Team:LCG-UNAM-Mexico/Description

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='''Description'''=
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='''Description'''=
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=='''Relevance of the project'''==
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=='''The Project'''==
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Bacteria play a fundamental role in human life and they are still the preferred models to study the molecular dynamics of organisms. One example are probiotics because of their vital importance in industry and food manufacturing. Infection by phages represents a relevant and expensive problem in these areas. For this reason we decided to construct a system to contend with bacteriophage infection at a population level.
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Given this global protection vision emerges the idea of dividing our project in two subsystems: '''''[[Team:LCG-UNAM-Mexico/Description#a) Delivery| delivery]]''''' and '''''[[Team:LCG-UNAM-Mexico/Description#b) Defense| defense]]'''''. Their coupled expression leads to a cascade dependent on the presence of an infectious phage. This property gives an extra versatility to the project because the defense subsystem turns on faster enough to hold back the infection and then lasts enough to give "immunity" to the population. Therefore, it is feasible to achieve a faster and wider protection response by amplifying the infection signal delivered by the phage in order to increase the number of "immune" bacteria at every lytic cycle.
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=='''Logic design of the project subsystems'''==
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<br>
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Bacteriophage infection represents an interesting process in science and industry. The idea of being able to contend at a population level with such infections is the main motivation for the development of our project.<br>
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The first level of the expression cascade consists on the delivery ('''''[[Team:LCG-UNAM-Mexico/Description#a) Delivery| Delivery susbsystem]]''''') of the protection system that will be immediately activated when a phage is detected ('''''[[Team:LCG-UNAM-Mexico/Description#Phage detection| Defense system: Phage detection and sabotage]]'''''). At the same time the formation of infectious viral particles is hold back, a diffusing signal warns the neighboring cells of the presence of infection ('''''[[Team:LCG-UNAM-Mexico/Description#Gossip and Paranoia| Defense system: Gossip]]'''''). The reaction of alarmed cells consists on turning on a device, which allows a delay in case the defense system is turned on('''''[[Team:LCG-UNAM-Mexico/Description#Gossip and Paranoia| Defense system: Paranoia]]''''').
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We propose a population level approach relaying on a defense system delivered by an engineered version of the enterobacteria phage P4. The purpose of the defense construction is to make a bacteria to hold back the process of infection by triggering a cellular death response when a cell encounters a specific component of the infective phage. Such response will be fast enough to stop the formation process of viral particles, thus preventing the phage proliferation and population decline.<br>
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[[Image:Cosa1.jpg]]
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Delivery of the defense system take advantage of the satellite properties of P4 phage. This means that a P4 phage engineered with the defense construction will be able to infect an ''E.coli'' strain which harbors some genes from the helper phage P2 that are used for complementing and completing P4 life cycle, hence creating a production line of our version of P4.<br>
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<br>
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On the other hand the defense system will consist of DNA and RNA degradation by toxins which will be transcribed by T3 or T7 RNA-Polymerases fast enough to stop phage assembly and scattering in the environment. Simultaneously, a quorum sensing signal will be difunding to the non-infected bacterias acting as a transcriptional activator of an antisense RNA against bacteriophage's transcriptional machinery , hence "warning" the population to prepare against further T3 or T7 infection.<br>
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Furthermore, we will implement a stochastic population model based on the basic properties of the bacterial cells and the phages such as movement, reproduction, etc. The model will make simulations of the infection processes and quantification of the efficiency of our system possible.<br>
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='''Project subsystems'''=
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<br>
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=='''a) Delivery'''==
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=='''Relevance of the project'''==
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==='''Main objective'''===
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'''The main goal of the delivery device is the construction of a new iGEM vector capable of being used in a system for transduction of biobricks and synthetic devices in several bacterial hosts.'''
 +
We propose a complete, standardized and controllable system for production of phage vectors for delivery of over 25 kb of synthetic constructs to a wide range of bacterial hosts. The relationships between bacteria and phages is quite rich and dynamic, so hacking this system for our control will be an interesting challenge!
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==='''Application areas'''===
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The system starts with a modified bacteriophage P4 genome. This viral vector will be modified to be compatible with iGEM standards for biobrick assembly. The second part of the system involves '''''[[Team:LCG-UNAM-Mexico/Description#P4sid1 standardized production| production]]''''' of the modified P4 phages under our control.
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As can be imagined, this promises to be a powerful tool in Synthetic Biology with a great potential for expansions and applications. We like the analogy of this modified P4 as an '''USB *** memory device''', where you can store information or entire programs and just "plug" them into another machine that will handle such information.
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Bacteria play a fundamental role in human life. They are still the preferred models in science for the study of the molecular dynamics of organisms; probiotics are of vital importance in industry and food manufacturing.  Infection by phages represents a relevant and expensive problem. That is the reason why we decided to construct a system to contend bacteriophage infection.
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<br>
 +
==='''Background'''===
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==='''Portability'''===
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====P2-P4 bacteriophages ====
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Bacteriophage P2 and P4 are double stranded DNA enterobacteria viruses. Phage P4 is a satellite phage because it is
 +
dependent on the machinery of  P2. [[Team:LCG-UNAM-Mexico/Description#References|(1,2,3)]] Sometimes, it is called a "parasite phage", since it takes over the elements of P2 and leaves its "host phage" practically neutralized. There are several interesting features of the P4 genome, including transactivation zones (the genes that respond to the presence of P2 along with P4 and vice versa) that
 +
function in domination of the late P2 genes. Important elements of this kind are gene P4 delta and P2 ogr[[Team:LCG-UNAM-Mexico/Description#References|(12,15,16)]], which work synergistically together in activating P2 genes. Given these interesting properties, P4 has been exhaustively studied.
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The project is designed in such a way that contributes on molecular biology as well as on industry. Our aim is to achieve this by making the defense system portable enough to be used as a tool for protection of profitable bacteria. With portability we mean that we will be able to work with the device in a wide range of bacterial species. Because of the system activation relies on the presence of the replication machinery of the infectious phage not depending on the identity of the protected bacteria, thus leaving the possibility to modify the multi promoter that controls the device to be triggered against specific phages. In the other hand, phage P4 seems to be able to infect a wide range of bacteria, which would contribute to the portability of the system.
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====P4 genome structure====
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We can divide P4 genome into two main regions: the essential and non-essential region. The essential region contains
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operons intended for replication and hijacking of P2, and the non-essential region contains accessory genes for special situations as lambda infections, as well as the integrase and attachment site[[Team:LCG-UNAM-Mexico/Description#References|(3)]]. Removing the latter two would result in a permanent plasmid-state P4 with a unique multicopy replication system.
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==='''Defence approach'''===
 
