infobiotics workbench, a computational framework …fran/tib/semana9.pdf3 top-down synthetic...

Infobiotics workbench, a computational framework for systems and synthetic biology

modelshttp://www.infobiotic.org/

Fran Romero

Dpt Computer Science and Artificial Intelligence

University of Seville

[email protected]/~fran

mailto:[email protected]

http://www.cs.us.es/~fran

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Synthetic Biology is …A) the design and construction of new biological parts, devices, and systems, and

B) the re-design of existing, natural biological systems for useful purposes.

C) Through rigorous mathematical, computational & engineering routes

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Top-Down Synthetic Biology: An Approach to Engineering Biology

Cells are information processors. DNA is their programming language.

DNA sequencing and PCR: Identification and isolation of cellular parts.

Recombinant DNA and DNA synthesis : Combination of DNA and construction of new systems.

Tools to make biology easier to engineer: Standardisation, encapsulation and abstraction (blueprints).

E. coli

Vibrio fischeri

Pseudomonas aeruginosa

plasmids

DNA synthesis

Discosoma sp.

Aequoreavictoria

Circuit BlueprintChassis

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Infobiotics: An Integrated Framework

http://www.infobiotics.org/infobiotics-workbench/

Synthetic Multi-cellular Systems

Libraries of Modules

P systems LPP systems

Multi Compartmental Stochastic Simulations

based on Gillespie’s algorithm

Spatio-temporal Dynamics Analysis

using Model Checking with PRISM and MC2

Automatic Design of Synthetic Gene

Regulatory Circuits using Evolutionary Algorithms

A compiler based on a BNF grammar

Single Cells

Cellular Parts

Synthetic Circuits

Module Combinations

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Ron Weiss’ Pulse Generator

gfpcI

luxR

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Two different bacterial strains carrying specific synthetic gene regulatory networks are used.

The first strain produces a diffusible signal AHL.

The second strain possesses a synthetic gene regulatory network which produces a pulse of GFP after AHL sensing.

These two bacterial strains and their respective synthetic networks are modelled as a combination of modules.

Ron Weiss‘ Pulse Generator

S. Basu, R. Mehreja, et al. (2004) Spatiotemporal control of gene expression with pulse generating networks, PNAS, 101, 6355-6360

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Single Cells

Cellular Parts

Synthetic Circuits

Module Combinations

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Characterisation/Encapsulation of Cellular Parts: Gene Promoters

A modeling language for the design of synthetic bacterial colonies.

A module, set of rules describing the molecular interactions involving a cellular part, provides encapsulation and abstraction.

Collection or libraries of reusable cellular parts and reusable models.

LuxRAHL

CI

PluxOR1({X},{c1, c2, c3, c4, c5, c6, c7, c8, c9},{l}) = {

type: promoter

sequence: ACCTGTAGGATCGTACAGGTTTACGCAAGAA ATGGTTTGTATAGTCGAATACCTCTGGCGGTGATA

rules: r1: [ LuxR2 + PluxPR.X ]_l -c1-> [ PluxPR.LuxR2.X ]_l r2: [ PluxPR.LuxR2.X ]_l -c2-> [ LuxR2 + PluxPR.X ]_l ... r5: [ CI2 + PluxPR.X ]_l -c5-> [ PluxPR.CI2.X ]_l r6: [ PluxPR.CI2.X ]_l -c6-> [ CI2 + PluxPR.X ]_l ... r9: [ PluxPR.LuxR2.X ]_l -c9-> [ PluxPR.LuxR2.X + RNAP.X ]_l}

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Module Variables: Recombinant DNA, Directed Evolution, Chassis

selection

A

Directed evolution: Variables for stochastic constants can be instantiated with specific values.

Recombinant DNA: Objects variables can be instantiated with the name of specific genes.

PluxOR1({X=tetR})PluxOR1({X=GFP})

PluxOR1({X=GFP},{...,c4=10,...}) Chassis Selection: The variable for the label can be instantiated with the name of a

chassis.

PluxOR1({X=GFP},{...,c4=10,...},{l=DH5α })

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Characterisation/Encapsulation of Cellular Parts: Riboswitches

A riboswitch is a piece of RNA that folds in different ways depending on the presence of absence of specific molecules regulating translation.

