1
|
Effect of vineyard row orientation on microclimate, phenolic compounds, individual anthocyanins, and free volatile compounds of Cabernet Sauvignon (Vitis vinifera L.) in a high-altitude arid valley. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-022-03961-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
2
|
Pietzke M, Zasada C, Mudrich S, Kempa S. Decoding the dynamics of cellular metabolism and the action of 3-bromopyruvate and 2-deoxyglucose using pulsed stable isotope-resolved metabolomics. Cancer Metab 2014; 2:9. [PMID: 25035808 PMCID: PMC4101711 DOI: 10.1186/2049-3002-2-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/23/2014] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Cellular metabolism is highly dynamic and continuously adjusts to the physiological program of the cell. The regulation of metabolism appears at all biological levels: (post-) transcriptional, (post-) translational, and allosteric. This regulatory information is expressed in the metabolome, but in a complex manner. To decode such complex information, new methods are needed in order to facilitate dynamic metabolic characterization at high resolution. RESULTS Here, we describe pulsed stable isotope-resolved metabolomics (pSIRM) as a tool for the dynamic metabolic characterization of cellular metabolism. We have adapted gas chromatography-coupled mass spectrometric methods for metabolomic profiling and stable isotope-resolved metabolomics. In addition, we have improved robustness and reproducibility and implemented a strategy for the absolute quantification of metabolites. CONCLUSIONS By way of examples, we have applied this methodology to characterize central carbon metabolism of a panel of cancer cell lines and to determine the mode of metabolic inhibition of glycolytic inhibitors in times ranging from minutes to hours. Using pSIRM, we observed that 2-deoxyglucose is a metabolic inhibitor, but does not directly act on the glycolytic cascade.
Collapse
Affiliation(s)
- Matthias Pietzke
- Integrative Metabolomics and Proteomics, Berlin Institute of Medical Systems Biology/Max-Delbrueck Center for Molecular Medicine, Robert Rossle Street 10, Berlin 13125, Germany
| | - Christin Zasada
- Integrative Metabolomics and Proteomics, Berlin Institute of Medical Systems Biology/Max-Delbrueck Center for Molecular Medicine, Robert Rossle Street 10, Berlin 13125, Germany
| | - Susann Mudrich
- Integrative Metabolomics and Proteomics, Berlin Institute of Medical Systems Biology/Max-Delbrueck Center for Molecular Medicine, Robert Rossle Street 10, Berlin 13125, Germany
- Present address: Faculté des Sciences, de la Technologie et de la Communication, University of Luxembourg, 162 A, Avenue de la Faïencerie L-1511, Luxembourg, Luxembourg
| | - Stefan Kempa
- Integrative Metabolomics and Proteomics, Berlin Institute of Medical Systems Biology/Max-Delbrueck Center for Molecular Medicine, Robert Rossle Street 10, Berlin 13125, Germany
| |
Collapse
|
3
|
Link H, Anselment B, Weuster-Botz D. Rapid media transition: an experimental approach for steady state analysis of metabolic pathways. Biotechnol Prog 2010; 26:1-10. [PMID: 19785030 DOI: 10.1002/btpr.290] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Commonly steady state analysis of microbial metabolism is performed under well defined physiological conditions in continuous cultures with fixed external rates. However, most industrial bioprocesses are operated in fed-batch mode under non-stationary conditions, which cannot be realized in chemostat cultures. A novel experimental setup-rapid media transition-enables steady state perturbation of metabolism on a time scale of several minutes in parallel to operating bioprocesses. For this purpose, cells are separated from the production process and transferred into a lab-scale stirred-tank reactor with modified environmental conditions. This new approach was evaluated experimentally in four rapid media transition experiments with Escherichia coli from a fed-batch process. We tested the reaction to different carbon sources entering at various points of central metabolism. In all cases, the applied substrates (glucose, succinate, acetate, and pyruvate) were immediately utilized by the cells. Extracellular rates and metabolome data indicate a metabolic steady state during the short-term cultivation. Stoichiometric analysis revealed distribution of intracellular fluxes, which differs drastically subject to the applied carbon source. For some reactions, the variation of flux could be correlated to changes of metabolite concentrations.
Collapse
Affiliation(s)
- Hannes Link
- Lehrstuhl für Bioverfahrenstechnik, Technische Universität München, Garching 85748, Germany
| | | | | |
Collapse
|
4
|
Picon A, de Mattos MJT, Postma PW. Protein production by Escherichia coli wild-type and ΔptsG mutant strains with IPTG induction at the onset. J Ind Microbiol Biotechnol 2008; 35:213-8. [DOI: 10.1007/s10295-007-0285-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 11/28/2007] [Indexed: 11/24/2022]
|
5
|
Weuster-Botz D, Hekmat D, Puskeiler R, Franco-Lara E. Enabling technologies: fermentation and downstream processing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 105:205-47. [PMID: 17408085 DOI: 10.1007/10_2006_034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Efficient parallel tools for bioprocess design, consequent application of the concepts for metabolic process analysis as well as innovative downstream processing techniques are enabling technologies for new industrial bioprocesses from an engineering point of view. Basic principles, state-of-the-art techniques and cutting-edge technologies are briefly reviewed. Emphasis is on parallel bioreactors for bioprocess design, biochemical systems characterization and metabolic control analysis, as well as on preparative chromatography, affinity filtration and protein crystallization on a process scale.