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An important artefact concerning with the defense system is the use of toxins as the main element in the disruption of phage’s assembly and scattering. Even though the contention of the infection implies that some bacteria will die, the use of a RNAse and a DNAse induces a delay of the phages production by beating host machinery. This in turn, avoids the possibility of the phage to getting resistance against toxins.
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====P4 sid mutation====
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Using a population approach makes feasible to achieve a faster and wider protection response by amplifying the infection signal of the delivery phage in order to increase the number of "immune" bacteria at every lytic cycle.
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As P4 thoroughly depends on P2 for capsid, tail and lysis functions, the difference in size between both genomes (+- 33kb for P2 whereas +-11kb for P4) came to attention. P4 protein sid is able to scaffold a smaller capsid with the same structural proteins as P2. A sid mutant was found that made P4 pack its genome inside bigger-sized capsids, which can hold up to 1, 2 or 3 copies of its genome[[Team:LCG-UNAM-Mexico/Description#References|(6)]]. The extra genome copies could be “something else”; this means P4 can transport over 20 kbs of extra foreign DNA attached to its genome.  
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==='''Standarization and delivery'''===
 
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====Cos sites====
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Standardization of biobricks has become an alternative in the development of easier and more profitable tools for genetic engineering. In this context, our project takes advantage of the phages property for infecting and transducing genetic material into bacteria. We will modify P4 bacteriophage in such a way that facilitates gene cloning into phage’s genome for its subsequent transduction into bacteria harboring the P2 genes for completing lytic cycle of the carrier phage and its exponential release.  
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Another important point is that the signal for encapsidation is located in the “cos” sites. It means that you only need this region (about 20 pb, but you increase the efficency of transduction with a region of  more than 100 pb) to encapsidate a double DNA strand disregarding the sequence in between the cos sites.
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<br><br>
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==='''P4sid1 standardized production'''===
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We thought of a way '''to overproduce our viral particles''' without being forced to infect with P2 or getting P2 particles as a byproduct. The solution planned was to construct an E. coli strain containing all the useful genes for P4 in P2 (capsid, tail and lysis operons). In addition to these genes, the''' helper cell''' would also contain the main P2  transactivators (cox and ogr)[[Team:LCG-UNAM-Mexico/Description#References|(12,15,16)]] under a lac operator. This way, after we transform the helper cell with our desired P4  plasmid, '''we would decide when to promote stock production by lysis of the helper bacteria''' by adding IPTG. Then we have our biobrick assembled inside ready-to-use phages that can deliver their genome to wildtype bacteria.
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=='''Design'''==
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We have also biobricked the cos sites of P4. This biobrick should be cloned in any vector with your construction. If you transform the P4 producing strain with this vector and then infect with P4, you will have as a result some
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P4 phages and some of your vectors with the P4 cos sites inside a capsid. It means you can encapsidate up to 33 kb
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with this system. Until your production is pure, you can add a marker in the plasmid (e.g. an antibiotic resistance or color) so after infection you select the colonies with the desired plasmid.
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<br>
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===Delivery system: benefits and perspectives===
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One of the main motivations for the construction of this delivery system using P4 as the vector is to achieve insertion of devices  into cells by transduction as an alternative way from traditional transformation. '''This extends the panorama of synthetic biology to the whole P4 host range, which involves especies of genera such as Rhizobium, Klebsiella, and Serratia besides Enterobacteria like E. coli'''. The delivery of parts into wildtype bacteria could be a pool for innovative applications and properties, such as the following:
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=='''Delivery'''==
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<br>1)[[Team:LCG-UNAM-Mexico/Description#b) Defense|''' A defense system against another phages for E. Coli delivered by P4 phage. ''']]
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The idea we love is '''hacking one system that is harmful''' (if you are a bacterium) '''and using it for your own protection''' against similar systems.
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<br>2) '''Refined phage therapy.'''
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In addition to bacterial protection, we propose the use of this system to protect humans. This could be done using phage therapy to transduce DNA into pathogenic bacteria. It would be an advantage in cases where extra control is needed, as in degrading toxins before killing the pathogen and so avoiding further immune response. Another benefit would be response specificity in '''hacking pathogen-specific regulators''' while '''the system is bypassed in non-hazardous strains'''.
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== '''The Defence System'''==
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As a first step in this area, we have adapted the [[Team:LCG-UNAM-Mexico/Description#Translation sabotage| kamikaze system]] to detect pathogenicity instead of phages. The target pathogen is EHEC and EPEC (Enterohemorragic and Enteropathogenic Escherichia coli). P4 will introduce a specific binding site for a pathogenicity-specific regulator LER, which in turn will activate the [[Team:LCG-UNAM-Mexico/Description#Translation sabotage| kamikaze system]] at the moment LER activates pathogenic [http://en.wikipedia.org/wiki/Locus_of_Enterocyte_Effacement effacement].
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{|
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<br>3) '''Phage mediated training '''
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|Defence system
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| System
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|Lab
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|Model
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| Phage Detection
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| When phage T7 or T3 transduce their DNA into the host cell, the phage's polymerase will be able to bind the promoter of the system, which will activate two subsequent actions: production of toxins to inhibit further phage propagation, and a neighborhood alarm. The first thing translated is GFP
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the part contents, in order of appearance, are as follows.-
