Design, construction and performance of the most efficient biomass producing E. coli bacterium

Inverse metabolic engineering based on elementary mode analysis was applied to maximize the biomass yield of Escherchia coli MG1655. Elementary mode analysis was previously employed to identify among 1691 possible pathways for cell growth the most efficient pathway with maximum biomass yield. The metabolic network analysis predicted that deletion of only 6 genes reduces the number of possible elementary modes to the most efficient pathway. We have constructed a strain containing these gene deletions and we evaluated its properties in batch and in chemostat growth experiments. The results show that the theoretical predictions are closely matched by the properties of the designed strain.     

Construction and elementary mode analysis of a metabolic model for Shewanella oneidensis MR-1

A stoichiometric model describing the central metabolism of Shewanella oneidensis MR-1 wild-type and derivative strains was developed and used in elementary mode analysis (EMA). Shewanella oneidensis MR-1 can anaerobically respire a diverse pool of electron acceptors, and may be applied in several biotechnology settings, including bioremediation of toxic metals, electricity generation in microbial fuel cells, and whole-cell biocatalysis. The metabolic model presented here was adapted and verified by comparing the growth phenotypes of 13 single- and 1 double-knockout strains, while considering respiration via aerobic, anaerobic fumarate, and anaerobic metal reduction (Mtr) pathways, and utilizing acetate, n-acetylglucosamine (NAG), or lactate as carbon sources. The gene ppc, which encodes phosphoenolpyruvate carboxylase (Ppc), was determined to be necessary for aerobic growth on NAG and lactate, while not essential for growth on acetate. This suggests that Ppc is the only active anaplerotic enzyme when cultivated on lactate and NAG. The application of regulatory and substrate limitations to EMA has enabled creation of metabolic models that better reflect biological conditions, and significantly reduce the solution space for each condition, facilitating rapid strain optimization. This wild-type model can be easily adapted to include utilization of different carbon sources or secretion of different metabolic products, and allows the prediction of single- and multiple-knockout strains that are expected to operate under defined conditions with increased efficiency when compared to wild type cells.     

Rational improvement of the engineered isobutanol-producing Bacillus subtilis by elementary mode analysis

ABSTRACT: BACKGROUND: Isobutanol is considered as a leading candidate for the replacement of current fossil fuels, and expected to be produced biotechnologically. Owing to the valuable features, Bacillus subtilis has been engineered as an isobutanol producer, whereas it needs to be further optimized for more efficient production. Since elementary mode analysis (EMA) is a powerful tool for systematical analysis of metabolic network structures and cell metabolism, it might be of great importance in the rational strain improvement. RESULTS: Metabolic network of the isobutanol-producing B. subtilis BSUL03 was first constructed for EMA. Considering the actual cellular physiological state, 239 elementary modes (EMs) were screened from total 11,342 EMs for potential target prediction. On this basis, lactate dehydrogenase (LDH) and pyruvate dehydrogenase complex (PDHC) were predicted as the most promising inactivation candidates according to flux flexibility analysis and intracellular flux distribution simulation. Then, the in silico designed mutants were experimentally constructed. The maximal isobutanol yield of the LDH- and PDHC-deficient strain BSUL05 reached 61 % of the theoretical value to 0.36 +/- 0.02 C-mol isobutanol/C-mol glucose, which was 2.3-fold of BSUL03. Moreover, this mutant produced approximately 70 % more isobutanol to the maximal titer of 5.5 +/- 0.3 g/L in fed-batch fermentations. CONCLUSIONS: EMA was employed as a guiding tool to direct rational improvement of the engineered isobutanol-producing B. subtilis. The consistency between model prediction and experimental results demonstrates the rationality and accuracy of this EMA-based approach for target identification. This network-based rational strain improvement strategy could serve as a promising concept to engineer efficient B. subtilis hosts for isobutanol, as well as other valuable products.     