Collapse
Affiliation(s)
- Dirk Weuster-Botz
- Lehrsthul für Bioverfahrenstechnik, Technischen Universität München, Boltzmannstr. 15, 85748 Garching, Germany.
| | | | | | | |
Collapse
|
6
|
Hiller J, Franco-Lara E, Weuster-Botz D. Metabolic profiling of Escherichia coli cultivations: evaluation of extraction and metabolite analysis procedures. Biotechnol Lett 2007; 29:1169-78. [PMID: 17479221 DOI: 10.1007/s10529-007-9384-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 03/21/2007] [Accepted: 03/26/2007] [Indexed: 11/30/2022]
Abstract
The quantitative estimation of intracellular metabolite concentrations (metabolic profiling) is a prerequisite for a better understanding of biological processes and thus inevitable for the rational improvement of microbial production strains and process design. Since pool sizes of substrates regulate flux through different enzymes, the accurate determination of intracellular metabolite concentrations is necessary to understand in vivo reaction kinetics. Quantification of intracellular concentrations of glycolytic intermediates in Escherichia coli K12 was achieved by using a novel in situ rapid sampling and quenching procedure. A new extraction procedure using buffered hot water was established. By use of simultaneous multi-substrate feeding with various ratios of glucose, fructose and acetate during continuous cultivations several metabolic states were induced. Metabolic flux analysis and the newly developed metabolic profiling procedure were used to determine in vivo enzyme kinetics as exemplified for fructose 1,6-bisphosphate aldolase and citrate synthase.
Collapse
Affiliation(s)
- Julia Hiller
- Lehrstuhl für Bioverfahrenstechnik, Technische Universität München, Boltzmannstr. 15, 85748, Garching, Germany.
| | | | | |
Collapse
|
7
|
Vemuri GN, Altman E, Sangurdekar DP, Khodursky AB, Eiteman MA. Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio. Appl Environ Microbiol 2006; 72:3653-61. [PMID: 16672514 PMCID: PMC1472329 DOI: 10.1128/aem.72.5.3653-3661.2006] [Citation(s) in RCA: 249] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 02/21/2006] [Indexed: 01/02/2023] Open
Abstract
Overflow metabolism in the form of aerobic acetate excretion by Escherichia coli is an important physiological characteristic of this common industrial microorganism. Although acetate formation occurs under conditions of high glucose consumption, the genetic mechanisms that trigger this phenomenon are not clearly understood. We report on the role of the NADH/NAD ratio (redox ratio) in overflow metabolism. We modulated the redox ratio in E. coli through the expression of Streptococcus pneumoniae (water-forming) NADH oxidase. Using steady-state chemostat cultures, we demonstrated a strong correlation between acetate formation and this redox ratio. We furthermore completed genome-wide transcription analyses of a control E. coli strain and an E. coli strain overexpressing NADH oxidase. The transcription results showed that in the control strain, several genes involved in the tricarboxylic acid (TCA) cycle and respiration were repressed as the glucose consumption rate increased. Moreover, the relative repression of these genes was alleviated by expression of NADH oxidase and the resulting reduced redox ratio. Analysis of a promoter binding site upstream of the genes which correlated with redox ratio revealed a degenerate sequence with strong homology with the binding site for ArcA. Deletion of arcA resulted in acetate reduction and increased the biomass yield due to the increased capacities of the TCA cycle and respiration. Acetate formation was completely eliminated by reducing the redox ratio through expression of NADH oxidase in the arcA mutant, even at a very high glucose consumption rate. The results provide a basis for studying new regulatory mechanisms prevalent at reduced NADH/NAD ratios, as well as for designing more efficient bioprocesses.
