Determination of key enzymes for threonine synthesis through in vitro metabolic pathway analysis

Engineering Escherichia coli for l-Threonine Hyperproduction Based on Multidimensional Optimization Strategies

Exploring effective remodeling strategies to further improve the productivity of high-yield strains is the goal of biomanufacturing. However, the lack of insight into host-specific metabolic networks prevents timely identification of useful engineering targets. Here, multidimensional engineering strategies were implemented to optimize the global metabolic network for improving l-threonine production. First, the metabolic bottleneck for l-threonine synthesis was eliminated by synergistic utilization of NADH and an enhanced ATP supply. Carbon fluxes were redistributed into the TCA cycle by rationally regulating the GltA activity. Subsequently, the stress global response regulator UspA was identified to enhance l-threonine production by a transcriptomic analysis. Then, l-threonine productivity was improved by enhancing the host's stress resistance and releasing the inhibitory reaction of glucose utilization. Eventually, the l-threonine yield of THRH16 reached 170.3 g/L and 3.78 g/L/h in a 5 L bioreactor, which is the highest production index reported. This study provides rational guidance for increasing the productivity of other chemicals.

Effect of low oxygen stress on the metabolic responses of tomato fruit cells

Postharvest losses of fruits and vegetables can occur due to cell breakdown and browning during controlled atmosphere storage as a result of low oxygen (O2) stress. Therefore, the study was designed to better understand the underlying mechanisms of the response of isolated tomato fruit cells incubated at low O2 (hypoxic and anoxic) conditions as a model system. The O2 stress conditions used for the experiment were based on the results of the Michaelis-Menten constant (Km) of respiration. A total of 56 polar metabolites belonging mainly to different functional groups, including amino acids, organic acids, sugars and sugar alcohols, were identified using GC-MS. O2 stress stimulated the biosynthesis of most of the free amino acids while decreasing the synthesis of most of the organic acids (especially those linked to the tricarboxylic acid cycle), sugars (except for ribose) and other nitrogen-containing compounds. The down-regulation of these TCA cycle metabolites served to provide energy to ensure the survival of the cell. Increases in the sugar alcohol levels and induction of fermentative metabolism were observed under low O2 stress. By employing multivariate statistics, metabolites were identified that were essential to the oxygen stress response and establishing the correlation between metabolite abundance, oxygen levels, and incubation period were achievable. A higher correlation was observed between the O2 levels and most of the metabolites.

Microbial Secondary Metabolites via Fermentation Approaches for Dietary Supplementation Formulations

Food supplementation formulations refer to products that are designed to provide additional nutrients to the diet. Vitamins, dietary fibers, minerals and other functional compounds (such as antioxidants) are concentrated in dietary supplements. Specific amounts of dietary compounds are given to the body through food supplements, and these include as well so-called non-essential compounds such as secondary plant bioactive components or microbial natural products in addition to nutrients in the narrower sense. A significant social challenge represents how to moderately use the natural resources in light of the growing world population. In terms of economic production of (especially natural) bioactive molecules, ways of white biotechnology production with various microorganisms have recently been intensively explored. In the current review other relevant dietary supplements and natural substances (e.g., vitamins, amino acids, antioxidants) used in production of dietary supplements formulations and their microbial natural production via fermentative biotechnological approaches are briefly reviewed. Biotechnology plays a crucial role in optimizing fermentation conditions to maximize the yield and quality of the target compounds. Advantages of microbial production include the ability to use renewable feedstocks, high production yields, and the potential for cost-effective large-scale production. Additionally, it can be more environmentally friendly compared to chemical synthesis, as it reduces the reliance on petrochemicals and minimizes waste generation. Educating consumers about the benefits, safety, and production methods of microbial products in general is crucial. Providing clear and accurate information about the science behind microbial production can help address any concerns or misconceptions consumers may have.

