Abstract: Background: Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded thermodynamic ( NET) analysis was introduced to address some of these open issues. Building upon principles of thermodynamics, this method allows for a quality check of measured metabolite concentrations and enables to spot metabolic reactions where active regulation potentially controls metabolic flux. So far, however, widespread application of NET analysis in metabolomics labs was hindered by the absence of suitable software. Results: We have developed in Matlab a generalized software called 'anNET' that affords a user-friendly implementation of the NET analysis algorithm. anNET supports the analysis of any metabolic network for which a stoichiometric model can be compiled. The model size can span from a single reaction to a complete genome-wide network reconstruction including compartments. anNET can (i) test quantitative data sets for thermodynamic consistency, (ii) predict metabolite concentrations beyond the actually measured data, (iii) identify putative sites of active regulation in the metabolic reaction network, and (iv) help in localizing errors in data sets that were found to be thermodynamically infeasible. We demonstrate the application of anNET with three published Escherichia coli metabolome data sets. Conclusion: Our user-friendly and generalized implementation of the NET analysis method in the software anNET allows users to rapidly integrate quantitative metabolome data obtained from virtually any organism. We envision that use of anNET in labs working on quantitative metabolomics will provide the systems biology and metabolic engineering communities with a mean to proof the quality of metabolome data sets and with all further benefits of the NET analysis approach.
Abstract: Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.
Abstract: The availability of suitable, well-characterized, and robust expression systems remains an essential requirement for successful metabolic engineering and recombinant protein production. We investigated the suitability of the Pseudomonas putida GPo1-derived AlkS/P-alkB expression system in strictly aqueous cultures. By applying the apolar inducer dicyclopropylketone (DCPK) to express green fluorescent protein (GFP) from this system in Escherichia coli and analyzing the resulting cultures on single-cell level by flow cytometry, we found that this expression system gives rise to a homogeneous population of cells, even though the overall system is expected to have a positive feed-back element in the expression of the regulatory gene alkS. Overexpressing E. coli's serine hydroxymethyltransferase gene glyA, we showed that the system was already fully turned in at inducer concentrations as low as 0.005% (v/v). This allows efficient mass production of recombinant enzymes even though DCPK concentrations from 0.05% to 0.01% over the course of a fully aerated cultivation in aqueous medium. Therefore, we elaborated the optimum induction procedure for production of the biocatalytically promising serine hydroxymethyltransferase and found volumetric and specific productivity to increase with specific growth rate in glucose-limited fed-batch cultures. Acetate excretion as a result of recombinant protein production could be avoided in an optimized fermentation protocol by switching earlier to a linear feed. This protocol resulted in a production of a final cell dry weight (CDW) concentration of 52 g/L, producing recombinant GlyA with a maximum specific activity of 6.3 U/mg total protein.
Abstract: Background: Synthesis of the Staphylococcus aureus peptidoglycan pentaglycine interpeptide bridge is catalyzed by the nonribosomal peptidyl transferases FemX, FemA and FemB. Inactivation of the femAB operon reduces the interpeptide to a monoglycine, leading to a poorly crosslinked peptidoglycan. femAB mutants show a reduced growth rate and are hypersusceptible to virtually all antibiotics, including methicillin, making FemAB a potential target to restore beta-lactam susceptibility in methicillin-resistant S. aureus (MRSA). Cis-complementation with wild type femAB only restores synthesis of the pentaglycine interpeptide and methicillin resistance, but the growth rate remains low. This study characterizes the adaptations that ensured survival of the cells after femAB inactivation. Results: In addition to slow growth, the cis-complemented femAB mutant showed temperature sensitivity and a higher methicillin resistance than the wild type. Transcriptional profiling paired with reporter metabolite analysis revealed multiple changes in the global transcriptome. A number of transporters for sugars, glycerol, and glycine betaine, some of which could serve as osmoprotectants, were upregulated. Striking differences were found in the transcription of several genes involved in nitrogen metabolism and the arginine-deiminase pathway, an alternative for ATP production. In addition, microarray data indicated enhanced expression of virulence factors that correlated with premature expression of the global regulators sae, sarA, and agr. Conclusion: Survival under conditions preventing normal cell wall formation triggered complex adaptations that incurred a fitness cost, showing the remarkable flexibility of S. aureus to circumvent cell wall damage. Potential FemAB inhibitors would have to be used in combination with other antibiotics to prevent selection of resistant survivors.
