Team:CoBRA/Project

   CoBRA iGEM Project Proposal Our research is to determine whether chitinase genes in transgenic E.coli will be produced and to what degree to reduce the BSF disease in pine trees. The CoBRA iGem team will attempt to engineer a new DNA biobrick containing a specific promoter gene, a gene of interest (one of three different Class I chitinases; PgeChia1-1, PgeChia1-2, and PcChia1-1,)3 and a terminator gene. This construct will then be placed in E.coli bacteria so that this bacteria, when subjected to pine tree resins, will secrete the chitinase which will kill the Gc.

   3N. Kolosova, J. Bohlmann, and C. Breuil. "Cloning and characterization of chitinases from interior spruce and lodgepole pine."Elsevier (2014): 1-8. Print.

   Background Information For our project, the CoBRA iGEM team has decided to attempt to manage the devastation that the mountain pine beetle (Dendroctonus ponderosae) has caused to the pine trees in forests along the Rocky Mountains in Alberta and British Columbia. This beetle burrows into the bark of the lodgepole pine of these Mountains and with the help of a fungus called the Blue Stain Fungus(Grosmannia clavigera), lays its eggs in the tree. The winter then kills the beetle off, but the eggs, which are protected from the cold by the tree, survive the winter and mature to be able to start the cycle all over again. The Gc spreads its mycelium into the phloem, and then feeds on this essential structure, thus choking off the supply of glucose to the tree. Research also shows the the BSF survives the pine trees defensive resin production, by using the monoterpene chemicals as its food source.

   These processes put the tree under tremendous stress and often kills it. The Mountain Pine Beetle has always been a factor in this ecosystem, but historically, winters have been harsh and cold enough to keep the beetle population in check. With global warming beginning to produce noticeable increases in winter temperatures, more and more beetles have been able to survive, and the population has reached a level where it is capable of ravaging huge chunks of forest, not only destroying the ecosystem, but rendering the lumber unusable.

   Looking at this problem from several angles, our team decided that the best way to combat this epidemic would be by killing off the Blue Stain Fungus or Gc. One reason is that the BSF is helpful, but not essential to the MPB survival. Secondly, by focussing on the BSF, we are attempting to minimize our disruption of MPB predator populations, such as woodpeckers and other birds. Thirdly, our objective is to focus specifically on the pathogenic BSF and not destroy the symbiotic relationships of a forest fungal ecosystem.

   Chitin is a structural component of the cell wall of many pathogenic fungi including BSF. Chitinases are enzymes that hydrolyze the polymer chitin breaking it down. Extensive research has been conducted to determine whether plant chitinases have a role in defense against fungal diseases. Expression of cloned chitinase genes in transgenic plants has provided further evidence for their role in plant defense. The level of protection observed in these plants is variable and may be influenced by the specific activity of the enzyme, its localization and concentration within the cell, the characteristics of the fungal pathogen, and the nature of the host-pathogen interaction. The expression of chitinase in combination with one or several different antifungal proteins should have a greater effect on reducing disease development, given the complexities of fungal-plant cell interactions and resistance responses in plants.

  Our project goal is to determine if a cloned chitinase cDNA can be successfully expressed in transgenic E.coli. Using recombinant DNA techniques our team will create an entirely new DNA biobrick, this biobrick will placed in the pSB1C3 vector and contain a specific inducible or constitutive promoter (LacI or TetR), a specific cDNA (one of three class 1 chitinases; PgeChia1-1, PgeChia1-2 and PcChia1-1), and a stop codon or terminator gene. This construct as previously mentioned will be placed into lab grade Top 10 and k12 lab strain E.coli bacteria thus allowing these new, genetically altered bacteria to successfully produce and secrete the chitinase enzyme thus showing proof of concept. It is important to note that our engineered bacteria will not be used outside of a controlled lab setting during our for the current project.

Materials and Method:

  As our ultimate goal is to express the chitinase gene in transgenic E.coli, we followed standard recombinant DNA techniques. To begin, our specific gene of interest, the chitinase, is not available in the iGEM registry. The Chitinase genes were received from Dr. Bohlmann at UBC. The DNA needed to go through some additional changes before they were usable. First of all, these pieces contained the PstI cut site in their coding region, which could wreak havoc on our restriction digest, by cutting the Chitinase at the wrong place with the enzymes. In addition, the biobrick prefix and suffix were not present, so the Chitinase parts could not be ligased to any of our other parts.

