Team:Caltech/Project

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==[[Team:Caltech/Project/Vitamins|<font face="verdana" style="color:#BB4400">Vitamin Production</font>]]==
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==[[Team:Caltech/Project/Oxidative Burst|<font face="verdana" style="color:#BB4400">Oxidative Burst</font>]]==
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Folate  is the generic term for the various forms of Vitamin B9, which include dihydrofolate (DHF), tetrahydrofolate (THF), and folic acid. An essential vitamin for cell survival, folate is involved in amino synthesis (and thus DNA synthesis) as well as single-carbon-transfer reactions. Though humans don't produce folate, folate deficiency can cause serious birth defects and anemia. As a result, most cereals and breads are supplemented with folate. Folate has also been shown to have good bioavailability in the large intestine, and so is more easily absorbed by the host than other vitamins.  
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Specialized white blood cells called neutrophils defend us from illness by killing bacteria with a potent concoction of degradative enzymes and oxidizing agents, including hydrogen peroxide. However, pathogens of the human large intestine are able to cause serious illness while being sheltered from neutrophils. We engineered a strain of ''Escherichia coli'' that is able to mimic a neutrophil by producing cytotoxic amounts of hydrogen peroxide in a controlled, inducible manner. Our engineered ''E. coli'' use the transcriptional activator LuxR to detect the presence of acyl-homoserine lactones, quorum sensing signaling molecules secreted by invading pathogens. LuxR activates production of the pyruvate oxidase of ''Streptococcus pneumoniae'', which produces large amounts of hydrogen peroxide by oxidizing pyruvate. The engineered ''E. coli'' is capable of killing certain strains of antibiotic resistant ''E. coli'' within six hours.  When translated into a probiotic strain such as Nissle 1917, this system has the potential to be an effective means of combating enteric pathogens.
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Our aim is to engineer a strain of ''E. coli'' that will overexpress folate such that a person without access to green, leafy vegetables or folate-supplemented foods can still obtain the necessary daily amount by having this strain residing in their gut.
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==[[Team:Caltech/Project/Lactose intolerance|<font face="verdana" style="color:#BB4400">Lactose Intolerance</font>]]==
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==[[Team:Caltech/Project/Phage Pathogen Defense|<font face="verdana" style="color:#BB4400">Phage Pathogen Defense</font>]]==
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Lactose intolerance is the inability to metabolize lactose in the small intestine. For a non lactose intolerant person, he or she is able to express β-galactosidase in the small intestine which cleaves lactose into glucose and galactose. Glucose and galactose are then taken up by the host. For a lactose intolerant person, lactose travels passed the small intestine into the large intestine where it is metabolized by the gut flora. The osmolarity changes in the large intestine due to the large amounts of sugar, pulling more water into the large intestine. Due to this rush of water, lactose intolerant persons may experience diarrhea. Lactose is metabolized in this order: Lactose --> glucose + galactose --> lactic acid + acetic acid --> H<sub>2</sub> --> methane. A different bacteria is involved in each step, so we can't engineer our strain to metabolize lactose, because it will eventually get metabolized into methane, which is the cause of abdominal pain and unwanted gas.
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Bacterial food poisoning is a prevalent problem around the world. In the year 2006, the United States had more than 325,000 hospitalizations from food borne illnesses. This subproject focuses on the prevention of food poisioning by the release of pathogen-specific bacteriophage. A model system for ‘manufacturing’ phage was built around ''Escherichia coli'' bacteriophage λ lysogens. We began with a strain of ''E. coli'' which does not express the receptor, LamB, necessary for λ infection. Next we expressed the receptor in the cell, allowing infection and lysogeny. Then the receptor was removed, again rendering the cell non-susceptible. Finally, a plasmid was constructed to control the induction of λ by regulating the expression of ''rcsA'' and ''cI''. When fully implemented, this system could be used to treat food poisoning due to pathogenic ''E. coli''. The system can also be modified to target other pathogenic species, such as ''Salmonella'', by replacing λ phage with other temperate bacteriophages and using similar methods to incorporate the non-native phage into ''E. coli''.
