Wiki/Team:Warsaw/igem project.htm

Aims of the project

One of the most important challenges in the field of modern medicine is to invent the efficacious anticancer therapy. The gene therapy appears to be the most effective strategy for metastasis remission without dangerous side effects, which are common disadvantages in the case of both radioand chemotherapy. Use of bare DNA particles is very inefficient, therefore new DNA delivery system is needed. The most common vectors used in genetic therapy are genetically altered viruses. However they generate problems that have not been solved yet. An integration into the host genome may lead to unpredictable sideeffects and increases cancer risk. Moreover this type of vector could cause acute immune response or symptoms of viral infection. Artificial systems of DNA or RNA delivery such as liposomes or alkaline polymers are characterized by low effectiveness and high toxicity.

The main aim of this project is to design a model system based on genetically modified Escherichia coli bacteria able to invade eukaryotic cells. This approach is the new alternative for established for years techniques. It has most of advantages of previously known viral vectors and, importantly, it does not induce negative changes in the patient’s genome. The created bacterial system will be applied to two problems. The first one is to create special bacterial strain, which is able to conjugate with the mitochondrion within the cytoplasm. It will enable effective DNA delivery in scientific or therapeutic approaches. The second strategy is to induce apoptosis of tumor cells by means of the proapoptotic proteins secreted to the cytoplasm by bacteria that exist within the cell.

Theoretical basis

Entrance of bacteria into eukaryotic cells

Many bacterial species are able to invade an eukaryotic cell. One of the crucial proteins for this process is invasin. It is capable of selective interaction with integrins, which are present on eukaryotic membrane. It triggers signalling cascade indispensable to start endocytosis [9]. This interaction occurs via the invasin N-terminal domain, which is able to promote effective endocytosis of bacteria that synthesize invasin by cells normally unable to undertake phagocytosis [3]. Majority of the enteropathogenic bacteria are incapable to divide within the phagosome, but after leaving the phagosome they can proliferate rapidly in the cytoplasm. Escape from the phagosome is possible because of hemolysin which causes membrane permeabilisation and phagosome disruption [16]. It was presented previously that transfection with gene encoding hemolysin is sufficient to enable Bacillus subtilis and Escherichia coli to escape phagosomal vesicle [1].

Mitochondrial transformation

Electron transport chain function can be impaired by a variety of defects acting on the DNA level: not only point mutation and local deletions in genes encoding proteins of the chain, but also deletions of huge fragments or even whole mitochondrial genome (mtDNA). Correct mitochondrion contains 2 to 10 copies of mtDNA. Defects in mitochondrial DNA result in severe medical disorders especially in tissues which consume large amount of energy like nervous and muscle tissue. Effects of this impairments are neuroand myopathies [20]. The standard therapy based on bypassing interrupted pathways does not apply under mentioned circumstances. Administration of enzyme cofactors or other metabolically active substances is not effective and may be applied only as supplementary therapy. We are forced to seek novel treatment strategies to cure patients suffering from mitochondrial disorders [7]. Currently the most commonly used method of mitochondrial transformation is the "gene gun" approach which is based on delivery of metal beads coated with DNA into the cell. This method is mostly limited to plants and yeast and has low therapeutic potential [7]. Current mammalian mitochondrial transformation techniques like electroporation are also limited. Whole process takes place ex vivo and causes irreversible mitochondrion destructions which make its efficient reintroduction to the cell almost impossible. The conjugation between bacteria and mitochondria free from these side effects. Moreover, this phenomenon has been proven to act in vitro. Conjugative plasmid had been placed in mitochondrion, where the expression of encoding genes occurred [22]. More recently a conjugation between two strains of bacteria within the cytoplasm of a mammalian cell has been observed . These findings suggest that conjugation between a bacterium and a mitochondrion is feasible [10].

Bacterial systems of protein secretion

Bacteria in natural environment use diverse, effective transport and secretion systems. In gram negative bacteria like E. coli common are type I secretion systems e.g. well characterized hemolysin secretion system. Hemolysin is responsible for pathogenicity of some E. coli strains. Systems using fusion of protein of interest to hemolysin C-terminus result in secretion of the protein into the growth medium[6] The same method can be use to secret bacterial proteins into the eukaryotic cell. It is currently used by designing new generation vaccines[5].

