Max Planck Institute for Dynamics of Complex Technical Systems...
Transcript of Max Planck Institute for Dynamics of Complex Technical Systems...
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Networks of Signal Transduction and Regulation in Cellular Systems
Max Planck Institute for Dynamics of Complex Technical Systems
Magdeburg
E.D. Gilles
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Magdeburg –Capital of Saxony-Anhalt
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MAX PLANCK INSTITUTEFOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS
MAGDEBURG
Founded in 1996 as 1st Max Planck Institute of EngineeringStart of research activities in 19984 departments:
Process Engineering (Sundmacher)Bioprocess Engineering (Reichl)Physical and Chemical Fundamentals (Seidel-Morgenstern)System Theory (Gilles)
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SYSTEM SCIENCES(SYSTEM THEORY)
Provides methods and
tools
ChemicalChemicalProcessesProcesses
Biochemical Biochemical ProcessesProcesses
Biological Biological Networks Networks
Integrating factor
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BROAD SPECTRUM OF PROCESSES TO DEAL WITH:
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SYSTEMS BIOLOGY
Data-bases
Visuali-zation
Hypo-theses
GeneticModi-fication
Analysis
Modeling ConceptSynthesis
ModelingTool
QuantitativeMeasurement
VirtualBiological
Laboratory
Interdisciplinary approach towards a quantitative and predictive biology
„Systems biology is the synergistic application ofexperiment, theory, andmodeling towards understanding biological processes as whole systemsinstead of isolated parts.“
Systems Biology Group/Caltech
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RESEARCH GROUP: SYSTEMS BIOLOGY
Research activities started in 199817 employees working in our groupContinuous extension of research activities on metabolic regulation and signal transduction Interdisciplinary composition of research groupClose cooperation with a network of external biology groupsFermentation laboratory to perform experiments for modelvalidation and hypotheses testing
Quantitative determination of cellular componentsConstruction of isogenic mutant strains of E.coli and other microorganisms
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OBJECTIVES OF RESEARCH
Improved understanding of cellular systemsNew solutions for biotechnological and medical problems (drug target identification)
APPROACH
Detailed mathematical modelingClose interconnection between theory and experiment
Model validation Model-based design of experimentsFormulation and testing of hypotheses
System-theoretical analysis of dynamics and structural propertiesDecomposition into functional units of limited autonomyModel reduction
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COMPLEXITY AND ROBUSTNESS
Complex Technical ProcessesPowerful concepts to cope with increasing complexity
Modularity techniquesHierarchical structuringRedundancy and diversity
Biological SystemsSimilar features of structuring
Natural modularity decomposition into functional units of limited autonomyHierarchical structuring of regulationRedundancy and diversity of pathways, sensors and other key units
Objectives of these concepts in both fieldsRobustness of functionalityReduction of fragilities
Methods and tools developed in engineering, also appropriate for biological systemsControl Theory, Nonlinear Dynamics, System Theory …
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SIGNAL TRANSDUCTION AND REGULATION IN BACTERIAL CELLS
Bacteria are ideally qualified to be studied in systems biology
Bacteria are very sensitive and respond very efficiently to changes in their environment
• Bacteria have a limited complexity compared to higher cells and multicellular organisms
• Well established experimental methods for large scale cultivationand genetic manipulations are available
• Lots of biochemical and genetic data are on-hand
• Broad spectrum of applications in biotechnology, medicine, agriculture
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PROCARIOTIC CELL
4800 genes50 metabolic units
100 genetically controlled regulatory units2500 proteins
50-70 sensors
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SIGNAL ORIENTED DESCRIPTION OF A BACTERIAL CELL
amino acidsnucleotides
substrates
daughter cells
substratesproducts
DNA, RNA, prot.cell. structures
metabolic network
products
sensor signals control actions
network of signal transduction
signal proteins signal complexes
stimulus response