In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates

Here, we present systems metabolic engineering driven by in-silico modeling to tailor Pseudomonas putida for synthesis of medium chain length PHAs on glucose. Using physiological properties of the parent wild type as constraints, elementary flux mode analysis of a large-scale model of the metabolism of P. putida was used to predict genetic targets for strain engineering. Among a set of priority ranked targets, glucose dehydrogenase (encoded by gcd) was predicted as most promising deletion target. The mutant P. putida Δgcd, generated on basis of the computational design, exhibited 100% increased PHA accumulation as compared to the parent wild type, maintained a high specific growth rate and exhibited an almost unaffected gene expression profile, which excluded detrimental side effects of the modification. A second mutant strain, P. putida Δpgl, that lacked 6-phosphogluconolactonase, exhibited a substantially decreased PHA synthesis, as was also predicted by the model. The production potential of P. putida Δgcd was assessed in batch bioreactors. The novel strain showed an increase of the PHA yield (+80%), the PHA titer (+100%) and cellular PHA content (+50%) and revealed almost unaffected growth and diminished by-product formation. It was thus found superior in all relevant criteria towards industrial production. Beyond the contribution to more efficient PHA production processes at reduced costs that might replace petrochemical plastics in the future, the study illustrates the power of computational prediction to tailor microbial strains for enhanced biosynthesis of added-value compounds.     

A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels

Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple crop with considerable variation in kernel carotenoid composition, maize (Zea mays L.) could have a widespread impact. We performed a genome-wide association study (GWAS) of quantified seed carotenoids across a panel of maize inbreds ranging from light yellow to dark orange in grain color to identify some of the key genes controlling maize grain carotenoid composition. Significant associations at the genome-wide level were detected within the coding regions of zep1 and lut1, carotenoid biosynthetic genes not previously shown to impact grain carotenoid composition in association studies, as well as within previously associated lcyE and crtRB1 genes. We leveraged existing biochemical and genomic information to identify 58 a priori candidate genes relevant to the biosynthesis and retention of carotenoids in maize to test in a pathway-level analysis. This revealed dxs2 and lut5, genes not previously associated with kernel carotenoids. In genomic prediction models, use of markers that targeted a small set of quantitative trait loci associated with carotenoid levels in prior linkage studies were as effective as genome-wide markers for predicting carotenoid traits. Based on GWAS, pathway-level analysis, and genomic prediction studies, we outline a flexible strategy involving use of a small number of genes that can be selected for rapid conversion of elite white grain germplasm, with minimal amounts of carotenoids, to orange grain versions containing high levels of provitamin A.     

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms

Rational engineering of metabolism is important for bio-production using microorganisms. Metabolic design based on in silico simulations and experimental validation of the metabolic state in the engineered strain helps in accomplishing systematic metabolic engineering. Flux balance analysis (FBA) is a method for the prediction of metabolic phenotype, and many applications have been developed using FBA to design metabolic networks. Elementary mode analysis (EMA) and ensemble modeling techniques are also useful tools for in silico strain design. The metabolome and flux distribution of the metabolic pathways enable us to evaluate the metabolic state and provide useful clues to improve target productivity. Here, we reviewed several computational applications for metabolic engineering by using genome-scale metabolic models of microorganisms. We also discussed the recent progress made in the field of metabolomics and ¹³C-metabolic flux analysis techniques, and reviewed these applications pertaining to bio-production development. Because these in silico or experimental approaches have their respective advantages and disadvantages, the combined usage of these methods is complementary and effective for metabolic engineering.     

Carotenoid production from n-alkanes with a broad range of chain lengths by the novel species Gordonia ajoucoccus A2T

A novel diesel-degrading bacterial strain, A2^T, was isolated from soil that was heavily contaminated with oil. Based on phenotypic, phylogenetic, and DNA analyses, strain A2^T was identified as a novel species of the genus Gordonia and named Gordonia ajoucoccus A2^T (KCTC 11900BP and CECT8382). G. ajoucoccus A2^T is able to synthesize carotenoids and produces mainly γ-carotene and keto-γ-carotene. G. ajoucoccus A2^T is also capable of assimilating n-alkanes with a broad range of chain lengths (C6, C8–C25). Batch culture of G. ajoucoccus A2^T in a bioreactor containing 1 % (v/v) hexadecane or 1 % (v/v) commercial diesel yielded 25 mg L^?1 and 2.6 mg L^?1 of carotenoids, respectively. Gas chromatography/mass spectrometry (GC-MS) analysis of hexadecane and hexane degradation metabolites suggested that G. ajoucoccus A2^T may possess a terminal oxidation pathway that allows it to utilize n-alkanes and hexane as carbon and energy sources. G. ajoucoccus A2^T could therefore serve as a good model system for understanding microbial n-alkane degradation pathways. Additionally, the metabolic capabilities of G. ajoucoccus A2^T suggest potential biotechnological applications, such as the bioproduction of carotenoids from industrial discharge or other sources of n-alkanes.     