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Another usage could be to "train" the bacterial population by P4 infection so that it is sensitive to a future
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|
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stimulus, like indirect activation of medicine producing devices inside bacteria through phage contact. For instance, imagine you load a device of interest in the P4 genome and you transduce native E. coli with it. Now this E. coli will turn the device on in response to a new stimulus, say a body substance like a hormone.
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<br><br>
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| Translation process Sabotage
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| One of the elements transcribed by T7 RNA polymerase at early stages of T7 cycle in our transformed bacteria is the suicide system which consists of a polycistronic mRNA that codes among other proteins, the rRNAse domain of colicin E3, this toxin cleaves 16s rRNAs in active ribosomes from E. Coli, which causes inactivation of the ribosome and a subsequent decay in the overall bacterial translation, this response of our system affect T7 Cycle by reducing the number of bacteriophage proteins and then lowering the number of T7 phages at the end of the cycle.
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|
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== '''b) Defense'''==
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| Alarm and Paranoia
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| luxI is another product from the suicide system, infected cells produce it in order to warn surrounding cells of phages' presence through AHL.
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When a neighboring cell has been reached by AHL it turns on an antisenseRNA against a T7 messenger to interrupt its life cycle if it becomes infected, this delay in the life cycle of T7 gives more time to colicins to act upon the translation machinery reducing active ribosomes to zero before the assembly of any T7 particle.
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==='''Main objective'''===
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A virus infection is a process that takes place inside and individual but the real consequences of the infection become important at the population scale.  In order to efficiently and accurately simulate the behaviour of our system we need to implement two different kinds of approaches: an individual-based simulation and a population simulation.
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'''The main goal of the defense device is to significantly reduce the burst size in order to allow bacteria to survive a phage infection process.''' To achieve this, we designed a [[Team:LCG-UNAM-Mexico/Description#Translation sabotage| kamikaze system]] that will prevent the spread of phage infections. When phages T7 and T3 infect protected E. coli, these will start producing toxins that deactivate ribosomes. The result: no translation machinery, no phages produced and heroic bacterial suicide. <br><br>
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<br>
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Initially, a viral infection is a process that takes place inside an individual but the real consequences of the infection become important at the population scale. In order to efficiently and accurately simulate the behaviour of the defence device we need to implement two different kinds of approaches: an individual-based simulation and a population simulation, and then integrate them in a Multi-Scale Model.<br><br>
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We designed a kamikaze system that will prevent the spreading of phage infection. We fused  T7’s promoter with toxin E3 and GFP genes. Naive T7 will infect protected ''E. Coli'' which will start producing toxins that deactivate ribosomes. The result: No translation Machinery, no phages production and a heroic bacterium’s death. We expect the burst size to be significantly reduced when our system is working.
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<br>
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<br>
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We designed and implemented a stochastic simulation for the essential reactions involved in the infection process: T7’s DNA insertion, transcription, translation, capsid assembly, toxins production, DNA degradation etc. With a fairly big number of simulations we are going to generate probability distributions for the number of molecules for each metabolite as a function of time. We are particularly interested in the Burst-Size Distribution (BSD); the burst-size is the number of phages an infected cell will produce.
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<br>
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<br>
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Once we have the BSD we are ready for the Spatial Population Model. The kamikaze system we designed is meant to increase the probability that the population as a whole survive an infection process.  We make infected-E. Coli commit suicide for the benefit of the population.  In case suicide wasn’t altruistic enough we thought an ‘’alarm system’’ might be useful. Once a bacterium is infected it will use Quorum Sensing  to communicate the message that phages are near, advised bacteria will produce antisense RNA against phage DNA Polymerase.
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To simulate this system we used two different approaches:
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<br>
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We solved the system of Ordinary Differential Equations (ODE’s) described in REFERENCE and We designed and implemented a Cellular Automaton (CA).
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Using the CA we simulate:
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* Bacteria’s duplication, movement, infection and lysis.
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* AHL and T7 Diffusion.
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* The alarm system.
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So let’s put all together:  
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In order to simulate the spatial dynamics of the defence device we designed and implemented a [[Team:LCG-UNAM-Mexico:CA|Celluar Automaton (CA).]] Using the CA we can approach several problems at the same time:  E. Coli movement and duplication, AHL and phage diffusion and the infection process.<br><br>
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The detailed parts of the defense subsystem are the following:
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==='''Phage detection'''===
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When phage T7 or T3 transduce their DNA into the host cell, the phage's polymerase will be able to bind the multi-promoter of the system, which will activate two subsequent actions: production of toxins to inhibit further phage propagation, and a neighborhood alarm. The first thing translated is GFP.
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The part contents, in order of appearance, are as follows:
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[[Image:Defense.jpg|center]]
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<br\>
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==='''Translation sabotage'''===
