Team:HKUST-Hong Kong/overview.html

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<h3>1. ASM</h3>
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<h4 align=left>1.1. Theory – how to select? </h4>
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The E. trojan is a synthetic E.coli strain that is engineered to lack an essential gene, nadE,  in its genomic DNA. To survive, this strain has to rely on a pre- introduced plasmid (pDummy) bearing the essential gene; thus forcing the bacteria to maintain the plasmid until an alternative source of nadE gene is present.  The pDummy, however, has been designed to have a temperature- sensitive origin of replication which would cease to function if the bacterial cells are incubated under higher incubation temperatures (>42ᵒC???). <br><br>
 
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For sub-cloning purposes, an E. trojan – compatible vector plasmid is designed. This carrier vector, like the pDummy, contains the nadE essential gene. Once a gene of interest is inserted into this  vector, the plasmid can be transformed to the E. trojan for amplification. Incubating the transformed bacteria at a temperature high enough to inactivate the heat sensitive replication origin  of the pDummy would result in pDummy loss, making it necessary for the cells to retain the insert- bearing pCarrier for survival. Bacterial cells that do not take up the pCarrier and its insert would be deprived of the nadE gene product and die; while those who do would survive and continue dividing.
 
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<a href=#back><img src="https://static.igem.org/mediawiki/2011/4/4a/Ust_back.gif" width=100 height=100 alt="Background"></a>
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<a href=#plan><img src="https://static.igem.org/mediawiki/2011/6/68/Ust_battle.gif" width=100 alt="The Battle Plan" height=100></a>
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<a href=#build>
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<img src="https://static.igem.org/mediawiki/2011/e/e4/Ust_build.gif" width=100 height=100 alt=" Building the horse - Engineering a novel strain for antibiotics-free selection"></a>
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<img src="https://static.igem.org/mediawiki/2011/2/23/Ust_army.gif" width=100 height=100 alt="The army inside - Toluene-4-Monooxygenase (T4MO)"></a>
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<b><font size=14> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Overview</font></b>
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&nbsp;  &nbsp;
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<a href=#back>Background</a> · &nbsp;
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<a href=#plan>The Battle Plan</a> · &nbsp;
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<a href=#build>Building the horse</a> · &nbsp;
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<a href=#army>The army inside</a>
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<b><a name=back></a>1. Background </b>
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<h4 align=left>1.2. Method of assembly</h4>
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In the past decade, the number of medical cases involving multi-antibiotic resistant microbes has seen a steady increase, and misuse of antibiotics has repeatedly been mentioned as one of the major reasons for the arise of such organisms. This situation provided the inspiration for our project, which is to attempt to improve the effectiveness of antibiotics, so that we can apply less of it to achieve the same effect as we do now.
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Our project name - E. trojan - has its origins rooted in the Trojan Horse found in the tale of the Trojan War. Similar to how the Greeks destroyed the city of Troy from within using a wooden horse filled with soldiers, our E. trojan also works to destroy an <i>E. coli</i>  population that is under antibiotic stress from within through indole quorum-sensing disruption.
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<a href=#top>[Top]</a>
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To study the population dynamics and behavior of a certain antibiotics sensitive strain of E Coli in a medium of antibiotic, our E. Trojan that is introduced into the culture medium must not process a wide spectrum of antibiotic resistance that impose a selective advantage. At the same time, E. Trojan needs to be transformed with the T4MO gene to carry out its job of signal disruption.
 
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Summarizing the above criteria, a solution where the bacteria can be transform with the gene of interest while remaining sensitive to antibiotics is needed. Therefore the requisite is to construct a new bacteria strain that can perform plasmid selection without the use of antibiotics, and contains as little antibiotics resistance gene as possible.<br><br>
 
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<b>Construction and maintenance of an antibiotic-resistance-gene-free plasmid through antibiotic selection – the unavoidable evil two plasmid system</b><br>
 
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Our ultimate goal is to construct our EX without conferring it any new antibiotic resistance. For this reason no resistance gene should be found in our dummy plasmid pDummy. <br><br>
 
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Yet, such a plasmid would not be maintained by itself unless the host bacterium develops an addiction to it (i.e. losses the essential gene in its genome and depends on extragenomic copies on pDummy), and inconveniently, the addiction can only be achieved after the introduction of the plasmid.<br><br>
 
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The solution is to develop a mutualistic relation between two plasmids and we planned to exploit positively regulated origin of replications. Well studied examples are those in pSC101 and R6K origins of replication, where the origins of replication (OR) appear together with a constitutive gene (G). Initiation of replication happens if and only if the trans element of the gene is provided.<br></p>
 
