Team:Imperial/EColi

From 2014.igem.org

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                             <div class="pure-u-1-2">
                                 <h2>Overview</h2>
                                 <h2>Overview</h2>
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                                 <p>Zombie ipsum reversus ab viral inferno, nam rick grimes malum cerebro. De carne lumbering animata corpora quaeritis. Summus brains sit​​, morbo vel maleficia? De apocalypsi gorger omero undead survivor dictum mauris. Hi mindless mortuis soulless creaturas, imo evil stalking monstra adventus resi dentevil vultus comedat cerebella viventium. Qui animated corpse, cricket bat max brucks terribilem incessu zomby. The voodoo sacerdos flesh eater, suscitat mortuos comedere carnem virus. Zonbi tattered for solum oculi eorum defunctis go lum cerebro. Nescio brains an Undead zombies. Sicut malus putrid voodoo horror. Nigh tofth eliv ingdead.</p>
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                                 <p><em>Escherichia coli</em> is a very unfussy strain. It is able to grow under a diverse range of conditions, it is very well understood, easy to engineer and there are numerous parts, control circuits, biological manufacturing platforms and various other complex constructs proven functional in this host. For these and other reasons, it is widely used in the Synthetic Biology community as a cloning host and for various other purposes. </p>
 +
<p>However, some <em>Escherichia coli</em> strains only produce cellulose at a specific set of phenotypical conditions (its secretion is generally linked to biofilm formation and stress situations). In order to encourage the use of bacterial cellulose as a functional, modular biomaterial that can become easy, cheap and quick to produce, it is necessary for its corresponding production machinery to be implemented in organisms that are easier and quicker to grow in manufacturing plants and bioreactors. </p>
 +
<p>Here, we confirm that the cellulose production machinery can be transferred into other organisms. We have proven portability of the Acs cellulose operon in <em>Escherichia coli</em> using Congo Red binding assays. </p>
                             </div>
                             </div>
                             <div class="pure-u-1-2">
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                     <section id="introduction">
                     <section id="introduction">
                         <h2>Introduction</h2>
                         <h2>Introduction</h2>
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                         <p>BEING UPDATED Despite its unique chemical, physical and mechanical features and great potential in a variety of industries, wider use of bacterial cellulose as a biomaterial has been limited due its high cost of production (mainly driven by the need of high medium volumes and large surface areas for the cellulose pellicle to grow on under optimized conditions), in addition to the slow and particularly low production yields, which do not meet the demands of an industrial setting. Therefore, it is essential to develop a sustainable, affordable and efficient approach for optimal cellulose productivity (alternative: optimal cellulose mass production)</p>
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                         <p>TEXT HERE</p>
                     </section>
                     </section>
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                     <section id="engineering">
                     <section id="engineering">
                         <h2>Engineering</h2>
                         <h2>Engineering</h2>
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                         <p>The cellulose production operon in Gluconacetobacter Xylinus is a 10kb genomic region, consisting of four main elements:</p>
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                         <p>The cellulose production operon in <em>Gluconacetobacter xylinus</em> is a 10kb genomic region, consisting of four main elements:</p>
                         <ul>
                         <ul>
-
                             <li>acsAB, the cellulose synthase element, which is in turn made up of two domains: acsA being the catalytic domain, and acsB being the cyclic-di-GMP-binding domain. This modular enzyme requires the second messenger cyclic-di-GMP in order to carry out efficient catalysis</li>
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                             <li>acsAB, known as cellulose synthase, is made up of two domains: acsA being the catalytic domain, and acsB being the cyclic-di-GMP-binding domain. This modular enzyme requires the second messenger cyclic-di-GMP in order to carry out efficient catalysis.</li>
-
                             <li>acsC codes for an oligomeric element that allows transport of the growing polymer across the cell membrane into the extracellular space</li>
+
                             <li>acsC codes for an oligomeric element that gets embedded in the extracellular membrane and allows transport of the growing polymer across the cell membrane into the extracellular environment.</li>
                             <li>acsD is believed to be a non-essential element, although it is a key player in the control of cellulose crystallinity and required for maximal cellulose productivity.</li>
                             <li>acsD is believed to be a non-essential element, although it is a key player in the control of cellulose crystallinity and required for maximal cellulose productivity.</li>
</ul>
</ul>
-
                             <p>The native operon has surprisingly high levels of internal regulation and its expression responds to a wide set of internal signalling events and environmental cues. The native RBS appear weak but are still able to efficiently maintain the stoichiometry of the system for all elements to be expressed and function at the right levels.</p>
+
                             <p>The native operon is highly regulated at transcriptional, translational and post-translational levels. Cellulose production responds to a wide set of internal signals and environmental cues. The native ribosomal binding sites (RBS) are predicted to be weak by translation rate calculators (The <a href="https://salis.psu.edu/software/"> Salis Lab RBS calculator </a> and <a href="http://sbi.postech.ac.kr/utr_designer"> Postech UTR designer </a>). This is perhaps to reduce noise in gene expression (strong promoter, weak RBS is less noisy that weak promoter strong RBS). The promoter region has not yet been characterized in <em>Gluconacetobacter xylinus</em>, however.</p>
-
                            <p>Unfortunately, the promoter region has not yet been characterized, and it was also noticed that there are overlapping regions between the 3’ end of an element, and the 5’ end of the following element downstream of it.</p>
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                            <p>The first step of our design engineering approach, was to identify the coding sequences and extract them from NCBI. We removed the native regulation by codon-optimizing the sequences for expression in E.coli and other standard hosts, and replaced the native RBS with stronger ones, but maintaining the strength differences amongst them so that the expression levels of each coding sequence could be replicated in any other organism. We replaced the existing promoter (uncharacterized and both negatively and positively regulated by native second messengers) with inducible promoters of our choice to develop the following strategy:</p>
+
-
                            <p>Gene Designer served as a very useful tool for assembling constructs and predicting cloning outcomes before proceeding with the experimental procedure. Find below the plasmid maps of our resulting constructs, and refer to Materials and Methods for a deeper insight into the assembly process.</p>
+
<p>The first step of our computational design engineering was to identify the coding sequences and extract them from NCBI. We removed some native regulation by codon-optimizing the sequences for expression in <em>E.coli</em> and replaced the native RBS’s with the strong B0034 sequence. The 6 base pairs either side of the B0034 RBS were edited with the Salis Lab RBS calculator design function to tune RBS strength output to better preserve the natural stoichiometry.</p>
 +
 
