs. KEY POINTS: • C. glutamicum accelerated anaerobic glucose consumption at elevated temperature. • The optimal temperature for glucose consumption was above the upper limit for growth. • Gene expression involved in glucose transport was upregulated at elevated temperature. Graphical abstract.

Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase

Succinic acid (SA), a dicarboxylic acid of industrial importance, can be efficiently produced by metabolically engineered Mannheimia succiniciproducens. Malate dehydrogenase (MDH) is one of the key enzymes for SA production, but has not been well characterized. Here we report biochemical and structural analyses of various MDHs and development of hyper-SA producing M. succiniciproducens by introducing the best MDH. Corynebacterium glutamicum MDH (CgMDH) shows the highest specific activity and least substrate inhibition, whereas M. succiniciproducens MDH (MsMDH) shows low specific activity at physiological pH and strong uncompetitive inhibition toward oxaloacetate (ki of 67.4 and 588.9 μM for MsMDH and CgMDH, respectively). Structural comparison of the two MDHs reveals a key residue influencing the specific activity and susceptibility to substrate inhibition. A high-inoculum fed-batch fermentation of the final strain expressing cgmdh produces 134.25 g L^-1 of SA with the maximum productivity of 21.3 g L^-1 h^-1, demonstrating the importance of enzyme optimization in strain development.

Synthesis of the character impact compound raspberry ketone and additional flavoring phenylbutanoids of biotechnological interest with Corynebacterium glutamicum

Background

The phenylbutanoid 4-(4-hydroxyphenyl)butan-2-one, commonly known as raspberry ketone, is responsible for the typical scent and flavor of ripe raspberries. Chemical production of nature-identical raspberry ketone is well established as this compound is frequently used to flavor food, beverages and perfumes. However, high demand for natural raspberry ketone, but low natural abundance in raspberries, render raspberry ketone one of the most expensive natural flavoring components.

Results

In this study, Corynebacterium glutamicum was engineered for the microbial synthesis of the character impact compound raspberry ketone from supplemented p-coumaric acid. In this context, the NADPH-dependent curcumin/dihydrocurcumin reductase CurA from Escherichia coli was employed to catalyze the final step of raspberry ketone synthesis as it provides a hitherto unknown benzalacetone reductase activity. In combination with a 4-coumarate: CoA ligase from parsley (Petroselinum crispum) and a monofunctional benzalacetone synthase from Chinese rhubarb (Rheum palmatum), CurA constitutes the synthetic pathway for raspberry ketone synthesis in C. glutamicum. The resulting strain accumulated up to 99.8 mg/L (0.61 mM) raspberry ketone. In addition, supplementation of other phenylpropanoids allowed for the synthesis of two other naturally-occurring and flavoring phenylbutanoids, zingerone (70 mg/L, 0.36 mM) and benzylacetone (10.5 mg/L, 0.07 mM).

Conclusion

The aromatic product portfolio of C. glutamicum was extended towards the synthesis of the flavoring phenylbutanoids raspberry ketone, zingerone and benzylacetone. Key to success was the identification of CurA from E. coli having a benzalacetone reductase activity. We believe, that the constructed C. glutamicum strain represents a versatile platform for the production of natural flavoring phenylbutanoids at larger scale.

Corynebacterium glutamicum, a natural overproducer of succinic acid?

Corynebacterium glutamicum is well known as an important industrial amino acid producer. For a few years, its ability to produce organic acids, under micro-aerobic or anaerobic conditions was demonstrated. This study is focused on the identification of the culture parameters influencing the organic acids production and, in particular, the succinate production, by this bacterium. Corynebacterium glutamicum 2262, used throughout this study, was a wild-type strain, which was not genetically designed for the production of succinate. The oxygenation level and the residual glucose concentration appeared as two critical parameters for the organic acids production. The maximal succinate concentration (4.9 g L-1) corresponded to the lower kLa value of 5 h-1. Above 5 h-1, a transient accumulation of the succinate was observed. Interestingly, the stop in the succinate production was concomitant with a lower threshold glucose concentration of 9 g L-1. Taking into account this threshold, a fed-batch culture was performed to optimize the succinate production with C. glutamicum 2262. The results showed that this wild-type strain was able to produce 93.6 g L-1 of succinate, which is one of the highest concentration reported in the literature.