Induction of apoptosis by p53

Mitochondrial outer membrane permabilization MOMP is one of the main programmed cell death mechanisms. The process is regulated by PTPc complex and Bcl2 family proteins [17]. Many cancer types involve disruption of this process therefore inducing MOMP in the tumour cells is regarded as potential therapeutic solution. Factors inducing MOMP include p53 protein. It is mutated in almost half of the cancer cases. Protein p53 by acting as a transcription regulator in the nucleus arrests the cell cycle and induce apoptosis [18]. In the cytoplasm p53 interacts with mitochondrial membrane and can enter the mitochondrium. It has been proven that these processes induce apoptosis and do not influence the cell cycle. In the mitochondrium p53 is an effector protein that activates soluble (cytochrom c, Smac) and insoluble (AIF, EndoG) apoptototic factors. Moreover interaction of p53 and Bax protein in vitro leads to permabilisation of lipid bilayer analogous to mitochondrial membrane. [12] Because p53 is inactive in tumour cells many research groups focused on designing gene therapies based on p53 gene delivery. Most frequently adenoviruses and eukaryotic plasmids were used. The research results confirmed increased effectiveness of chemotherapeutic drugs after introduction of p53 gene copy into the cell [4]. It has been shown that p53 with the mitochondrial leader sequence is enough to induce apoptosis in mammalian cells. The fusion protein Lp53 with mitochondrial leader sequence from ornithine transcarbamylase was used. In terms of apoptosis induction fusion protein was almost as effective as standard p53. Previous research did not include delivery of p53 into tumour cells by bacterial vectors. Secretion of p53 into the cytoplasm by bacteria has an advantage over gene therapy because it does not disrupt genome integrity. Results of p53 integration with host genome are not fully characterized yet, but too high level of p53 is shown to accelerate ageing. Our project proposes a method to induce apoptosis without arresting the cell cycle. Cell cycle arrest decreases the sensitivity of cancer cells to chemotherapeutic agents, because they can affect only proliferating cells [14].

Detailed research project

Introduction

Fig 1. The overview of the system. Gene regulatory network is composed of three modules: invasion operon, endosome detection operon and cytoplasmic operon. Invasion and cytoplasmic operon are bistable switches regulated by endosome detection operon.

We are going to create E. coli strain able to enter the eukaryotic cells using the controlled expression of invasin from Yersinia sp. It leads to internalization of the bacteria into the fagosome of the host cell. To escape the endosome we will use controlled expression of bacterial hemolysin (listeriolysin) from Listeria monocytogenes. The coordination of protein expression is based on switching the E. coli cells between four physiological states: growth in the growth medium, ability to enter mammalian cells, presence in the endosome, and escape from the endosome into the cytoplasm. (Fig1.). Two component system phoP/phoQ from Salmonella typhimurium will be used to detect states. It activates PhoP dependent promoters in the endosomal conditions (low pH, low metal ions concentration). Each of the states is going to be stabilised by two feedback loops based on natural regulatory systems. System is composed of three synthetic operons [18].

Invasion operon

Fig 2. The overview of the invasion operon. It is a lacI/cI bistable switch. After thermal activation (42°C) the expression of genes that enable invasion of mammalian cells is activated. The invasion operon is composed of lacI – lactose operon repressor, llo – hemolysin from Listeria monocytogenes, inv – invasin from Yersinia sp., phoQ/phoP two component system detecting endosomal conditions from Salmonella typhimurium, GFP – Green Fluorescent Protein. Proteins are fused with LVA sequence that provides quick proteolytic degradation by bacteria.

The invasion operon includes lacI – lactose operon repressor, llo – hemolysin from Listeria monocytogenes, inv – inwasin from Yersinia sp., phoQ/phoP two component system that detects endosomal conditions from Salmonella typhimurium, GFP – green fluorescent protein. (Fig.2.). These genes are under the control of bacteriophage promoter (PR) that is repressed by CL protein. The second part of the operon is gene clts that codes for thermosensitive version of the CI repressor protein from phage . It is under control of lactose promoter (Plac). This λ system of promoters and regulatory genes creates two mutually exclusive negative feedback loops and is called bistable switch[19]. It has two states depending on conditions within the cell. Cl protein binds the PR promoter inhibiting its activity and expression of the invasion operon genes. Cl protein is inactivated by high temperature 42°C it allows the expression of invasion operon that codes for LacI. LacI stops gene expression from the Plac promoter ( the expression of Cl protein). IPTG that binds and inactivates LacI can be used to switch on the expression from Plac promoter. Another way to control the operon is in trans expression of CL or LacI genes. Activated invasion operon causes internalisation of bacteria by mammalian cells. It also detects endosomal localisation using phoP/phoQ system. Expression of green fluorescence protein allows observation of the process using confocal microscopy.

Endosome detection operon

Fig 3. Overview of endosomal detection operon. It is composed of cro – antirepressor from phage λ, tetR – repressor of tetracycline resistance operon, cI – repressor from phage λ and cfp – Cyan Fluorescent Protein.

