First Seminar on Synthetic Biology for Biotechnology Decision Makers

I I C A H E A D Q U A R T E R S , C O S T A R I C A 1 6 T H A N D 1 7 T H M A R C H , 2 0 1 6

FIRST SEMINAR ON SYNTHETIC BIOLOGY FOR BIOTECHNOLOGY DECISION MAKERS

SYNBIO INDUSTRIAL APPLICATIONS NATALIA VERZA

STATE UNIVERSITY OF CAMPINAS, BRAZIL

WHAT IS SYNTHETIC BIOLOGY?

• Synthetic biology is the engineering of

biology: the synthesis of complex, biologically

based (or inspired) systems, which display functions

that do not exist in nature

• may be applied at all levels of the hierarchy of

biological structures – from individual molecules

to whole cells, tissues and organisms

• enable the design of ‘biological systems’ in a

rational, standardized and systematic way

Source: Synthetic Biology: Applying Engineering to Biology. Molecular Systems Biology (2007) 3:158


Synthetic biology aims to use modular, well-

characterized biological parts to predictably

construct novel genetic devices and complex cell-

based systems following engineering principles (Drew

Endy, 2005)

Synthetic Biology Open Language (SBOL)


• Synthetic biology aims to make biology

easier to engineer. Synthetic biology is the

convergence of advances in chemistry,

biology, computer science, and

engineering that enables us to go from idea

to product faster, cheaper, and with greater

precision than ever before

Source: SYNTHETIC BIOLOGY ENGINEERING RESEARCH CENTER (SynBerc, NSF, USA)

SYNBIO X GENETIC ENGINEERING WHAT ARE THE DIFFERENCES?

Species of interest: maize calli (Zea mays)

Goal: improve crop tolerance to drought stress

Target gene Co-chaperonin GroES

Donor species: Clostridium acetobutylicum (anaerobic

bacterium)

Codon usage divergences




bacterium)

Anaerobic chamber

Gene amplification and isolation

Construction of DNA expression

cassete

2X35S BlpR

TVSP TEV NptR

UbiPro

T35S

Act1F

Zea mays calli

transformation

Classic genetic engineering Special equipment and new protocols

Methods development and validation


Construction of DNA cassette

2X35S BlpR

TVSP TEV NptR

UbiPro

T35S

Act1F

Zea mays calli transformation

Synthetic biology

Design and order optimized, synthetic gene



bacterium)


“Synthetic biology is not an entirely new science. Rather,

aspects of it are an outgrowth of what plant and animal

breeders have been doing for thousands of years and

genetic engineers have been doing for decades—mixing

and matching genetic material with the goal of “creating”

novel plants and animals with desirable traits. What

differentiates synthetic biology from genetic engineering is its

goal of designing new genetic systems and organisms using

standardized parts from the “ground up.”

The Science and Applications of Synthetic and Systems Biology: Workshop Summary

SYNBIO – STATE OF SCIENCE

• In 2006, Dr. Jay Keasling, director of the Berkeley Center for Synthetic

Biology and CEO of the Joint BioEnergy Institute, and three post-

doctoral researchers discovered and re-engineered a yeast

containing bacterial and wormwood genes into a chemical factory to

produce a precursor to artemisinin for use as an inexpensive anti-

malarial drug. The breakthrough originated the Biotech company

Amyris (CA, USA)

Oil-producing yeast under the microscope


Amyris multi-products platform


Nature Reviews Microbiology 12, 355–367 (2014)

doi:10.1038/nrmicro3240

Iterative cycle of testing

and learning that spins

faster with help of

synbio tools


• In May 2010, researchers at the JCVI published the

first functional, self-replicating bacterium whose

entire nuclear genome had been synthesized

artificially in the laboratory, albeit using a naturally

occurring genome sequence as a template

(Gibson et al., 2010).


• The CRISPR revolution – editing genomes in vivo. The CRISPR/Cas9

technique, derived from a microbial defense system, has enormous

potential application, including altering the germline of humans,

animals and other organisms, and modifying the genes of food crops.