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One of the elements transcribed by T7 RNA polymerase at early stages of T7 cycle in our transformed bacteria is the [[Team:LCG-UNAM-Mexico/Description#Translation process sabotage| kamikaze system]] which consists of a polycistronic mRNA that codes, among other proteins, the rRNAse domain of colicin E3. This toxin cleaves 16s rRNAs in active ribosomes from E. Coli, which causes inactivation of the ribosome and a subsequent decay in the overall bacterial translation. This response of our system affect T7 cycle by reducing the number of bacteriophage proteins and then lowering the number of T7 phages at the end of the cycle.
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==='''Gossip and Paranoia'''===
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luxI is another product from the kamikaze system. Infected cells produce it in order to warn surrounding cells of phages' presence through AHL.
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When a neighboring cell has been reached by AHL, it turns on an antisense RNA against a T7 messenger to interrupt its life cycle if it becomes infected. This delay in the life cycle of T7 gives more time to colicins to act upon the translation machinery reducing active ribosomes to zero before the assembly of any T7 particle.
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[[Image:Gossip.jpg|center]]
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<br\>
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===Model Validation===
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We expect the Burst-Size to be significantly reduced. An optimal result would be a Burst-Size of 0. Implementing a [[Team:LCG-UNAM-Mexico:BSD |sensitivity analysis]] we found that the [[Team:LCG-UNAM-Mexico:BSD|burst size distribution]] is dependent on the rate of ribosome inactivation by colicin E3. The [[Team:LCG-UNAM-Mexico:BSD|wild type Burst Size Distribution]] has mean 176 and standard deviation 102. This results are consistent with [[Team:LCG-UNAM-Mexico:BSD|existing experimental data]], the reported values for the burst size present a wide variation.
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The [[Team:LCG-UNAM-Mexico:CA|Celluar Automaton]] and the system of [[Team:LCG-UNAM-Mexico:odes|Delay Differential Equations]] generate growth curves that can be compared with those obtained experimentally.<br>
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Results generated by the [[Team:LCG-UNAM-Mexico:CA| Cellular Automaton]] are in good agreement with those obtained experimentally.<br>
<br>
<br>
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Our [[Team:LCG-UNAM-Mexico:Molecular model|Molecular Model]] has proved to be a reliable tool for sampling molecular distributions in order to make sensitivity analysis and to assemble more complex models as we did with our Cellular Automaton.<br>
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Parameters of the events occurring in the CA are random variables that take values according to a corresponding Probability Distribution.  We have distributions from literature and distributions generated by our simulations. So, for instance, when a bacterium gets infected we sample the Burst-Size Distribution, when a bacterium duplicate we sample the Duplication Time Distribution to assign lifetime to the newborn bacteria and so on. Sampling the distributions is the link between kinetic and population simulations: Random Variables in the population simulations take values from the kinetic simulations and ''voila'' we have our multi-scale stochastic model.
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<br><br>
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See [https://2009.igem.org/Team:LCG-UNAM-Mexico/Modelling Modelling Section] for detailed information.
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==='''System Specifications'''===
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<br><br><br>
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<br>Construction: 
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<br>E Coli Strain:  
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==='''Defense system: benefits and perspectives'''===
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<br>Toxins:
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<br>Bacteriophages:
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One of the most important mechanisms concerning the [[Team:LCG-UNAM-Mexico/Description#Defense|defense subsystem]] is the use of toxins as the main element in the disruption of phage’s assembly and scattering. Even though the contention of the infection implies that some bacteria will die, the use of a RNAse and a DNAse induces a delay of the phages production by beating host machinery. This in turn, avoids the possibility of the phage to gain resistance against toxins.
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<br>
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====1)Lytic phage-induced responses====
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==='''Model Validation'''===
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One interesting internal property of this system that could be exploited for novel purposes is the use of an entire wild-type biological entity (phages) as the activator of an internal system. Phage infection neutralization makes the population survive to the initial signal, while phage-mediated signal triggering makes the stimulus arrive to non-infected cells. This makes phages act merely as "external activators" analogous to quorum sensing molecules.
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<br>
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We expect the Burst-Size to be significantly reduced. An optimal result would be a Burst-Size of 0;   we see in our results that this is not the case. The BSD has mean ___ and variance___. We can calculate the likelihood of the model (BSD) given the observed burst size for both the wild type and modified E.Coli.   The CA and the ODE’s generate growth curves that can be compared with those obtained experimentally.
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====2)Internal Negative Autoregulation====
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One of the ideal situations in synthetic biology is the "friendly get-along" of humans and biological machines for the benefit of the former, as projected with medicine production from genetic circuits. We propose that activation of such circuits could rely on the usage of bacteriophages and their population equilibrium with bacteria. While a bacterial population could tolerate a phage infection with our alarm system and hence initiate extra responses (like medicine production), an overdose of the initial phage activation signal, instead of killing individuals by icreasing the production of medicine, could cause the extintion of the biological machine inside the body. This would bring the individual to an initial pre-medication state.
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=='''References'''==
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1.Propagation of satellite phage P4 as a plasmid. Goldstein R, Sedivy J, Ljungquist E. Proc Natl Acad Sci U S A. 1982 Jan;79(2):515-9
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2.Nonessential region of bacteriophage P4: DNA sequence, transcription, gene products, and functions. Ghisotti D, Finkel S, Halling C, Deh˜ G, Sironi G, Calendar R. J Virol. 1990 Jan;64(1):24-36.
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3.Mechanisms of Genome Propagation and Helper Exploitation by Satellite Phage P4. Lindqvist BH, Deh˜ G, Calendar R. Microbiol Rev. 1993 Sep;57(3):683-702.
 +
 