Requirement of de novo synthesis of pyruvate carboxylase in long-term succinic acid production in Corynebacterium glutamicum

Protein turnover through de novo synthesis is critical for sustainable cellular functions. We previously found that glucose consumption rate in Corynebacterium glutamicum under anaerobic conditions increased at temperature higher than the upper limit of growth temperature. Here, we showed that production of lactic and succinic acids increased at higher temperature for long-term (48 h) anaerobic reaction in metabolically engineered strains. At 42 °C, beyond the upper limit of growth temperature range, biomass-specific lactic acid production rate was 8% higher than that at 30 °C, the optimal growth temperature. In contrast, biomass-specific succinic acid production rate was highest at 36 °C, 28% higher than that at 30 °C, although the production at 42 °C was still 23% higher than that at 30 °C. As enzymes are usually unstable at high temperatures, we investigated whether protein turnover of metabolic enzymes is required for the production of lactic and succinic acids under these conditions. Interestingly, when de novo protein synthesis was inhibited by addition of chloramphenicol, after 6 h, only succinic acid production was inhibited. Because glycolytic enzymes are involved in both lactic and succinic acids synthesis, enzymes in the anaplerotic pathway and the tricarboxylic acid (TCA) cycle leading to succinic acid synthesis were likely to be responsible for its decreased production. Among the five enzymes examined, the specific activity of only pyruvate carboxylase was drastically decreased after 48 h at 42 °C. Thus, the de novo synthesis of pyruvate carboxylase is required for long-term production of succinic acid. Graphical abstract KEY POINTS: • Long-term reaction for organic acids can be improved at temperature beyond ideal growth conditions. • De novo synthesis of pyruvate carboxylase is required for long-term succinic acid production.

Effect of dissolved oxygen on L-methionine production from glycerol by Escherichia coli W3110BL using metabolic flux analysis method

L-Methionine is an essential amino acid in humans, which plays an important role in the synthesis of some important amino acids and proteins. In this work, metabolic flux of batch fermentation of L-methionine with recombinant Escherichia coli W3110BL was analyzed using the flux balance analysis method, which estimated the intracellular flux distributions under different dissolved oxygen conditions. The results revealed the producing L-methionine flux of 4.8 mmol/(g cell·h) [based on the glycerol uptake flux of 100 mmol/(g cell·h)] was obtained at 30% dissolved oxygen level which was higher than that of other dissolved oxygen levels. The carbon fluxes for synthesizing L-methionine were mainly obtained from the pathway of phosphoenolpyruvate to oxaloacetic acid [15.6 mmol/(g cell·h)] but not from the TCA cycle. Hence, increasing the flow from phosphoenolpyruvate to oxaloacetic acid by enhancing the enzyme activity of phosphoenolpyruvate carboxylase might be conducive to the production of L-methionine. Additionally, pentose phosphate pathway could provide a large amount of reducing power NADPH for the synthesis of amino acids and the flux could increase from 41 mmol/(g cell·h) to 51 mmol/(g cell·h) when changing the dissolved oxygen levels, thus meeting the requirement of NADPH for L-methionine production and biomass synthesis. Therefore, the following modification of the strains should based on the improvement of the key pathway and the NAD(P)/NAD(P)H metabolism.

Selection of Thermotolerant Corynebacterium glutamicum Strains for Organic Acid Biosynthesis

In recent years, Corynebacterium glutamicum has been considered as producer of many valuable chemical compounds. Among them, organic acids such as l-lactic and succinic acids are the most important ones. It is known that the wild-type C. glutamicum grows well in the temperature range between 25 and 37 °C. Above 40 °C, the biomass growth usually abruptly stops; however, the bacteria remain metabolically active. High temperature affects the metabolic activity of C. glutamicum cells and can lead to changes in the composition and quantity of the fermentation products. Therefore, in a series of subsequent selection steps, we tried to obtain prototrophic strains capable of growing at 44 °C from the culture of homoserine auxotroph C. glutamicum ATCC 13287. During selection, we used complex and mineral media containing succinic and citric acids. As a result, we obtained 47 clones able to grow at elevated temperature. Moreover, the estimated optimal growth temperature for several of them was about 40 °C or higher. Under oxygen limitation conditions, C. glutamicum strains produce organic acids. Regardless of the tested clone, l-lactic acid was the main product. However, its concentration was the highest in the cultures performed at 44 °C. The elevated temperature also affected the biosynthesis of other organic acids. Compared to the parental strain, the concentration of acetic acid increased, and of succinic acid decreased in the cultures of thermotolerant strains. Strain RCG44.3 exhibited interesting properties; it was able to synthesise 27.1 g/L l-lactic acid, with production yield of 0.57 g/g, during 24 h of fermentation at 44 °C.

