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Synthetic Biology and Industrial Biotechnology

Jens NielsenSystems and Synthetic Biology

ChalmersGothenburg, Sweden

Volume of Product

Valu

e of

Pro

duct

Pharmaceuticals

Fine Chemicals

Food Ingredients

Bulk Chemicals

Product value vs. volume

AntibioticsChiral building blocksEnzymes

VitaminsAntioxidantsFlavours

EthanolSolventsFeed additives (amino acids)Polymer building blocks

Over the whole range of products it is relevant to develop efficient cell factories for industrial production

Recombinant proteinsStatins and other natural products

Biotech Products

2

Chemical sales(100%=€1.383 billion)

Biotech sales(100%=€48 billion)

Between 2007 and 2012 chemical sales is expected to grow about 25% (to €1.748 billion) whereas biotech sales is expected to grow by more than 180% (to €135 billion)

Festel (2010) Ind. Biotech. 6:88-94

The Chemical Market

3

Enzymes

Polylactate

Sorona

Cephalexin

Vitamin B2

Move towards a biobased economy

Many success stories already implemented

Many novel processes are in the development phase

Time

White Biotechnology

Bio-feedstocks• Replacement of fossil fuel by sugars and starch

Bio-processes• Production of chemicalsusing bioprocesses, e.g. vitamins

Bio-products• polymers• enzymes• food ingredients

Today

Marked

Thepotential

Industrial Biotechnology

4

Pre‐treatment

Fermen‐tation

Purifi‐cation

Formu‐lation

RawMaterial

Chemicals&

Fuels

The research intensive partDesire to develop plug and play 

solutions, i.e. common cell factory platforms for many 

products

The Value Chain in Industrial Biotechnology

Biobutanol

2. Generationbioethanol

There is a trend towards partnerships – sharing competences, risks, and capital investments5

Yeast is a widely used cell factoryEthanolBaker’s yeastWine & BeerResveratrolInsulin precursorsVaccines (HPV, Hepatatis)

Many ongoing attempts to develop novel cell factoriesProduction of fuels (butanol, biodiesel), commodity chemicals (malate, succinate, 3-OH propionic acid), fine chemicals (isoprenoids), food ingredients (PUFAs) and protein drugs

Platform Cell Factories

6

Metabolic Engineering

The enabling technology that will allow for design of novel cell factories that can be constructed through the use of genetic engineering

The genomics revolution has resulted in a technology pushMetabolic Engineering:• bioanalytics• genomics• quantitative physiology

Xylitol

Phosphate Glu NAD

Xylitol

Phosphate Glu NADPhosphate Glu NAD

Enabling Technologies

7

Industrial Systems Biology

B&B (2010) 105:439-4608

+

+

Components and their abundance

Interactions and information flow

SystemMecha

nical 

system

Biological  

system

Systems Biology

9FEMS Yeast Research (2008) 8:122-131

Ana Paula Oliveira, PhD thesis (2008) DTU

Can we expand in silico design and analysis of cell factories?

Yeast Platform for Succinate ProductionModel guided ME strategy

SerineGlycine Biomass Demand Succinate Biomass 

Coupled

Reference (CEN.PK113‐5D) 

Mutant 8D(Δsdh3 Δser3Δser33)

+ 500 mg/L glycine

Genetic engineering

Specific Growth Rate (1/h)

Maximum Titer (g/L)

Maximum Yield (g/g‐biomass)

Maximum Yield (g/g‐glucose)

REF 0.33 0.03 0.01 0.008D 0.22 0.40 0.14 0.02

0

0.1

0.2

0.3

0.4

0.5

Proof of Concept

10

Evolved 8D(Δsdh3 Δser3 Δser33)

Mutant 8D(Δsdh3 Δser3Δser33) 500 375 250 125 25

+ mg/L glycine supplemented, Directed Evolution

0

Select for Faster Growth

0.09 0.100.13

0.10

0.39

0.69

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

YXSuc[g‐suc/g‐DCW]

500 mg/L375 mg/L250 mg/L125 mg/L25 mg/L0 mg/L

Glycine Supplemented

SF1 SF2 SF3

Growth Rate 0.03 0.08 0.14Yield 0.69 0.27 0.27

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

YXSuc[g‐suc/g‐DCW]

Growth Rate [1/h]

Growth Rate

Yield

Error bars represent ± 99% CI (n=3)

Yeast Platform for Succinate ProductionThrough evolution a glycine-prototroph could be evolved

11

Substrate A B

C D E

Product

By-product

X Y

Substrate A B

C D E

Product

By-product

X Y

Substrate A B ProductX Y

Metabolic Engineering

Synthetic Biology

Metabolic Engineering vs.Synthetic Biology

12

Glucose

Sucrose

Xylose

Arabinose

Fine chemicals

Biofuels

Commodity chemicals

Protein drugs

Volume

Value

Butanol

Biodiesel

3-HPA

Succinic acid

Sesquiterpenes

Antibiotics

Human insulin

S. cerevisiae

Yeast as a Platform OrganismAn extensive technology base for wider use of yeast as platform cell factory has been established in our group

Metabolic Engineering

Systems Biology

13

Acknowledgements Funding

YSBN

14