presented by leo seak chi u(team leader) ricky chan wai ... -...

Presented by

Leo Seak Chi U(Team leader)

Ricky Chan Wai Lun(Wet lab team)

Joe Ho Cho Tai(Modeling team)

Elaine Chiu Yee Ting(Human Practice team)

1

AzotoBacter vinelandii Cluster-transformable

& Deoxygenated protein Expression system

(ABCDE system)

2

ABCDE System

Introduction

3

Problem: Energy and Environment

𝐶𝑂2 𝐶𝐻4nitrogenase

Hydrogenase III (H2ase) ADP Nitrogenase(N2ase)

H2

H+

Ferredoxin reduced

Ferredoxin oxidized

ATP

Fe protein oxidized

Fe protein reduced

MoFe protein reduced

MoFe protein oxidized

CH4

CO2

Supported by Guiral et.al.,2005 5

Mechanism

Byproduct of nitrogenase

Needed for CH4

production𝐶𝑂2

Problem of Introducing Nitrogenase

•Oxygen sensitive (degenerated by oxygen)

•Anaerobic condition is needed

6Zhi-Yong Yang et al., PNAS 2012

2013 Bielefeld-Germany iGEM team 2013 Copenhagen iGEM team

7

Previous iGEM Team

AzotoBacter vinelandii Cluster-transformable &

Deoxygenated protein Expression system

(ABCDE system)

8

Solution: ABCDE System

Why Azotobacter vinelandii

Azotobacter vinelandii (strain DJ)

June 2014

• Intracellular anaerobic environment

• Stable genome integration

• Safety level: group 1 bacteria

• nifH promoter

(ammonium-repressible)

Sabra, W., Zeng, A. P., Lünsdorf, H., & Deckwer, W. D. (2000)Applied and environmental microbiology, 66(9), 4037-4044.

AzotoBacter vinelandii Cluster-transformable &

Deoxygenated protein Expression system (ABCDE system)

10

Biobricks and CharacterizationAmmonium-Repressible T7 Protein Expression System

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ABCDE: Basic Parts

Parts Description

BBa_K1314000 Ammonia repressible nifH promoter

BBa_K1314002 150bp random sequence (sequence for homology)

BBa_K1314003 part of mRFP(sequence for homology)

BBa_K1314012 nif K homologous sequence

Status

Submitted and accepted

Submitted and accepted

Not submitted

Not submitted

12

Characterization of BBa_K1314000: nifH Promoter

transcriptional regulation mechanism of

nifHDK operon in A. vinelandii

Hamilton, T. L., Ludwig, M., Dixon, R., Boyd, E. S., Dos Santos, P. C., Setubal, J. C., ... &

Peters, J. W. (2011). Transcriptional profiling of nitrogen fixation in Azotobacter vinelandii.

Journal of bacteriology, 193(17), 4477-4486 13

Characterization of BBa_K1314000: nifH Promoter

300bp

200bp

100bp

Gel photo of EcoRI PstI double digest

check of BBa_K1314000

nifH regulated RFP expression(left) versus

constitutive RFP expression(right) in DH5α

14

nifH promoter

Parts Description

BBa_K1314001 nifH promoter with mRFP reporter

BBa_K1314004 Ptet mRFP with random sequence

BBa_K1314005 Ammonia- repressible T7 RNA polymerase generator(strong)

BBa_K1314006 Ammonia- repressible T7 RNA polymerase generator(weak)

BBa_K1314007 Ammonia- repressible T7 RNA polymerase generator(strong) with ptet mRFP reporter

BBa_K1314008 Ammonia- repressible T7 RNA polymerase generator(weak) with ptet mRFP reporter

BBa_K1314009 Amilcp reporter with part of rfp

BBa_K1314010 T7 promoter with random sequence

ABCDE: Composite Parts

Status

Submitted and accepted

Submitted and accepted

Submitted and accepted

Submitted and accepted

Submitted and accepted

Submitted and accepted

Submitted and accepted

Submitted and accepted15

ABCDE: Composite Parts

Composite PartsParts Description Status

BBa_K1314010 T7 promoter with random sequence Submitted and accepted

BBa_K1314011 T7 promoter amilcp reporter with homologous sequence

Submitted and accepted

BBa_K1314013 Ammonia- repressible T7 RNA polymerase generator(strong) with ptet mRFP reporter( site-specific integration version)

