Integrating metabolomics into a systems biology framework to exploit metabolic complexity: strategies and applications in microorganisms

As an important functional genomic tool, metabolomics has been illustrated in detail in recent years, especially in plant science. However, the microbial category also has the potential to benefit from integration of metabolomics into system frameworks. In this article, we first examine the concepts and brief history of metabolomics. Next, we summarize metabolomic research processes and analytical platforms in strain improvements. The application cases of metabolomics in microorganisms answer what the metabolomics can do in strain improvements. The position of metabolomics in this systems biology framework and the real cases of integrating metabolomics into a system framework to explore the microbial metabolic complexity are also illustrated in this paper.

[1]  D. Schomburg,et al.  GC–MS libraries for the rapid identification of metabolites in complex biological samples , 2005, FEBS letters.

[2]  Jens Nielsen,et al.  The next wave in metabolome analysis. , 2005, Trends in biotechnology.

[3]  David I. Ellis,et al.  Metabolomics: Current analytical platforms and methodologies , 2005 .

[4]  Douglas B. Kell,et al.  Functional Genomics Via Metabolic Footprinting: Monitoring Metabolite Secretion by Escherichia Coli Tryptophan Metabolism Mutants Using FT–IR and Direct Injection Electrospray Mass Spectrometry , 2003, Comparative and functional genomics.

[5]  K. Nickerson,et al.  Single-run separation and detection of multiple metabolic intermediates by anion-exchange high-performance liquid chromatography and application to cell pool extracts prepared from Escherichia coli. , 1995, Analytical biochemistry.

[6]  A. Sinskey,et al.  Disparity between changes in mRNA abundance and enzyme activity in Corynebacterium glutamicum:implications for DNA microarray analysis , 2003, Applied Microbiology and Biotechnology.

[7]  S. Oliver.  Functional genomics: lessons from yeast. , 2002, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[8]  I. Wilson,et al.  Understanding 'Global' Systems Biology: Metabonomics and the Continuum of Metabolism , 2003, Nature Reviews Drug Discovery.

[9]  J J Heijnen,et al.  Improved rapid sampling for in vivo kinetics of intracellular metabolites in Saccharomyces cerevisiae. , 2001, Biotechnology and bioengineering.

[10]  Kristian Fog Nielsen,et al.  Fungal metabolite screening: database of 474 mycotoxins and fungal metabolites for dereplication by standardised liquid chromatography-UV-mass spectrometry methodology. , 2003, Journal of chromatography. A.

[11]  R. Takors,et al.  Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques. , 2001, Analytical biochemistry.

[12]  D. Fell.  Beyond genomics. , 2001, Trends in Genetics.

[13]  Jochen Förster,et al.  A functional genomics approach using metabolomics and in silico pathway analysis. , 2002, Biotechnology and bioengineering.

[14]  Gregory Stephanopoulos,et al.  High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts. , 2005, The Biochemical journal.

[15]  F. Létisse,et al.  An intracellular metabolite quantification technique applicable to polysaccharide-producing bacteria , 2000, Biotechnology Letters.

[16]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[17]  H. Westerhoff,et al.  Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway , 2001, FEBS letters.

[18]  Oliver Fiehn,et al.  Metabolic networks of Cucurbita maxima phloem. , 2003, Phytochemistry.

[19]  T. Ferenci,et al.  Global metabolite analysis: the influence of extraction methodology on metabolome profiles of Escherichia coli. , 2003, Analytical biochemistry.

[20]  Nigel W. Hardy,et al.  A proposed framework for the description of plant metabolomics experiments and their results , 2004, Nature Biotechnology.

[21]  R. Goodacre,et al.  Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis , 2003, Springer US.

[22]  T. Ferenci,et al.  Effect of Slow Growth on Metabolism of Escherichia coli, as Revealed by Global Metabolite Pool (“Metabolome”) Analysis , 1998, Journal of bacteriology.

[23]  Sven Pedersen,et al.  Metabolite profiling for analysis of yeast stress response during very high gravity ethanol fermentations , 2005, Biotechnology and bioengineering.

[24]  T. Nishioka,et al.  Determination of pyridine and adenine nucleotide metabolites in Bacillus subtilis cell extract by sweeping borate complexation capillary electrophoresis. , 2003, Journal of chromatography. A.

[25]  M. Tomita,et al.  Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. , 2003, Journal of proteome research.

[26]  Sang Yup Lee,et al.  Systems biotechnology for strain improvement. , 2005, Trends in biotechnology.

[27]  E. Horning,et al.  Human Metabolic Profiles Obtained by GC and GC/MS , 1971 .

[28]  J. Dalluge,et al.  Potential of fermentation profiling via rapid measurement of amino acid metabolism by liquid chromatography-tandem mass spectrometry. , 2004, Journal of chromatography. A.

[29]  M. Reuss,et al.  In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model. , 1997, Biotechnology and bioengineering.