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Let’s consider the following scenario: <br>
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<b><a name=plan></a>2. The Battle Plan</b>
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i. G is placed on pDummy with no selection marker but with a normal replication origin<br>
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ii. OR is the sole origin of replication of another plasmid (pToolkit) with a selection marker<br>
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iii. pDummy and pToolkit are co-transformed to a bacterium which is under selection stress</p>
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We would obtain three possible outcomes:<br>
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<b>1. only pDummy is uptaken</b><br>
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- since pDummy has no selection marker, the host bacteria die under selection pressure and cannot propagate<br><br>
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<b>2. only pToolkit is uptaken</b><br>
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- the host bacterium that uptakes pToolkit survives. Yet during propagation, pToolkit is not replicated because proteins of G are absent. Therefore daughter cells of the host bacterium will not receive copies of the pToolkit and die under selection pressure.<br><br>
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<b>3. both pDummy and pToolkit are uptaken</b><br>
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- in presence of pDummy, pToolkit is maintained and confers the host bacterium with stress resistance. Daughters that receive copies of both plasmids will survive and eventually develop into a colony.<br><br></p>
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Indole has been proposed as a key signalling molecule for <i>E. coli</i> in mediating resistance to environmental stress.[1] In particular, indole is found to stimulate passive resistance against antibiotics by triggering stress-response mechanisms inside cells, including increased expression of drug efflux pumps and oxidative-damage repair systems.
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Using this mutualistic relation, the desired pDummy can be maintained once the host bacterium develops an addiction it, and pToolkit can be lost in bacteria propagation if the expression of G can be shut off manually. Eventually, the bacteria not obtain any new antibiotic resistance genes but keep pDummy.
 
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<b>Development of addiction – use of the lambda RED recombination system</b><br>
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In a normal <i>E. coli</i> population containing wild type and naturally resistant mutants, the mutants will supply indole to nearby cells that are under antibiotic stress. This is considered to be a 'charity' action as the mutant does so at a fitness cost to itself. Our aim is to introduce E. trojan into the population and proceed to degrade indole via an enzyme (T4MO) and remove the charity effect. If the charity effect is significant, removal of its presence will cause a notable increase in the effectiveness of antibiotics.
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<a href=#top>[Top]</a>
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To develop the addiction in the host bacterium to pDummy, an essential gene for survival is to be deleted from the bacteria genome, provided that the bacteria can survive on extra-genomic copies after the deletion.<br><br>
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The deletion here is mediated through the lambda RED recombination system.<br><br>
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The lambda RED recombination cassette is located on the pToolkit (and hence the name of the plasmid). Once the recombination is successful, it can be eliminated from the host bacterium together with the antibiotic resistance gene. <br><br>
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Therefore, once the co-transformation of pDummy and pToolkit is successful, linear dsDNAs having a reporter gene flanked by homologous sequences to the essential gene can be introduced into the bacteria. When the recombination is kicked started, the essential gene will be swapped out and the reporter gene will be incorporated into the bacteria genome.<br><br>
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Since the linear dsDNAs do not have origin of replications, they are not inherited in daughters unless they are swapped into the genomes. Thus, any observable signals from the reporter would allow identification of successful recombination. Identified colonies can then be further treated to induce loss of pToolkit, which afterwards would be the completed strain of EX.<br><br>
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<b>Complementation between reporter genes – manifesting completion of EX engineering</b><br>
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To ensure that the final strain of EX has: 1. successfully had its essential gene deleted from genome, 2. maintained the pDummy, a complementation reporter system between the pDummy and swapped gene is preferred over a single reporter at the swapped site.<br><br>
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Different methods can achieve the above aim:<br>
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i. Alpha complementation can be used in E. Coli strains where the lacZ gene is completely removed. The larger fragment ω can be swapped for the essential gene while the smaller α fragment can stay on pDummy. In a X-gal rich medium, blue colonies suggest the desired engineered strains.<br><br>
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ii. Complementation between split fluorescent proteins (sFP). 2010 iGEM Slovenia team has demonstrated the principle that N-terminal and C-terminal fragments of sFPS are able to complement in vivo and two sets of sfFPS are able to undergo Förster resonance energy transfer (FRET). This idea is adopted but an alternative set of candidate, split superfolder GFPs (sfGFP), was developed.</p>
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<h5 align=left>Summary of construction flow:</h5>
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<p>1. Assembly pDummy and pToolkit<br>
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2. Co-transform both plasmid into E Coli and maintain stable strains<br>
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3. Introduce linear dsDNAs and induce recombination<br>
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4. Isolate recombinants<br>
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5. Induce loss of pToolkit
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<h4 align=left>1.3. Component details</h4>
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<b><a name=build></a>3. Building the horse - Engineering a novel strain for antibiotics-free selection</b>
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Temperature-sensitive origin of replication_oriR101 & repA101-ts (BBa_K524000)
 
