Genom Transkriptom Proteom Metabolom

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1 Genom Transkriptom Proteom Metabolom
Stofffluss Informationsfluss Speicher DNA (Gen) ATG.CTC.. Botschaft mRNA AUG.CUC… Produkt Metabolit A Protein (Enzym) Metabolit B Met.Leu... Genom Transkriptom Proteom Metabolom Abb.1

2 R P T P A B Hg(II) Abb.2 Regulator 144 aa Promotor Transport Peri-
plasma 116 aa Transport Membrane 91 aa Mercury- Reductase 561 aa Mercury- Lyase 212 aa Abb.2

3 Operon mRNA Metabolite P Enzyme Abb. 3
RG Promotor Operator TF Struc. DNA Repressor Apo- repressor Transcription mRNA Degradation Feedback repression Inhibition Translation Metabolite P Enzyme Secretion Degradation The production of metabolites is determined at the end by gene expression. The interactions of gene expression with cellular metabolism are an important issue in many fields including metabolic engineering. The metabolites can interact with almost all the essential steps on the path from DNA to metabolites such as transcrption, translation and enzymatic catalysis. Of particular relevance are feedback repression of the operator activity, inhibition of enzyme activities and global regulation. There are also several regulatory genes coded in the near of the structure genes. Together with the promoter and operator these regulatory and structure genes form a genetic unit called operon or regulon. We have mathematically modeled and analyzed the operons for propanediol formation and tryptophan biosynthesis. I am not going to talk about the models in detail. In principle, for each of the steps from DNA to metabolite P, such a differential equation can be formulated. The mathematic modeling can help to assess the relative importance of these regulation mechanisms and to formulate experimental hypothesis. Abb. 3

4 Transkription GEN Translation Metabolische Flüsse PRODUKT Abb.4

5 The interactions of gene expression and cellular metabolism can lead to strong nonlinear dynamics of cells such as oscillations and multiplicity. This graph shows for example oscillations of mRNA, enzyme and tryptophan concentrations in the tryptophan biosynthesis under certain conditions. The study of cellular dynamics requires the expertise of engineers in system analysis and dynamic modeling and is also within my research interest. Abb. 5

6 2-D IEF/SDS-PAGE Gel Electrophoretic Separation
Abb. 6

7 Abb. 7

8 Genome Enzymes Connection matrix Reactions
Abb. 8 Genome Annotation Enzymes EC EC EC Reversibility information Connection matrix C00013-C00009 C00022-C00900 C01083-C00267 Reactions Homoserine + NAD+ = Aspartate- Glycerol + NAD+ = Glycerone + Mannitol 1-P + NAD+ = F6P + N ………………… Reaction database (e.g. Ligand, Brenda Nonenzymatic reactions Ma & Zeng (2003) Bioinformatics. 19: Reaction Metabolite

9 Glycolysis, pyruvate TCA Abb. 9 Methionine Cysteine sulfur Purine
Methane Pentose phosphate fructose, mannose galactose Lysine Purine de novo One carbon, folate, glycine, serine, threonine Glycolysis, pyruvate Glycerolipid, glycosphingolipid TCA Fatty acid Valine, leucine isoleucine Urea cycle, nitrogen, glutamate, arginine, proline, pyrimidine Phenylalanine tyrosine tryptophan EC numbers: 434 Metabolites: 1172

10 Global regulators Regulatory modules Abb. 10 . rpoE fis soxR cspA rpoS
phoB crp ihf argP cspE rpoN dnaA hns cytR Global regulators Regulatory modules Abb. 10 .

11 Nahrung = 350 Signale A B Abb. 11 pH-Wert Osmolarität Temperatur
Gen mRNA Protein Temperatur Antibiotika Sauerstoff A B Gift/Gefahr Licht Erdanziehungskraft Nährstoff- limitierung Botschaften anderer Bakterien Scherstress Druck Abb. 11

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15 Abb. 15 Shaking Flask Couette flow bioreactor g = 0.028 s-1
1µm cata Abb. 15

16 Abb. 16 1 2 3 4 Sporen Sporenpakete Primäre Aggregation Keimung
2 Stunden Keimung 2 50 µm 8 Stunden Sekundäre Aggregation 3 100 µm 12 Stunden Pellet Wachstum 4 Abb. 16

17 Abb.17 t = 80 h Aktivität [µKat/mL Pelletvolumen]
Pelletdurchmesser [mm] 0,1 1,0 10,0 106 1,8 180 Aktivität [µKat/mL Pelletvolumen] Aktivität [µKat/L Reaktorvolumen] t = 80 h 1,6 160 1,4 140 1,2 120 Pelletkonzentration [1/L] 1,0 100 105 0,8 80 0,6 60 0,4 40 0,2 20 104 0,050 0,060 0,070 0,080 0,090 0,100 spezifischer Leistungseintrag [W/kg] Abb.17

18 Zellphysiologie Kinetik metabolisches Netzwerk
Genom- Sequenzen Proteom (Proteine) Transkriptom (mRNA) gezielte Exp. Metabolic Eng. Zellphysiologie Kinetik Metabolom Fluxom Bioprozesse & Bioprodukte Environom Verfahrenstechnik metabolisches Netzwerk genetisches Netzwerk Abb. 18