[30]  Matthias Reuss,et al.  New bioreactor-coupled rapid stopped-flow sampling technique for measurements of metabolite dynamics on a subsecond time scale. , 2002, Biotechnology and bioengineering.

[31]  Vassily Hatzimanikatis,et al.  Insights into the relation between mrna and protein expression patterns: ii. Experimental observations in Escherichia coli 1 , 2003, Biotechnology and bioengineering.

[32]  Jeffrey E. Barrick,et al.  Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria , 2003, Cell.

[33]  Christophe Junot,et al.  Liquid chromatography-mass spectrometry and 15N metabolic labeling for quantitative metabolic profiling. , 2005, Analytical chemistry.

[34]  Andrew Hayes,et al.  An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. , 2003, Phytochemistry.

[35]  Christoph Wittmann,et al.  Dynamics of intracellular metabolites of glycolysis and TCA cycle during cell-cycle-related oscillation in Saccharomyces cerevisiae. , 2005, Biotechnology and bioengineering.

[36]  J. Heijnen,et al.  Rapid sampling for analysis of in vivo kinetics using the BioScope: a system for continuous-pulse experiments. , 2002, Biotechnology and bioengineering.

[37]  Mariët J. van der Werf,et al.  Towards replacing closed with open target selection strategies , 2005 .

[38]  Koji Otsuka,et al.  Capillary electrophoretic techniques toward the metabolome analysis , 2001 .

[39]  S. Stein,et al.  Deconvolution gas chromatography/mass spectrometry of urinary organic acids--potential for pattern recognition and automated identification of metabolic disorders. , 1999, Rapid communications in mass spectrometry : RCM.

[40]  J. François,et al.  A rapid and reliable method for metabolite extraction in yeast using boiling buffered ethanol , 1997, Yeast.

[41]  H. Mori,et al.  Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout , 2003, Biotechnology and bioengineering.

[42]  D. Kell,et al.  High-throughput classification of yeast mutants for functional genomics using metabolic footprinting , 2003, Nature Biotechnology.

[43]  J. Visser,et al.  Determination of intermediary metabolites in Aspergillus niger. , 1996 .

[44]  J. Smedsgaard.  Micro-scale extraction procedure for standardized screening of fungal metabolite production in cultures. , 1997, Journal of chromatography. A.

[45]  Christophe Junot,et al.  Combined Proteome and Metabolite-profiling Analyses Reveal Surprising Insights into Yeast Sulfur Metabolism* , 2005, Journal of Biological Chemistry.

[46]  J. Collado-Vides,et al.  Identifying global regulators in transcriptional regulatory networks in bacteria. , 2003, Current opinion in microbiology.

[47]  W. Gams,et al.  Variations in random amplified polymorphic DNA patterns and secondary metabolite profiles withinFusariumspecies from cereals from various parts of The Netherlands , 1997 .

[48]  D Weuster-Botz,et al.  Automated sampling device for monitoring intracellular metabolite dynamics. , 1999, Analytical biochemistry.

[49]  Weihong Jiang,et al.  A Novel Two-Component System amrB-amkB Involved in the Regulation of Central Carbohydrate Metabolism in Rifamycin SV-Producing Amycolatopsis mediterranei U32 , 2003, Current Microbiology.

[50]  T. Ebbels,et al.  NMR-based metabonomic toxicity classification: hierarchical cluster analysis and k-nearest-neighbour approaches , 2003 .

[51]  C. Schmidt.  Metabolomics takes its place as latest up-and-coming "omic" science. , 2004, Journal of the National Cancer Institute.

[52]  K. Dam,et al.  A method for the determination of changes of glycolytic metabolites in yeast on a subsecond time scale using extraction at neutral pH. , 1992 .

[53]  Masaru Tomita,et al.  Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. , 2002, Analytical chemistry.

[54]  J. Nielsen,et al.  Fermentation performance and intracellular metabolite patterns in laboratory and industrial xylose-fermenting Saccharomyces cerevisiae , 2002, Applied Microbiology and Biotechnology.

[55]  Manor Askenazi,et al.  Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains , 2003, Nature Biotechnology.

[56]  O. Fiehn.  Metabolomics – the link between genotypes and phenotypes , 2004, Plant Molecular Biology.

[57]  D B Kell,et al.  Genomic computing. Explanatory analysis of plant expression profiling data using machine learning. , 2001, Plant physiology.

[58]  Jian Yang,et al.  Metabolomics spectral formatting, alignment and conversion tools (MSFACTs) , 2003, Bioinform..

[59]  Karl-Heinz Ott,et al.  Metabonomics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts. , 2003, Phytochemistry.

[60]  R. Goodacre,et al.  Phenotypic and genotypic differences between certain strains of Clostridium acetobutylicum , 1995 .

[61]  Jens Nielsen,et al.  Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics. , 2005, Journal of experimental botany.

[62]  G. Stephanopoulos,et al.  Exploiting biological complexity for strain improvement through systems biology , 2004, Nature Biotechnology.

