Expanding the chemistry of life using synthetic biology

Jessica Perez Monday, May 5th, 2014

Life is diverse and complex

Biological systems are a powerful, untapped technology

Engineering biology will transform food, energy, chemicals, materials, and medicine

Synthetic biology = Biology + Engineering

Synthetic Biology is:

an emerging field dedicated to designing biological systems to have new functions

“Programming” cells to have new functions

Jeffrey Tabor et al. Cell, Volume 137, Issue 7, 1272-1281, 26 June 2009

Synthetic Biology is adding new functionality: Bacteria can see light!

500 million people each year are infected by malaria

Artemisinin is harvested from plantations

Producing Artemisinin in a microbe lowers cost from $2.40 per dose to $0.25 per dose.

Dae-Kyun Ro et al. Nature 440, 940-943 Apr 2006

Synthetic Biology is addressing global health: combating malaria

Synthetic Biology is synthesizing small molecules: materials and biofuels

Target Institutions Time to market

1,3, propanediol 15 years (1992-2007)

artemisinin 13 years(2000-2013)

farnesene 4 years (2008-2012)

isobutanol X years??(2005-201X)

- Data from Zach Serber, Amyris

My research focus:Harnessing biology’s biosynthetic potential

Biological systems can synthesize proteins very quickly and efficiently: ~15 amino acids/sec/ribosome and 10-4 error rate

Can we use bacteria to synthesize proteins made of novel building blocks (amino acids)?

Can we produce new materials inside cells?

Central Dogma

Codon table are instructions for translating mRNA code into proteins

20 amino acids for building life

Structural biology

Fluorescent Redox-active and heavy metal containing

Photo-cross-linkable and unique reactivity

Biocatalysis

Therapeutics

Engineered organism requires novel amino acids

NH2 CO2HNH2 CO2H

HN

SO

N

O

NH2 CO2H

ONH2 O

H3C NH2 CO2H

OH

NH2

NH2 CO2H

OH

OH

NH2 CO2H

Br

NH2 CO2H

NH

HO

NH2 CO2H

O

NH2 CO2H

N3

NH2 CO2H

O

Expanded chemistry of life using novel amino acids

Biocontainment

Hijack codon table to encode a new amino acid

Novel amino acid

NH2 CO2H

O

Current challenges in engineering biology to have new functions

1)Incomplete knowledge of how life works2)Unwieldy complexity of cells, unforeseen interference3)Living cells have their own growth and adaptation objectives that are usually diametrically opposed to the overproduction of a single biomolecular product

17

Research goals:• Expand chemistry of life by making proteins that contain

novel amino acids

How am I doing it?• Hijacking stop codons to encode an additional amino acid

Why is this important?• Push the limits of what is possible with biology• Synthesize new materials and medicines

Summary

How non-scientists interface with synthetic biology outside the classroom?

How non-scientists interface with synthetic biology outside the classroom?

Case study: replicating synthetic biology in the classroom

Computer Aided Design (CAD) tool for synthetic biology

Allows you to visually construct and then simulate/analyze a biological network

HS-ETS1-4: Use a computer simulation for modeling of real-world problems

Case study: replicating synthetic biology in the classroom

Questions/Discussion

How I became interested in science

Summer engineering programs

Interactive

Problem Solving

Freedom to explore

High expectations