 +
4.Phasmid P4: manipulation of plasmid copy number and induction from the integrated state. Lagos R, Goldstein R. J Bacteriol. 1984 Apr;158(1):208-15.
 +
 
 +
5.Integration of satellite bacteriophage P4 in Escherichia coli. DNA sequences of the phage and host regions involved in site-specific recombination. Pierson LS 3rd, Kahn ML. J Mol Biol. 1987 Aug 5;196(3):487-96.
 +
 
 +
6.Determination of capsid size by satellite bacteriophage P4.  Shore D, Deh˜ G, Tsipis J, Goldstein R. Proc Natl Acad Sci U S A. 1978 Jan;75(1):400-4.
 +
 
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7.Recombinant P4 Bacteriophages Propagate as Viable Lytic Phages or as Autonomous Plasmids in Klebsiella pneumoniae. David W. Ow and Frederick M. Ausubel. Molec. gen. Genet. 180, 165 175 (1980)
 +
 
 +
8.Engineered bacteriophage-defence systems in bioprocessing. Sturino JM, Klaenhammer TR. Nat Rev Microbiol. 2006 May;4(5):395-404.
 +
 
 +
9.Interactions between a satellite bacteriophage and its helper. Barrett KJ, Marsh ML, Calendar R. J Mol Biol. 1976 Sep 25;106(3):683-707
 +
 
 +
10.Engineering BioBrick vectors from BioBrick parts. Shetty RP, Endy D, Knight TF Jr. J Biol Eng. 2008 Apr 14;2:5.
 +
 
 +
11.The Locus of Enterocyte Effacement (LEE)-Encoded Regulator Controls Expression of Both LEE- nd Non-LEE-Encoded Virulence Factors in Enteropathogenic and Enterohemorrhagic Escherichia coli. Eliott J. et al.(2000).  Infection and immnity, Nov. 2000, p 6115-6126
 +
 
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12.Activation of prophage P4 by the P2 Cox protein and the sites of action of the Cox protein on the two phage genomes. PNAS. Vol 86:pp. 3973-3977 Shamol Saha et al.(1989)
 +
 
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13.Eliott J. et al.(2000). The Locus of Enterocyte Effacement (LEE)-Encoded RegulatorControls Expression of Both LEE- and Non-LEE-Encoded
 +
 