The low endosomal pH limits the concentration of metal ions. In these conditions transmembrane receptor kinase phoQ is less likely to bind its ligands – divalent cations. It allows the phosphorylation of phoP by phoQ. Phosphorylated phoP activates the gene expression from phoQ promoter expression of proteins encoded by endosome detection operon. Cl protein inactivates the invasion operon. TetR protein activates cytoplasmic operon. But not all genes encoded by cytoplasmic operon are expressed in endosome because operon contains cro box that binds cro protein which stops transcription. Cro protein is encoded by endosome detection operon. After bacterium escapes into cytoplasm the endosome detection operon genes are no longer expressed because phoP is not phosphorylated in cytoplasmic conditions. Process can be monitored using CFP fluorescence protein.

The cytoplasmic operon.

Fig 4. Overview of endosomal detection operon. It is composed of YFP – Yellow Fluorescent Protein, tetR – repressor of a tetracycline resistance operon, cro box regulatory sequence from phage and λ desired genes and genes specific for desired function of bacterial strain. In this case p53 – apoptosis inducer.

Cytoplasmic operon like the invasion operon is a bistable switch. The regulatory elements are: synthetic promoter inhibited by TetR, promoter inhibited by araC, araC protein (inactivated by L-arabinose) and TetR protein (repressor of tetracycline resistance gene inactivated by tetracycline). [18] This switch controls genes expressed in the cytoplasm. Cro box confines the gene expression to the cytoplasm only. Cro protein bound to it stops the transcription while the endosome detection operon is expressed. The yellow florescence protein is expressed to allow detection of the cytoplasmic operon activity. The set of genes in the cytoplasmic operon depends on the desired functionality of bacterial strain. In case of anticancer therapy it would be p53 protein with mitochondrial leader sequence. In the strain able to conjugate with mitochondria cytoplasmic operon will control genes responsible for conjugation process.

The mechanism of proposed regulatory system.

In the medium the expression of all genetic circuits is inactive. After temperature increase to 42°C the system is activated by thermal deactivation of cI. Genes from invasion operon are transcribed. They maintain their own expression, cause internalisation of E. coli by mammalian cells and enable escape from endosome. When bacterial cell is inside the endosome the endosome detection module is activated by phoP/phoQ system. In trans expression of regulatory genes cI and tetR deactivates invasion operon and activates cytoplasmic operon. However its genes are not expressed as long as bacterial cell is inside endosome due to cro protein activity. When bacterium escapes from the endosome, the transcription from endosome detection operon is repressed and cytoplasmic operon genes are expressed.

Conjugation with mitochondria.

To place the copy of the mitochondrial genome into bacterial cell the pBACrNESd plasmid will be used. It is built basing the Bacterial Artificial Chromosome. Replication origin (ori R6K), kanamycin resistance gen (kanR) and replication complex genes (repE, parA, parC) from pBACrNESd plasmid will be fused with origin of transfer (oriTF) from natural conjugative F plasmid. Unique restriction site will be introduced to the mitochondrial genome by PCR reaction and the described gene construct will be inserted into mitochondrion. To enable conjugation proteins encoded on RP4 plasmid (Tc, MuKm, Tn7) will be placed in the cytoplasmic operon. These genes are responsible for pillus formation and transport of single stranded DNA. The cell with this system will conjugate with any structure surround by lipid bilayer. We will prepare mitochondrial DNA deficient cells using procedure described in [2]. The occurrence of conjugation will be confirmed by PCR reaction specific for sequences added to mitochondrial DNA. The quality of the DNA will be determined by analysis of restriction patterns. The expression of mitochondrial genes will be confirmed by semiquantitative time PCR [2].

Secretion of p53 into the cytoplasm

To efficiently transport p53 to the eukaryotic cells the endogenic E. coli secretion system responsible for secretion of hemolysin by uropathogenic strains will be used. It is composed of three transport proteins HlyB, HlyD and TolC [10]. TolC is present in the genome of the lab strain derived from K12 strain. To ensure efficient secretion hlyB and hlyD have to be introduced into the genome and proapoptotic protein has to be fused with 60 amino acid long C-terminal sequence of hemolysin. [5].

Directing bacterial proteins to mammalian mitochondria.

We need to be able to direct to the mammalian mitochondria some of the proteins secrete by bacteria into the cytoplasm of the host cell. It is going to be archived by fusion of mitochondrial leader sequence from human protein Suv3 to the N-terminus of proteins. It has been shown that 40 amino acids long N-terminal sequence is enough for effective transport of Suv3 through the mitochondrial membrane. [21]. First the efficiency of the process will be assessed by detection of Red Fluorescent Protein with confocal microscopy. The red fluorescence should be visible in the mitochondria of the cells invaded by bacteria expressing RFP fused with mitochondrial leader sequence. Then the ability to induce apoptosis by mitochondrially directed p53 will be investigated. Apoptosis induction will be confirmed by flow cytometry [8]. In addition we will use confocal microscopy to monitor the process. In both cases cells will be stained with propidium iodide and annexin V.