Abstract: Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis synthetic biology's system fabrication process-supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds. Contact: panke@ipe.mavt.ethz.ch.
Abstract: The rapid progress in biocatalysis in the identification and development of enzymes over the last decade has enormously enlarged the chemical reaction space that can be addressed not only in research applications, but also on industrial scale. This enables us to consider even those groups of reactions that are very promising from a synthetic point of view, but suffer from drawbacks on process level, such as an unfavourable position of the reaction equilibrium. Prominent examples stem from the aldolase-catalyzed enantioselective carbon-carbon bond forming reactions, reactions catalyzed by isomerising enzymes, and reactions that are kinetically controlled. On the other hand, continuous chromatography concepts such as the simulating moving bed technology have matured and are increasingly realized on industrial scale for the efficient separation of difficult compound mixtures - including enantiomers - with unprecedented efficiency. We propose that coupling of enzyme reactor and continuous chromatography is a very suitable and potentially generic process concept to address the thermodynamic limitations of a host of promising biotransformations. This way, it should be possible to establish novel in situ product recovery processes of unprecedented efficiency and selectivity that represent a feasible way to recruit novel biocatalysts to the industrial portfolio. (c) 2006 Elsevier B.V. All rights reserved.
Abstract: In this study, full-genome DNA microarrays based on the sequence of Staphylococcus aureus N315 were used to compare the transcriptome of a clinical S. aureus strain with a normal phenotype to that of its isogenic mutant with a stable small-colony-variant (SCV) phenotype (hemB::ermB). In addition to standard statistical analyses, systems biology advances were applied to identify reporter metabolites and to achieve a more detailed survey of genome-wide expression differences between the hemB mutant and its parental strain. Genes of enzymes involved in glycolytic and fermentative pathways were found to be up-regulated in the hemB mutant. Furthermore, our analyses allowed identification of additional differences between the normal-phenotype S. aureus and the SCV, most of which were related to metabolism. Profound differences were identified especially in purine biosynthesis as well as in arginine and proline metabolism. Of particular interest, a hypothetical gene of the Crp/Fnr family (SA2424) that is part of the arginine-deiminase (AD) pathway, whose homologue in Streptococcus suis is assumed to be involved in intracellular persistence, showed significantly increased transcription in the hemB mutant. The hemB mutant potentially uses the up-regulated AD pathway to produce ATP or (through ammonia production) to counteract the acidic environment that prevails intracellularly. Moreover, genes involved in capsular polysaccharide and cell wall synthesis were found to be significantly up-regulated in the hemB mutant and therefore potentially responsible for the changed cell morphology of SCVs. In conclusion, the identified differences may be responsible for the SCV phenotype and its association with chronic and persistent infections.
Abstract: The suitability of a teicoplanin-aglycone based chiral stationary phase for the simulated moving bed (SMB) enantioseparation of amino acids under enzyme-compatible conditions was shown following a procedure that is based solely on model-based simulations and HPLC experiments. A set of eight amino acids could be separated employing aqueous solvent containing only 10% (v/v) methanol, five of them with baseline resolution. The impact of type and concentration of organic modifier and pH modifier and pH on the separation characteristics of racemic methionine was investigated. Invariant elution profiles of repetitive adsorption/desorption of large amounts of methionine representing SMB-like conditions suggest stable adsorption behavior. Competitive loading capacity (20 mg of methionine per g of chiral stationary phase (CSP)) and SMB productivity (1 g Of D-methionine per g of CSP per day) were predicted. The applied transport-dispersive model based on a competitive Bi-Langmuir isotherm was validated and its parameter estimated by model-based experimental analysis. (c) 2006 Elsevier B.V. All rights reserved.
