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One-Step Construction of a Bioplastic Production Pathway in E. coli

We, the determined and motivated Duke University iGEM 2009 team of 6 undergraduate students and 3 graduate students, have developed a practical and powerful method to deliver on the promise of sustainable green synthetic biology!

Due to the high costs and inefficiency of the gene and pathway cloning process, we invented a new procedure which lowers costs and increases efficiency. This method, Circular Polymerase Extension Cloning (CPEC), saves time as well, since it does not involve ligation or restriction enzymes. See publication of our method here.

We have applied our method to the production of biologically derived plastics. The rising costs of the current method of producing biodegradable plastics in an environmentally sound manner has hindered its widespread use. However, we have discovered a more efficient pathway to produce these biodegradable plastics.

*We were also proud to help Team Valencia with their survey.

Abstract

A convenient ligation-free, sequence-independent one-step plasmid assembly and cloning method is developed [Quan J, Tian J (2009) Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways. PLoS ONE 4(7): e6441]. This strategy, Circular Polymerase Assembly Cloning (CPEC), relies solely on polymerase extension to assemble and clone multiple fragments into any vector. Using this method, we are able to quickly assemble a metabolic pathway consisting of multiple enzymes and regulatory elements for the production of a biocompatible as well as biodegradable plastic polymer in E. coli.

What is CPEC?

Circular Polymerase Extension Cloning (CPEC) is the development of a much simplified sequence-independent cloning technology based entirely on the polymerase extension mechanism. This method extends overlapping regions between the insert and vector fragments to form a complete circular plasmid. (Refer to Fig. 1a and 1b.) The basic principle of this strategy is that, after denaturation, both single-stranded vector and inserts overlap with each other by end sequences and extend by using the other as the primer in a typical PCR reaction. After complete circular plasmids with one nick in each strand are formed, the relaxed plasmids are transformed to competent cells and sealed as closed plasmids. CPEC strategy is not only suitable for the cloning of an individual gene but also for gene libraries, combinatorial libraries and multi-fragment plasmid assembling. With its simplicity, cost-effectiveness and high transformation efficiency, CPEC has become the most convenient, economical and accurate cloning method at the present day, especially for cloning applications with high complexity. {| style="background:transparent; margin:auto" |- || [[Image:CPEC.jpg|thumb|350px|Figure 1a. Biobrick spliced into vector using CPEC]] || [[Image:multicomponent.jpg|thumb|350px|Figure 1b. Multicomponent Biobrick system spliced into vector simulatenously using CPEC]] |}

What are the benefits?

The process of high-throughput cloning is bottle necked at the restriction and ligation stages. A combination of high costs, requirements for restriction site specific enzymes and general inefficiency of the process makes cloning on a large combinatorial gene library inviable. Circular Polymerase Extension Cloning (CPEC) addresses this issue by eliminating the need for restriction and ligation enzymes and thereby streamlining and condensing the procedure into the duration of 5 minutes.

One-Step Construction of a Bioplastic Production Pathway using CPEC

We applied CPEC in the construction of a multi-component pathways in a single reaction. The proposed multi-way cloning mechanism is shown in Figure 1b. First, we constructed the biobrick parts containing genes involved in this pathway. Then we used multi-way CPEC for construction of a metabolic pathway for synthesizing a biodegradable plastic, poly(3HB-co-4HB) in E. coli..

Biodegradable Plastic Synthesis Pathway in E. coli

Polyhydroxyalkanoic acids (PHA), naturally occurring storage polymers found in a variety of bacteria, have received increased attention for their potential use as bioplastics that are both biodegradable and reduce reliance on petroleum-based plastics. In particular, the copolymer poly(3-hyroxybutyrate-co-4-hydroxybutyrate), or poly(3HB-co-4HB), which combines the 3HB and 4HB polymers from different bacteria (Figure 2 shows the pathway), has elastic properties ideal for a wide range of thermoplastic applications. The high cost of PHA, however, is the biggest impediment to widespread use of bioplastics. Moreover, poly(3HB-co-4HB) pathways developed so far in E. coli have yielded undesirably low and unpredictable 4HB-to-3HB ratios.

Thus, this project aims to develop a more efficient biopathway for poly(3HB-co-4HB) while increasing the 4HB monomer composition predictably. It was hypothesized that optimizing codon permutations of the phaC gene would greatly increase affinity of PHA synthase to the 4HB monomer. To date, the phaCAB and cat2 operons have been cloned into pUC19 and PCR Blunt II-TOPO vectors for successful independent production of the 3HB and 4HB polymers (Figure 4). Ligation and transformation into E. coli as six different recombinant constructs will soon be completed and allow for engineering of the poly(3HB-co4HB) biopathway. Future directions would be to test the hypothesis to see if phaC can be manipulated to increase 4HB-to-3HB composition in poly(3HB-co-4HB) and to increase efficient production of the bioplastic by engineering the FtsZ cell division protein to allow for cells to accumulate larger quantities of PHA granules before dividing. Ultimately, once an optimal biopathway is found, the goal would be to explore a model for mass production of PHA bioplastics so that novel applications of bioplastics can be feasible economically.