 +
14.Virulence Factors in Enteropathogenic and Enterohemorrhagic Escherichia coli. Infection and immnity, Nov. 2000, p 6115-6126
 +
 
 +
15.Bacteriophage P2 ogr and P4 delta genes act independently and are essential for P4 multiplication. Journal of Bacteriology. Halling, C. (1990)  172(7):3549-3558
 +
 
 +
16.Regulation of bacteriophage P2 late-gene expression: The ogr gene. Christie, G. (1986)  PNAS Vol.83 3238-3242
 +
 
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Latest revision as of 03:51, 22 October 2009

Description

Contents


Relevance of the project

Bacteria play a fundamental role in human life and they are still the preferred models to study the molecular dynamics of organisms. One example are probiotics because of their vital importance in industry and food manufacturing. Infection by phages represents a relevant and expensive problem in these areas. For this reason we decided to construct a system to contend with bacteriophage infection at a population level.

Given this global protection vision emerges the idea of dividing our project in two subsystems: delivery and defense. Their coupled expression leads to a cascade dependent on the presence of an infectious phage. This property gives an extra versatility to the project because the defense subsystem turns on faster enough to hold back the infection and then lasts enough to give "immunity" to the population. Therefore, it is feasible to achieve a faster and wider protection response by amplifying the infection signal delivered by the phage in order to increase the number of "immune" bacteria at every lytic cycle.

Logic design of the project subsystems


The first level of the expression cascade consists on the delivery ( Delivery susbsystem) of the protection system that will be immediately activated when a phage is detected ( Defense system: Phage detection and sabotage). At the same time the formation of infectious viral particles is hold back, a diffusing signal warns the neighboring cells of the presence of infection ( Defense system: Gossip). The reaction of alarmed cells consists on turning on a device, which allows a delay in case the defense system is turned on( Defense system: Paranoia).

Cosa1.jpg


Project subsystems


a) Delivery

Main objective

The main goal of the delivery device is the construction of a new iGEM vector capable of being used in a system for transduction of biobricks and synthetic devices in several bacterial hosts.

We propose a complete, standardized and controllable system for production of phage vectors for delivery of over 25 kb of synthetic constructs to a wide range of bacterial hosts. The relationships between bacteria and phages is quite rich and dynamic, so hacking this system for our control will be an interesting challenge!

The system starts with a modified bacteriophage P4 genome. This viral vector will be modified to be compatible with iGEM standards for biobrick assembly. The second part of the system involves production of the modified P4 phages under our control.

As can be imagined, this promises to be a powerful tool in Synthetic Biology with a great potential for expansions and applications. We like the analogy of this modified P4 as an USB *** memory device, where you can store information or entire programs and just "plug" them into another machine that will handle such information.


Background

P2-P4 bacteriophages

Bacteriophage P2 and P4 are double stranded DNA enterobacteria viruses. Phage P4 is a satellite phage because it is dependent on the machinery of P2. (1,2,3) Sometimes, it is called a "parasite phage", since it takes over the elements of P2 and leaves its "host phage" practically neutralized. There are several interesting features of the P4 genome, including transactivation zones (the genes that respond to the presence of P2 along with P4 and vice versa) that function in domination of the late P2 genes. Important elements of this kind are gene P4 delta and P2 ogr(12,15,16), which work synergistically together in activating P2 genes. Given these interesting properties, P4 has been exhaustively studied.

P4 genome structure

We can divide P4 genome into two main regions: the essential and non-essential region. The essential region contains operons intended for replication and hijacking of P2, and the non-essential region contains accessory genes for special situations as lambda infections, as well as the integrase and attachment site(3). Removing the latter two would result in a permanent plasmid-state P4 with a unique multicopy replication system.


P4 sid mutation

As P4 thoroughly depends on P2 for capsid, tail and lysis functions, the difference in size between both genomes (+- 33kb for P2 whereas +-11kb for P4) came to attention. P4 protein sid is able to scaffold a smaller capsid with the same structural proteins as P2. A sid mutant was found that made P4 pack its genome inside bigger-sized capsids, which can hold up to 1, 2 or 3 copies of its genome(6). The extra genome copies could be “something else”; this means P4 can transport over 20 kbs of extra foreign DNA attached to its genome.


Cos sites

Another important point is that the signal for encapsidation is located in the “cos” sites. It means that you only need this region (about 20 pb, but you increase the efficency of transduction with a region of more than 100 pb) to encapsidate a double DNA strand disregarding the sequence in between the cos sites.

P4sid1 standardized production

We thought of a way to overproduce our viral particles without being forced to infect with P2 or getting P2 particles as a byproduct. The solution planned was to construct an E. coli strain containing all the useful genes for P4 in P2 (capsid, tail and lysis operons). In addition to these genes, the helper cell would also contain the main P2 transactivators (cox and ogr)(12,15,16) under a lac operator. This way, after we transform the helper cell with our desired P4 plasmid, we would decide when to promote stock production by lysis of the helper bacteria by adding IPTG. Then we have our biobrick assembled inside ready-to-use phages that can deliver their genome to wildtype bacteria.