Evaluation of pyruvate decarboxylase-negative Saccharomyces cerevisiae strains for the production of succinic acid

Dicarboxylic acids are important bio‐based building blocks, and Saccharomyces cerevisiae is postulated to be an advantageous host for their fermentative production. Here, we engineered a pyruvate decarboxylase‐negative S. cerevisiae strain for succinic acid production to exploit its promising properties, that is, lack of ethanol production and accumulation of the precursor pyruvate. The metabolic engineering steps included genomic integration of a biosynthesis pathway based on the reductive branch of the tricarboxylic acid cycle and a dicarboxylic acid transporter. Further modifications were the combined deletion of GPD1 and FUM1 and multi‐copy integration of the native PYC2 gene, encoding a pyruvate carboxylase required to drain pyruvate into the synthesis pathway. The effect of increased redox cofactor supply was tested by modulating oxygen limitation and supplementing formate. The physiologic analysis of the differently engineered strains focused on elucidating metabolic bottlenecks. The data not only highlight the importance of a balanced activity of pathway enzymes and selective export systems but also shows the importance to find an optimal trade‐off between redox cofactor supply and energy availability in the form of ATP.

Metabolic engineering of Corynebacterium glutamicum for hyperproduction of polymer-grade L- and D-lactic acid

Strain development is critical for microbial production of bio-based chemicals. The stereo-complex form of polylactic acid, a complex of poly-L- and poly-D-lactic acid, is a promising polymer candidate due to its high thermotolerance. Here, we developed Corynebacterium glutamicum strains producing high amounts of L- and D-lactic acid through intensive metabolic engineering. Chromosomal overexpression of genes encoding the glycolytic enzymes, glucokinase, glyceraldehyde-3-phosphate dehydrogenase, phosphofructokinase, triosephosphate isomerase, and enolase, increased L- and D-lactic acid concentration by 146% and 56%, respectively. Chromosomal integration of two genes involved in the Entner-Doudoroff pathway (6-phosphogluconate dehydratase and 2-dehydro-3-deoxyphosphogluconate aldolase), together with a gene encoding glucose-6-phosphate dehydrogenase from Zymomonas mobilis, to bypass the carbon flow from glucose, further increased L- and D-lactic acid concentration by 11% and 44%, respectively. Finally, additional chromosomal overexpression of a gene encoding NADH dehydrogenase to modulate the redox balance resulted in the production of 212 g/L L-lactic acid with a 97.9% yield and 264 g/L D-lactic acid with a 95.0% yield. The optical purity of both L- and D-lactic acid was 99.9%. Because the constructed metabolically engineered strains were devoid of plasmids and antibiotic resistance genes and were cultivated in mineral salts medium, these strains could contribute to the cost-effective production of the stereo-complex form of polylactic acid in practical scale.

Carboxylic acid consumption and production by Corynebacterium glutamicum

Corynebacterium glutamicum is well-known as an industrial workhorse, most notably for its use in the bulk production of amino acids in the feed and food sector. Previous studies of the effect of gradients in scale-down reactors with complex media disclosed an accumulation of several carboxylic acids and a parallel decrease of growth and product accumulation. This study, therefore, addresses the impact of carboxylic acids, for example, acetate and l-lactate, on the cultivation of the cadaverine producing strain C. glutamicum DM1945Δact3:P_tuf -ldcC^opt and their potential role in scale up related performance losses. A fluctuating power input in shake flask and stirred tank cultivations with mineral salt was applied to mimic discontinuous oxygen availability. Results demonstrate, whenever sufficient oxygen was available, C. glutamicum recovered from previously occurring stressful conditions like an oxygen limiting phase. Reassimilation of acids was detected simultaneously. In cultures, which were supplemented with either acetate or l-lactate, a rapid cometabolization of both acids in presence of glucose was observed, showing conversion rates of 7.8 and 3.8 mmol g_{cell dry weight} ^-1 hr^-1 , respectively. Uptake of these acids was accompanied by increased oxygen consumption. Proteins related to oxidative stress response, glycogen synthesis, and the main carbon metabolism were found in altered concentrations under oscillatory cultivation conditions. (Proteomics data are available via ProteomeXchange with identifier PXD012760). Virtually no impact on growth or product formation was observed. We conclude that the reduced growth and product formation in scale-down cultivations when complex media was used is not caused by the accumulation of carboxylic acids.