Figure 3. Plasmid vector and genes used for transformation in E. coli

Figure 3a. Maggie add a caption

Figure 4. The reddish tint present on some colonies indicates the presence of PHA granules in the bacteria

Biobricks

In order to facilitate the completion of this project, several biobricks were created and used. The two foremost (the ones submitted) were phaAB and a double terminator.

phaAB

Part: BBa_K282000
Used in the creation of bioplastics. Contains both the PhaA gene and the PhaB gene. Part of the pathway PhaAB - Terminator - Cat2PhaC .

Terminator

Part: BBa_K282001
Based off of Part:BBa_B0014. Comprised of forward terminator Part:BBa_B0010 and reverse terminator Part:BBa_B0012.

Contents 1 Calendar 2 Protocols 2.1 CPEC Cloning 2.2 DNA Purification 2.3 PCA (Polymerase Cycle Assembly) 2.4 PCR Product Clean-up for DNA Sequencing 2.5 PCR 2.6 Single Colony PCR 2.7 Transformation 2.8 NMR 3 Lab Safety

Calendar

Protocols

CPEC Cloning

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Materials

• Phusion™ High-Fidelity PCR Kit (FINNZYMES, Cat. No. F-553)
• Thermocycler

Preparation

5x Phusion HF Buffer    4 ul
10 mM dNTPs	        0.4 ul	
Vector		        50 ng/1kb	
Insert		        x ng*	
Phusion DNA Polymerase  0.2 ul
-------------------------------
H2O		        to 20 ul

*The amount of insert is determined so that the molar ratio for vector and insert is 1 to 2.

Procedures

98°C                  30sec
  10X
     98°C             10 sec
     Annealing**      30 sec
     72°C             x sec***
72°C                  5min
4°C                   hold

** Anneal at Tm + 3°C. The Tm should be calculated with the nearest-neighbor method.
***The extension time is usually calculated according to the shortest piece with 15 sec /kb if the cloning is not complicated. For example, if there is only one insert and is shorter than the vector, say, 600 bp, then I will use 15 sec for extension. Refer to the published paper for detailed information.

DNA Purification

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Materials :

• E.Z.N.A Gel Purification Kit (Omega Bio-Tek, Cat No. D2500-02 )
• Water bath equilibrated to 55-65C
• Microcentrifuge capable of at least 10,000 x g
• Nuclease-free 1.5 ml centrifuge bottles
• Absolute (95%-100%) ethanol
• Protective eye-wear
• Isopropanol (for fragments < 500 bp only)

Protocol:

1. Perform agarose gel electrophoresis to fractionate DNA fragments. Any type or grade of agarose may be used. It is strongly recommended, however, that fresh TAE buffer or TBE buffer be used as running buffer. Do not re-use running buffer as its pH will increase and reduce yields.
2. When adequate separation of bands has occurred, carefully excise the DNA fragment of interest using a wide, clean scalpel.
3. Determine the approximate volume of the gel slice by weighing it in a clean 1.5 ml microfuge tube. Assuming a density of 1 g/ml of gel, the volume of gel is derived as follows: A gel slice of mass 0.3 g will have a volume of 0.3 ml. Add equal volume of Binding Buffer (XP2). Incubate the mixture at 55C-60C for 7 min or until the gel has completely melted. Mix by shaking or inverting the tube every 2-3 minutes. Centrifuge the tube briefly to collect all the liquid to the bottom of the tube.

Note: For DNA fragment less than 500bp, add 1 sample volume of isopropanol after the addition of Binding Buffer (XP2).