Exploring the Feasibility of Cell-Free Synthesis as a Platform for Polyhydroxyalkanoate (PHA) Production: Opportunities and Challenges

The extensive utilization of traditional petroleum-based plastics has resulted in significant damage to the natural environment and ecological systems, highlighting the urgent need for sustainable alternatives. Polyhydroxyalkanoates (PHAs) have emerged as promising bioplastics that can compete with petroleum-based plastics. However, their production technology currently faces several challenges, primarily focused on high costs. Cell-free biotechnologies have shown significant potential for PHA production; however, despite recent progress, several challenges still need to be overcome. In this review, we focus on the status of cell-free PHA synthesis and compare it with microbial cell-based PHA synthesis in terms of advantages and drawbacks. Finally, we present prospects for the development of cell-free PHA synthesis.

The OxyR and SoxR transcriptional regulators are involved in a broad oxidative stress response in Paraburkholderia xenovorans LB400

Background

Aerobic metabolism generates reactive oxygen species that may cause critical harm to the cell. The aim of this study is the characterization of the stress responses in the model aromatic-degrading bacterium Paraburkholderia xenovorans LB400 to the oxidizing agents paraquat and H₂O₂.

Methods

Antioxidant genes were identified by bioinformatic methods in the genome of P. xenovorans LB400, and the phylogeny of its OxyR and SoxR transcriptional regulators were studied. Functionality of the transcriptional regulators from strain LB400 was assessed by complementation with LB400 SoxR of null mutant P. aeruginosa ΔsoxR, and the construction of P. xenovorans pIZoxyR that overexpresses OxyR. The effects of oxidizing agents on P. xenovorans were studied measuring bacterial susceptibility, survival and ROS formation after exposure to paraquat and H₂O₂. The effects of these oxidants on gene expression (qRT-PCR) and the proteome (LC–MS/MS) were quantified.

Results

P. xenovorans LB400 possesses a wide repertoire of genes for the antioxidant defense including the oxyR, ahpC, ahpF, kat, trxB, dpsA and gorA genes, whose orthologous genes are regulated by the transcriptional regulator OxyR in E. coli. The LB400 genome also harbors the soxR, fumC, acnA, sodB, fpr and fldX genes, whose orthologous genes are regulated by the transcriptional regulator SoxR in E. coli. The functionality of the LB400 soxR gene was confirmed by complementation of null mutant P. aeruginosa ΔsoxR. Growth, susceptibility, and ROS formation assays revealed that LB400 cells were more susceptible to paraquat than H₂O₂. Transcriptional analyses indicated the upregulation of the oxyR, ahpC1, katE and ohrB genes in LB400 cells after exposure to H₂O₂, whereas the oxyR, fumC, ahpC1, sodB1 and ohrB genes were induced in presence of paraquat. Proteome analysis revealed that paraquat induced the oxidative stress response proteins AhpCF and DpsA, the universal stress protein UspA and the RNA chaperone CspA. Both oxidizing agents induced the Ohr protein, which is involved in organic peroxide resistance. Notably, the overexpression of the LB400 oxyR gene in P. xenovorans significantly decreased the ROS formation and the susceptibility to paraquat, suggesting a broad OxyR-regulated antioxidant response.

Conclusions

This study showed that P. xenovorans LB400 possess a broad range oxidative stress response, which explain the high resistance of this strain to the oxidizing compounds paraquat and H₂O₂.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40659-022-00373-7.

Identification of a rate-limiting step in a metabolic pathway using the kinetic model and in vitro experiment

Identification of the rate-limiting step in a metabolic pathway is an important challenge in metabolic engineering for enhancing pathway flow. Although specific enzyme activities (V_max) provide valuable clues for the identification, it is time-consuming and difficult to measure multiple enzymes in the pathway because different assay protocols are required for each enzyme. In the present study, we propose a method to simultaneously determine the V_max values of multiple enzymes using a kinetic model with a time course of the intermediate concentrations through an in vitro experiment. To demonstrate this method, nine glycolysis reactions for converting glucose-6-phosphate (G6P) to pyruvate in Escherichia coli were considered. In a reaction mixture containing G6P and cofactors, glycolysis was initiated by adding a crude cell extract obtained from stationary phase cells. The V_max values were optimized to minimize the difference between the measured and simulated time-courses using a kinetic model. Metabolic control analysis using the kinetic model with the estimated V_max values revealed that fructose bisphosphate aldolase (FBA) was the rate-limiting step in the upper part of glycolysis. The addition of FBA in the reaction mixture successfully increased the glycolytic flux in vitro. Furthermore, in vivo, the specific glucose consumption rate of an FBA overexpression strain was 1.4 times higher than that of the control strain during the stationary phase. These results confirmed that FBA was the rate-limiting step in glycolysis under the stationary phase. This approach provides V_max values of multiple enzymes in a pathway for metabolic control analysis with a kinetic model.