Metabolic Engineering of Escherichia coli for Efficient Conversion of Glycerol to Ethanol

Based on elementary mode analysis, an Escherichia coli strain was designed for efficient conversion of glycerol to ethanol. By using nine gene knockout mutations, the functional space of the central metabolism of E. coli was reduced from over 15,000 possible pathways to a total of 28 glycerol-utilizing pathways that support cell function. Among these pathways are eight aerobic and eight anaerobic pathways that do not support cell growth but convert glycerol into ethanol with a theoretical yield of 0.50 g ethanol/g glycerol. The remaining 12 pathways aerobically coproduce biomass and ethanol from glycerol. The optimal ethanol production depends on the oxygen availability that regulates the two competing pathways for biomass and ethanol production. The coupling between cell growth and ethanol production enabled metabolic evolution of the designed strain through serial dilution that resulted in strains with improved ethanol yields and productivities. In defined medium, the evolved strain can convert 40 g/liter of glycerol to ethanol in 48 h with 90% of the theoretical ethanol yield. The performance of the designed strain is predicted by the property space of remaining elementary modes.With the recent rising prices of fossil fuels, development of alternative renewable fuels, such as biodiesel, has become attractive. However, the increase in biodiesel production generates a surplus of crude glycerol since this compound is an inevitable waste by-product resulting directly from the transesterification of vegetable oils or animal fats. For every 3 mol of biodiesel produced, 1 mol of glycerol (about 5 to 10% weight equivalent of biodiesel) is generated. To maximize the full economic potential of the biodiesel process, it is important to convert crude glycerol into useful chemicals (9, 25).Both chemical conversion and biological conversion of crude glycerol into value-added products have been considered. For instance, chemical conversion based on the etherification of glycerol with either alcohols (methanol or ethanol) or alkenes (isobutene or 2-methylpropene) can produce useful fuels or solvents, or steam reforming of glycerol can result in methanol and hydrogen production (7). Biological conversion utilizes species belonging to the Enterobacteriaceae family, such as Klebsiella pneumoniae (11), Citrobacter freundii (5), Clostridium butyricum (4), and Pantoea agglomerans (3), to convert glycerol to 1,3-propanediol by fermentation.Even though Escherichia coli belongs to the family Enterobacteriaceae, it cannot ferment glycerol due to a lack of the dha regulon encoding glycerol dehydratase (dhaB) and 1,3-propanediol oxidoreductase (dhaT), which constitute the fermentative 1,3-propanediol-producing pathway (18). However, introduction of this pathway from K. pneumoniae into E. coli can facilitate glycerol fermentation (18), presumably because the redox potential is balanced. In fact, it is well documented that a wild-type E. coli strain cannot grow on glycerol anaerobically in defined medium except after addition of specific electron acceptors (18). Such electron acceptors can come from external sources, including nitrate, nitrite, fumarate, dimethyl sulfoxide, or trimethylalamine-N-oxide, or from internal sources through added fermentative pathways, such as the 1,3-propanediol-producing pathway.A recent study suggested the feasibility of fermenting glycerol into fuels and other reduced chemicals by inducing the dormant, native 1,2-propanediol fermentative pathway in E. coli without using external electron acceptors (10, 14). This approach, however, faces several critical challenges, such as low specific growth rates resulting in low chemical productivities and coproduction of unavoidable by-products, such as 1,2-propanediol. The reported specific growth rate appears to limit any practical application since a minimal doubling time of about 17 h results in consumption of only 8 to 10 g/liter glycerol after 110 h (10, 14). In addition, glycerol fermentation apparently worked only when complex components, such as yeast extract, tryptone, or amino acids that are required for biomass synthesis, were added to the medium (10, 14).Here, we took a different approach by employing oxygen as the electron acceptor in well-defined microaerobic growth conditions. We used elementary mode (EM) analysis to rationally design an E. coli cell with minimized metabolic functionality tailored to efficiently convert glycerol to ethanol under these microaerobic growth conditions. EM analysis is a metabolic pathway analysis tool that identifies all pathway options in a metabolic network (16). Knowledge of these pathway options allows rational implementation of only the efficient pathways of interest by removing the inefficient pathways, resulting in a cell with minimal but specialized functionality (20-22, 24). Furthermore, the cell developed is engineered to tightly couple cell growth and ethanol production. This unique characteristic facilitates metabolic evolution of the minimal cell to improve ethanol productivity because faster-growing cells also produce ethanol at a higher rate. We demonstrate here that the performance of the designed strain falls into the range defined by the EMs that are possible.     