1. Apply up to 700 ul of the DNA/agarose solution to a HiBind® DNA spin column assembled in a clean 2 ml collection tube (provided) and centrifuge in a microcentrifuge at 8,000-10,000 x g for 1 min at room temperature. Discard the liquid. Re-use the collection tube in Steps 5-8. For volumes greater than 700 ul, load the column and centrifuge successively, 700 ul at a time. Each HiBind® spin-column has a total capacity of 25-30 ug DNA.
2. Discard liquid and add 300ul Binding Buffer. Centrifuge at 10,000 x g for 1 minutes.
3. Add 700 ul of SPW Buffer diluted with absolute ethanol into the column and wait 2-3 minutes. Centrifuge at 10,000 x g for 1 min at room temperature to wash the sample.
4. Discard liquid and repeat step 6 with another 700 ul SPW Buffer.
5. Discard liquid and, re-using the collection tube, centrifuge the empty column for 1 min at maxi speed (>13,000 x g) to dry the column matrix. This drying step is critical for good DNA yields.
6. Place column into a clean 1.5 ml microcentrifuge tube (not provided). Add 30-50 ul depending on desired concentration of final product) Elution Buffer (or sterile deionized water) directly to the center of the column matrix, then incubate for 1 minute. Centrifuge 1 min at maxi speed (>13,000 x g) to elute DNA. This represents approximately 70% of bound DNA. An optional second elution will yield any residual DNA, though at a lo

PCA (Polymerase Cycle Assembly)

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Materials

• Phusion™ High-Fidelity PCR Kit (FINNZYMES, Cat. No. F-553)
• Thermocycler

Preparation

5x Phusion HF Buffer	5 ul
10 mM dNTPs	0.5 ul
Oligo mixture	125 ng /250 ng /500 ng /
Phusion DNA Polymerase	0.25 ul
---------------------	--------
H2O	to 25 ul

Procedures

98°C              30sec 
  40X
      98°C        7 sec
      70-50°C     slow ramp, 0.1°C/sec
      50°C        30 sec 
      72°C        15 sec /kb
72°C              5 min
4°C               hold

PCR Product Clean-up for DNA Sequencing

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Materials:

• ExoSAP-IT® (usb, Cat. No. 78200)
• Thermocycler

Protocol:

1. Remove ExoSAP-IT from -20°C freezer and keep on ice throughout this procedure.
2. Mix 5 μl of a post-PCR reaction product with 2 μl of ExoSAP-IT for a combined 7 μl reaction volume.
3. Incubate at 37°C for 15 min to degrade remaining primers and nucleotides.
4. Incubate at 80°C for 15 min to inactivate ExoSAP-IT.
5. The PCR product is now ready for use in DNA sequencing etc.

PCR

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Materials

• Phusion™ High-Fidelity PCR Kit (FINNZYMES, Cat. No. F-553)
• Thermocycler

Preperation

5x Phusion HF Buffer	10 ul
10 mM dNTPs	1 ul
DNA template	1 pg – 10 ng
Forward primer (10 uM)	2.5 ul
Reverse primer (10 uM)	2.5 ul
Phusion DNA Polymerase	0.5 ul
--------------------	-----
H2O	to 50 ul

Procedure

98°C	30sec	30X
98°C	10 sec
Annealing*	30 sec
72°C	15 sec per 1 kb
72°C	5min
4°C	hold

* Anneal at Tm + 3°C. The Tm should be calculated with the nearest-neighbor method.

Single Colony PCR

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Materials

• Taq DNA Polymerase with Standard Taq Buffer (NEB, Cat. No. M0273)
• 10 mM dNTP Mix (NEB, Cat. No. N0447)
• Thermocycler

Preperation

10x Standard Taq Buffer	2 ul
10 mM dNTPs	0.4 ul
Bacteria culture*	1 ul
Forward primer (10 uM)	1 ul
Reverse primer (10 uM)	1 ul
Taq DNA Polymerase	0.2 ul
H2O	to 20 ul

*Bacteria culture refers to E. coli cultured in LB solution overnight.

Procedures

94°C	5 min	25X
94°C	15 sec
Annealing **	30 sec
72°C	1 min /1 kb
72°C	5min
4°C	hold

**Anneal at Tm which is calculated with salt-adjusted method.

Transformation

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Materials:

• GC5 Chemical Competent Cells (Genesee Scientific, Cat. No. 42-653)
• SOC Medium (Sigma, Cat. No. S1797)
• LB Agar (Sigma, Cat. No. L3027)
• Petri Dishes (VWR, Cat. No. SC25373-187)
• Cell Spreader (VWR, Cat. No. 89042-018)
• 37°C incubator
• 37°C shaker
• water bath

Protocol:

1. Thaw 1 tube of competent cells on ice;

2. Add 3 ul of cloning product or 1-50 ng of plasmid into competent cells while stirring gently;

3. Keep the tube covered by ice for 30min;

4. Heat-shock the competent cells in water bath for 45 sec at 42°C;

5. Put the tube on ice for 2 minutes;

6. Add 450 ul of SOC medium and then put it in a 37°C shaker for 1 hour;

7. Dilute and spread an appropriate amount on an LB agar plate with the appropriate antibiotics;

8. Place the plate up-side-down in 37°C incubator for 16-18 hours (overnight).

NMR

1. Login and start NMR program.

2. Click Acqi. Load sample. Make sure spin is on and lock is off.

3. Go to lock. Decrease number of sine waves to 1 to obtain step function.

       Make sure Zo is 1100, lockpower is below 30, lockgain is 36, lockphase is 352, and spin is 20.