We have also biobricked the cos sites of P4. This biobrick should be cloned in any vector with your construction. If you transform the P4 producing strain with this vector and then infect with P4, you will have as a result some P4 phages and some of your vectors with the P4 cos sites inside a capsid. It means you can encapsidate up to 33 kb with this system. Until your production is pure, you can add a marker in the plasmid (e.g. an antibiotic resistance or color) so after infection you select the colonies with the desired plasmid.


Delivery system: benefits and perspectives

One of the main motivations for the construction of this delivery system using P4 as the vector is to achieve insertion of devices into cells by transduction as an alternative way from traditional transformation. This extends the panorama of synthetic biology to the whole P4 host range, which involves especies of genera such as Rhizobium, Klebsiella, and Serratia besides Enterobacteria like E. coli. The delivery of parts into wildtype bacteria could be a pool for innovative applications and properties, such as the following:


1) A defense system against another phages for E. Coli delivered by P4 phage.

The idea we love is hacking one system that is harmful (if you are a bacterium) and using it for your own protection against similar systems.


2) Refined phage therapy.

In addition to bacterial protection, we propose the use of this system to protect humans. This could be done using phage therapy to transduce DNA into pathogenic bacteria. It would be an advantage in cases where extra control is needed, as in degrading toxins before killing the pathogen and so avoiding further immune response. Another benefit would be response specificity in hacking pathogen-specific regulators while the system is bypassed in non-hazardous strains.

As a first step in this area, we have adapted the kamikaze system to detect pathogenicity instead of phages. The target pathogen is EHEC and EPEC (Enterohemorragic and Enteropathogenic Escherichia coli). P4 will introduce a specific binding site for a pathogenicity-specific regulator LER, which in turn will activate the kamikaze system at the moment LER activates pathogenic [http://en.wikipedia.org/wiki/Locus_of_Enterocyte_Effacement effacement].


3) Phage mediated training

Another usage could be to "train" the bacterial population by P4 infection so that it is sensitive to a future stimulus, like indirect activation of medicine producing devices inside bacteria through phage contact. For instance, imagine you load a device of interest in the P4 genome and you transduce native E. coli with it. Now this E. coli will turn the device on in response to a new stimulus, say a body substance like a hormone.

b) Defense

Main objective

The main goal of the defense device is to significantly reduce the burst size in order to allow bacteria to survive a phage infection process. To achieve this, we designed a kamikaze system that will prevent the spread of phage infections. When phages T7 and T3 infect protected E. coli, these will start producing toxins that deactivate ribosomes. The result: no translation machinery, no phages produced and heroic bacterial suicide.

Initially, a viral infection is a process that takes place inside an individual but the real consequences of the infection become important at the population scale. In order to efficiently and accurately simulate the behaviour of the defence device we need to implement two different kinds of approaches: an individual-based simulation and a population simulation, and then integrate them in a Multi-Scale Model.

In order to simulate the spatial dynamics of the defence device we designed and implemented a Celluar Automaton (CA). Using the CA we can approach several problems at the same time: E. Coli movement and duplication, AHL and phage diffusion and the infection process.

The detailed parts of the defense subsystem are the following:


Phage detection

When phage T7 or T3 transduce their DNA into the host cell, the phage's polymerase will be able to bind the multi-promoter of the system, which will activate two subsequent actions: production of toxins to inhibit further phage propagation, and a neighborhood alarm. The first thing translated is GFP.

The part contents, in order of appearance, are as follows:

Defense.jpg


Translation sabotage

One of the elements transcribed by T7 RNA polymerase at early stages of T7 cycle in our transformed bacteria is the kamikaze system which consists of a polycistronic mRNA that codes, among other proteins, the rRNAse domain of colicin E3. This toxin cleaves 16s rRNAs in active ribosomes from E. Coli, which causes inactivation of the ribosome and a subsequent decay in the overall bacterial translation. This response of our system affect T7 cycle by reducing the number of bacteriophage proteins and then lowering the number of T7 phages at the end of the cycle.


Gossip and Paranoia

luxI is another product from the kamikaze system. Infected cells produce it in order to warn surrounding cells of phages' presence through AHL. When a neighboring cell has been reached by AHL, it turns on an antisense RNA against a T7 messenger to interrupt its life cycle if it becomes infected. This delay in the life cycle of T7 gives more time to colicins to act upon the translation machinery reducing active ribosomes to zero before the assembly of any T7 particle.

Gossip.jpg


Model Validation

We expect the Burst-Size to be significantly reduced. An optimal result would be a Burst-Size of 0. Implementing a sensitivity analysis we found that the burst size distribution is dependent on the rate of ribosome inactivation by colicin E3. The wild type Burst Size Distribution has mean 176 and standard deviation 102. This results are consistent with existing experimental data, the reported values for the burst size present a wide variation. The Celluar Automaton and the system of Delay Differential Equations generate growth curves that can be compared with those obtained experimentally.
Results generated by the Cellular Automaton are in good agreement with those obtained experimentally.