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oriR101 & repA101-ts is a set of low copy origin of replication derived from the pSC101 origin of replication. The repA101-ts gene codes for a heat-labile protein that is required in trans for the initiation of replication at oriR101. In our construct, our characterization has shown that plasmids with this origin of replication can only be maintained below than 300C, and partial maintenance of plasmid was observed within temperature range from 290C to 330C. This part was cloned out from pKD46 plasmid (courtesy of The Coli Genetic Stock Center), and standardized by a nucleotide mutation.<br>
 
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To study the interaction and population dynamics of the naturally-coexisting HR (high resistance) and LR (low resistance) <i>E. coli</i> strains under antibiotic selection pressure, the E. trojan - which is to be introduced to HR/ LR mixed culture - should harbor the T4MO gene to allow it to perform quorum sensing disruption between the two strains. In addition, the E. trojan should not possess a wide spectrum of antibiotic resistance as this would give it an inherent selective advantage, thus interfering with the relationship between MICs and indole degradation in our study.
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split superfolder green fluroscent protein_split sfGFPsplit superfolder green fluroscent <br>
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protein_split sfGFP<br>
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sfGFP1-10 (BBa_K524001)<br>
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sfGFP11 ((BBa_K524002)
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To fulfill the above criteria, it becomes necessary for us to first construct a new, pre-E. trojan bacterial strain (E. CRAFT) that is capable of performing plasmid selection without antibiotics and consequently contains as few antibiotic resistance genes as possible. Due to some limitations of the various alternative (non-antibiotic) selection methods[2] available today, we have designed E. CRAFT in a way that causes it to perform selection by imposing internal pressure of holding an essential gene for survival. Upon the completion of this precursor strain, the E. trojan can be easily constructed by transformation of the T4MO gene into it. In the long run, however, we hold a hope that this novel strain will prove to be a versatile, effective alternative to the widely- used antibiotic selection method.<a href=#top>[Top]</a>
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The sfGFPs are mutated variants of GFPs that has improved folding kinetics and resistance to chemical denaturants. Split sfGFPs at amino acid residues 214 and 215 have been reported to undergo spontaneous complementation to give green fluorescence. The two split constructs were produced from an existing biobrick – pBAD driven sfGFP BBa_I746908. CDS of sfGFP amino acid residues 1-214 were copied out for sfGFP1-10 using PCR and stop codon was added to the end. The sfGFP11 was produced in a similar fashion, with a start codon added to the front of the CDS of amino acid residues 215 to 238.
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<b><a name=army></a>4. The army inside - Toluene-4-Monooxygenase (T4MO)</b>
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Toluene-4-Monooxygenase (T4MO) is a three-component enzyme system that is naturally able to degrade a variety of hydrocarbons. In particular, its ability to oxidize small aromatic compounds has caught the attention of scientists looking for biological means of producing certain useful organic chemicals for industrial use, resulting in extensive research on modifying its activity and affinity. </p>
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For our project, a mutated form of T4MO (double mutations at G103L & A107G) was chosen as the candidate for indole degradation. While there were several possible candidates, this particular one was known to convert almost 50% of the indole into 7-hydroxyindole (7-HI)[2]. This is of great interest to us as 7-HI has been documented to inhibit biofilm formation in Enterohemorrhagic <i>E. coli</i>[3], and quite possibly for other strains of <i>E. coli</i> as well. Biofilm formation is a major element that reduces the efficiency of antibiotics due to reduced area of action, and hence we were keen to take advantage of this synergistic effect to improve our construct.<a href=#top>[Top]</a>
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<b>Essential gene nadE (BBa_K524003)</b><br>
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<i>nadE</i> is a vital gene in <i>E. Coli.</i> It codes for NAD+ synthetase. In principle, removal of such gene from the genome would cause addiction of bacteria to a plasmid that has a copy of the gene. CyaR (a sRNA) regulates the expression of nadE post-transcriptionally. This feature is retained in our construct. Transcription of <i>nadE</i> operon requires the sigma-70 factor and is terminated by downstream extragenic sites. The <i>nadE</i> gene was cloned out from the genome of strain BL21(DE3), and was completed the <i>nadE</i> by having B0015 terminator assembled to its end.
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<b>4.1 Soldiers need shields...maybe - Multidrug Efflux Pump (Bcr)</b>
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<b>Replication initiator pi protein and ori-gamma from R6K plasmid</b><br>
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ori-gamma is one of three replication origins (the other two being alpha and beta) of the R6K origin. Initiation of replication at ori-gamma requires the pi protein in trans, which is encoded by the pir gene. Yet doubling the concentration of pi protein would effectively shut down the replication as well. Expression of pi protein is autogenously regulated. The pir construct was cloned out from the genome of strain BW25141 (courtesy of The Coli Genetic Stock Center) and standardized. The ori-gamma was adopted from the R6K origin of replication BBa_J61001.
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As our novel strain will have one of its essential genes maintained in a plasmid, a lot of uncertainties are present regarding its fitness. It is quite possible that it will be more vulnerable to antibiotics compared with wild type and thus will be selected against when cultured together with wild type <i>E. coli</i>. This would reduce the effectiveness of our construct and is not desirable. Hence we planed an additional component to be maintained in the plasmid, known as Bcr, which we hope will boost the resistance of E. trojan. You will find more details on its construction <a href="asm.html"  target=_top><b>here</b></a>.<a href=#top>[Top]</a></p>
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<b>iGEM 2010 Slovenia Split/FRET constructs</b><br>  
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The split CFP and YFP from the biobricks of Slovenia team last year were used as alternative reporters. The idea is to put one of the terminal fragments of a split fluorescence protein into the pDummy, and swap out the essential nadE gene from the genome with the other terminal fragment. Driven by pLac R0010, both fragments should express simultaneously when induced by IPTG and fluorescence signal would be observed as an indicator of successful recombination.
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[1] <a href=http://www.nature.com/nature/journal/v467/n7311/pdf/nature09354.pdf>Bacterial charity work leads to population-wide resistance</a>
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[2] <a href=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941680/pdf/1475-2859-9-65.pdf>Antibiotic-free selection in <i>E. coli</i>: new considerations for optimal design and improved production</a>
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[3] <a href=aem.asm.org/cgi/reprint/71/9/5476.pdf>Mutations of Toluene-4-Monooxygenase That Alter Regiospecificity of Indole Oxidation and Lead to Production of Novel Indigoid Pigments</a>
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[4] <a href=aem.asm.org/cgi/reprint/73/13/4100.pdf>Enterohemorrhagic Escherichia coli Biofilms Are Inhibited by 7-Hydroxyindole and Stimulated by Isatin</a><br><br>
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<h2>Overview</h2>
 