Rebalancing microbial carbon distribution for L-threonine maximization using a thermal switch system

In metabolic engineering, unbalanced microbial carbon distribution has long blocked the further improvement in yield and productivity of high-volume natural metabolites. Current studies mostly focus on regulating desired biosynthetic pathways, whereas few strategies are available to maximize L-threonine efficiently. Here, we present a strategy to guarantee the supply of reduced cofactors and actualize L-threonine maximization by regulating cellular carbon distribution in central metabolic pathways. A thermal switch system was designed and applied to divide the whole fermentation process into two stages: growth and production. This system could rebalance carbon substrates between pyruvate and oxaloacetate by controlling the heterogenous expression of pyruvate carboxylase and oxaloacetate decarboxylation that responds to temperature. The system was tested in an L-threonine producer Escherichia coli TWF001, and the resulting strain TWF106/pFT24rp overproduced L-threonine from glucose with 111.78% molar yield. The thermal switch system was then employed to switch off the L-alanine synthesis pathway, resulting in the highest L-threonine yield of 124.03%, which exceeds the best reported yield (87.88%) and the maximum available theoretical value of L-threonine production (122.47%). This inducer-free genetic circuit design can be also developed for other biosynthetic pathways to increase product conversion rates and shorten production cycles.

Transcriptomic analysis of an l-threonine-producing Escherichia coli TWF001

Wild-type Escherichia coli usually does not accumulate l-threonine, but E. coli strain TWF001 could produce 30.35 g/L l-threonine after 23-H fed-batch fermentation. To understand the mechanism for the high yield of l-threonine production in TWF001, transcriptomic analyses of the TWF001 cell samples collected at the logarithmic and stationary phases were performed, using the wild-type E. coli strain W3110 as the control. Compared with W3110, 1739 and 2361 genes were differentially transcribed in the logarithmic and stationary phases, respectively. Most genes related to the biosynthesis of l-threonine were significantly upregulated. Some key genes related to the NAD(P)H regeneration were upregulated. Many genes relevant to glycolysis and TCA cycle were downregulated. The key genes involved in the l-threonine degradation were downregulated. The gene rhtA encoding the l-threonine exporter was upregulated, whereas the genes sstT and tdcC encoding the l-threonine importer were downregulated. The upregulated genes in the glutamate pathway might form an amino-providing loop, which is beneficial for the high yield of l-threonine production. Many genes encoding the 30S and 50S subunits of ribosomes were also upregulated. The findings are useful for gene engineering to increase l-threonine production in E. coli.

Deletion of arcA, iclR, and tdcC in Escherichia coli to improve l-threonine production

l-Threonine is an important amino acid supplemented in food, medicine, or feed. Starting from glucose, l-threonine production in Escherichia coli involves the glycolysis, TCA cycle, and the l-threonine biosynthetic pathway. In this study, how the l-threonine production in an l-threonine producing E. coli TWF001 is controlled by the three regulators ArcA, Cra, and IclR, which control the expression of genes involved in the glycolysis and TCA cycle, has been investigated. Ten mutant strains were constructed from TWF001 by different combinations of deletion or overexpression of arcA, cra, iclR, and tdcC. l-Threonine production was increased in the mutants TWF015 (ΔarcAΔcra), TWF016 (ΔarcAPcra::Ptrc), TWF017 (ΔarcAΔiclR), TWF018 (ΔarcAΔiclRΔtdcC), and TWF019 (ΔarcAΔcraΔiclRΔtdcC). Among these mutant strains, the highest l-threonine production (26.0 g/L) was obtained in TWF018, which was a 109.7% increase compared with the control TWF001. In addition, TWF018 could consume glucose more efficiently than TWF001 and produce less acetate. The results suggest that deletion of arcA, iclR, and tdcC could efficiently increase l-threonine production in E. coli.

