Team:UNIPV-Pavia/Project/solution
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Different studies demonstrated that bacteria, such as ''V. fischeri'', can communicate through a mechanism called ''quorum sensing'' and can regulate gene expression relying on cell culture density. One of the most studied organisms is ''V. fischeri'', for which the quorum sensing is regulated by two genes: luxI and luxR. The first one encodes a protein responsible for the synthesis of 3-oxo-C6-homoserine-lactone (3OC6HSL or simply HSL), a small molecule called ''autoinducer''. The second one encodes a protein capable to bind the HSL. The ''lux pR'' promoter, which is normally off, can be activated by the LuxR-HSL complex when the autoinducer reaches a critical concentration. | Different studies demonstrated that bacteria, such as ''V. fischeri'', can communicate through a mechanism called ''quorum sensing'' and can regulate gene expression relying on cell culture density. One of the most studied organisms is ''V. fischeri'', for which the quorum sensing is regulated by two genes: luxI and luxR. The first one encodes a protein responsible for the synthesis of 3-oxo-C6-homoserine-lactone (3OC6HSL or simply HSL), a small molecule called ''autoinducer''. The second one encodes a protein capable to bind the HSL. The ''lux pR'' promoter, which is normally off, can be activated by the LuxR-HSL complex when the autoinducer reaches a critical concentration. | ||
- | When a cell population expresses luxI, the concentration of HSL is an increasing function of cell culture density and so the induction of the ''lux pR'' promoter occurs only when the | + | When a cell population expresses luxI, the concentration of HSL is an increasing function of cell culture density and so the induction of the ''lux pR'' promoter occurs only when the cells reach a threshold density. |
- | In ''V. fischeri'', the ''lux pR'' regulates a set of genes involved in the bioluminescence of the bacteria | + | Taking inspiration from this natural regulation mechanism, a library of self-inducible devices was built by engineering quorum sensing circuits in ''E. coli''. The critical cell density was modulated by changing the autoinducer molecule synthesis rate. In this way, the library members can initiate the ''lux pR'' gene expression at different cell densities of the host strain. In ''V. fischeri'', the ''lux pR'' regulates a set of genes involved in the bioluminescence of the bacteria, but in synthetic circuits based on this regulatory mechanism users can regulate the expression of the desired genes. |
Revision as of 19:42, 23 October 2010
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Thus, these BioBrick parts can be used to express recombinant proteins without adding an inducer to trigger the transcription initiation of downstream genes; in large-scale production of such proteins this strategy can be cost saving and ease the entire process.
Integrative standard vector for E. coliThe integration of the genetic circuits of interest into the microbial host genome can eliminate the need of expensive selection techniques, such as antibiotics or auxotrophic media, in cell cultures. In order to simplify the engineering of the host genome, two standard and modular integrative vectors have been designed for Escherichia coli and Saccharomyces cerevisiae, two commonly used hosts for industrial protein production. Here, a detailed description of the integrative vector for E. coli is reported, while the following section deals with the integrative vector for yeast.
This vector can be considered as a base vector, which can be specialized to target the desired integration site in the host genome. The default version of this backbone has the bacteriophage Phi80 attP (<partinfo>BBa_K300991</partinfo>) as integration site. This vector enables multiple integrations in different positions of the same genome.
GlossaryThe passenger is the desired DNA part to be integrated into the genome. The guide is the DNA sequence that is used to target the passenger into a specific locus in the genome.
The main design features for vector engineering and for the genome integration of the vector are reported below. Vector engineering features:
Genome integration features:
How to use it<partinfo>BBa_K300000</partinfo> can be:
How to propagate it before performing genome integrationThe default version of this vector contains the <partinfo>BBa_I52002</partinfo> insert, so it *must* be propagated in a ccdB-tolerant strain such as DB3.1 (<partinfo>BBa_V1005</partinfo>). After the insertion of the desired BioBrick part in the cloning site, this vector does not contain a standard replication origin anymore, so it *must* be propagated in a pir+ or pir-116 strain such as BW25141 (<partinfo>BBa_K300984</partinfo>) or BW23474 (<partinfo>BBa_K300985</partinfo>) that can replicate the R6K conditional origin (<partinfo>BBa_J61001</partinfo>).
