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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

• • •

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

•••

assemblyreactions

envelope

nucleoid

cytosol

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catabolism

precursor

C-1

•••

polymer-synthesis

••

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!