	Pc 1-1	Pge 1-1	Pge 1-2
Before optimization
After optimization

  We optimized our DNA using BioBasics Inc. Once we received the optimized DNA we proceeded to create our new biobricks. The vector for our chitinase DNA was different than the standardized vector required by iGEM. Utilization of the iGEM protocols for DNA recombination techniques enabled our team to create transgenic E.coli DH5-alpha cells in the proper iGEM pSB1C3 backbone. At this point we then needed to identify that our transformed DH5a cells contained our correct plasmids. We performed two sets of gel tests. First we digested the J04450 cells containing our gene of interest, as well as the pSB1c3 backbone and tested using gel electrophoresis, comparing our results to a standard ladder. Next we digested our J04500 cells which was a construct consisting of our chosen promoter, RBS, gene of interest and terminator comparing the results to a ladder.

To end we submitted all six of our biobricks to iGEM. We performed all of our protocols under aseptic conditions and were conducted at room temperature unless stated otherwise.

Result

Figure 1. DIY Shaking Incubator: Hova-Bator Incubator Atop Fisher-Price Electric Plug-In Baby Swing

Figure 2. Failed Bacterial Transformation Plates Using NEB Top 10 E.coli May 11, 2014

Notice the odd fringe of growth around the central core. Notice the colony shape is not circular or dense in the core.

Figure 4. Successful Ligation Transformation Plates Using DH5a E.coli June 3, 2014

Ligated DH5a with chitinase cells in J04500 backbone (pictured on left); Ligated DH5a with chitinase cells in J04450 backbone (pictured on right)

Figure 5. Gel Results of Digestion with Restriction Enzymes on J4450 Plasmids To Isolate Chitinase Protein in our DH5a E.coli cells with 1 Kb Invitrogen Ladder (June 14)

Moving from right the first well is a track it 1kb invitrogen DNA ladder, the second and third wells consist of a construct made up of PcChia 1-1 in a pSB1C3 backbone. In well 2 this construct was cut by restriction enzymes PstI and EcoRI, causing the chitinase coding region to become detached from the backbone. In well 3 this construct was only cut at the EcoRI cut site, causing the plasmid to be linearized. Wells 4 and 5 followed the same process as wells 2 and 3 with the exception that the chitinase coding region in wells 4 and 5 is of the PgeChia 1-2 variety. Wells 6 and 7 contain the PgeChia 1-1 gene. Using the ladder, our chitinase genes look to be approximately 1000 base pairs (lanes 2, 4, and lowest band), the pSB1C3 backbone appears to be approximately 2000 base pairs (lanes 2, 4, and 6 second lowest band), and the linearized construct looks to be about 3000 base pairs (lanes 3, 5, and 7). These numbers match up with our theoretical values.

2 uL ladder
4 uL loading dye + 20 uL plasmid digest
pH TAE buffer solution at 8 and at Room temperature

Figure 6. Gel Results of Digestion with Restriction Enzymes on J4500 Plasmids To Isolate Chitinase Protein in our DH5a E.coli cells from the Vector (June 17)

Moving left to right, lanes 1, 8 and 9 contain our two ladders, 1 kb Invitrogen 0.9% Ethidium bromide/Agarose (lane 8) and 1 kb Ready 1% TBE/Agarose (lane 1 6 uL of ladder; lane 9 12 uL of ladder). In well 2 this construct (PgeChia 1-1) was only cut at the EcoRI cut site, causing the plasmid to be linearized. In well 3 this construct (PgeChia 1-1) was cut by restriction enzymes PstI and EcoRI, causing the chitinase coding region to become detached from the backbone. Wells 4 and 5 followed the same process as wells 2 and 3 with the exception that the chitinase coding region in wells 4 and 5 is of the PgeChia 1-2 variety. Wells 6 and 7 contain the PcChia 1-1 gene. Using the ladder on the right, our chitinase genes look to be approximately 1000 base pairs (lanes 3, 5, and 7 lowest band), the pSB1C3 backbone appears to be approximately 2000 base pairs (lanes 3, 5, and 7 second lowest band), and the linearized construct looks to be about 3000 base pairs (lanes 2, 4, and 6). These numbers match up with our theoretical values.