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong" target=_top>
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<b><font color="#FFE1E1" size=3>Home</font></b>
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<b><font color="green">Our Project</font></b></p>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/overview.html" target=_top>Overview</a><font color="green"> | </font>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/data.html" target=_top>Data Page</a><br></p>
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<b><font color="green">Experiments and Results</font></b></p>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/asm.html"  target=_top>Strain Construction</a><font color="green"> | </font>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/mic.html"  target=_top>Culture Tests</a><font color="green"> | </font>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/modeling.html"  target=_top>Modeling</a><br></p>
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<b><font color="green">Miscellaneous</font></b></p>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/notebook.html" target=_top>Notebook</a></p>
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<b><font color="#FFF4D0">iGEM Resources</font></b></p>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/acknowledgement.html" target=_top>Acknowledgements</a></p>
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<b><font color="#FFF4D0">The Team</font></b></p>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/team.html" target=_top>iGEM Member List</a><font color="#FFF4D0"> | </font>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/contribution.html" target=_top>Contributions</a><br></p>
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<b><font color="#FFF4D0">Achievements</font></b></p>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/medal.html" target=_top>Medal Requirements</a><font color="#FFF4D0"> | </font>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/biosafety.html" target=_top>BioSafety</a><br></p>
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong" target=_top><font face="Verdana, Arial, Helvetica, sans-serif" size="4" color="#FFE1E1" font color=white><span style="font-weight:700">Home</span></font></a></font></b></p>
 
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<a href="https://2011.igem.org/Team:HKUST-Hong_Kong/characterization.html" target=_top>Master List & Characterization Data</a><br></p>
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Our Project</font></b></p>
 
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Latest revision as of 17:51, 28 October 2011


Background The Battle Plan  Building the horse - Engineering a novel strain for antibiotics-free selection The army inside - Toluene-4-Monooxygenase (T4MO)              Overview
    Background ·   The Battle Plan ·   Building the horse ·   The army inside



1. Background

In the past decade, the number of medical cases involving multi-antibiotic resistant microbes has seen a steady increase, and misuse of antibiotics has repeatedly been mentioned as one of the major reasons for the arise of such organisms. This situation provided the inspiration for our project, which is to attempt to improve the effectiveness of antibiotics, so that we can apply less of it to achieve the same effect as we do now.