[63]  Ross D. King,et al.  Application of metabolomics to plant genotype discrimination using statistics and machine learning , 2002, ECCB.

[64]  S. Stein.  An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data , 1999 .

[65]  Dietmar Schomburg,et al.  Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry , 2004, Biological chemistry.

[66]  Woo-Sik Kim,et al.  Separation of astaxanthin from red yeast Phaffia rhodozyma by supercritical carbon dioxide extraction , 2002 .

[67]  I. Wilson,et al.  Physiological variation in metabolic phenotyping and functional genomic studies: use of orthogonal signal correction and PLS‐DA , 2002, FEBS letters.

[68]  Paul Christakopoulos,et al.  Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. , 2005, Journal of biotechnology.

[69]  W. Matson,et al.  Analytical precision, biological variation, and mathematical normalization in high data density metabolomics , 2005, Metabolomics.

[70]  D B Kell,et al.  Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks. , 1998, Microbiology.

[71]  J. Villadsen,et al.  Determination of the phosphorylated sugars of the Embden-Meyerhoff-Parnas pathway in Lactococcus lactis using a fast sampling technique and solid phase extraction. , 1999, Biotechnology and bioengineering.

[72]  D. Kell,et al.  Rapid and Quantitative Detection of the Microbial Spoilage of Meat by Fourier Transform Infrared Spectroscopy and Machine Learning , 2002, Applied and Environmental Microbiology.

[73]  C. Wittmann,et al.  In-Depth Profiling of Lysine-Producing Corynebacterium glutamicum by Combined Analysis of the Transcriptome, Metabolome, and Fluxome , 2004, Journal of bacteriology.

[74]  Hyung-Kyoon Choi,et al.  Metabolic fingerprinting of wild type and transgenic tobacco plants by 1H NMR and multivariate analysis technique. , 2004, Phytochemistry.

[75]  J. Selbig,et al.  Parallel analysis of transcript and metabolic profiles: a new approach in systems biology , 2003, EMBO reports.

[76]  A. Delort,et al.  NMR and microbiology: from physiology to metabolomics. , 2003, Biochimie.

[77]  J. Heijnen,et al.  Changes in the metabolome of Saccharomyces cerevisiae associated with evolution in aerobic glucose-limited chemostats. , 2005, FEMS yeast research.

[78]  D. Kell,et al.  Metabolomics by numbers: acquiring and understanding global metabolite data. , 2004, Trends in biotechnology.

[79]  Oliver Fiehn,et al.  Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks , 2001, Comparative and functional genomics.

[80]  J. Lindon,et al.  'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. , 1999, Xenobiotica; the fate of foreign compounds in biological systems.

[81]  C. Wittmann,et al.  In vivo quantification of intracellular amino acids and intermediates of the methionine pathway in Corynebacterium glutamicum. , 2005, Analytical biochemistry.

[82]  L. Larsson,et al.  Evaluation of chromatographic methods for the detection of bacterial contamination in biotechnical processes , 1992 .

[83]  D. Kell,et al.  A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations , 2001, Nature Biotechnology.

[84]  E. Heinzle,et al.  Quantification of intracellular amino acids in batch cultures of Saccharomyces cerevisiae , 2001, Applied Microbiology and Biotechnology.

[85]  J. François,et al.  Sampling techniques and comparative extraction procedures for quantitative determination of intra- a , 1998 .

[86]  R. D'ari.  Systematic functional analysis of the yeast genome , 1998 .

[87]  Stefan Schuster,et al.  A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. , 2003, Bio Systems.

[88]  M. Reuss,et al.  In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae : I. Experimental observations. , 1997, Biotechnology and bioengineering.

[89]  R. Takors,et al.  Metabolomics: quantification of intracellular metabolite dynamics. , 2002, Biomolecular engineering.

[90]  Age K. Smilde,et al.  ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data , 2005, Bioinform..

[91]  J J Heijnen,et al.  MIRACLE: mass isotopomer ratio analysis of U‐13C‐labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites , 2004, Biotechnology and bioengineering.

[92]  R. Takors,et al.  Applying metabolic profiling techniques for stimulus-response experiments: chances and pitfalls. , 2005, Advances in biochemical engineering/biotechnology.

[93]  L. Olsson,et al.  Cleanup and analysis of sugar phosphates in biological extracts by using solid-phase extraction and anion-exchange chromatography with pulsed amperometric detection. , 1998, Analytical biochemistry.

[94]  J. Heijnen,et al.  Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards. , 2005, Analytical biochemistry.

[95]  Douglas B. Kell,et al.  Metabolomics and Machine Learning: Explanatory Analysis of Complex Metabolome Data Using Genetic Programming to Produce Simple, Robust Rules , 2004, Molecular Biology Reports.

[96]  Transcriptional, translational and metabolic regulation of glycolysis in Lactococcus lactis subsp. cremoris MG 1363 grown in continuous acidic cultures. , 2003, Microbiology.