Abstract: Background: The availability of genome sequences for many organisms enabled the reconstruction of several genome-scale metabolic network models. Currently, significant efforts are put into the automated reconstruction of such models. For this, several computational tools have been developed that particularly assist in identifying and compiling the organism-specific lists of metabolic reactions. In contrast, the last step of the model reconstruction process, which is the definition of the thermodynamic constraints in terms of reaction directionalities, still needs to be done manually. No computational method exists that allows for an automated and systematic assignment of reaction directions in genome-scale models. Results: We present an algorithm that - based on thermodynamics, network topology and heuristic rules - automatically assigns reaction directions in metabolic models such that the reaction network is thermodynamically feasible with respect to the production of energy equivalents. It first exploits all available experimentally derived Gibbs energies of formation to identify irreversible reactions. As these thermodynamic data are not available for all metabolites, in a next step, further reaction directions are assigned on the basis of network topology considerations and thermodynamics-based heuristic rules. Briefly, the algorithm identifies reaction subsets from the metabolic network that are able to convert low-energy co-substrates into their high-energy counterparts and thus net produce energy. Our algorithm aims at disabling such thermodynamically infeasible cyclic operation of reaction subnetworks by assigning reaction directions based on a set of thermodynamics-derived heuristic rules. We demonstrate our algorithm on a genome-scale metabolic model of E. coli. The introduced systematic direction assignment yielded 130 irreversible reactions ( out of 920 total reactions), which corresponds to about 70% of all irreversible reactions that are required to disable thermodynamically infeasible energy production. Conclusion: Although not being fully comprehensive, our algorithm for systematic reaction direction assignment could define a significant number of irreversible reactions automatically with low computational effort. We envision that the presented algorithm is a valuable part of a computational framework that assists the automated reconstruction of genome-scale metabolic models.
Abstract: As one of the most recent members of the omics family, large-scale quantitative metabolomics data are currently complementing our systems biology data pool and offer the chance to integrate the metabolite level into the functional analysis of cellular networks. Network-embedded thermodynamic analysis (NET analysis) is presented as a framework for mechanistic and model-based analysis of these data. By coupling the data to an operating metabolic network via the second law of thermodynamics and the metabolites' Gibbs energies of formation, NET analysis allows inferring functional principles from quantitative metabolite data; for example it identifies reactions that are subject to active allosteric or genetic regulation as exemplified with quantitative metabolite data from Escherichia coli and Saccharomyces cerevisiae. Moreover, the optimization framework of NET analysis was demonstrated to be a valuable tool to systematically investigate data sets for consistency, for the extension of sub-omic metabolome data sets and for resolving intracompartmental concentrations from cell-averaged metabolome data. Without requiring any kind of kinetic modeling, NET analysis represents a perfectly scalable and unbiased approach to uncover insights from quantitative metabolome data.
Abstract: In this work, a systematic examination of various parameters of adsorptive immobilization of alcohol dehydrogenases (ADHs) on solid support is performed and the impact of these parameters on immobilization efficiency is studied. Depending on the source of the enzymes, these parameters differently influence the immobilization efficiency, expressed in terms of residual activity and protein loading. Residual activity of 79% was achieved with ADH from bakers' yeast (YADH) after optimizing the immobilization parameters. A step-wise drying process has been found to be more effective than one-step drying. A hypothesis of deactivation through bubble nucleation during drying of the enzyme/glass bead suspension at low drying pressure (< 45 kPa) is experimentally verified. In the case of ADH from Lactobacillus brevis (LBADH), > 300% residual activity was found after drying. Hyperactivation of the enzyme is probably caused by structural changes in the enzyme molecule during the drying process. ADH from Thermoanaerobacter species (ADHT) is found to be stable under drying conditions (> 15 kPa) in contrast to LBADH and YADH.
Abstract: A new method based on Raman spectroscopy is presented for non-invasive, quantitative determination of the spatial polymer distribution in alginate beads of approximately 4 mm diameter. With the experimental setup, a two-dimensional image is created along a thin measuring line through the bead comprising one spatial and one spectral dimension. For quantitative analysis of the Raman spectra, the method of indirect hard modeling was applied to make use of the information contained in the entire recorded spectra. For quantification of the alginate signals from within the beads, a calibration curve acquired from sodium alginate solutions was used after it was shown that only negligible differences occur between signals from alginate solutions and alginate gels. The distribution of alginate over the bead gel matrix was acquired with high spatial (51 mu m) and time (12 s) resolution. The inhomogeneous distribution obtained using the new measuring technique is qualitatively in excellent agreement with data from the literature. In contrast to known measuring techniques, correct quantitative information about the spatial polymer distribution within the matrix was derived. It gave an alginate mass fraction of approximately 0.045 g/g at the edges and 0.02 g/g in the center of the beads. Next to the determination of mere polymer concentrations, the excellent time resolution of the presented method will enable investigation of the dynamic process of gel formation and it will also serve as a basis for investigation of mass transfer of small diffusing molecules in alginate matrices.