Increasing L-threonine production in Escherichia coli by overexpressing the gene cluster phaCAB

L-Threonine is an important branched-chain amino acid and could be applied in feed, drugs, and food. In this study, L-threonine production in an L-threonine-producing Escherichia coli strain TWF001 was significantly increased by overexpressing the gene cluster phaCAB from Ralstonia eutropha. TWF001/pFW01-phaCAB could produce 96.4-g/L L-threonine in 3-L fermenter and 133.5-g/L L-threonine in 10-L fermenter, respectively. In addition, TWF001/pFW01-phaCAB produced 216% more acetyl-CoA, 43% more malate, and much less acetate than the vector control TWF001/pFW01, and meanwhile, TWF001/pFW01-phaCAB produced poly-3-hydroxybutyrate, while TWF001/pFW01 did not. Transcription analysis showed that the key genes in the L-threonine biosynthetic pathway were up-regulated, the genes relevant to the acetate formation were down-regulated, and the gene acs encoding the enzyme which converts acetate to acetyl-CoA was up-regulated. The results suggested that overexpression of the gene cluster phaCAB in E. coli benefits the enhancement of L-threonine production.

Improved Efficiency of the Desulfurization of Oil Sulfur Compounds in Escherichia coli Using a Combination of Desensitization Engineering and DszC Overexpression

The 4S pathway of biodesulfurization, which can specifically desulfurize aromatic S-heterocyclic compounds without destroying their combustion value, is a low-cost and environmentally friendly technology that is complementary to hydrodesulfurization. The four Dsz enzymes convert the model compound dibenzothiophene (DBT) into the sulfur-free compound 2-hydroxybiphenyl (HBP). Of these four enzymes, DszC, the first enzyme in the 4S pathway, is the most severely affected by the feedback inhibition caused by HBP. This study is the first attempt to directly modify DszC to decrease its inhibition by HBP, with the results showing that the modified protein is insensitive to HBP. On the basis of the principle that the final HBP product could show a blue color with Gibbs reagent, a high-throughput screening method for its rapid detection was established. The screening method and the combinatorial mutagenesis generated the mutant AKWC (A101K/W327C) of DszC. After the IC₅₀ was calculated, the feedback inhibition of the AKWC mutant was observed to have been substantially reduced. Interestingly, the substrate inhibition of DszC had also been reduced as a result of directed evolution. Finally, the recombinant BL21(DE3)/BADC*+C* (C* represents AKWC) strain exhibited a specific conversion rate of 214.84 μmol_HBP/g_DCW/h, which was 13.8-fold greater than that of the wild-type strain. Desensitization engineering and the overexpression of the desensitized DszC protein resulted in the elimination of the feedback inhibition bottleneck in the 4S pathway, which is practical and effective progress toward the production of sulfur-free fuel oil. The results of this study demonstrate the utility of desensitization of feedback inhibition regulation in metabolic pathways by protein engineering.

Fermentative production of the unnatural amino acid L-2-aminobutyric acid based on metabolic engineering

Background

l-2-aminobutyric acid (l-ABA) is an unnatural amino acid that is a key intermediate for the synthesis of several important pharmaceuticals. To make the biosynthesis of l-ABA environmental friendly and more suitable for the industrial-scale production. We expand the nature metabolic network of Escherichia coli using metabolic engineering approach for the production of l-ABA.

Results

In this study, Escherichia coli THR strain with a modified pathway for threonine-hyperproduction was engineered via deletion of the rhtA gene from the chromosome. To redirect carbon flux from 2-ketobutyrate (2-KB) to l-ABA, the ilvIH gene was deleted to block the l-isoleucine pathway. Furthermore, the ilvA gene from Escherichia coli W3110 and the leuDH gene from Thermoactinomyces intermedius were amplified and co-overexpressed. The promoter was altered to regulate the expression strength of ilvA* and leuDH. The final engineered strain E. coli THR ΔrhtAΔilvIH/Gap-ilvA*-Pbs-leuDH was able to produce 9.33 g/L of l-ABA with a yield of 0.19 g/L/h by fed-batch fermentation in a 5 L bioreactor.

