SYNBIOLOGY - An Analysis of Synthetic Biology Research in Europe and North America 4,5/4,5 CM SYNBIOLOGY: An Analysis of Synthetic Biology Research in Europe and North America Definition of Synthetic Biology Activities 30th May 2006 European Commission, Brussels

SYNBIOLOGY Brussels, 30 May 2006 Introduction (1) Definition of Synthetic Biology Activities - -Synbiology project provided discussion and structuring of synthetic biology activities in Analysis of Synthetic Biology Literature and Statistical Review - -No single agreed definition on synthetic biology activities - -Definition provided by NEST High-Level Expert Group (2006) - -Synopsis will be provided in upcoming paper : Consensus Synthetic Biology - a Structured View

SYNBIOLOGY Brussels, 30 May 2006 Definition of Synthetic Biology Activities - -Synthetic biology represents missing interdisciplinary links from molecular biology to engineering technologies close to IT and advanced nano-technology sciences - -Synthetic biology application potential is enormous and universal to all life science based industries - -As well as other industries for improving processes and generating totally new products and services Introduction (2)

SYNBIOLOGY Brussels, 30 May 2006 Integrity of the Basic Genetic System RNA-World Cellular Systems Szostack Group Minimal Cell Project Piere Luigi Luisi – Group „Intermediate Up“ - Approach Reduction of Natural on Basic Function Graig Venter Group Genetic Engineering & Metabolic Engineering Consecutive Substitution or Expansion of Natural Function General Recombinant DNA Technologies focus on „Metabolic Engineering“ Continuous increase of complexity Affecting the integrity of the basic genetic system ->Use of not natural nucleotides as artificial genetic information store and -> use of not triplet codons System Integration „de novo“ – Approach Prof. Norman Packard Group, Prof. Mark A. Bedau Proto Life SRL – Los Alamos Bug - PACE Cellular Differentiation & Mitotic Engineering Éngineering „Bottom Up“ – Approach „Top Down“ - Approach Signal Transduction Éngineering Creation of new artificial genetic system Synthetic Biology Artificial Biology Definition of Synthetic Biology Activities

SYNBIOLOGY Brussels, 30 May 2006 Differentiation by type of genetic element : Gene Regulatory Circuits are composed of different genetic functions : regulating function (regulators) versus regulated function Regulated Gene Functions for Biocatalysis (Enzymes, Ribozymes) Structure Formation ((Glyco)proteins, RNA) Biosensing (Proteins) Regulators Catalysts Structural Elements Sensors Signal Sensors Signal Input Parameters Signal Processing Signal Integration Output Parameters Actuator/ Signal/ Product in vitroin vivo ex vivo in silico Regulating Gene Functions in CIS or TRANS : Regulation of Regulatory Elements by Regulation of Proliferation Regulation of Cellular Differentiation Regulation Chemical Differentiation Definition of Synthetic Biology Activities

SYNBIOLOGY Brussels, 30 May 2006 Development Stages Definition of Synthetic Biology Activities - -Three developmental stages of synthetic biology can be identified - -Mainly influenced by steadily increasing technical feasibilities of enabling technologies - the basis for generating a general trend to more complex system oriented thinking. - -These stages of can be described as shifts in paradigm - -Class III Synthetic Biology Activities (SB3) - -Class II Synthetic Biology Activities (SB2) - -Class I Synthetic Biology Activities (SB1)

SYNBIOLOGY Brussels, 30 May 2006 Class III Synthetic Biology Activities (SB3) Definition of Synthetic Biology Activities - -Synthetic biology as an expression of early genetic engineering experiments mainly focused on in vivo synthetic biology - -Simple and individual modifications of natural function (e.g. improvement of a promoter) performed on natural genetic parts without standardization - -Aimed at single functional improvements for bio-production in mostly heterogenious expression rather than generation of functional defective mutations of DNA constructions for unraveling genetic function

SYNBIOLOGY Brussels, 30 May 2006 Class II Synthetic Biology Activities (SB2) Definition of Synthetic Biology Activities - -Intentional design of systemic functional interactions of new assemblies genes and its products and appropriate regulatory circuits - -Such as in Biochemical Pathway Designs consisting of new configurations of regulators and regulated parts like sensors, catalysts and structural elements - -Mixing natural genetic elements, artificially modified by rational designed or evolved by molecular breeding - -Mosaics of natural and partially designed parts