 +
<p>Finally, in order to allow for even more customizable fine-tuning of the system, the operon was divided and cloned into two separate expression vectors: the AcsAB element was cloned under the control of the inducible pBAD promoter contained within pSB1C3, a high copy plasmid that would contribute to higher expression of Cellulose Synthase. Alternatively, AcsC and AcsD, believed to be expressed at lower levels in <em>G.xylinus</em>, was put under the control of the pLAC promoter and was transferred into a low copy plasmid, pSB3K3 so as to maintain lower levels of expression. This approach provided the following advantages:</p>
 +
<ul>
 +
<li>Reducing the size of the final expression vector avoids complications during assembly and vector take-up, and it also prevents a large construct from becoming a burden for cell growth and vector propagation. </li>
 +
<li>By expressing the cellulose production machinery from two separate expression vectors, the following levels of control become available to us: the first being the changes in vector copy number, which directly affects gene expression levels throughout induction, and the second being the ability to activate the system using two different inducers. These key features of our system allow for a larger scope for fine-tuning and optimization of cellulose production levels. </li>
 +
 
 +
</ul>
 +
<p>ith this approach, we allow for our system to be implemented in new range of hosts because a larger set of growth conditions, inducer concentrations and growth phases can be tested in order to achieve the required stoichiometry for the system to become functional.  </p>
 +
 