Metabolic pathway analysis and kinetic studies for production of nattokinase in Bacillus subtilis

We have constructed a reaction network model of Bacillus subtilis. The model was analyzed using a pathway analysis tool called elementary mode analysis (EMA). The analysis tool was used to study the network capabilities and the possible effects of altered culturing conditions on the production of a fibrinolytic enzyme, nattokinase (NK) by B. subtilis. Based on all existing metabolic pathways, the maximum theoretical yield for NK synthesis in B. subtilis under different substrates and oxygen availability was predicted and the optimal culturing condition for NK production was identified. To confirm model predictions, experiments were conducted by testing these culture conditions for their influence on NK activity. The optimal culturing conditions were then applied to batch fermentation, resulting in high NK activity. The EMA approach was also applied for engineering B. subtilis metabolism towards the most efficient pathway for NK synthesis by identifying target genes for deletion and overexpression that enable the cell to produce NK at the maximum theoretical yield. The consistency between experiments and model predictions proves the feasibility of EMA being used to rationally design culture conditions and genetic manipulations for the efficient production of desired products.     

基元模式分析在生物网络和途径分析中的应用

基元模式分析是应用最广泛的代谢途径分析方法。基元模式分析的研究对象从代谢网络发展到信号传导网络;研究尺度从细胞到生物反应器,甚至生态系统;数学描述从稳态分解到动态解析;研究领域从微生物代谢到人类疾病。以下综述了基元模式分析的算法和软件开发现状,以及其在代谢途径与鲁棒性、代谢通量分解、稳态代谢通量分析、动态模型与生物过程模拟、网络结构与调控、菌株设计和信号传导网络等方面的应用。开发新的算法解决组合爆炸问题,探索基元模式与代谢调控的关系以及提高菌株设计算法效率是今后基元模式的重要发展方向。     

Lycopene,but not zeaxanthin,serves as a skeleton for the formation of an orthorhombic organization of intercellular lipids within the lamellae in the stratum corneum: Molecular dynamics simulations of the hydrated ceramide NS bilayer model

Carotenoids play an important role in the protection of biomembranes against oxidative damage. Their function depends on the surroundings and the organization of the lipid membrane they are embedded in. Carotenoids are located parallel or perpendicular to the surface of the lipid bilayer. The influence of carotenoids on the organization of the lipid bilayer in the stratum corneum has not been thoroughly considered. Here, the orientation of the exemplary cutaneous carotenoids lycopene and zeaxanthin in a hydrated ceramide NS24 bilayer model and the influence of carotenoids on the lateral organization of the lipid bilayer model were studied by means of molecular dynamics simulations for 32 °C and 37 °C. The results confirm that lycopene is located parallel and zeaxanthin perpendicular to the surface of the lipid bilayer. The lycopene-loaded lipid bilayer appeared to have a strong orthorhombic organization, while zeaxanthin-loaded and pure lipid bilayers were organized in a disordered hexagonal-like and liquid-like state, respectively. The effect is stronger at 32 °C compared to 37 °C based on p-values. Therefore, it was assumed that carotenoids without hydroxyl polar groups in their structure facilitate the formation of the orthorhombic organization of lipids, which provides the skin barrier function. It was shown that the distance between carotenoid atoms matched the distance between atoms in the lipids, indicating that parallel located carotenoids without hydroxyl groups serve as a skeleton for lipid membranes inside the lamellae. The obtained results provide reasonable prediction of the overall qualitative properties of lipid model systems and show the importance of parallel-oriented carotenoids in the development and maintenance of the skin barrier function.     

Structure and function of carotenoids in the photoreaction center from Rhodospirillum rubrum