Submitted and accepted

BBa_K1314014 Ammonia- repressible T7 RNA polymerase generator(weak) with ptet mRFP reporter( site-specific integration version)

Submitted and accepted

16

BBa_K1314013/14: T7 RNA Polymerase into A.vinelandii

Reciprocal recombination in A.vinelandii

Patricia Dos Santos, Molecular Biology and Genetic Engineering in Nitrogen Fixation17

Foreign DNA as a

Vector

Wild type A.vinelandii

genome

Mutated A.vinelandii

genome

Circular DNA of BBa_K1314013 with Ampicillin resistance gene 18

BBa_K1314013/14: Making the Vector

Linearized DNA of BBa_K1314013 with Ampicillin

resistance gene by cutting XhoISingle

Digestion

using XhoI

BBa_K1314013/14: Modifying the A. vinelandii genome

genomic sequence of nifHDK operon in wild type A. vinelandii

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Linearized DNA of BBa_K1314013 with

Ampicillin resistance gene by cutting XhoI

Hamilton, T. L., Ludwig, M., Dixon, R., Boyd, E. S., Dos

Santos, P. C., Setubal, J. C., ... & Peters, J. W. (2011).

Transcriptional profiling of nitrogen fixation in Azotobacter

vinelandii. Journal of bacteriology, 193(17), 4477-4486.

Characterization of BBa_K1314013/14

5000bp

Gel electrophoresis of EcoRI

PstI double digestion check of

BBa_K1314013/14

20

Characterization of BBa_K1314013/14

Ammonium replete condition

BBa_K1314014(no growth) BBa_K1314013

(no growth)

BBa_K1314001(RFP

expression but poor

growth)

Wildtype

A.vinelandii

Normal nitrogenase

expression

High RFP expression

High RFP expression

well grown but no red RFP

expression

21Ammonium depleted condition

Introduce gene under T7 promoter into A.vinelandii

Strain Colour change from red to blue

Part of genome sequence of A.vinelandii with BBa_K1314013 integrated

Sequence of DNA Vector BBa_K1314011 22

Characterization of BBa_K1314011

BL21 BFP expression of K1314011(right,10mM IPTG added) and negative control(left, no IPTG added) 23

BBa_K1314015: Vector for insertion of desired protein for T7 expression

Plasmid Backbone

3000bp

2000bp

EcoRI PstI double digest check gel photo

Status

Submitted (Kanamycin resistance)

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~2500bp insert

Description

Part:BBa_K1314015 Homology integration toolkit

Genome Integration Has Never Been Easier

Plasmid map of

BBa_K1314015

Quick method for making desired vector

25

Restriction + Ligation = Vector for integration

Modeling

26

ABCDE (Protein Expression)-solve the contradiction

ABCDE system (Methane Energy)- rate & efficiency

Problem in protein expression

27

ɑ-RNA

polymerase

nifH

promoter T7polymeraseT7 promoter Target

proteins

repressed by ammonia

needs ammonia

ABCDE (Protein Expression)-solve the contradiction

Solution: Separate into two stages

Stage one

Producing T7

polymerase

28

Stage two

Producing target

proteins

𝑁𝐻3𝑁𝐻3

𝑁𝐻3

𝑁𝐻3

𝑁𝐻3

𝑁𝐻3

ABCDE (Protein Expression)-solve the contradiction

We have the following equation for the rate of change of [N]:

𝑑[𝑁]

𝑑𝑡=-A

𝑑[𝑇7]

𝑑𝑡-B

𝑑[𝑇𝑃]

𝑑𝑡−

𝐶[𝑁]

𝐷+[𝑁]

• A: nitrogen needed to expression one T7 polymerase;

• B: nitrogen needed to expression one target protein;

• C: maximum speed of nitrogen consumption of unmodified bacteria;

• D: concentration needed for the rate of nitrogen consumption equals to half of maximum speed.