How to engineer itThe DNA guide can be changed as follows:
How to perform genome integrationThe integration into the E. coli chromosome can exploit the bacteriophage attP-mediated integration or the homologous recombination. Detailed protocols about attP-mediated integration can be found here:
Detailed protocols about homologous recombination can be found here:
This integration method is applicable when the host strain does not have prophages in the att(Phi80) locus. TOP10 (<partinfo>BBa_V1009</partinfo>) and DH5alpha (<partinfo>BBa_V1001</partinfo>) strains have the Phi80 prophage and so their chromosome cannot be engineered with this procedure. The genomic integration of the desired BioBrick part into the attP(Phi80) locus has to be mediated by co-transforming a helper plasmid, such as the Amp-resistant <partinfo>BBa_J72008</partinfo> plasmid) which carries the IntPhi80 site-specific integrase gene under the control of a thermoinducible promoter (see Fig.5). The helper plasmid also has a heat-sensitive replication origin, whose replication can be inhibited at temperatures of 37-42°C, while a permissive temperature for this vector is 30°C. For this reason, it can be cured at high temperatures, when the integrase expression is triggered at the same time. The Phi80 integrase mediates the site-specific recombination between the attP site in the integrative vector and the attB site in the bacterial genome (for a schematic description of this process, see Fig.6 and http://partsregistry.org/Recombination). Thanks to its R6K conditional replication origin, the integrative vector cannot be replicated in common E. coli strains, so the Chloramphenicol resistant bacteria are actual integrants. In the Materials and Methods section (https://2010.igem.org/Team:UNIPV-Pavia/Project/results), a detailed protocol to target the desired BioBrick part into the Phi80 locus is reported. How to perform multiple integrations in the same genomeWhen this vector is integrated into the genome, the desired passenger should be maintained into the host, as well as the Chloramphenicol resistance marker and the R6K conditional replication origin. The CmR and the R6K can be excised from the genome by exploiting the two FRT recombination sites that flank them. The Flp recombinase protein mediates this recombination event (for a schematic description of this process, see Fig.7 and http://partsregistry.org/Recombination), so it has to be expressed by a helper plasmid, such as pCP20 (CGSC#7629). This enables the sequential integration of several parts using the same antibiotic resistance marker, which can be each time eliminated.
Detailed protocols about homologous recombination can be found here:
Integrative standard vector for yeastHere, a detailed description of the integrative vector for the yeast S. cerevisiae is reported. The structure of the designed vector, here named BBa_K300001, is shown in Fig.1. Most of its features have been inspired by the pUG6 plasmid (GenBank: AF298793.1), constructed by [Guldener U et al., 1996]. This is an integrative vector which can be used to insert the desired RFC10-compatible BioBrick parts/devices/systems into the genome of S. cerevisiae. This vector can also be specialized to target the desired integration site in the host genome. The default version of this backbone targets the Gal system of the S288C strain (<partinfo>BBa_K300979</partinfo>) through the two homologous regions <partinfo>BBa_K300986</partinfo> and <partinfo>BBa_K300987</partinfo>. The Gal system is not essential for yeast survival if the strain is grown on carbon sources other than galactose. This vector enables multiple integrations in different positions of the same genome. The usage of the KanMX dominant selection marker can avoid the usage of auxotrophic markers. In the industrial framework auxotrophies are usually deleterious for the process productivity because they affect the growth rate of cells. For this reason, this vector can be a concrete solution for the design of industrial yeast strains with novel user-defined functions.
GlossaryA HR (Homologous Region) is a sequence that can recombine with the host genome. As explained for the integrative vector for E. coli, The passenger is the desired DNA part to be integrated into the genome.