The bacteriochlorophyll (P-800 and P-870) of the carotenoidless photoreaction center isolated from Rhodospirillum rubrum (strain G9) is bleached irreversibly when the preparations are exposed to intense near infrared light in the presence of oxygen. This effect is much smaller in preparations, extracted from the wild type, which contain, as shown earlier, 1 mol of spirilloxanthin per mol of P-870. This photodynamic effec is shown to be due to singlet O₂. The oxidation of adrenaline in the presence of superoxide dismutase and the oxidation of 1,3-diphenylisobenzofuran are used as reporter reactions. Singlet oxygen is presumably generated by the triplet-triplet energy transfer ³bacteriochlorophyll → O₂ (³Σ).Four purified bacterial carotenoids, spirilloxanthin, sphaeroidene, sphaeroidenone and chloroxanthin were attached onto the carotenoidless photoreaction center from strain G9 in nearly 1 : 1 mol ratios with respect to P-870. Once fixed, these carotenoids confer protection against the photodynamic bleaching of bacteriochlorophyll. The relative photoprotection efficiency was 1.0 for spirilloxanthin and sphaeroidene, 0.4 for chloroxanthin and 0.2 for sphaeroidenone. The fixed carotenoids display optical activity and their molar ellipticity appears to be correlated with their relative photoprotection efficiency. The efficiency of energy transfer to P-870 is 0.90 for sphaeroidene, 0.35 for sphaeroidenone, 0.30 for chloroxanthin and 0.20 for spirilloxanthin. The energy transfer efficiency from the carotenoids to bacteriochlorophyll is suggested to be governed by the rate of the internal conversion processes of the excited singlet state of the carotenoids.A study of the difference absorption and CD spectra of the reconstituted minus carotenoidless preparations leads to the interpretation that the fixed carotenoids are in a central monocis conformation.     

From crude glycerol to carotenoids by using a Rhodotorula glutinis mutant

In this work eighteen red yeasts were screened for carotenoids production on glycerol containing medium. Strain C2.5t1 of Rhodotorula glutinis, that showed the highest productivity, was UV mutagenized. Mutant 400A15, that exhibited a 280 % increase in β–carotene production in respect to the parental strain, was selected. A central composite design was applied to 400A15 to optimize carotenoids and biomass productions. Regression analyses of the quadratic polynomial equations obtained (R² = 0.87 and 0.94, for carotenoids and biomass, respectively) suggest that the models are reliable and significant (P < 0.0001) in the prediction of carotenoids and biomass productions on the basis of the concentrations of crude glycerol, yeast extract and peptone. Accordingly, total carotenoids production achieved (14.07 ± 1.45 mg l^?1) under optimized growth conditions was not statistically different from the maximal predicted (14.64 ± 1.57 mg l^?1) (P < 0.05), and it was about 100 % higher than that obtained under un-optimized conditions. Therefore mutant 400A15 may represent a biocatalyst of choice for the bioconversion of crude glycerol into value-added metabolites, and a tool for the valorization of this by-product of the biodiesel industry.     

Substrate specificities and availability of fucosyltransferase and beta-carotene hydroxylase for myxol 2'-fucoside synthesis in Anabaena sp. strain PCC 7120 compared with Synechocystis sp. strain PCC 6803

To elucidate the biosynthetic pathways of carotenoids, especially myxol 2'-glycosides, in cyanobacteria, Anabaena sp. strain PCC 7120 (also known as Nostoc sp. strain PCC 7120) and Synechocystis sp. strain PCC 6803 deletion mutants lacking selected proposed carotenoid biosynthesis enzymes and GDP-fucose synthase (WcaG), which is required for myxol 2'-fucoside production, were analyzed. The carotenoids in these mutants were identified using high-performance liquid chromatography, field desorption mass spectrometry, and (1)H nuclear magnetic resonance. The wcaG (all4826) deletion mutant of Anabaena sp. strain PCC 7120 produced myxol 2'-rhamnoside and 4-ketomyxol 2'-rhamnoside as polar carotenoids instead of the myxol 2'-fucoside and 4-ketomyxol 2'-fucoside produced by the wild type. Deletion of the corresponding gene in Synechocystis sp. strain PCC 6803 (sll1213; 79% amino acid sequence identity with the Anabaena sp. strain PCC 7120 gene product) produced free myxol instead of the myxol 2'-dimethyl-fucoside produced by the wild type. Free myxol might correspond to the unknown component observed previously in the same mutant (H. E. Mohamed, A. M. L. van de Meene, R. W. Roberson, and W. F. J. Vermaas, J. Bacteriol. 187:6883-6892, 2005). These results indicate that in Anabaena sp. strain PCC 7120, but not in Synechocystis sp. strain PCC 6803, rhamnose can be substituted for fucose in myxol glycoside. The beta-carotene hydroxylase orthologue (CrtR, Alr4009) of Anabaena sp. strain PCC 7120 catalyzed the transformation of deoxymyxol and deoxymyxol 2'-fucoside to myxol and myxol 2'-fucoside, respectively, but not the beta-carotene-to-zeaxanthin reaction, whereas CrtR from Synechocystis sp. strain PCC 6803 catalyzed both reactions. Thus, the substrate specificities or substrate availabilities of both fucosyltransferase and CrtR were different in these species. The biosynthetic pathways of carotenoids in Anabaena sp. strain PCC 7120 are discussed.     