29

ABCDE (Protein Expression)-solve the contradiction

Stage one: producing T7 polymerase

Reference:Michaelis, L.; Menten, M.L. (1913). "Die Kinetik der Invertinwirkung". Biochem Z 49: 333–369

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𝑁𝐻3

𝑑[𝑇7]

𝑑𝑡= 𝐸[𝑁]𝑒−𝐹[𝑁]

ABCDE (Protein Expression)-solve the contradiction

Stage one: producing T7 polymerase

Stage two: producing target protein

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ABCDE (Protein Expression)-solve the contradiction

𝑁𝐻3𝑁𝐻3𝑁𝐻3𝑁𝐻3

𝑁𝐻3

𝑑[𝑇𝑃]

𝑑𝑡= 𝑉𝑚𝑎𝑥( 𝑇7 )

0

1

2

3

4

5

6

7

8

0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2

Co

nce

ntr

atio

n

time

Analysis: rate equations for CH4 production

Reference: 1.G. P. Moss(1981)” Symbolism and Terminology in Enzyme Kinetics"http://www.chem.qmul.ac.uk/iubmb/kinetics/2. Michael W.W. Adams(1990)” The structure and mechanism of iron-hydrogenases “Biophysica Acta, 1020 (1990) 115-145

𝑑[𝐶𝐻4]

𝑑𝑡= 𝐾1 𝐻+ [𝐶𝑂2]=𝐾1𝐾2 𝐻+ = 𝐾 𝐻+

𝑑[𝐻+]

𝑑𝑡= 𝐾3[𝐻2][oxidized ferredoxin]-k’’

𝑑[𝐶𝐻4]

𝑑𝑡

=𝐾3𝐾4 𝐶𝐻4 [oxidized ferredoxin] -k’’𝑑[𝐶𝐻4]

𝑑𝑡

=𝐾3𝐾4𝐾5 𝐶𝐻4 −k’’𝑑[𝐶𝐻4]

𝑑𝑡

=K’ 𝐶𝐻4 -k’’𝑑[𝐶𝐻4]

𝑑𝑡

𝐾1 = rate constant; 𝐾2 = 𝐶𝑂2𝑛; K = K1K2;

𝐾3= rate constant; [𝐻+]=𝐾4 𝐶𝐻4 ; [oxidized ferredoxin]=𝐾5; K’ = K3K4K5. K’’=𝐾4+8

ABCDE system (Methane Energy)- rate & efficiency

33

ABCDE system (Methane Energy)- rate & efficiency

[𝐶𝐻4] = 𝑐1exp 𝑐2𝑡 + 𝑐3exp(𝑐4𝑡)

Result: Energy Efficiency

34

ABCDE system (Methane Energy)- rate & efficiency

Energy Output (𝐸𝑜𝑢𝑡𝑝𝑢𝑡):

𝐸𝑐: combustion energy of CH4

Energy input (𝐸𝑖𝑛𝑝𝑢𝑡):

𝐸1: ATP energy for enzyme activity – producing 𝐶𝐻4

𝐸2: ATP energy for producing 𝐻2

𝐸𝑚: Metabolic energy

𝐸𝐸: Environmental consumption

Energy Efficiency = = = 5.36 % 𝐸𝑜𝑢𝑡𝑝𝑢𝑡

𝐸𝑖𝑛𝑝𝑢𝑡

𝐸𝑐

𝐸1+𝐸2 + 𝐸𝑚+𝐸𝐸

16 ATP2 ATP

𝐶𝑂2

𝐶𝐻4+2𝐻2𝑂𝐻2

~ 2 times of photosynthesis in crop plants(2%)Reference: Govindjee, What is photosynthesis?

Human Practice and Safety

35

Collaboration

Cooperate with CityU_HK, Hong_Kong_HKUST, Berlin

-Cloning

-Modelling

-Ideas exchanging

Material Exchanging Platform

36

Collaboration

37

BBa_K1472614(3384bp)

Invitrogen 1kb plus ladder

3000bp4000bp

~3600bp

Colony PCR with biobricksequencing primer

What do people think about our project

38

Do you think this project is beneficial to the human being?

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Yes No No opinion

HS (102) UG (408) PG (61) Other* (32)

%

HS: High SchoolUG: Under-graduatePG: Post-graduateOther: Any responders other than these three

What is the most attractive highlight to you in this project?

40

%

0102030405060708090

Environmentalfriendly

Bacterial-based Creativity Practical None Other

HS (102) UG (408) PG (61) Other* (32)HS: High SchoolUG: Under-graduatePG: Post-graduateOther: Any responders other than these three

(Interesting)

In which aspect do you think this project is helpful and therefore worth-conducting?

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0

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Energy Crisis Global Warming None Other

HS (102) UG (408) PG (61) Other* (32)

%

HS: High SchoolUG: Under-graduatePG: Post-graduateOther: Any responders other than these three

What will be your main concern of this project?