Our project name - E. trojan - has its origins rooted in the Trojan Horse found in the tale of the Trojan War. Similar to how the Greeks destroyed the city of Troy from within using a wooden horse filled with soldiers, our E. trojan also works to destroy an E. coli population that is under antibiotic stress from within through indole quorum-sensing disruption. [Top]

2. The Battle Plan

Indole has been proposed as a key signalling molecule for E. coli in mediating resistance to environmental stress.[1] In particular, indole is found to stimulate passive resistance against antibiotics by triggering stress-response mechanisms inside cells, including increased expression of drug efflux pumps and oxidative-damage repair systems.

In a normal E. coli population containing wild type and naturally resistant mutants, the mutants will supply indole to nearby cells that are under antibiotic stress. This is considered to be a 'charity' action as the mutant does so at a fitness cost to itself. Our aim is to introduce E. trojan into the population and proceed to degrade indole via an enzyme (T4MO) and remove the charity effect. If the charity effect is significant, removal of its presence will cause a notable increase in the effectiveness of antibiotics. [Top]

3. Building the horse - Engineering a novel strain for antibiotics-free selection

To study the interaction and population dynamics of the naturally-coexisting HR (high resistance) and LR (low resistance) E. coli strains under antibiotic selection pressure, the E. trojan - which is to be introduced to HR/ LR mixed culture - should harbor the T4MO gene to allow it to perform quorum sensing disruption between the two strains. In addition, the E. trojan should not possess a wide spectrum of antibiotic resistance as this would give it an inherent selective advantage, thus interfering with the relationship between MICs and indole degradation in our study.

To fulfill the above criteria, it becomes necessary for us to first construct a new, pre-E. trojan bacterial strain (E. CRAFT) that is capable of performing plasmid selection without antibiotics and consequently contains as few antibiotic resistance genes as possible. Due to some limitations of the various alternative (non-antibiotic) selection methods[2] available today, we have designed E. CRAFT in a way that causes it to perform selection by imposing internal pressure of holding an essential gene for survival. Upon the completion of this precursor strain, the E. trojan can be easily constructed by transformation of the T4MO gene into it. In the long run, however, we hold a hope that this novel strain will prove to be a versatile, effective alternative to the widely- used antibiotic selection method.[Top]

4. The army inside - Toluene-4-Monooxygenase (T4MO)

Toluene-4-Monooxygenase (T4MO) is a three-component enzyme system that is naturally able to degrade a variety of hydrocarbons. In particular, its ability to oxidize small aromatic compounds has caught the attention of scientists looking for biological means of producing certain useful organic chemicals for industrial use, resulting in extensive research on modifying its activity and affinity.

For our project, a mutated form of T4MO (double mutations at G103L & A107G) was chosen as the candidate for indole degradation. While there were several possible candidates, this particular one was known to convert almost 50% of the indole into 7-hydroxyindole (7-HI)[2]. This is of great interest to us as 7-HI has been documented to inhibit biofilm formation in Enterohemorrhagic E. coli[3], and quite possibly for other strains of E. coli as well. Biofilm formation is a major element that reduces the efficiency of antibiotics due to reduced area of action, and hence we were keen to take advantage of this synergistic effect to improve our construct.[Top]

4.1 Soldiers need shields...maybe - Multidrug Efflux Pump (Bcr)

As our novel strain will have one of its essential genes maintained in a plasmid, a lot of uncertainties are present regarding its fitness. It is quite possible that it will be more vulnerable to antibiotics compared with wild type and thus will be selected against when cultured together with wild type E. coli. This would reduce the effectiveness of our construct and is not desirable. Hence we planed an additional component to be maintained in the plasmid, known as Bcr, which we hope will boost the resistance of E. trojan. You will find more details on its construction here.[Top]


[1] Bacterial charity work leads to population-wide resistance
[2] Antibiotic-free selection in E. coli: new considerations for optimal design and improved production
[3] Mutations of Toluene-4-Monooxygenase That Alter Regiospecificity of Indole Oxidation and Lead to Production of Novel Indigoid Pigments
[4] Enterohemorrhagic Escherichia coli Biofilms Are Inhibited by 7-Hydroxyindole and Stimulated by Isatin

Home

Our Project

Overview | Data Page

Experiments and Results

Strain Construction | Culture Tests | Modeling

Miscellaneous

Notebook

iGEM Resources

Acknowledgements

The Team

iGEM Member List | Contributions

Achievements

Medal Requirements | BioSafety

BioBricks

Master List & Characterization Data

Human Practice

Workshop | Survey