Our Molecular Model has proved to be a reliable tool for sampling molecular distributions in order to make sensitivity analysis and to assemble more complex models as we did with our Cellular Automaton.


See Modelling Section for detailed information.


Defense system: benefits and perspectives

One of the most important mechanisms concerning the defense subsystem is the use of toxins as the main element in the disruption of phage’s assembly and scattering. Even though the contention of the infection implies that some bacteria will die, the use of a RNAse and a DNAse induces a delay of the phages production by beating host machinery. This in turn, avoids the possibility of the phage to gain resistance against toxins.

1)Lytic phage-induced responses

One interesting internal property of this system that could be exploited for novel purposes is the use of an entire wild-type biological entity (phages) as the activator of an internal system. Phage infection neutralization makes the population survive to the initial signal, while phage-mediated signal triggering makes the stimulus arrive to non-infected cells. This makes phages act merely as "external activators" analogous to quorum sensing molecules.

2)Internal Negative Autoregulation

One of the ideal situations in synthetic biology is the "friendly get-along" of humans and biological machines for the benefit of the former, as projected with medicine production from genetic circuits. We propose that activation of such circuits could rely on the usage of bacteriophages and their population equilibrium with bacteria. While a bacterial population could tolerate a phage infection with our alarm system and hence initiate extra responses (like medicine production), an overdose of the initial phage activation signal, instead of killing individuals by icreasing the production of medicine, could cause the extintion of the biological machine inside the body. This would bring the individual to an initial pre-medication state.

References

1.Propagation of satellite phage P4 as a plasmid. Goldstein R, Sedivy J, Ljungquist E. Proc Natl Acad Sci U S A. 1982 Jan;79(2):515-9

2.Nonessential region of bacteriophage P4: DNA sequence, transcription, gene products, and functions. Ghisotti D, Finkel S, Halling C, Deh˜ G, Sironi G, Calendar R. J Virol. 1990 Jan;64(1):24-36.

3.Mechanisms of Genome Propagation and Helper Exploitation by Satellite Phage P4. Lindqvist BH, Deh˜ G, Calendar R. Microbiol Rev. 1993 Sep;57(3):683-702.

4.Phasmid P4: manipulation of plasmid copy number and induction from the integrated state. Lagos R, Goldstein R. J Bacteriol. 1984 Apr;158(1):208-15.

5.Integration of satellite bacteriophage P4 in Escherichia coli. DNA sequences of the phage and host regions involved in site-specific recombination. Pierson LS 3rd, Kahn ML. J Mol Biol. 1987 Aug 5;196(3):487-96.

6.Determination of capsid size by satellite bacteriophage P4. Shore D, Deh˜ G, Tsipis J, Goldstein R. Proc Natl Acad Sci U S A. 1978 Jan;75(1):400-4.

7.Recombinant P4 Bacteriophages Propagate as Viable Lytic Phages or as Autonomous Plasmids in Klebsiella pneumoniae. David W. Ow and Frederick M. Ausubel. Molec. gen. Genet. 180, 165 175 (1980)

8.Engineered bacteriophage-defence systems in bioprocessing. Sturino JM, Klaenhammer TR. Nat Rev Microbiol. 2006 May;4(5):395-404.

9.Interactions between a satellite bacteriophage and its helper. Barrett KJ, Marsh ML, Calendar R. J Mol Biol. 1976 Sep 25;106(3):683-707

10.Engineering BioBrick vectors from BioBrick parts. Shetty RP, Endy D, Knight TF Jr. J Biol Eng. 2008 Apr 14;2:5.

11.The Locus of Enterocyte Effacement (LEE)-Encoded Regulator Controls Expression of Both LEE- nd Non-LEE-Encoded Virulence Factors in Enteropathogenic and Enterohemorrhagic Escherichia coli. Eliott J. et al.(2000). Infection and immnity, Nov. 2000, p 6115-6126

12.Activation of prophage P4 by the P2 Cox protein and the sites of action of the Cox protein on the two phage genomes. PNAS. Vol 86:pp. 3973-3977 Shamol Saha et al.(1989)

13.Eliott J. et al.(2000). The Locus of Enterocyte Effacement (LEE)-Encoded RegulatorControls Expression of Both LEE- and Non-LEE-Encoded

14.Virulence Factors in Enteropathogenic and Enterohemorrhagic Escherichia coli. Infection and immnity, Nov. 2000, p 6115-6126

15.Bacteriophage P2 ogr and P4 delta genes act independently and are essential for P4 multiplication. Journal of Bacteriology. Halling, C. (1990) 172(7):3549-3558

16.Regulation of bacteriophage P2 late-gene expression: The ogr gene. Christie, G. (1986) PNAS Vol.83 3238-3242



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