2 uL ladder
4 uL loading dye + 20 uL plasmid digest
pH TAE buffer solution at 8 and Room Temperature

Future goals

• We establish that Gc is heterothallic, and report evidence for repeat-induced point mutation. We report insights, from genome and transcriptome analyses, into how Gc tolerates conifer-defense chemicals, including oleoresin terpenoids, as they colonize a host tree. RNA-seq data indicate that terpenoids induce a substantial antimicrobial stress in Gc, and suggest that the fungus may detoxify these chemicals by using them as a carbon source. *Terpenoid treatment strongly activated a ∼100-kb region of the Gc genome that contains a set of genes that may be important for detoxification of these host-defense chemicals. This work is a major step toward understanding the biological interactions between the tripartite MPB/fungus/forest system.

*Terpenoid - Any of a large class of organic compounds including terpenes, diterpenes, and sesquiterpenes. They have unsaturated molecules composed of linked isoprene units, generally having the formula (C 5H 8)

Surface display: Instead of sending things to the media outside the cell, you can also stick things onto the outside of the cell to be displayed. As Magda suggested, this normally works just fine, however sometimes it can impair the function of your protein. The only way to tell for sure is to try however- usually you fuse the protein (as described for the secretion tag) to the N terminus (start) of the protein for one construct, and the c terminus (end) of the protein for a second construct, and test both to see if one works better. The part that Magda suggested has been shown to work. http://parts.igem.org/wiki/index.php/Part:BBa_K103006. An alternative would be something like this https://2012.igem.org/Team:Penn/SurfaceDisplayBBa. It won best biobrick, and was also shown to work. Chitinase APPEARS to be a monomer (meaning that the enzyme is formed from a single protein chain, and not from more than one protein associating together (Protein subunits)). I think this article brings strong support in favour of targeting the blue stain fungus with a bacteria-displayed chitinase. And the fact that the surface display part (http://parts.igem.org/Part:BBa_K811005) is available in the registry, and even won the best biobrick award (!) adds to the promise of this project. Thanks for digging these out, Lisa

Idea #3 - Saturday March 29 from Richard Lee

Arming Trees Against Pine Beetle Invasions

Our iGEM experiment purported that if we engineered an E. coli construct with a spruce/pine tree chitinase, then that transgenic E. coli will produce the tree chitinase. In doing so, our research will lend further support for a biological solution to a major ecological problem facing Canada and the USA.

   To begin, our specific gene of interest, the chitinase, is not available in the iGEM registry. The cloned Chitinase genes were received from Dr. Bohlmann at UBC. The DNA needed to go through some additional changes before they were usable. These pieces contained the PstI cut site in their coding region, which could wreak havoc on our restriction digest by cutting the Chitinase at the wrong place with the enzymes. In addition, the biobrick prefix and suffix were not present, so the Chitinase parts could not be ligased to any of our other parts. Use of NEBCutter website was beneficial in determining that our sequence was problematic and what was required to fix the situation. BioBasics Inc optimized our DNA so that the illegal cut sites were removed and we were able to utilize this DNA for our experimental purposes.

   Transformation of iGEM’s NEBTop 10 E.coli cells proved extremely difficult. In the end, after several attempts, it was decided that we switch to DH5-alpha E.coli cells. This strain has worked under our laboratory conditions. DH5 alpha cells maintain plasmids well and can be made competent on a more consistent basis. Modifications of the transformation protocol included suspending cells in CaCl2 on ice for 15 min prior to removing the second supernatant, increasing the spin RPMs in order to collect a greater volume of pellet while making cells competent, increasing the heat shock 45 s, floating on ice for 5 min, increasing the volume of solution taken for growth on plates, addition of more luria broth media before growing colonies on plates and including control plates along with the experimental plates. Modifications to our miniprepping protocol included increasing our volumes of ingredients added to the culture tubes and ensuring that the dry spinning was achieved before adding the elution buffer. Restriction digest and ligation protocols were following specifically using addgene website and iGEM methods. For identification of plasmids or genes we used gel electrophoresis. We had issues with the integrity of our bands and ladders and consequently with our purported results. Part of the issue was that our plasmids floated out of the wells while loading which meant that we did not dry spin the centrifuge column enough. We corrected this step and had greater success as seen in Figures 5 and 6. As for the choice of ladders, it appears from Figures 5 and 6 that the 1 kb Invitrogen 0.9% Ethidium bromide/Agarose DNA ladders worked the best in our TAE buffer solution and in our high school laboratory conditions.