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Instead, we will engineer a strain of ''E. coli'' that will express the β-Gal gene in the large intestine to quickly cleave lactose. The host will then be able to reabsorb the glucose and galactose from the large intestine.
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==[[Team:Caltech/Project/Oxidative Burst|<font face="verdana" style="color:#BB4400">Oxidative Burst</font>]]==
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==[[Team:Caltech/Project/Lactose intolerance|<font face="verdana" style="color:#BB4400">Lactose Intolerance</font>]]==
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Several types of bacteria can cause illness in humans by infecting the gut. ''Salmonella'' and ''E. coli'' are probably the two people most frequently associate with food poisoning. There are other pathogenic bacteria that can infect our gut as well. ''Shigella'' and ''Campylobacter'' can cause cramping, diarrhea and dysentery. ''Vibrio cholerae'', which also infects the gut, is the cause of cholera. The body normally relies on white blood cells (neutrophils) to clear bacteria from the body. Once a bacterium is engulfed, the neutrophil releases a sudden and toxic amount of reactive oxygen species, comprised of a mixture of superoxide, hydrogen peroxide, and hypochlorous acid. This is event is termed the oxidative burst. However, white blood cells do not patrol the gut lumen and so there is no active clearance of pathogens. The goal of this project is to engineer a beneficial gut microbe capable of detecting a harmful bacterium and, in turn, generate an oxidative burst sufficient to kill the pathogen.
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Approximately 75% of adults worldwide suffer from lactose intolerance, the inability to metabolize lactose in the small intestine. We propose to treat lactose intolerance by engineering a strain of ''Escherichia coli'' that can reside in the large intestine. The engineered strain will sense lactose and subsequently release ß-galactosidase to convert lactose into glucose and galactose, both of which can be reabsorbed by the host. To treat lactose intolerance, our engineered bacterial strain will contain two plasmids: one with constitutive expression of a mutant lactose permease and ß-galactosidase, and the second with lactose-inducible expression of the λ phage lysis cassette. The mutant lactose permease allows the cells to import lactose under all conditions. When the cells uptake enough lactose, the second plasmid will induce cell lysis through activation of the λ phage lysis cassette, resulting in cell lysis and release of ß-galactosidase into the large intestine. Data covering the construction and characterization of these plasmid constructs is [[Team:Caltech/Project/Lactose_intolerance|<font style="color:#BB4400">discussed</font>]].
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==[[Team:Caltech/Project/Phage Pathogen Defense|<font face="verdana" style="color:#BB4400">Phage Pathogen Defense</font>]]==
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==[[Team:Caltech/Project/Vitamins|<font face="verdana" style="color:#BB4400">Vitamin Production</font>]]==
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Another aspect of bacterial pathogen defense for our probiotic is to produce bacteriophages, which would rapidly infect and wipe out all of the pathogens. There are basically methods to approach phage production, differentiated by the type of phage used. The first uses the bacteriophage λ, which targets E. Coli. The other is exploring the use of a temperate bacteriophage from B. Subtilis, however this method, if successful, can be adapted to temperate bacteriophages of any bacterial strain.
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Folate, a term which encompasses the various forms of the vitamin B9, is an essential vitamin involved in everyday cell functions such as DNA replication. Unable to naturally produce folate, humans must obtain it from vegetables or folate-supplements. In regions with little or no access to these foods, folate deficiencies can cause serious birth defects. One possible solution to alleviate the effects of folate deficiency is to engineer a strain of gut microbes to produce bioavailable folate directly in the colon. We tested a total of four heterologous genes, two from the folate biosynthesis gene cluster and two from the paraaminobenzoic acid (pABA) synthesis pathway. Using standardized genetic sequences, folate biosynthesis genes extracted from the ''Lactoccocus lactis'' genome were cloned into Biobricks plasmids, transformed into ''Escherichia coli'' and overexpressed. We measured the effects of overexpression