ToppRibo({X},{c1, c2, c3, c4, c5, c6},{l}) = {

type: riboswitch

sequence:GGTGATACCAGCATCGTCTTGATGCCCTTGG CAGCACCCCGCTGCAAGACAACAAGATG rules: r1: [ RNAP.ToppRibo.X ]_l -c1-> [ ToppRibo.X ]_l r2: [ ToppRibo.X ]_l -c2-> [ ]_l r3: [ ToppRibo.X + theop ]_l –c3-> [ ToppRibo*.X ]_l r4: [ ToppRibo*.X ]_l –c4-> [ ToppRibo.X + theop ]_l r5: [ ToppRibo*.X ]_l –c5-> [ ]_l r6: [ ToppRibo*.X ]_l –c6-> [ToppRibo*.X + Rib.X ]_l}

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Characterisation/Encapsulation of Cellular Parts: Degradation Tags

Degradation tags are amino acid sequences recognised by proteases. Once the corresponding DNA sequence is fused to a gene the half life of the protein is reduced considerably.

degLVA({X},{c1, c2},{l}) = {

type: degradation tag

sequence: CAGCAAACGACGAAAACTACGCTTTAGTAGCT

rules: r1: [ Rib.X.degLVA ]_l -c1-> [ X.degLVA ]_l r2: [ X.degLVA ]_l -c2-> [ ]_l}

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Single Cells

Cellular Parts

Synthetic Circuits

Module Combinations

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Gene Constructs

Promoter Gene(s) RBS Term TAATAA

Transcription Initiation

TranscriptionTermination

Translation Initiation

Translation Initiation

Genes

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Higher Order Modules: Building Synthetic Gene Circuits

PluxOR1 GFPToppRibo degLVA

3OC6_repressible_sensor = { PluxOR1({X=ToppRibo.GFP.degLVA},{...},{l=DH5α}) ToppRibo({X=GFP.degLVA},{...},{l=DH5α}) degLVA({X=GFP},{...},{l=DH5α})}

X=GFP

Plux({X=ToppRibo.geneCI.degLVA},{...},{l=DH5α}) ToppRibo({X=geneCI.degLVA},{...},{l=DH5α}) degLVA({CI},{...},{l=DH5α})

PtetR({X=ToppRibo.geneLuxR.degLVA},{...},{l=DH5α}) Weiss_RBS({X=LuxR},{...},{l=DH5α}) Deg({X=LuxR},{...},{l=DH5α})

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• Using P systems modules one can model a large variety of commonly occurring BRN: Gene Regulatory Networks, Signaling Networks and Metabolic Networks

• This can be done in an incremental and parsimonious way.

F. J. Romero-Campero, J. Twycross, M. Camara, M. Bennett, M. Gheorghe, and N. Krasnogor. Modular assembly of cell systems biology models using p systems. International Journal of Foundations of Computer Science, 2009

Rapid Model Prototyping

Co-design of parts and their models hence improves and makes both processes more reliable

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Single Cells

Cellular Parts

Synthetic Circuits

Module Combinations

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Sending Cells

Pconst

LuxI AHL

AHL

Pconst({X = luxI },…)

PostTransc({X=LuxI},{c1=3.2,…})

Diff({X=AHL},{c=0.1})

luxI

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luxRPconst

cIPlux

gfpPluxOR1

LuxR

CI

GFPAHL

AHL

Pconst({X=luxR},…)

PluxOR1({X=gfp},…)

Plux({X=cI},…)

…

…

Diff({X=AHL},…)

Pulse Generating Cells

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Single Cells

Cellular Parts

Synthetic Circuits

Module Combinations

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Specification of Multi-cellular Systems: LPP systems

luxIPconst

LuxI AHL

AHL

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luxIPconst

LuxI AHL

AHL

luxRPconst

cIPlux

gfpPluxOR1

LuxR

CI

GFPAHL

AHLSpecification of Multi-cellular

Systems: LPP systems

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Simulation of the propagation of a wave of gene expression

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A Step forward in Synthetic Biology: Controlling Cell Differentation

Validation of hypothesis about the functioning of cellular systems by implementing them in vivo.

Specific pattern formation in several organisms is produced by transcriptional networks with a double negative feedback loop at their core.

The ZEB/miR-200 feedback loop—a motor of cellular plasticity in development and cancer?Simone Brabletz & Thomas BrabletzEMBO reports (2010) 11, 670 - 677

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PLtet01 luxR cI

Ptac rhlR cI434

Plux,R lacI cherry

PrhlA tetR gfp

PR luxI

PR434 rhlI

LuxR

RhlR

CI

CI434

LacI

TetR

3OC6

C4

Synthetic Double Negative Feedback Loop

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PLtet01 luxR cI

Ptac rhlR cI434

Plux,R lacI cherry

PrhlA tetR gfp

PR luxI

PR434 rhlI

LuxR

RhlR

CI

CI434

LacI

C4

3OC6 C4

C4

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PLtet01 luxR cI

Ptac rhlR cI434

Plux,R lacI cherry

PrhlA tetR gfp

PR luxI

PR434 rhlI

LuxR

RhlR

CI

CI434

TetR

3OC6

3OC6 3OC6 3OC6

3OC6 3OC6

C4 C4

C4C4

Ondas de Expresión Génica en Colonias de Bacterias Sintéticas

Pattern Formation in synthetic bacterial colonies

infobiotics workbench, a computational framework …fran/tib/semana9.pdf3 top-down synthetic...

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