 +
<p>In order to ease synthesis, the operon sequence was split into 4 fragments of similar sizes. We took advantage of the presence of two restriction sites: An NcoI present within the AcsAB sequence, and a PvuII site contained within AcsC. Furthermore, the BioBrick prefix and suffix were included and any additional sites removed elsewhere. </p>
 +
 
 +
<p>By standard cloning, these fragments could easily be put together to yield the following constructs:</p>
 +
 
 +
<p>Gene Designer served as a very useful tool for assembling constructs and predicting cloning outcomes before proceeding with the experimental procedure. Find above the plasmid maps of our resulting constructs, and refer to Materials and Methods for a deeper insight into the assembly process. </p>
                          
                          
                     </section>
                     </section>

Revision as of 20:10, 17 October 2014

Imperial iGEM 2014

Team E. coli

Overview

Escherichia coli is a very unfussy strain. It is able to grow under a diverse range of conditions, it is very well understood, easy to engineer and there are numerous parts, control circuits, biological manufacturing platforms and various other complex constructs proven functional in this host. For these and other reasons, it is widely used in the Synthetic Biology community as a cloning host and for various other purposes.

However, some Escherichia coli strains only produce cellulose at a specific set of phenotypical conditions (its secretion is generally linked to biofilm formation and stress situations). In order to encourage the use of bacterial cellulose as a functional, modular biomaterial that can become easy, cheap and quick to produce, it is necessary for its corresponding production machinery to be implemented in organisms that are easier and quicker to grow in manufacturing plants and bioreactors.

Here, we confirm that the cellulose production machinery can be transferred into other organisms. We have proven portability of the Acs cellulose operon in Escherichia coli using Congo Red binding assays.

Key Achievements

  • We have contributed significantly to the Registry of Standard Parts by providing the necessary components for the assembly of a 10kB operon for cellulose production in a wide range of organisms.
  • We have proven system portability by transferring the cellulose production machinery from Gluconacetobacter xylinus into Escherichia coli and demonstrating its functionality in the latter.
  • Assembled a fully synthetic, functional, cellulose-producing system in Escherichia coli without engineering signal peptides, indicating that these and the signal peptides of G. xylinus must be of high similarity.
  • We were able to successfully maintain the native stoichiometry and ratios of expression of the native host to ensure proper protein folding, complex assembly and correct levels of activity of each of the parts in the process of making cellulose.
  • In summary, we have majorly contributed to the Synthetic Biology community by encouraging the implementation of non-native, complex functions and systems into new hosts and by encouraging the production and uses of bacterial cellulose by a broader range of hosts to widen the applications of such useful biomaterial.

Introduction

TEXT HERE

Aims

By aiming to transfer the cellulose production operon from its native organism Gluconacetobacter xylinus into the lab-friendly strain E. coli, we aimed to emphasize the importance of increasing cellulose production per unit time to achieve a reduction in pellicle growth timeframe and production costs. We also aim to optimize growth conditions by potentially allowing shaking incubation, and to ease genetic engineering and cloning procedures due to the wider availability of functional, already characterized Biobricks to work with cellulose (by having the two highest expressed elements in a high copy plasmid (pSB1C3) and the lowest expressed elements in a low copy plasmids (pSB3k3), and by having two different inducible promoters that allow for an even finer tuning of expression).

Engineering

The cellulose production operon in Gluconacetobacter xylinus is a 10kb genomic region, consisting of four main elements:

  • acsAB, known as cellulose synthase, is made up of two domains: acsA being the catalytic domain, and acsB being the cyclic-di-GMP-binding domain. This modular enzyme requires the second messenger cyclic-di-GMP in order to carry out efficient catalysis.
  • acsC codes for an oligomeric element that gets embedded in the extracellular membrane and allows transport of the growing polymer across the cell membrane into the extracellular environment.
  • acsD is believed to be a non-essential element, although it is a key player in the control of cellulose crystallinity and required for maximal cellulose productivity.