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0

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Safety Efficiency Cost Other Not at all

HS (102) UG (408) PG (61) Other* (32)

%

HS: High SchoolUG: Under-graduatePG: Post-graduateOther: Any responders other than these three

Safety

• Lab safety training course

• Proper handling of biological and chemical materials

• Proper disposal of biological and chemical waste

• Personal protective equipment

• Only organisms in risk group 1 are used

• Negative pressure laboratory

• Communication with supervisors regularly

43

Workshops

Laboratory Demonstration

-Introduce simple lab tools

-Some simple cloning techniques

-*Focus on increasing safety awareness

44

Have you heard of International GeneticalEngineered Machine(iGEM) or Synthetic Biology?

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0

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Neither iGEM only Synthetic Biology Only Both

HS (102) UG (408) PG (61) Other* (32)

%

HS: High SchoolUG: Under-graduatePG: Post-graduateOther: Any responders other than these three

Do you think there are enough ways for public to reach Synthetic Biology?

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0

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Yes No Not sure

HS (102) UG (408) PG (61) Other* (32)

%

HS: High SchoolUG: Under-graduatePG: Post-graduateOther: Any responders other than these three

In your point of view, which is the most effective way to raise public awareness towards synthetic biology?

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0

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Leaflet Poster Workshop Other

HS (102) UG (408) PG (61) Other* (32)

%

HS: High SchoolUG: Under-graduatePG: Post-graduateOther: Any responders other than these three

(Banner)

Outreach

University

Art Fair

Energy Day Collaboration

High School

WorkshopsCUHK

Orientation Day

Industry

Energy Day

International

Poster Collaboration

48

Outreach

University

Art Fair

Energy Day Collaboration

High School

WorkshopsCUHK

Orientation Day

Industry

Energy Day

International

Poster Collaboration

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Energy day

Poster presentation

-Promote our project

-Receive professional comments

There are industries interested in our project

50

Outreach

University

Art Fair

Energy Day Collaboration

High School

WorkshopsCUHK

Orientation Day

Industry

Energy Day

International

Poster Collaboration

51

Art fair, CUHK Orientation Day, Workshops & Poster Exhibition

Poster Exhibition

-Promotion of iGEM

and Synthetic Biology

-Promotion of Project

-Recruitment of next year iGEM team

Leaflet Distribution

52

Would you join activities related to Synthetic Biology (say, iGEM), if you were given a chance?

53

0

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Yes No

HS (102) UG (408) PG (61) Other* (32)

%

HS: High SchoolUG: Under-graduatePG: Post-graduateOther: Any responders other than these three

More!

• First intracellular anaerobic protein expression system

• Introduce Azotobacter vinelandii to iGEM

• Try to make registry biobricks usable in the chassis

• Carbon fixation with the bacteria

54

Bronze Completed Judging form

Wiki

Sliver Characterize Bba_K1314000,

Bba_K1314001, Bba_K1314011,

Bba_K1314013, Bba_K1314014

16 biobricks submitted and accepted

Gold Improved and characterized E1010 and

K529009

Helped CityU to construct a functional

biobrick with some characterization

Analyzed difference between postgraduate,

high school and college student

Linking all the iGEM together by material

changing platform

Medal?

• Electricity production

• Magnetosome production

• Carbon fixation

• Nitrogen fixation

• ……More to be discovered

55

ABCDE is just a beginning!

And Further More…

Acknowledgement

Our Sponsors:

56

Special Acknowledgement:• Professor CHAN King Ming (Associate Professor, School of Life Sciences)

• Professor CHAN Ting Fung (Associate Professor, School of Life Sciences)

Thank you both for giving advices and guidance throughout the project.

• Professor Pun To, Douglas YUNG (Assistant Professor)

• Mr. Nelson So (Technician - BME Teaching Lab)

Thank you both for providing place and support to the project.

• Professor Jimmy C. M. YU (Professor of Chemistry)

Thank you for giving suggestions of the project.

• Thank you Professor Dennis R. Dean and Ms. Valerie Cash for giving DNA and strain dj of Azotobactor Vinlandii.

• Thank you Dr. Marianne Guira for giving frozen pellet of Aquifex Aeolicus.

• Thank you Dr. Zhu Yuan (Dept. of Biology and Chemistry, City University of Hong Kong) for modelling work.

57

Q&A

Thank You!

58