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in terms of total folate and paraaminobenzoic acid levels. PABA, an intermediate in folate synthesis, was detected using [[Team:Caltech/Protocols/PABA_HPLC_assay|<font style="color:#BB4400">high performance liquid chromatography</font>]] (HPLC). Folate detection was achieved via a [[Team:Caltech/Protocols/Folate_assay|<font style="color:#BB4400">microbiological assay</font>]]. A measurable increase in folate production in ''E. coli'' provides proof-of-concept for both the feasibility of engineering overproduction of folate in ''E. coli'', as well as using standardized genetic components to do so.
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Bacteriophage λ is a temperate phage with an E. Coli. host, λ infects E. Coli through the lamB receptor, and absence of this receptor prevents λ infection. We will takes advantage of this aspect of bacteriophage λ to create E. Coli which are resistant to the phage, but release the phage to destroy susceptible pathogenic E. Coli.
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The second approach is more versatile, and can target more strains of pathogenic bacteria. The goal is to create a phasmid out of the genome of a temperate bacteriophage. A phasmid combines a E. Coli plasmid Origin of Replication with a linear phage genome, circularizing it. This allows the phasmid to pass on as a plasmid within E. Coli, however when transferred to its native host, the phage phage is induced.  
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Given that we have created four different states for a cell to be in, we need to in some manner combine them into one system. However, we need to ensure that any particular cell is in only one of these states, and not more than one, or else the load on the cell may be too big. In other words, we want to make these states mutually exclusive.  
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As more complicated and interconnected biological circuits are built, there is an increasing need for the simple integration of multiple functions into a single bacterial cell line. However, some of these functions may be incompatible or may kill the cell, such that each cell can only express a single function at any time or must be regenerated if the functionality is fatal. We aim to combine multiple mutually exclusive and potentially fatal functions into a single bacterial cell line that, as a population, exhibits the entire set of functions.  
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In particular, we want only one of the four subprojects described above to be turned on in any given cell, or else the cell may be overburdened by our constructs. At the same time, we want our bacterial population to have the capability to exhibit all four functions. In addition, three of the four subprojects result in the death of the host cell through different methods of self-induced lysis. Therefore, we need a system that is able to combine all subprojects into one coherent system and that allows for self-renewal of the population.
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To do so, two new devices have been created: a randomly activated off-to-on switch and a population variation generator. Initially, a cell is in a default state (S0), the switch is off, and the fate of the cell is undetermined. However, each time a cell replicates the plasmid that contains the switch, there is a chance that the switch turns on. Once the switch is on, it activates the population variation generator, which in turn determines the fate of the cell by setting it to one of three states - S1, S2, or S0 (the original default). That cell and all of its descents then stay in the determined state.  
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We propose a system in which a single bacterial strain encodes all four functions in its genome and can access each function independently through probabalistic molecular events. The engineered bacterial cells start in an undifferentiated state and randomly differentiate into one of three possible final states. To build this system, we designed two genetic devices. One relies on DNA polymerase slippage upon replication of a long stretch of short nucleotide repeats, a phenomenon termed slipped-strand mispairing (SSM). The other device uses the recombinase protein FimE to flip DNA segments. The two devices can form a system that permits the novel introduction of random multi-state differentiation into bacterial cells. Our experimental results demonstrate that short nucleotide repeats can be used as a stochastic switch and that FimE activity depends on the length of the segment being flipped.  
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Latest revision as of 20:49, 29 October 2008