The native operon is highly regulated at transcriptional, translational and post-translational levels. Cellulose production responds to a wide set of internal signals and environmental cues. The native ribosomal binding sites (RBS) are predicted to be weak by translation rate calculators (The Salis Lab RBS calculator and Postech UTR designer ). This is perhaps to reduce noise in gene expression (strong promoter, weak RBS is less noisy that weak promoter strong RBS). The promoter region has not yet been characterized in Gluconacetobacter xylinus, however.

The first step of our computational design engineering was to identify the coding sequences and extract them from NCBI. We removed some native regulation by codon-optimizing the sequences for expression in E.coli and replaced the native RBS’s with the strong B0034 sequence. The 6 base pairs either side of the B0034 RBS were edited with the Salis Lab RBS calculator design function to tune RBS strength output to better preserve the natural stoichiometry.

Finally, in order to allow for even more customizable fine-tuning of the system, the operon was divided and cloned into two separate expression vectors: the AcsAB element was cloned under the control of the inducible pBAD promoter contained within pSB1C3, a high copy plasmid that would contribute to higher expression of Cellulose Synthase. Alternatively, AcsC and AcsD, believed to be expressed at lower levels in G.xylinus, was put under the control of the pLAC promoter and was transferred into a low copy plasmid, pSB3K3 so as to maintain lower levels of expression. This approach provided the following advantages:

  • Reducing the size of the final expression vector avoids complications during assembly and vector take-up, and it also prevents a large construct from becoming a burden for cell growth and vector propagation.
  • By expressing the cellulose production machinery from two separate expression vectors, the following levels of control become available to us: the first being the changes in vector copy number, which directly affects gene expression levels throughout induction, and the second being the ability to activate the system using two different inducers. These key features of our system allow for a larger scope for fine-tuning and optimization of cellulose production levels.

ith this approach, we allow for our system to be implemented in new range of hosts because a larger set of growth conditions, inducer concentrations and growth phases can be tested in order to achieve the required stoichiometry for the system to become functional.

In order to ease synthesis, the operon sequence was split into 4 fragments of similar sizes. We took advantage of the presence of two restriction sites: An NcoI present within the AcsAB sequence, and a PvuII site contained within AcsC. Furthermore, the BioBrick prefix and suffix were included and any additional sites removed elsewhere.

By standard cloning, these fragments could easily be put together to yield the following constructs:

Gene Designer served as a very useful tool for assembling constructs and predicting cloning outcomes before proceeding with the experimental procedure. Find above the plasmid maps of our resulting constructs, and refer to Materials and Methods for a deeper insight into the assembly process.

Materials and Methods

Cell Strains and Media Components

Escherichia coli strain DH10B were made chemically competent following a standard protocol and were used to clone the pSB-AraC-pBAD and pSB-LacI-pLAC elements. Additionally, High Efficiency chemically competent DH10B E.coli were purchased from New England Biolabs for assembly of the Acs cellulose-producing operon, which was codon-optimized for expression in E.coli and synthesized by GenArt. Both strains were grown overnight in liquid cultures (supplemented with specific antibiotics), or on semi-solid LB-Agar plates, provided with the specific antibiotic, as listed on the table below.

Luria Broth Miller (LB) and LB Agar were purchased from ????, prepared using standard protocols and used throughout the experimental procedure. During characterization, Acs-containing strains were supplemented with 1% D-glucose, 0.1% Arabinose and 0.5mM IPTG.

Plasmid name Vector backbone Antibiotic concentration (ug/ml)
pSB-AraC-pBAD pSB1C3 Chloramphenicol 50
pSB-LacI-pLAC pSB3K3 Kanamycin 25
pSB-AcsAB pSB1C3 Chloramphenicol 50
pSB-AcsCD pSB1C3 Chloramphenicol 50
pSB-AraC-pBAD-AcsAB pSB1C3 Chloramphenicol 50
pSB-LacI-pLAC-CD pSB3K3 Kanamycin 25
List of antibiotics used, in relation to their respective constructs

Chemicals

Congo Red was purchased from Sigma Aldrich (Steiheim, Germany) and diluted in 1x PBS to a concentration of 350 uM. The final Congo Red concentration used during system characterization steps was 20 uM.