Whole Cell Actinobacteria as Biocatalysts

Production of fuels, therapeutic drugs, chemicals, and biomaterials using sustainable biological processes have received renewed attention due to increasing environmental concerns. Despite having high industrial output, most of the current chemical processes are associated with environmentally undesirable by-products which escalate the cost of downstream processing. Compared to chemical processes, whole cell biocatalysts offer several advantages including high selectivity, catalytic efficiency, milder operational conditions and low impact on the environment, making this approach the current choice for synthesis and manufacturing of different industrial products. In this review, we present the application of whole cell actinobacteria for the synthesis of biologically active compounds, biofuel production and conversion of harmful compounds to less toxic by-products. Actinobacteria alone are responsible for the production of nearly half of the documented biologically active metabolites and many enzymes; with the involvement of various species of whole cell actinobacteria such as Rhodococcus, Streptomyces, Nocardia and Corynebacterium for the production of useful industrial commodities.

Pyruvate Carboxylase Variants Enabling Improved Lysine Production from Glucose Identified by Biosensor-Based High-Throughput Fluorescence-Activated Cell Sorting Screening

Pyruvate carboxylase is an anaplerotic carbon dioxide-fixing enzyme replenishing the tricarboxylic acid cycle with oxaloacetate during growth on sugars. In this study, we applied a lysine biosensor to identify pyruvate carboxylase variants in Corynebacterium glutamicum that enable improved l-lysine production from glucose. A suitable reporter strain was transformed with a pyc gene library created by error-prone PCR and screened by fluorescence-activated cell sorting (FACS) for cells with increased fluorescence triggered by an elevated cytoplasmic lysine concentration. Two pyruvate carboxylase variants, PCx^T343A,I1012S and PCx^T132A were identified allowing 9% and 19% increased lysine titers upon plasmid-based expression. Chromosomal expression of PCx^T132A and PCx^T343A variants led to 6% and 14% higher l-lysine levels. The new PCx variants can be useful also for other microbial strains producing TCA cycle-derived metabolites. Our approach indicates that a biosensor such as pSenLys enables directed evolution of many enzymes involved in converting a carbon source into the target metabolite.

Engineering of Corynebacterium glutamicum as a prototrophic pyruvate-producing strain: Characterization of a ramA-deficient mutant and its application for metabolic engineering

To construct a prototrophic Corynebacterium glutamicum strain that efficiently produces pyruvate from glucose, the effects of inactivating RamA, a global regulator responsible for activating the oxidative tricarboxylic acid (TCA) cycle, on glucose metabolism were investigated. ΔramA showed an increased specific glucose consumption rate, decreased growth, comparable pyruvate production, higher formation of lactate and acetate, and lower accumulation of succinate and 2-oxoglutarate compared to the wild type. A significant decrease in pyruvate dehydrogenase complex activity was observed for ΔramA, indicating reduced carbon flow to the TCA cycle in ΔramA. To create an efficient pyruvate producer, the ramA gene was deleted in a strain lacking the genes involved in all known lactate- and acetate-producing pathways. The resulting mutant produced 161 mM pyruvate from 222 mM glucose, which was significantly higher than that of the parent (89.3 mM; 1.80-fold).

Metabolic engineering of Corynebacterium glutamicum for production of sunscreen shinorine

Ultraviolet-absorbing chemicals are useful in cosmetics and skin care to prevent UV-induced skin damage. We demonstrate here that heterologous production of shinorine, which shows broad absorption maxima in the UV-A and UV-B region. A shinorine producing Corynebacterium glutamicum strain was constructed by expressing four genes from Actinosynnema mirum DSM 43827, which are responsible for the biosynthesis of shinorine from sedoheptulose-7-phosphate in the pentose phosphate pathway. Deletion of transaldolase encoding gene improved shinorine production by 5.2-fold. Among the other genes in pentose phosphate pathway, overexpression of 6-phosphogluconate dehydrogenase encoding gene further increased shinorine production by 60% (19.1 mg/L). The genetic engineering of the pentose phosphate pathway in C. glutamicum improved shinorine production by 8.3-fold in total, and could be applied to produce the other chemicals derived from sedoheptulose-7-phosphate.