4. Go to shim. Increase lock level.

5. Click main menu. Click set up. Click H1CDCl3.

       Type ‘nt=64’ (number of scans), ‘ss=2’ (dummy scans), ‘go’, ‘lb=0.2’ (line broadening).

6. Viewing: Type ‘wft’, ‘dscale’, ‘dfp’ to display peak frequency.

7. Zooming in: Click display. Go to interactive. Type ‘cr=8p, delta=8p’ to set width of zoom.

       Use cursor to set boundaries. Click to cut.

8. Printing: Type “pL pscale(0) pltext ppf page’ to print spectra with text and peak frequencies.

Lab Safety

None of our project ideas raised any safety issues whether it be researcher, environmental, or public safety. Duke has an in-house review board for projects and they did not raise any flags regarding our project. The biobrick parts created also do not pose any safety issues.

Not Including: Andrew Ang and Kevin Chien

Students

	Andrew Ang andrew.ang(at)duke.edu Andrew Ang is a freshman at Duke, majoring in Biomedical Engineering. Apart from class and iGEM, he is involved in the Jazz Ensembles program and Asian Students Association at Duke. His hobbies include piano, saxophone, tennis, and squash. He is interested in molecular and synthetic biology, biomolecular engineering and medical research. He has previously worked as part of the MIT 2008 team, and he is excited to participate in iGEM again this year, and many more years to come.
	Kevin Chien kevin.chien(at)duke.edu Kevin Chien is a freshman at duke, majoring in Biomedical Engineering. He wants to explore his options in many different careers. He occasionally plays Club Frisbee and is interested in many different areas of knowledge, ranging from Astrophysics to Public Policy (and even sometimes History). He worked on this iGEM team last year as well and enjoyed his stay in Boston(hopes to have a good one this year too!).
	Yaoyao Fu yf21(at)duke.edu Yaoyao Fu is a master's student in Biomedical Engineering. She is interested in molecular synthetic biology. Her hobbies are traveling and sports.
	Faith Kung fk8(at)duke.edu Faith Kung is a senior at Duke majoring in Biomedical Engineering with minors in Music and Biology. She enjoys working in a lab. Besides academics, her hobbies include arts and crafts, dance, and figure skating. Also, she is actively involved in the IV Christian Fellowship. Faith is applying to PhD programs in Biomedical Science and hopes to pursue a career in scientific research and education. She is excited about attending the iGEM competition this year.
	Sahil Prasada sahil.prasada(at)duke.edu Sahil Prasada is a freshman at Duke. He plans to pursue medicine as a career. His interests lie in Detroit sports, tennis, and dancing. He is a member of the DBS Raas team on campus. He is currently in the Trinity School of the Arts and Sciences but is considering transferring to the Pratt School of Engineering. He hopes that the Detroit Lions may one day win the Superbowl. While waiting for this to occur, he will attend the iGEM competition and is looking forward to winning an award.
	Nicholas Tang nicholas.tang(at)duke.edu Nicholas Tang is a junior Biomedical Engineering/Electrical and Computer Engineering student. He plans to pursue his interests in computational biology and biological engineering. His hobbies include cycling, playing the violin and playing the piano. As a participant in the 2006, 2007, and 2008 Duke iGEM teams, he is excited to contribute to the progress of the synthetic biology community, and hopes to help in any way he can.
	Peter Zhu peter.zhu(at)duke.edu Peter Zhu Is a freshman at Duke University and a North Carolina local. Though he's not sure yet what to do with his life, he thinks Biomedical Engineering and pre-Law is looking pretty good. When he's not busy with the routines of life, he is listening to the Billboard Top 100, playing Chopin Preludes, searching for new places to eat, playing tennis, studying poker, and gaming Starcraft/DoTA. Peter is a regular at Bail Hai Mongolian Grill, Lime and Basil Vietnamese Pho, and Five Guy's Burgers---bacon cheeseburger with all toppings of course.

Faculty Advisors

Dr. Jingdong Tian jtian(at)duke.edu Department of Biomedical Engineering & IGSP

Dr. Lingchong You you(at)duke.edu Department of Biomedical Engineering & IGSP

Dr. Fan Yuan fyuan(at)duke.edu Department of Biomedical Engineering

Maggie Jiayuan Quan jq7(at)duke.edu Graduate Student

Faisal Reza faisal.reza(at)duke.edu Graduate Student