iGEM 2008



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Subprojects
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Oxidative Burst

Specialized white blood cells called neutrophils defend us from illness by killing bacteria with a potent concoction of degradative enzymes and oxidizing agents, including hydrogen peroxide. However, pathogens of the human large intestine are able to cause serious illness while being sheltered from neutrophils. We engineered a strain of Escherichia coli that is able to mimic a neutrophil by producing cytotoxic amounts of hydrogen peroxide in a controlled, inducible manner. Our engineered E. coli use the transcriptional activator LuxR to detect the presence of acyl-homoserine lactones, quorum sensing signaling molecules secreted by invading pathogens. LuxR activates production of the pyruvate oxidase of Streptococcus pneumoniae, which produces large amounts of hydrogen peroxide by oxidizing pyruvate. The engineered E. coli is capable of killing certain strains of antibiotic resistant E. coli within six hours. When translated into a probiotic strain such as Nissle 1917, this system has the potential to be an effective means of combating enteric pathogens.

Phage Pathogen Defense

Bacterial food poisoning is a prevalent problem around the world. In the year 2006, the United States had more than 325,000 hospitalizations from food borne illnesses. This subproject focuses on the prevention of food poisioning by the release of pathogen-specific bacteriophage. A model system for ‘manufacturing’ phage was built around Escherichia coli bacteriophage λ lysogens. We began with a strain of E. coli which does not express the receptor, LamB, necessary for λ infection. Next we expressed the receptor in the cell, allowing infection and lysogeny. Then the receptor was removed, again rendering the cell non-susceptible. Finally, a plasmid was constructed to control the induction of λ by regulating the expression of rcsA and cI. When fully implemented, this system could be used to treat food poisoning due to pathogenic E. coli. The system can also be modified to target other pathogenic species, such as Salmonella, by replacing λ phage with other temperate bacteriophages and using similar methods to incorporate the non-native phage into E. coli.

Lactose Intolerance

Approximately 75% of adults worldwide suffer from lactose intolerance, the inability to metabolize lactose in the small intestine. We propose to treat lactose intolerance by engineering a strain of Escherichia coli that can reside in the large intestine. The engineered strain will sense lactose and subsequently release ß-galactosidase to convert lactose into glucose and galactose, both of which can be reabsorbed by the host. To treat lactose intolerance, our engineered bacterial strain will contain two plasmids: one with constitutive expression of a mutant lactose permease and ß-galactosidase, and the second with lactose-inducible expression of the λ phage lysis cassette. The mutant lactose permease allows the cells to import lactose under all conditions. When the cells uptake enough lactose, the second plasmid will induce cell lysis through activation of the λ phage lysis cassette, resulting in cell lysis and release of ß-galactosidase into the large intestine. Data covering the construction and characterization of these plasmid constructs is discussed.

Vitamin Production

Folate, a term which encompasses the various forms of the vitamin B9, is an essential vitamin involved in everyday cell functions such as DNA replication. Unable to naturally produce folate, humans must obtain it from vegetables or folate-supplements. In regions with little or no access to these foods, folate deficiencies can cause serious birth defects. One possible solution to alleviate the effects of folate deficiency is to engineer a strain of gut microbes to produce bioavailable folate directly in the colon. We tested a total of four heterologous genes, two from the folate biosynthesis gene cluster and two from the paraaminobenzoic acid (pABA) synthesis pathway. Using standardized genetic sequences, folate biosynthesis genes extracted from the Lactoccocus lactis genome were cloned into Biobricks plasmids, transformed into Escherichia coli and overexpressed. We measured the effects of overexpression in terms of total folate and paraaminobenzoic acid levels. PABA, an intermediate in folate synthesis, was detected using high performance liquid chromatography (HPLC). Folate detection was achieved via a microbiological assay. A measurable increase in folate production in E. coli provides proof-of-concept for both the feasibility of engineering overproduction of folate in E. coli, as well as using standardized genetic components to do so.

Population Variation

As more complicated and interconnected biological circuits are built, there is an increasing need for the simple integration of multiple functions into a single bacterial cell line. However, some of these functions may be incompatible or may kill the cell, such that each cell can only express a single function at any time or must be regenerated if the functionality is fatal. We aim to combine multiple mutually exclusive and potentially fatal functions into a single bacterial cell line that, as a population, exhibits the entire set of functions.

In particular, we want only one of the four subprojects described above to be turned on in any given cell, or else the cell may be overburdened by our constructs. At the same time, we want our bacterial population to have the capability to exhibit all four functions. In addition, three of the four subprojects result in the death of the host cell through different methods of self-induced lysis. Therefore, we need a system that is able to combine all subprojects into one coherent system and that allows for self-renewal of the population.

We propose a system in which a single bacterial strain encodes all four functions in its genome and can access each function independently through probabalistic molecular events. The engineered bacterial cells start in an undifferentiated state and randomly differentiate into one of three possible final states. To build this system, we designed two genetic devices. One relies on DNA polymerase slippage upon replication of a long stretch of short nucleotide repeats, a phenomenon termed slipped-strand mispairing (SSM). The other device uses the recombinase protein FimE to flip DNA segments. The two devices can form a system that permits the novel introduction of random multi-state differentiation into bacterial cells. Our experimental results demonstrate that short nucleotide repeats can be used as a stochastic switch and that FimE activity depends on the length of the segment being flipped.

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