Collapse
Affiliation(s)
- G N Vemuri
- Center for Molecular BioEngineering, Driftmier Engineering, University of Georgia, Athens, GA 30602, USA
| | | | | | | | | |
Collapse
|
8
|
Banerjee S, Nandyala A, Podili R, Katoch VM, Hasnain SE. Comparison of Mycobacterium tuberculosis isocitrate dehydrogenases (ICD-1 and ICD-2) reveals differences in coenzyme affinity, oligomeric state, pH tolerance and phylogenetic affiliation. BMC BIOCHEMISTRY 2005; 6:20. [PMID: 16194279 PMCID: PMC1260013 DOI: 10.1186/1471-2091-6-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Accepted: 09/29/2005] [Indexed: 11/10/2022]
Abstract
BACKGROUND M.tb icd-1 and M.tb icd-2, have been identified in the Mycobacterium tuberculosis genome as probable isocitrate dehydrogenase (ICD) genes. Earlier we demonstrated that the two isoforms can elicit B cell response in TB patients and significantly differentiate TB infected population from healthy, BCG-vaccinated controls. Even though immunoassays suggest that these proteins are closely related in terms of antigenic determinants, we now show that M.tb icd-1 and M.tb icd-2 code for functional energy cycle enzymes and document the differences in their biochemical properties, oligomeric assembly and phylogenetic affiliation. RESULTS Functionally, both M.tb ICD-1 and ICD-2 proteins are dimers. Zn+2 can act as a cofactor for ICD-1 apart from Mg+2, but not for ICD-2. ICD-1 has higher affinity for metal substrate complex (Km (isocitrate) with Mg++: 10 microM +/- 5) than ICD-2 (Km (isocitrate) with Mg++: 20 microM +/- 1). ICD-1 is active across a wider pH range than ICD-2, retaining 33-35% activity in an acidic pH upto 5.5. Difference in thermal behaviour is also observed with ICD-2 being active across wider temperature range (20 degrees C to 40 degrees C) than ICD-1 (optimum temperature 40 degrees C). The isozymes are NADP+ dependent with distinct phylogenetic affiliations; unlike M.tb ICD-2 that groups with bacterial ICDs, M.tb ICD-1 exhibits a closer lineage to eukaryotic NADP+ dependent ICDs. CONCLUSION The data provide experimental evidence to show that the two open reading frames, Rv3339c (ICD-1) and Rv0066c (ICD-2), annotated as probable ICDs are functional TCA cycle enzymes with identical enzymatic function but different physio-chemical and kinetic properties. The differences in biochemical and kinetic properties suggest the possibility of differential expression of the two ICDs during different stages of growth, despite having identical metabolic function.
Collapse
Affiliation(s)
- Sharmistha Banerjee
- Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad, 500076, India
| | - Ashok Nandyala
- Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad, 500076, India
| | - RaviPrasad Podili
- Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad, 500076, India
| | | | - Seyed E Hasnain
- Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad, 500076, India
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560012, India
| |
Collapse
|
9
|
Huang GS, Hong MY, Liu YC. Incorporation of DNA chip technology to the simulation and validation of flux analysis in yeast diauxic growth. Life Sci 2003; 72:2525-31. [PMID: 12650861 DOI: 10.1016/s0024-3205(03)00138-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We incorporated gene expression information from cDNA microarray into flux analysis to simulate yeast diauxic growth. Expression ratios of both growth phases were applied to assign the split ratio at glyoxylate shunt during simulation, in which the equation was mathematically unsolvable due to the singularity and artificial split ratios, which were traditionally introduced without biological evidence. In addition, the directionality of microarray dataset was used as a further constraint during simulation. Metabolic fluxes obtained by this modified approach are in general consistent with microarray analysis. However, discrepancies occurred when the quantity of fluxes was compared, probably due to the substantial reduction of substrates at phase II in which the increase in the enzymatic levels was not proportional to the increase of substrate flow, as would be predicted from microarray dataset. The modified flux analysis might have brought a new approach to investigate other cellular pathways.
Collapse
Affiliation(s)
- Guewha Steven Huang
- Institute of Chinese Pharmaceutical Sciences, China Medical College, 91 Hsueh-Shih Road, 404, Taichung, Taiwan, ROC.
| | | | | |
Collapse
|
10
|
Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M. GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Res 2002; 30:4574-82. [PMID: 12384605 PMCID: PMC137121 DOI: 10.1093/nar/gkf555] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2002] [Revised: 08/08/2002] [Accepted: 08/08/2002] [Indexed: 11/15/2022] Open
Abstract
We present a prototype of a new database tool, GeneCensus, which focuses on comparing genomes globally, in terms of the collective properties of many genes, rather than in terms of the attributes of a single gene (e.g. sequence similarity for a particular ortholog). The comparisons are presented in a visual fashion over the web at GeneCensus.org. The system concentrates on two types of comparisons: (i) trees based on the sharing of generalized protein families between genomes, and (ii) whole pathway analysis in terms of activity levels. For the trees, we have developed a module (TreeViewer) that clusters genomes in terms of the folds, superfamilies or orthologs--all can be considered as generalized 'families' or 'protein parts'--they share, and compares the resulting trees side-by-side with those built from sequence similarity of individual genes (e.g. a traditional tree built on ribosomal similarity). We also include comparisons to trees built on whole-genome dinucleotide or codon composition. For pathway comparisons, we have implemented a module (PathwayPainter) that graphically depicts, in selected metabolic pathways, the fluxes or expression levels of the associated enzymes (i.e. generalized 'activities'). One can, consequently, compare organisms (and organism states) in terms of representations of these systemic quantities. Develop ment of this module involved compiling, calculating and standardizing flux and expression information from many different sources. We illustrate pathway analysis for enzymes involved in central metabolism. We are able to show that, to some degree, flux and expression fluctuations have characteristic values in different sections of the central metabolism and that control points in this system (e.g. hexokinase, pyruvate kinase, phosphofructokinase, isocitrate dehydrogenase and citric synthase) tend to be especially variable in flux and expression. Both the TreeViewer and PathwayPainter modules connect to other information sources related to individual-gene or organism properties (e.g. a single-gene structural annotation viewer).
Collapse
Affiliation(s)
- J Lin
- Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520, USA
| | | | | | | | | | | | | | | | | |
Collapse
|