Synthetic biology Arnold Driessen Molecular Microbiology, - - PowerPoint PPT Presentation

Synthetic biology

Arnold Driessen Molecular Microbiology, University of Groningen a.j.m.driessen@rug.nl

Groningen Biomolecular Sciences and Biotechnology Institute

Centre of Synthetic Biology, Groningen

Definition Synthetic Biology

Design and construction of new biological parts, devices and systems, and the re-design of excising natural biological systems for useful purposes

Synthetic Biology

‘ Let me now comment on the question "what next". Up to now we are working

• n the descriptive phase of molecular biology. ... But the real challenge will

start when we enter the synthetic biology phase of research in our field. We will then devise new control elements and add these new modules to the existing genomes or build up wholly new genomes. This would be a field with the unlimited expansion potential and hardly any limitations to building "new better control circuits" and ..... finally other "synthetic" organisms, like a "new better mouse". ... I am not concerned that we will run out of exciting and novel ideas, ... in the synthetic biology, in general (Szybalski, 1974) ,

Areas of research

• Understanding of how does life

work (origin of life) (protocells, selfreplication, re-build a minimal cell from parts … … )

• Use to benefit society (bio-

technology, certain areas of biological and biomedical engineering) Creation of new biological systems with a focus on:

Key enabling technologies

• Genetic engineering:
• Increased speed/ lower costs of

DNA sequencing and synthesis

• Use modular principles – building blocks,

standardization (Biobricks)

• Use to:
• Build new biological systems
• Rewriting, re-building of natural systems

De nov o DNA synthesis

Tim eline: 2000: 9.6 kbp Hepatitis C virus genome (60-to 80-mers) 2002: 7.7 kbp Polivirus genome 2003: 5.4 kbp bacteriophage Phi X 174 (in 2 weeks) 2006: Synthetic genome of Mycoplasm a genitalium (laboratorium ) 2010: Introduction of synthetic genome of M. m ycoides into M. capricolum (acclaimed synthetic cell) 2012: Church’s Book (5.3 Mb) encoded in DNA

Synthetic biology requires rapid & reliable & cheap methods for de novo DNA synthesis and assembly of DNA fragments

Greg Venter

Biobricks

Standard of interchangable genetic parts

• Parts – a finite DNA sequence with a specific function

(promoters, coding genes, terminators, ribosome binding sites)

• Devices – multiple parts with a higher level of

functioning (translational units, riboregulators, reporters, inverters, sensors etc)

• System s – multiple devices hooked up together

by Drew Andy

Im pact of synthetic biology on research

• Synthetic genomes – rewire cells
• Synthetic operons – re-arrange gene order / introduce

new genes / ease transfer to heterologous hosts

• Refactoring: codon racemise to remove regulatory

sequences; re-order genes in operon; screen

• Design novel enzymes that specify new catalytic

activities or other functionalities

• Biosensors – bacteria that sense pollutants,

cancer, artificial nose, etc (critters-on-a-chip)

• Hydrogen from water with cyanobacteria

Exam ples of synthetic biology Designer ‘bugs,

• Biofuels and base chemicals biosynthesis from renewable

feedstocks

• Biosynthesis of medicines (f.i. artemisinin)
• Nitrogen fixation by non-fixing plants
• Expand sugar crops by plants
• Increase seasonable tolerance of plants/ trees

• Biosynthetic route towards the

fermentative production of caprolactam: building block nylon 6

• Rewiring the Bacterial ester-based phospholipid bio-

synthetic pathway of Escherichia coli for Archaeal ether- lipids (create an archaeabacterium ) (evolutionary studies)

Ether lipids Ester lipids

What are we doing?

Protocells

Reproduce protein, lipid, DNA and RNA synthesis and division from a synthetic genome encapsulated in a liposome

• r droplet

Bottom-up approach to explore path between living and nonliving systems (Origin of Life / Evolution)

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Sy nthetic biology to benefit society