Abstract: Though lipases are frequently applied in ester synthesis, fundamental information on optimal pH or substrate concentration, can almost only be found for the reverse reaction - hydrolysis. This study demonstrates that the pH-optima of lipase-catalysed esterifications differ significantly from the optima of the hydrolysis reaction. In the esterification of n-butanol and propionic acid with lipases of Candida rugosa (CRL) and Thermomyces lanuginosa (TLL) pH-optima of 3.5 and 4.25, respectively, were found. This is about 3-4 units (CRL) and 7 units (TLL) in pH lower than optimum for hydrolysis. Enzyme activity increased with increasing concentrations of protonated acid indicating that the protonated acid rather than the deprotonated form is the substrate for esterification. The rate of esterification can be drastically increased by ensuring acid concentrations up to 1000 mmol L-1 for CRL and 600 mmol L-1 for TLL in the reaction system.
Abstract: A genome-scale metabolic model of the Gram-positive, facultative anaerobic opportunistic pathogen Staphylococcus aureus N315 was constructed based on current genomic data, literature, and physiological information. The model comprises 774 metabolic processes representing approximately 23% of all protein-coding regions. The model was extensively validated against experimental observations and it correctly predicted main physiological properties of the wild-type strain, such as aerobic and anaerobic respiration and fermentation. Due to the frequent involvement of S. aureus in hospital-acquired bacterial infections combined with its increasing antibiotic resistance, we also investigated the clinically relevant phenotype of small colony variants and found that the model predictions agreed with recent findings of proteome analyses. This indicates that the model is useful in assisting future experiments to elucidate the interrelationship of bacterial metabolism and resistance. To help directing future studies for novel chemotherapeutic targets, we conducted a large-scale in silico gene deletion study that identified 158 essential intracellular reactions. A more detailed analysis showed that the biosynthesis of glycans and lipids is rather rigid with respect to circumventing gene deletions, which should make these areas particularly interesting for antibiotic development. The combination of this stoichiometric model with transcriptomic and proteomic data should allow a new quality in the analysis of clinically relevant organisms and a more rationalized system-level search for novel drug targets. (c) 2005 Wiley Periodicals, Inc.
Abstract: Both, experimental investigation of protein adsorption processes and mathematical models describing such processes indicate, that the pH in the absorbent particle might be the key factor for an improved understanding of these chromatographic processes. Thus, a technique aiming at the spatially resolved pH measurement in macroscopic large absorbent particles is presented. The first application of this method, being based on confocal laser scanning microscopy (CLSM), revealed an apparent dependence of the pH calibration curve on the scanning depth. By a model-based approach, factors distorting the measurement signal are identified: The wavelength-dependent light scattering and the re-absorption of emitted light. The resulting consequences for further development and application of CLSM based techniques to measure pH in macroscopic large absorbent particles are illustrated and discussed. (C) 2003 Elsevier B.V. All rights reserved.
Abstract: Enzymatic gas-phase reactions are usually performed in continuous reactors, and thus very stable and active catalysts are required to perform such transformations on cost-effective levels. The present work is concerned with the reduction of gaseous acetophenone to enantiomerically pure (R)-1-phenylethanol catalyzed by solid alcohol dehydrogenase from Lactobacillus brevis (LBADH), immobilized onto glass beads. Initially, the catalyst preparation displayed a half-life of 1 day under reaction conditions at 40 degreesC and at a water activity of 0.5. It was shown that the observed decrease in activity is due to a degradation of the enzyme itself (LBADH) and not of the co-immobilized cofactor NADP. By the addition of sucrose to the cell extract before immobilization of the enzyme, the half-life of the catalyst preparation (at 40 degreesC) was increased 40 times. The stabilized catalyst preparation was employed in a continuous gas-phase reactor at different temperatures (25-60 degreesC). At 50 degreesC, a space-time yield of 107 g/L/d was achieved within the first 80 h of continuous reaction.