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model

A genome-scale metabolic model of the lactic acid bacterium Lactobacillus plantarum WCFS1 was constructed based on genomic content and experimental data. The complete model includes 721 genes, 643 reactions, and 531 metabolites. Different stoichiometric modeling techniques were used for interpretation of complex fermentation data, as L. plantarum is adapted to nutrient-rich environments and only grows in media supplemented with vitamins and amino acids. (i) Based on experimental input and output fluxes, maximal ATP production was estimated and related to growth rate. (ii) Optimization of ATP production further identified amino acid catabolic pathways that were not previously associated with free-energy metabolism. (iii) Genome-scale elementary flux mode analysis identified 28 potential futile cycles. (iv) Flux variability analysis supplemented the elementary mode analysis in identifying parallel pathways, e.g. pathways with identical end products but different co-factor usage. Strongly increased flexibility in the metabolic network was observed when strict coupling between catabolic ATP production and anabolic consumption was relaxed. These results illustrate how a genome-scale metabolic model and associated constraint-based modeling techniques can be used to analyze the physiology of growth on a complex medium rather than a minimal salts medium. However, optimization of biomass formation using the Flux Balance Analysis approach, reported to successfully predict growth rate and by product formation in Escherichia coli and Saccharomyces cerevisiae, predicted too high biomass yields that were incompatible with the observed lactate production. The reason is that this approach assumes optimal efficiency of substrate to biomass conversion, and can therefore not predict the metabolically inefficient lactate formation.     

Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses

To obtain an efficient ethanologenic Escherichia coli strain, we reduced the functional space of the central metabolic network, with eight gene knockout mutations, from over 15,000 pathway possibilities to 6 pathway options that support cell function. The remaining pathways, identified by elementary mode analysis, consist of four pathways with non-growth-associated conversion of pentoses and hexoses into ethanol at theoretical yields and two pathways with tight coupling of anaerobic cell growth with ethanol formation at high yields. Elimination of three additional genes resulted in a strain that selectively grows only on pentoses, even in the presence of glucose, with a high ethanol yield. We showed that the ethanol yields of strains with minimized metabolic functionality closely matched the theoretical predictions. Remarkably, catabolite repression was completely absent during anaerobic growth, resulting in the simultaneous utilization of pentoses and hexoses for ethanol production.     

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm,GEM-Path

The production of 75% of the current drug molecules and 35% of all chemicals could be achieved through bioprocessing (Arundel and Sawaya, 2009). To accelerate the transition from a petroleum-based chemical industry to a sustainable bio-based industry, systems metabolic engineering has emerged to computationally design metabolic pathways for chemical production. Although algorithms able to provide specific metabolic interventions and heterologous production pathways are available, a systematic analysis for all possible production routes to commodity chemicals in Escherichia coli is lacking. Furthermore, a pathway prediction algorithm that combines direct integration of genome-scale models at each step of the search to reduce the search space does not exist. Previous work (Feist et al., 2010) performed a model-driven evaluation of the growth-coupled production potential for E. coli to produce multiple native compounds from different feedstocks. In this study, we extended this analysis for non-native compounds by using an integrated approach through heterologous pathway integration and growth-coupled metabolite production design. In addition to integration with genome-scale model integration, the GEM-Path algorithm developed in this work also contains a novel approach to address reaction promiscuity. In total, 245 unique synthetic pathways for 20 large volume compounds were predicted. Host metabolism with these synthetic pathways was then analyzed for feasible growth-coupled production and designs could be identified for 1271 of the 6615 conditions evaluated. This study characterizes the potential for E. coli to produce commodity chemicals, and outlines a generic strain design workflow to design production strains.     