REFERENCES

1. Bielecki J, Youngman P, Connelly P, Portnoy DA. Bacillus subtilis expressing a haemolysin gene from Listeria monocytogenes can grow in mammalian cells. Nature. 1990 May 10;345(6271):1756
2. Cao J, Liu Y, Jia L, Zhou HM, Kong Y, Yang G, Jiang LP, Li Q J, Zhong LF. Curcumin induces apoptosis through mitochondrial hyperpolarization and mtDNA damage in human hepatoma G2 cells. Free Radic Biol Med. 2007 Sep 15;43(6):96875
3. Dersch P, Isberg RR. An immunoglobulin superfamilylike domain unique to the Yersinia pseudotuberculosis invasin protein is required for stimulation of bacterial uptake via integrin receptors. Infect Immun. 2000 May;68(5):29308
4. Fuster JJ, SanzGonzález SM, Moll UM, Andrés V. Classic and novel roles of p53: prospects for anticancer therapy. Trends Mol Med. 2007 May;13(5):1929
5. Gentschev I, Dietrich G, Spreng S, KolbMäurer A, Daniels J, Hess J, Kaufmann SH, Goebel W. Delivery of protein antigens and DNA by virulenceattenuated strains of Salmonella typhimurium and Listeria monocytogenes. J Biotechnol. 2000 Sep 29;83(12): 1926
6. Gentschev I, Mollenkopf H, Sokolovic Z, Hess J, Kaufmann SH, Goebel W. Development of antigen delivery systems, based on the Escherichia coli hemolysin secretion pathway. Gene. 1996 Nov7;179(1):13340
7. Johnston SA, Anziano PQ, Shark K, Sanford JC, Butow RA. Mitochondrial transformation in yeast by bombardment with microprojectiles. Science. 1988 Jun 10;240(4858):1
8. Krysko DV, Vanden Berghe T, D’Herde K, Vandenabeele P. Apoptosis and necrosis: detection, discrimination and phagocytosis. Methods. 2008 Mar;44(3):20521
9. Leong JM, Fournier RS, Isberg RR. Identification of the integrin binding domain of the Yersinia pseudotuberculosis invasin protein. EMBO J. 1990 Jun;9(6):197989
10. Lim YM, de Groof AJ, Bhattacharjee MK, Figurski DH, Schon EA. Bacterial conjugation in the cytoplasm of mouse cells. Infect Immun. 2008 Nov;76(11):51109
11. Mahoney DJ, Parise G, Tarnopolsky MA. Nutritional and exercisebased therapies in the treatment of mitochondrial disease. Curr Opin Clin Nutr Metab Care. 2002 Nov;5(6):61929
12. Mihara M, Erster S, Zaika A, Petrenko O, Chittenden T, Pancoska P, Moll UM. p53 has a direct apoptogenic role at the mitochondria. Mol Cell. 2003 Mar;11(3):57790
13. MIT registry of standard biological parts http://partsregistry.org
14. Palacios G, Crawford HC, Vaseva A, Moll UM. Mitochondrially targeted wildtype p53 induces apoptosis in a solid human tumor xenograft model. Cell Cycle. 2008 Aug 15;7(16):258490
15. Patil SD, Rhodes DG, Burgess DJ. DNAbased therapeutics and DNA delivery systems: a comprehensive review. AAPS J. 2005 Apr 8;7(1):E6177
16. Polekhina G, Giddings KS, Tweten RK, Parker MW. Insights into the action of the superfamily of cholesteroldependent cytolysins from studies of intermedilysin. Proc Natl Acad Sci USA. 2005 Jan 18;102(3):6005
17. Reed JC. Proapoptotic multidomain Bcl2/ Baxfamily proteins: mechanisms, physiological roles, and therapeutic opportunities. Cell Death Differ. 2006 Aug;13(8):137886
18. Riley T, Sontag E, Chen P, Levine A. Transcriptional control of human p53regulated genes. Nat Rev Mol Cell Biol. 2008 May;9(5):40212
19. Sayut DJ, Kambam PK, Sun L. Engineering and applications of genetic circuits. Mol Biosyst. 2007 Dec; 3(12):83540
20. Smith PM, Ross GF, Taylor RW, Turnbull DM, Lightowlers RN. Strategies for treating disorders of the mitochondrial genome. Biochim Biophys Acta. 2004 Dec 6;1659(23):2329
21. Stepien PP, Margossian SP, Landsman D, Butow RA. The yeast nuclear gene suv3 affecting mitochondrial posttranscriptional processes encodes a putative ATPdependent RNA helicase. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):68137
22. Yoon YG, Koob MD. Transformation of isolated mammalian mitochondria by bacterial conjugation. Nucleic Acids Res. 2005 Sep 12;33(16):e139