Conclusions

This novel metabolically tailored strain offers a promising approach to fulfill industrial requirements for production of l-ABA.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1095-z) contains supplementary material, which is available to authorized users.

Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates

Isoprenoids are an attractive class of metabolites for enzymatic synthesis from renewable substrates. However, metabolic engineering of microorganisms for monoterpenoid production is limited by the need for time-consuming, and often non-intuitive, combinatorial tuning of biosynthetic pathway variations to meet design criteria. Towards alleviating this limitation, the goal of this work was to build a modular, cell-free platform for construction and testing of monoterpenoid pathways, using the fragrance and flavoring molecule limonene as a model. In this platform, multiple Escherichia coli lysates, each enriched with a single overexpressed pathway enzyme, are mixed to construct the full biosynthetic pathway. First, we show the ability to synthesize limonene from six enriched lysates with mevalonate substrate, an adenosine triphosphate (ATP) source, and cofactors. Next, we extend the pathway to use glucose as a substrate, which relies on native metabolism in the extract to convert glucose to acetyl-CoA along with three additional enzymes to convert acetyl-CoA to mevalonate. We find that the native E. coli farnesyl diphosphate synthase (IspA) is active in the lysate and diverts flux from the pathway intermediate geranyl pyrophospahte to farnesyl pyrophsophate and the byproduct farnesol. By adjusting the relative levels of cofactors NAD+, ATP and CoA, the system can synthesize 0.66 mM (90.2 mg l-1) limonene over 24 h, a productivity of 3.8 mg l-1 h-1. Our results highlight the flexibility of crude lysates to sustain complex metabolism and, by activating a glucose-to-limonene pathway with 9 heterologous enzymes encompassing 20 biosynthetic steps, expands an approach of using enzyme-enriched lysates for constructing, characterizing and prototyping enzymatic pathways.

A metabolic control analysis approach to introduce the study of systems in biochemistry: the glycolytic pathway in the red blood cell

Metabolic control analysis (MCA) is a promising approach in biochemistry aimed at understanding processes in a quantitative fashion. Here the contribution of enzymes and transporters to the control of a given pathway flux and metabolite concentrations is determined and expressed quantitatively by means of numerical coefficients. Metabolic flux can be influenced by a wide variety of modulators acting on one or more metabolic steps along the pathway. We describe a laboratory exercise to study metabolic regulation of human erythrocytes (RBCs). Within the framework of MCA, students use these cells to determine the sensitivity of the glycolytic flux to two inhibitors (iodoacetic acid: IA, and iodoacetamide: IAA) known to act on the enzyme glyceraldehyde-3-phosphate-dehydrogenase. Glycolytic flux was estimated by determining the concentration of extracellular lactate, the end product of RBC glycolysis. A low-cost colorimetric assay was implemented, that takes advantage of the straightforward quantification of the absorbance signal from the photographic image of the multi-well plate taken with a standard digital camera. Students estimate flux response coefficients for each inhibitor by fitting an empirical function to the experimental data, followed by analytical derivation of this function. IA and IAA exhibit qualitatively different patterns, which are thoroughly analyzed in terms of the physicochemical properties influencing their action on the target enzyme. IA causes highest glycolytic flux inhibition at lower concentration than IAA. This work illustrates the feasibility of using the MCA approach to study key variables of a simple metabolic system, in the context of an upper level biochemistry course. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):502-515, 2018.

Increasing L-threonine production in Escherichia coli by engineering the glyoxylate shunt and the L-threonine biosynthesis pathway