SYNBIOLOGY Brussels, 30 May 2006 Class I Synthetic Biology Activities (SB1) Definition of Synthetic Biology Activities - -Artificial designs of genetic circuits and pathways using only rational engineered or evolved standardized parts which meet technical requirement specifications. - -Will be used for future artificial regulation, catalysis, structural parts - -Or for sensing in vivo or for biobased nano-technology applications in vitro synthetic biology (nanowires, biocomputing, bioelectronics, self-assembly), artificial biology and artificial life

SYNBIOLOGY Brussels, 30 May 2006 Class I Synthetic Biology Activities (SB1) Definition of Synthetic Biology Activities - -New Paradigm : Drew Endy (2005): Artificial Synthetic Biology molecular parts of biological function and devices of higher functional order built thereof have some mandatory features of proven quality which are necessary to assure its function in vivo as well as in vitro - -Should be compatible with defined interfaces to other parts with defined robust function showing reproducible behavior - -Ideally the function can be established independently of the host system - -Excellent documentation and standardisation of parts are prerequisites

SYNBIOLOGY Brussels, 30 May 2006 in vivo Synthetic Biology in silico SB Structural in vivo Synthetic Biology in silico SB Systemic in vitro Synthetic Biology in silico SB Theory general Bioinformatics Systems Biology system oriented Bioinformatics Structural Bioinformatics classical Genomics functional Genomics in silico Genomicsstructural Genomics Synthetic Biology 1 (SB1) : Artificial Systems Functional Devices Artificial Standard Parts Synthetic Biology 2 (SB2) : Systems Modified Natural Parts Synthetic Biology 3 (SB3) : Natural and slightly modified natural Parts SB1 - Transition Point : mixed Systems natural and artificial parts generating mixed devices Artificial devices of standardized functional behaviour is the unique feature of SB1 SB1 - Transition Point : simple artificial arrangements of natural parts generating simple artificial systems All Artificial All Natural SB2 – Transition Point : Complex artificial arrangements of natural and slightly modified natural parts generating simple individual systems Definition of Synthetic Biology Activities Specific Functional Interactions on the Structural Level At least a Minimum of two Designed Functional Interactions

SYNBIOLOGY Brussels, 30 May 2006 Mandatory features of Synthetic Biology molecular parts and devices standardized compatible defined interfaces robust reproducible behavior well documented independent of host system Devices are small integrated genetic circuits Functional genetic circuits of regulated parts with defined behavior/ properties (see parts) The difference parts will be public domain, wheras devices will start to be patented intensive and frequently Systems functionally integrated genetic circuit systems composed of parts and devices extended compatible crosstalking regulator parts/ devices networks with defined properties net of networks (e.g. regulatory and catalyst, metabolic) networks with defined properties Source : Drew Endy (2005) Foundations for engineering biology, Nature Review, 438: SB1 - Parts, Devices and Systems Standardisation Decoupling (Design & DNA-Synthesis) Abstraction (circuitry design models, simulation, improvement) Evolution Definition of Synthetic Biology Activities

SYNBIOLOGY Brussels, 30 May 2006 Synthetic Biology Aspects of Scope Only in vivo SB ? -> in vitro SB is accepted to be SB Self organizing molecular systems (DNA; RNA; Proteis, Sugars) Biomineralisation (Silicon, Magnetite, Hydroxylapatite) application of biomolecules in vitro (Polyproteins, Biomimetics) Only regulation in vivo = SB ? Clearly not – there is a clear focus on materials and biobased replicative production Only SB1 = SB ? with few exemptions the applications were at the transition point to SB1 and not hard core SB1 - adressed at the SB2.0 Conference Definition of Synthetic Biology Activities Conclusions : Answers to Questions Raised during Synbiology Project

SYNBIOLOGY Brussels, 30 May 2006 Definition of Synthetic Biology Activities Examples for Synthetic Biology - Design Files : (1) SB-design.pdf (2) omnibus.uni-freiburg.de.pdf by Andrey Kuznetsov