   Looking at our data, we believe that the length of the parts that were restriction digested with two enzymes should add together to equal the length of the parts that were restricted with one enzyme. By the ladder on the right of both Figures 5 and 6, our chitinase genes look to be approximately 1058 base pairs for PgeChia 1-1 and PcChia 1-1 and 1067 base pairs for PgeChia 1-2 (1), the pSB1C3 backbone appears to be approximately 2070 base pairs (2), and together the constructs look to be about 3128 base pairs for PgeChia 1-1 and PcChia 1-1 and 3137 for PgeChia 1-2. These lines match up with our theoretical values. The genes for the production of chitinase were the same ones tested in Kolosova, N., et al (3).

   We are currently in the process of attempting to prove the production of chitinase from our transformed DH5alpha cells in the presence of lab grade chitin agar plates. Results to be determined.

   Accessibility to high tech equipment and critical chemicals was a hinderance with the wet lab component of our project. For example, we do not have a optical density machine, which made many of our calculations that required knowledge of how much plasmid our solutions contained unpredictable. Also, as we try to achieve proof of concept, we are missing some of the compounds that would help us make a different kind of agar plate that is optimal for testing for the breakdown of chitin. Furthermore, looking at our gels that we ran in the results section, although the lines look to be close to where they would be expected to be, they are not exact. We see two lines where the double digested parts are and one line where the single digested parts are, but these lines are not exactly where they should be in regards to the ladder. Seeing the rounded edges of the lines in our gel, we believe that our TAE buffer may be have been incorrectly made, which could cause our samples to run incorrectly.

   Despite our relative inexperience in the field of genetics and phytochemistry we were presented with the opportunity to work alongside Dr. Bohlmann and Dr. Kolosova, two researchers at UBC’s Michael Smith Laboratory and members of the TRIA project. Their coauthored paper on chitinase and their in depth knowledge of phytochemistry, the mountain pine beetle and the blue stain fungus proved to be a very valuable resource to our team as we set out to test chitinase production in transgenic E.coli4.

   Our project, although parallel to the work done by Dr. Bohlmann and Dr. Kolosova, has provided iGEM with 6 new chitinase biobricks that will go on to aid future teams in their endeavors. In addition to our lab work we have also completed a high school level lab manual which combines tested lab protocols with high school level terms and directions, thus making synthetic biology more accessible to high school students. In the context of iGEM we have blazed a trail by creating six new BioBricks in a single iGEM cycle and providing iGEM with a multitude of high school level protocols to make synthetic biology more applicable and accessible at the secondary level

   Our project is by no means ready to be put into a real world application. Firstly, the cell walls of the blue-stain fungus are not made exclusively of chitin. In Kolosova et al3 Phytochemistry, when the chitinase was tested on the blue-stain fungus, no antifungal activity was observed, as the cell walls contain many more compounds which are not degraded by chitinase. In future years, we may research these compounds, and see if we can alter our plasmid to also degrade them. Also, we currently are using the LacI promoter in our constructs. This promoter will not function if IPTG is present. For the forest ecosystem, this could be hazardous, as there are many beneficial fungi in forests which we would risk killing. For next year we hope to try and find a promoter which functions only when the tree is producing stress hormones such as terpenes or other indicators. This would help the tree fight off the infections with minimal, if any damage to the other fungi of the forest. Additionally, we need to find a method of delivery of our plasmid. The DH5alpha cells that we used are not able to survive in an environment such as a forest. Hopefully we could use a bacteria that is naturally present in the tree, to avoid introducing an alien species to the forest. Producing chitinase in E Coli is just the first step in combating the blue-stain fungus.

Vancouver Referencing Guides
1. http://store.biobasic.com/
2. http://parts.igem.org/Part:pSB1C3
3. Kolosova, N., et al. Cloning and characterization of chitinases from interior spruce and lodgepole pine. Phytochemistry (2014).
4. http://www.for.gov.bc.ca/hfp/mountain_pine_beetle/