How to use it<partinfo>BBa_K300001</partinfo> can be:
How to propagate it before performing genome integrationThis vector can be easily propagated in E. coli thanks to the high-copy replication origin and the Ampicillin resistance selection marker, both derived from the <partinfo>pSB1A2</partinfo> vector backbone.
How to integrate a BioBrick into the yeast genome
Users can change the integration site by engineering the vector: <partinfo>BBa_K300986</partinfo> and <partinfo>BBa_K300987</partinfo> are flanked by two AvrII and two NheI respectively and for this reason the two Homologous Regions can be excided. New homologous sequences compatible with RFC10 can be digested with XbaI-SpeI and assembled because AvrII, NheI, XbaI and SpeI have compatible sticky ends. Note that this assembly is not directional and the correct orientation can be validated through sequencing with standard VF2 and VR primers.
How to perform the KanMX marker excisionThe KanMX dominant selection marker is flanked by two loxP recombination sites and for this reason it can be excided upon Cre recombinase activity. The Cre recombinase has to be expressed by a helper plasmid.
Self-cleaving affinity tags to easily purify proteinsConventional affinity-based protein purification methods rely on specific binding of the fusion tag to an immobilized ligand, but they are affected by severe limitations []. Firstly, they imply the use of expensive proteases for tag removal from the fusion protein, requiring the appropriate amminoacidic sequence to be included between the tag and the target protein. Secondly, the cost of the affinity resins used in the process is far from negligible, especially on industrial scale. The use of self-cleaving protein elements coupled with innovative affinity tags has been subsequently proposed to overcome these limitations. For all these reasons in this module a technique compliant to the BioBrick assembly standard and based on self-splicing affinity tags derived from the fusion of Phasins, Inteins and a short and flexible linker sequence is proposed []. TagPhasinPhasins are proteins involved in formation and stabilization of PolyHydroxyAlkanoates (PHA) intracytoplasmic inclusions in microorganisms like Ralstonia eutropha, which serve as carbon and energy storage []. As such, phasins exhibit highly specific binding to PHA granules; these granules and the associated Phasins can thus be used to create tags for proteins. BioBrick <partinfo>K208001</partinfo>, coding for Ralstonia eutropha‘s Phasin, has been improved and mutagenized through PCR using custom primers to build and submit two new BioBrick parts:
These two new parts allow the synthesis of composite constructs built using an arbitrary number of Phasins (it has been shown [] that best affinity is achieved by fusions of two or more Phasins). In this work a flexible linker sequence (<partinfo>BBa_K105012</partinfo>) that connects the Phasins has also been used in order to test if it can improve or facilitate the binding and folding of the tag. PHA productionPHA production in R. eutropha is achieved by the PhaCAB operon, which contains three genes, phbC, phbA and phbB, each encoding for an enzyme essential for the formation of PHA inclusions. Production of polyhydroxybutirrate (PHB, a kind of polyhydroxyalkanoate) granules in E. coli for use as an affinity matrix has been achieved in E. Coli strain DMSZ15372 which harbours pBHR68 plasmid shown below.
Protein purification systemInteinInteins (Intervening Proteins) are sequences capable of self-exciding from a host precursor protein through a process known as self-splicing, forming a peptide bond between the flanking proteins (exteins). Many so-called mini-inteins have been engineered, whose key feature is the capability to completely release a flanking extein (the target protein) in response to a simple stimulus, either chemical or physical, with no need for expensive endonucleases. One mini-intein in particular was obtained through deletion of the endonuclease domain and subsequent mutagenesis of Mycobacterium tuberculosis Mtu RecA intein []. The sequence of this intein, referred to as ΔI-CM, allows for pH- and temperature-controlled C-terminal cleavage. Once properly modified, it was synthesized for testing and submitted as <partinfo>BBa_K300004</partinfo>.
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