Abstract: Biotransformations have moved far beyond the classic one-reaction approach. Progress in genomic science enables the rapid assembly of complex multi-enzyme catalysts that allow [i] utilizing cheaper starting materials, as in the case of 5-acetylneuraminic acid formation from N-acetylglucosamine; [ii] increasing the yield, for example by exploiting racemization as in the hydantoinase carbamoylase technology; [iii] and recycling coenzymes as in the D-transaminase technology. However, recent examples demonstrate that modern multi-enzyme technology can handle systems that address combinations of these points. in our view, this constitutes a novel enabling technology that allows accessing cell-like catalytic complexity with the tools of enzyme technology.
Abstract: The partitioning behavior of the reactants 1-butanol, propionic acid and butyl propionate in an aqueous-organic two-phase system consisting of alginate beads suspended in hexane was investigated. Partitioning experiments with a single reactant showed that, even in the dilute region, the equilibrium concentrations of 1-butanol and propionic acid cannot be described by constant partition coefficients as is normally done in the field of biocatalysis. Besides the aqueous alginate beads, two other aqueous phases with different compositions (solutions with and without electrolytes) were also used for partitioning experiments. The equilibrium concentrations of the reactants obtained from the systems with the three different aqueous phases (water, water plus electrolytes, alginate beads) demonstrated that the partitioning behavior of the reactants is scarcely influenced by the presence of the electrolytes or by the alginate matrix, at least up to reactant concentrations of 80 mmol/l in the organic phase. The comparison of the experimental equilibrium concentrations with predicted values obtained from simulations with the modified UNIFAC (Dortmund) model showed a generally good agreement. However, in the dilute region, differences of up to 100% occurred between experimental and predicted values. Thus, for the later detailed mathematical modeling of processes occurring inside the alginate beads (such as mass transfer and enzymatic reaction), the modified UNIFAC (Dortmund) model is not adequate. Therefore, empirical correlations were derived for the mathematical description of the reactants' partitioning behavior. Experiments, conducted with two reactants simultaneously present in the two-phase system, showed that at reactant concentrations in the organic phase higher than 10 mmol/l the partitioning behavior of the investigated reactants is influenced by the presence of the second component. Thus, in systems with multiple reactants the derived correlations are strictly only valid up to this concentration.
Abstract: To investigate the spatial distribution of white egg albumin (WEA) in alginate beads, a new method based on confocal laser scanning microscopy (CLSM) was developed. In contrast to the existing CLSM methods, misleading conclusions are prevented with the application of the new method which does not allow the attenuation of the exciting and emitted light by the opaque hydrogel matrices to be disregarded. By the application of this method, the distribution of WEA in alginate beads was shown to be dependent on the amount of protein loading. At low quantities of protein, a higher protein concentration occurs in the shell layer of the alginate bead while at higher loadings a more or less homogeneous distribution is observed.
Abstract: Gel-stabilized aqueous phases entrapping enzymes and surrounded by organic solvents have become promising tools for the biocatalytic conversion of hydrophobic compounds. In this work, we provide methods for an improvement of the solvent phase with special regard to the avoidance of gel agglomeration in batch as well as fluidized-bed reactors, and resulting effects on the catalyzed reaction. With alginate beads entrapping a lipase from Candida rugosa as investigation system, it was demonstrated that increasing the solvent polarity was only a limited measure to separate agglomerated beads, as water-unsaturated polar solvents extracted large amounts of water from the hydrogel. Water-saturated alcohols, however, were incorporated into side product esters by the entrapped enzyme. With non-polar solvents, like hexane, bead separation in batch reactors was achieved by the addition of certain surfactants to the organic phase, Best results were obtained with the cationic surfactant cetyl trimethyl ammonium chloride (CTAC), which in contrast to other surfactants only slightly affected the entrapped lipase and revealed no effects on the hydrogel structure. For the suspension of alginate beads in a fluidized-bed reactor, not only CTAC, but an additional increase in the solvent density was necessary, which affected the system's productivity. (C) 2002 Elsevier Science B.V. All rights reserved.