Construct Assembly

Cloning of pSB-AraC-pBAD

The AraC and pBAD elements were obtained by PCR, using the Biobricks BBa_K325108, BBa_K325218 and BBa_K325219 as DNA templates, all of which follow the standard structure showed on the image below (left hand side, add legend, add figure number). The primers used during this procedure were as follows:

  • Forward: TACTAGTAGCGGCCGCTGCAG
  • Reverse: GCTAGCCCAAAAAAACGGGTATGGAG
Figure 1 - Plasmid maps describing both the original (left) and engineered (right) AraC-pBAD-containing parts, including all relevant elements. These were designed and cloned in silico on GeneDesigner.

The amplified elements were DpnI-treated following a standard procedure (New England Biolabs), and were subsequently submitted to a purification step (Qiaquick PCR clean up, Qiagen) prior to self-ligation. Three different template concentrations were tested during ligation (specifically 3 ng, 7.5 ng and 15 ng), and were incubated at room temperature for 1h+. The ligation mix was then transformed into chemically competent DH10B E.coli using a standard chemical transformation protocol and plated out on Chloramphenicol-specific LB plates.

Cloning of pSB-LacI-pLAC

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Assembly of Acs elements

The AcsABCD operon was designed in silico as described in the previous section. It was ordered for synthesis at GenArt in the form of four separate elements of similar sizes, named AcsA, AcsB, AcsC and AcsD, respectively. After synthesis, the constructs were directly transformed into DH10B E.coli using a standard chemical transformation protocol and plated overnight supplied with 50 ug/ml Kanamycin. 5 ml LB were inoculated with a freshly growing colony and grown overnight at 37°C, under shaking conditions. Glycerol stocks were produced prior to proceeding with the assembly process.

In order to meet the Registry standards, we aimed to clone these elements into pSB1C3. To do so, the vector backbone (pSB1C3), AcsA and AcsB were submitted to SpeI/PstI, XbaI/SpeI and XbaI/PstI double digests, respectively, to later yield pSB-AcsAB. AcsC, AcsD were digested in a similar manner, and would be cloned into pSB1C3 to yield pSB-AcsCD. Prior to ligation, the vector backbone was dephosphorylated using AP phosphorylase (Roche). A three-part ligation was then set up, keeping equimolar ratios amongst all three parts, and incubated at 4 degrees overnight. The resulting ligation mix was transformed using the NEB High Efficiency Transformation protocol into NEB 10B cells (New England Biolabs), which were in turn plated and incubated overnight at 37 degrees. 5ml LB supplied with 50ug/ml Chloramphenicol were inoculated with a selection of colonies for further.

Results

Constructs

pSB-AraC-pBAD Assembly

The pSB-AraC-pBAD construct was assembled as described in Materials and Methods. As a preliminary verification step, a restriction analysis was carried out using XbaI and PstI, and results were visualized on a 1% Agarose Gel. A 2-band pattern was obtained, indicating the presence of a ~2kb DNA fragment potentially corresponding to the pSB1C3 vector backbone, and a ~1kb fragment corresponding to the AraC and pBAD elements being cloned. Final confirmation of successful cloning was obtained by gene sequencing of the part in question, using the BioBrick Verification Primers, shown below: (refer to the “Sequencing” section to find a compilation of all confirmed parts)

  • Verification Primer Forward: T GCC ACC TGA CGT CTA AGA A
  • Verification Primer Reverse: ATT ACC GCC TTT GAG TGA GC
Figure x: pSB-AraC-pBAD

pSB-AcsAB and pSB-AcsCD Assembly

Figure x: pSB-AcsAB
Figure x: pSB-AcsCD

pSB-AraC-pBAD-AcsAB Assembly

Figure x: pSB-AraC-pBAD-AcsAB and pSB-LacI-AcsAB

Characterising Cellulose Production

Preliminary Characterization: Congo Red Assay

Data Analysis

Future Work

References