regulatory network
enzymes regulatory proteins
sensor signals control actions
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METABOLIC NETWORK
daughtercell
trans-port
products(in)
substrate(in)
monomer-synthesis
amino acids
nucleotides
sugars
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assemblyreactions
envelope
nucleoid
cytosol
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catabolism
precursor
C-1
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polymer-synthesis
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DNA
RNA
proteins
energy redox coenzyme alarmones
substrate(ex)
products(ex)
metabolic network
regulatory network
signal transduction
lipid
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CATABOLISM AND GLYCOLYSISGLCglycolysis
G6P
PGI
F6P
FDP
ATP
T3-P
G3P-DHNAD NADH
1,3PDG
PGKADP ATP
3PG
PGM/ENO
PEP
PSYPYK
PYR
ATPATP ADPADP
catabolism
precursor
Acetyl CoA
precursor
TCA
precursor
PPW
precursorADP
glycolysis
GLK
PFK FDP
ALD
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REGULATORY NETWORK
cellcycle
modulon
regulonoperon
level ofsequential control
genetic level of regulation
condensation of measuring information
covalent and allosterical modificationmetaboliclevel ofregulation
sensor signalcontrol action
detailing of controlaction
metabolic network
regulatory network
signal transduction
σ - factor
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METABOLISM
REGULATION
BACTERIAL CELL
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CELLULAR FUNCTIONAL UNIT
metabolic network
regulatory network
signal transduction
sensorsignals
control actions
part of the metabolic network
assigned part of the regulatory network
part of the signal network
sensorsignals
controlactions
functional unit of metabolism with regulation
functional unitof signal transduction with regulation
metabolic flux
stimulus
assigned part of the regulatory network
response metabolic flux
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CRITERIA TO DEMARCATE CELLULAR FUNCTIONAL UNITS
Physiological function:Components of a functional unit fulfil by interaction common physiological task (quest for food, respiration, sporulation, stress management ...)
Genetic structuring:Genes of a functional unit are expressed in a coordinated way (operon, regulon, modulon)
Regulation:A functional unit owes a certain degree of autonomy to closed control circuits in its interior
Signal transduction:The components of a functional unit establish a network of transfer elements for signal processing and signal integration
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CATABOLITE REPRESSION IN E. coli
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VALIDATION OF THE MODEL BY EXPERIMENTS
Experimental strategyIsogenic mutant strainsDifferent mixtures of the main substratesDifferent preculture conditionsBatch experiments (µ is constant)Feeding strategy (µ is changing)Continuous culture (µ is constant, but sub-maximal)
Time dependent measurement of componentsExtra cellular carbohydratesGlycolytic metabolites (Glc, Glc6P, F6P, Pep, Prv)Degree of phosphorylation (EIIA, P~EIIA)Enzyme activity (LacZ)
Desired and in preparation PCR technologyTranscriptome (cDNA arrays)Proteome
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EXPERIMENTS WITH DIFFERENT STRAINS AND CULTURE CONDITIONS
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COMPARISON SIMULATION – EXPERIMENT(wild type)
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REDOX CONTROL OF PHOTOSYNTHETIC BACTERIA
Fructose-6-phosphate
Glyceraldehyde-3-phosphate
3-Phospho-glycerate
NADHFADH
2-OG
SCoAOATCA-
Cycle
ATP
ATPNADH
CO2
C4/C5/C6/C7-Intermediates
Ribulose-1,5-bisphosphate
3-Phospho-glycerate
Glyceraldehyde-3-phosphate CBB-
Cycle
EMP
Fructose
FormiateAcetate
NADH
NADH
NADH
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PHOTOTAXIS IN HALOBACTERIUM SALINARUM
Orange light as energy source for photosynthesis through the light driven proton pump bacteriorhodopsin.
Simple kind of colour vision (blue, orange, ultraviolet).
H. swims to those sites where optimal light conditions exist.
Continues to swim in forward direction when sensing increasing intensity of orange light.
Flees blue or ultraviolet light by reversing its swimming direction
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PHOTOTAXIS IN HALOBACTERIUM SALINARUM
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MOLECULAR ORIENTED:
SIGNAL ORIENTED:
BLOCK-DIAGRAM OF PHOTOTAXIS
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THANK YOU!