L-threonine is an important amino acid that can be added in food, medicine, or feed. Here, the influence of glyoxylate shunt on an L-threonine producing strain Escherichia coli TWF001 has been studied. The gene iclR was deleted, and the native promoter of the aceBA operon was replaced by the trc promoter in the chromosome of TWF001, the resulting strainTWF004 could produce 0.39 g L-threonine from1 g glucose after 36-h flask cultivation. Further replacing the native promoter of aspC by the trc promoter in the chromosome of TWF004 resulted in the strain TWF006. TWF006 could produce 0.42 g L-threonine from 1 g glucose after 36-h flask cultivation. Three key genes in the biosynthetic pathway of L-threonine, thrA ^* (a mutated thrA), thrB, and thrC were overexpressed in TWF006, resulting the strain TWF006/pFW01-thrA ^* BC. TWF006/pFW01-thrA ^* BC could produce 0.49 g L-threonine from 1 g glucose after 36-h flask cultivation. Next, the genes asd, rhtA, rhtC, or thrE were inserted into the plasmid TWF006/pFW01-thrA ^* BC, and TWF006 was transformed with these plasmids, resulting the strains TWF006/pFW01-thrA ^* BC-asd, TWF006/pFW01-thrA ^* BC-rhtA, TWF006/pFW01-thrA ^* BC-rhtC, and TWF006/pFW01-thrA ^* BC-thrE, respectively. These four strains could produce more L-threonine than the control strain, and the highest yield was produced by TWF006/pFW01-thrA ^* BC-asd; after 36-h flask cultivation, TWF006/pFW01-thrA ^* BC-asd could produce 15.85 g/l L-threonine, i.e., 0.53 g L-threonine per 1 g glucose, which is a 70% increase relative to the control strain TWF001. The results suggested that the combined engineering of glyoxylate shunt and L-threonine biosynthesis pathway could significantly increase the L-threonine production in E. coli.

Metabolic Profile of Oral Squamous Carcinoma Cell Lines Relies on a Higher Demand of Lipid Metabolism in Metastatic Cells

Tumor cells are subjected to a broad range of selective pressures. As a result of the imposed stress, subpopulations of surviving cells exhibit individual biochemical phenotypes that reflect metabolic reprograming. The present work aimed at investigating metabolic parameters of cells displaying increasing degrees of metastatic potential. The metabolites present in cell extracts fraction of tongue fibroblasts and of cell lines derived from human tongue squamous cell carcinoma lineages displaying increasing metastatic potential (SCC9 ZsG, LN1 and LN2) were analyzed by ¹H NMR (nuclear magnetic resonance) spectroscopy. Living, intact cells were also examined by the non-invasive method of fluorescence lifetime imaging microscopy (FLIM) based on the auto fluorescence of endogenous NADH. The cell lines reproducibly exhibited distinct metabolic profiles confirmed by Partial Least-Square Discriminant Analysis (PLS-DA) of the spectra. Measurement of endogenous free and bound NAD(P)H relative concentrations in the intact cell lines showed that ZsG and LN1 cells displayed high heterogeneity in the energy metabolism, indicating that the cells would oscillate between glycolysis and oxidative metabolism depending on the microenvironment’s composition. However, LN2 cells appeared to have more contributions to the oxidative status, displaying a lower NAD(P)H free/bound ratio. Functional experiments of energy metabolism, mitochondrial physiology, and proliferation assays revealed that all lineages exhibited similar energy features, although resorting to different bioenergetics strategies to face metabolic demands. These differentiated functions may also promote metastasis. We propose that lipid metabolism is related to the increased invasiveness as a result of the accumulation of malonate, methyl malonic acid, n-acetyl and unsaturated fatty acids (CH₂)_n in parallel with the metastatic potential progression, thus suggesting that the NAD(P)H reflected the lipid catabolic/anabolic pathways.

Our microbes not only produce antibiotics, they also overproduce amino acids

Fermentative production of amino acids is an important goal of modern biotechnology. Through fermentation, micro-organisms growing on inexpensive carbon and nitrogen sources can produce a wide array of valuable products including amino acids. The amino acid market is $8 billion and mainly impacts the food, pharmaceutical and cosmetics industries. In terms of tons of amino acids produced per year by fermentation, L-glutamate is the most important amino acid produced (3.3 million), followed by L-lysine (2.2 million). The bacteria producing these amino acids are among the top fermentation organisms with respect to titers. Corynebacterium glutamicum is the best producer.The Journal of Antibiotics advance online publication, 1 November 2017; doi:10.1038/ja.2017.142.