Is carotenoid ornamentation linked to the inner mitochondria membrane potential? A hypothesis for the maintenance of signal honesty

Several mechanistic hypotheses have been proposed for how carotenoid pigmentation of integumentary structures can serve as an honest signal of individual quality. These hypotheses are founded on proposed links between carotenoids, immuno responsiveness, and oxidative stress, but an absence of biochemical information on the oxidative pathways of carotenoids has limited the sophistication of such hypotheses. Based on published evidence, we propose that the oxidation of carotenoids for the purpose of ornamentation in birds and reptiles is coupled to the inner mitochondria membrane. We predict that several carotenoid oxidation reactions yielding ornamental pigments occur on the inner mitochondrial membrane. Three of these reactions are proposed to occur within the ubiquinone biosynthesis cluster known as the Coq cluster consisting of approximately a dozen Coq members, tightly integrated and intimately associated with Complex I and III of the electron transport system. Ubiquinone and highly oxidized ornamental carotenoids share a stereochemically-conserved binding region suggesting that these two molecules may have shared similar pathways in the past. Carotenoids and ubiquinones may cooperate as redox participants in anti-radical reactions or independently in helping to maintain membrane or supra-complex stabilization during times of high-energy demand. Under this hypothesis, oxidation of carotenoids is coupled to the inner mitochondria membrane potential such that ornamental coloration reflects the efficiency of cellular respiration.     

Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation

Lactococcus lactis subsp. cremoris MG1363 is a paradigm strain for lactococci used in industrial dairy fermentations. However, despite of its importance for process development, no genome-scale metabolic model has been reported thus far. Moreover, current models for other lactococci only focus on growth and sugar degradation. A metabolic model that includes nitrogen metabolism and flavor-forming pathways is instrumental for the understanding and designing new industrial applications of these lactic acid bacteria. A genome-scale, constraint-based model of the metabolism and transport in L. lactis MG1363, accounting for 518 genes, 754 reactions, and 650 metabolites, was developed and experimentally validated. Fifty-nine reactions are directly or indirectly involved in flavor formation. Flux Balance Analysis and Flux Variability Analysis were used to investigate flux distributions within the whole metabolic network. Anaerobic carbon-limited continuous cultures were used for estimating the energetic parameters. A thorough model-driven analysis showing a highly flexible nitrogen metabolism, e.g., branched-chain amino acid catabolism which coupled with the redox balance, is pivotal for the prediction of the formation of different flavor compounds. Furthermore, the model predicted the formation of volatile sulfur compounds as a result of the fermentation. These products were subsequently identified in the experimental fermentations carried out. Thus, the genome-scale metabolic model couples the carbon and nitrogen metabolism in L. lactis MG1363 with complete known catabolic pathways leading to flavor formation. The model provided valuable insights into the metabolic networks underlying flavor formation and has the potential to contribute to new developments in dairy industries and cheese-flavor research.     

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori

MOTIVATION: We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy. RESULTS: The comparisons we performed were as follows. (1) We compared two predictions of the pathway complements of Helicobacter pylori that were computed by an early version of our pathway-prediction algorithm: prediction A used the EcoCyc E. coli pathway DB as the reference database (DB) for prediction, and prediction B used the MetaCyc pathway DB (a superset of EcoCyc) as the reference pathway DB. The MetaCyc-based prediction contained 75% more pathway predictions, but we believe a significant number of those predictions were false positives. (2) We compared two predictions of the pathway complement of H. pylori that used MetaCyc as the reference pathway DB, but that used different algorithms: the original PathoLogic algorithm, and an enhanced version of the algorithm designed to eliminate false-positive pathway predictions. The improved algorithm predicted 30\% fewer metabolic pathways than the original algorithm; all of the eliminated pathways are believed to be false-positive predictions. (3) We compared the 98 pathways predicted by the enhanced algorithm with the results of a manual analysis of the pathways of H. pylori. Results: 40 of the computationally predicted pathways were consistent with the manual analysis, 13 pathways are considered false-positive predictions, and four pathways had partially overlapping topologies. Twenty-six predicted pathways were not mentioned in the manual analysis; we believe these are correct predictions by PathoLogic that were not found by the manual analysis. Five pathways from the manual analysis were not found computationally. Agreement between the computational and manual predictions was good overall, with the computational analysis inferring many pathways that the manual analysis did not identify. Ultimately the manual analysis is also partially speculative, and therefore is not an absolute measure of correctness. The algorithm is designed to err on the side of more false positives to bring more potential pathways to the user's attention. The resulting H. pylori pathway DB is freely available at http://ecocyc.org:1555/HPY/organism-summary?object=HPY. AVAILABILITY: The Pathway Tools software is freely available to academic users, and is available to commercial users for a fee. Contact pkarp@ai.sri.com for information on obtaining the software.