Genome editing was selected by Nature Methods as the 2011 Method

of the Year, and CRISPR-Cas system was selected by Science

Magazine as 2015 Breakthrough of the Year

Emmanuelle Charpentier Max-Plank Institute, Germany

Jennifer Doudna

University of California, Berkeley


Source: http://www.livemint.com; UC Berkeley

In vivo

genome

editing

INDUSTRIAL SYNBIO MAIN DEVELOPERS

Leading consumer biotech companies building novel biological systems

for bioproducts, biofuels, and the healthcare sector

INDUSTRIAL SYNBIO MAIN DEVELOPERS

Genome-editing technology companies

Companies developing efficient methods to create engineered microbes

to order

Companies that sell synthetic DNA (oligonucleotides, genes, genomes,

genome editing tools)

INDUSTRIAL SYNBIO: POTENTIAL FOR COMMERCIAL PRODUCTS

• BioIsoprene™ - fermentation – based synthetic rubber

made by engineered microbes expressing plant

genes. Synthetic biology has enabled the construction

of a gene that encodes the same amino acid

sequence as the plant enzyme but that is optimized

for expression in the engineered microorganism of

choice (DuPont and The Goodyear Tire & Rubber

Company)

• Cephalexin, a synthetic antibiotic. Starting with a

penicillin-producing microbial strain, DSM introduced

and optimized two enzyme-encoding genes for a

one-step direct fermentation of adipoyl-7-ADCA,

which is converted into Cephalexin via two enzymatic

steps. (DSM)


• Sitagliptin (dipeptidyl peptidase-4 inhibitor

to treat for type II diabetes). Codexis and

Merck collaborated to develop a novel,

environmentally benign alternative

manufacturing route. Using synthetic

biology and its directed evolution

technologies, Codexis discovered and

developed a transaminase capable of

enabling the new biocatalytic route,

which is currently in scale-up towards

commercial manufacture


• BioAcrylic - fermentation – based acrylic

from sugar feedstock — OPX Biotech

partnering with the Dow Chemical

Company(OPX – Cargill and Dow

Chemical)

• BiofeneTM –the Amyris-brand farnesene, a

hydrocarbon building block that can

replace petrochemicals in a wide variety

of products in the cosmetics, flavors and

fragrances, consumer product, polymers,

lubricants and fuel markets (Amyris)

BIO-FUELS PIPELINE PRODUCTS (BY ORGANIZATIONS)

Source: Presidential Commission for the Study of Bioethical Issues (Transparency Market Research Report)


• BDO - 1,4-butanediol, a solvent and in the

manufacture of some types of plastics, elastic

fibers and polyurethanes. Genomatica’s GENO

BDO™ process has been licensed by BASF and

by Novamont; BASF has announced its first

commercial production; over nine million

pounds have been produced to date

• GM Mosquitos – Oxitec’s (Intrexon)solution for

controlling harmful insect populations through

the production of ‘sterile’, self-limiting insects

whose offspring do not survive. Intrexon will

further use Oxitec’s technology to combat

diseases and agricultural pests worldwide


• Plants as bio-factories - Scientists at the

John Innes Centre in the UK have

developed technology for the rapid

expression of proteins in plants. Medicago

Inc. licensed the technology to produce

10M doses of H1N1 swine flu VLP Vaccine in

just a month, outperforming the traditional

method which takes 9-12 months

TECHNOLOGIES AND APPLICATIONS

SynBio enabling technologies

• Enabling Technologies

• Bioinformatics

• Gene Synthesis

• Genome Engineering

• Microfluidics

• Measurement and Modeling

• Nanotechnology

• Cloning and Sequencing

• Site-saturation Mutagenesis

• Enabled Technologies

• Pathway Engineering

• Next-generation Sequencing

SynBio applications

• Environmental Application

• Bioremediation

• Whole-cell Biosensors

• Medical Application

• Artificial Tissue and Tissue

Regeneration

• Drug Discovery and Therapeutics

• Pharmaceuticals

• Industrial Application

• Biofuels and Renewable Energy

• Biomaterials and Green

Chemicals

• Industrial Enzymes

SYNBIO MARKET SEGMENTATION

Source: Transparency Market Research Report, 2013-2019

2009 – 2015 INVESTMENT IN SYNBIO COMPANIES

Source: SynBio Beta

2009 – 2015 SYNBIO COMPANIES FUNDED

Source: SynBio Beta

2015 INVESTMENT IN SYNBIO COMPANIES

Source: SynBio Beta

SYNBIO REGULATION IS NEEDED

• In our view, synthetic biology is an extension of the continuum of genetic science that has been used safely for more than 40 years by the biotechnology industry in the development of commercial products. Examples of synthetic biology use by biotechnology companies illustrate the potential to substantially reduce research and development time and to increase speed to market (Erickson et al. Science (2011)Vol 333, Issue 6047:1254-1256)

• NIH has assessed its “Guidelines for Research Involving Recombinant DNA” with regard to synthetic biology and found that the distinction between recombinant and synthetic techniques is immaterial in discerning the need for biosafety oversight. Rather it is the biological attributes of the final product that should be taken into account.

Natalia Verza

State University of Campinas

Structural Genomics Consortium [email protected]

[email protected]

Documents

First Seminar on Synthetic Biology for Biotechnology Decision Makers