Enzymes of industrial interest

For many years, industrial enzymes have played an important role in the benefit of our society due to their many useful properties and a wide range of applications. They are key elements in the progress of many industries including foods, beverages, pharmaceuticals, diagnostics, therapy, personal care, animal feed, detergents, pulp and paper, textiles, leather, chemicals and biofuels. During recent decades, microbial enzymes have replaced many plant and animal enzymes. This is because microbial enzymes are widely available and produced economically in short fermentations and inexpensive media. Screening is simple, and strain improvement for increased production has been very successful. The advances in recombinant DNA technology have had a major effect on production levels of enzymes and represent a way to overproduce industrially important microbial, plant and animal enzymes. It has been calculated that 50-60% of the world enzyme market is supplied with recombinant enzymes. Molecular methods, including genomics and metagenomics, are being used for the discovery of new enzymes from microbes. Also, directed evolution has allowed the design of enzyme specificities and better performance.

Metabolic systems modeling for cell factories improvement

Techniques for modeling microbial bioproduction systems have evolved over many decades. Here, we survey recent literature and focus on modeling approaches for improving bioproduction. These techniques from systems biology are based on different methodologies, starting from stoichiometry only to various stoichiometry with kinetics approaches that address different issues in metabolic systems. Techniques to overcome unknown kinetic parameters using random sampling have emerged to address meaningful questions. Among those questions, pathway robustness seems to be an important issue for metabolic engineering. We also discuss the increasing significance of databases in biology and their potential impact for biotechnology.

Cell-Free Mixing of Escherichia coli Crude Extracts to Prototype and Rationally Engineer High-Titer Mevalonate Synthesis

Cell-free metabolic engineering (CFME) is advancing a powerful paradigm for accelerating the design and synthesis of biosynthetic pathways. However, as most cell-free biomolecule synthesis systems to date use purified enzymes, energy and cofactor balance can be limiting. To address this challenge, we report a new CFME framework for building biosynthetic pathways by mixing multiple crude lysates, or extracts. In our modular approach, cell-free lysates, each selectively enriched with an overexpressed enzyme, are generated in parallel and then combinatorically mixed to construct a full biosynthetic pathway. Endogenous enzymes in the cell-free extract fuel high-level energy and cofactor regeneration. As a model, we apply our framework to synthesize mevalonate, an intermediate in isoprenoid synthesis. We use our approach to rapidly screen enzyme variants, optimize enzyme ratios, and explore cofactor landscapes for improving pathway performance. Further, we show that genomic deletions in the source strain redirect metabolic flux in resultant lysates. In an optimized system, mevalonate was synthesized at 17.6 g·L^-1 (119 mM) over 20 h, resulting in a volumetric productivity of 0.88 g·L^-1·hr^-1. We also demonstrate that this system can be lyophilized and retain biosynthesis capability. Our system catalyzes ∼1250 turnover events for the cofactor NAD⁺ and demonstrates the ability to rapidly prototype and debug enzymatic pathways in vitro for compelling metabolic engineering and synthetic biology applications.

Developing a high-throughput screening method for threonine overproduction based on an artificial promoter

BACKGROUND

L-Threonine is an important amino acid for animal feed. Though the industrial fermentation technology of threonine achieved a very high level, there is still significant room to further improve the industrial strains. The biosensor-based high-throughput screening (HTS) technology has demonstrated its powerful applications. Unfortunately, for most of valuable fine chemicals such as threonine, a HTS system has not been established mainly due to the absence of a suitable biosensor. In this study, we developed a HTS method to gain high-yielding threonine-producing strains.

RESULTS

Novel threonine sensing promoters including cysJp and cysHp were discovered by proteomic analyses of Escherichia coli in response to extracellular threonine challenges. The HTS method was constructed using a device composed of the fused cysJp and cysHp as a promoter and a linked enhanced green fluorescent protein gene as a reporter. More than 400 strains were selected with fluorescence activated cell sorting technology from a library of 20 million mutants and tested within 1 week. Thirty-four mutants have higher productivities than the starting industrial producer. One mutant produced 17.95 % more threonine in a 5-L jar fermenter.

CONCLUSIONS

This method should play a functional role for continuous improvement of threonine industry. Additionally, the threonine sensor construction using promoters obtained by proteomics analyses is so convenient that it would be easily extended to develop HTS models for other biochemicals.