Difference between revisions of "Team:Marburg/Results"
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| + | <h1 class="heading"> | ||
| + | R E S U L T S <!-- Titel austauschen--> | ||
| + | </h1> | ||
| + | <hr class="line"> | ||
| + | <img src="https://static.igem.org/mediawiki/2019/a/ac/T--Marburg--logo.svg" | ||
| + | class="logo" | ||
| + | alt="Syntex Logo"> | ||
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| − | <div | + | <div style="margin-top: 10vh;"> |
| − | + | <section class="section"> | |
| − | + | <h1 class="title"> </h1> | |
| − | + | <p style="text-align: justify;"> <!-- Text--> | |
| − | + | The way to the results we demonstrate here was full of success and failure. Therefore, it was necessary to | |
| − | + | compare and revise our theoretical plans with the practical work and the associated results. After trying our | |
| − | + | best to implement our plans, we would like to show you on this page that we have managed to realize some of our | |
| − | + | goals and are able to show some achievements for every sub-group. | |
| − | + | </p> | |
| − | + | </section> | |
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| − | + | <h1><!-- Titel von Pop up in schwarzer Box--> | |
| − | + | S T R A I N<br> | |
| − | + | E N G I N E E R I N G | |
| − | + | </h1> | |
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| − | + | </div> | |
| − | + | <div class="sub-content"> | |
| − | + | <p> <!-- Untertitel im Popup --> | |
| − | + | At this passage we show how to do genetic modifications to regain the natural | |
| − | + | competence of <i>Synechococcus elongatus</i> UTEX 2973. With these methods we succeed the | |
| − | + | natural | |
| − | + | transformation of plasmids in UTEX2973. | |
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| − | + | <h1 class="title">Colony pictures</h1> <!-- Titel im pop up--> | |
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| + | onclick="hide('rbn1')">X</button> <!-- nummer aendern --> | ||
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| − | <div class="popup-content" style="text-align: justify; | + | <div class="popup-content" |
| − | <p> | + | style="text-align: justify;"> |
| − | < | + | <section class="section"> <!-- Inhalt Pop up start--> |
| − | + | <h2> <b> The Colony picture Collaboration </b></h2> | |
| − | + | <p> | |
| − | + | <h1>Results</h1> | |
| − | + | <h2>Natural competence</h2> | |
| − | + | ||
| − | + | <p> | |
| − | + | Reintroducing natural competence into our <i>S. elongatus</i> strain was an important goal for us. To make sure | |
| − | + | that | |
| − | + | our <i>S. elongatus</i> UTEX 2973 actually holds the point mutation in the <i>pilN</i> gene we thought it has, | |
| − | + | we sequenced | |
| − | + | this region - and the results showed the expected mutation | |
| − | + | <figure Style="text-align:center"> | |
| − | </figcaption> | + | <img style="height: 50ex; width: 90ex" |
| + | src=https://static.igem.org/mediawiki/2019/e/ed/T--Marburg--Seq_UTEX-pilN-with-o_iGEM_1_650.png | ||
| + | alt="sequencing results"> | ||
| + | <figcaption> | ||
| + | Fig.1: Sequencing results | ||
| + | </figcaption> | ||
| + | </figure> | ||
| + | As there were multiple methods at hand that we could use to get our strain naturally competent again, we tried | ||
| + | all those at hand, making sure we do everything we can to tackle this issue. <br> | ||
| + | Although not our favorite method, we tried integrating an intact copy of the <i>pilN</i> gene into neutral site | ||
| + | II of | ||
| + | <i>S. elongatus</i> UTEX 2973 following the example of <a href=https://doi.org/10.1016/j.ymben.2018.06.002> Li | ||
| + | et al., 2018 </a> . We received pSII-trc-pilN, the same plasmid used by Li et al., as a gift from Petra | ||
| + | Wurmser from the research group of Prof. Kaldenhoff in Darmstadt and conjugated it into our strain via | ||
| + | triparental conjugation. <figure Style="text-align:center"> | ||
| + | <img style="height: 40ex; width: 50ex" | ||
| + | src=https://static.igem.org/mediawiki/2019/d/d4/T--Marburg--p_pilN-NSII.png alt="map"> | ||
| + | <figcaption> | ||
| + | Fig. 2: Plasmidmap of pSII-trc-<i> pilN </i>. | ||
| + | </figcaption> | ||
</figure> | </figure> | ||
| − | + | Beforehand, Petra Wurmser told us that she was not able to successfully reproduce the experiment, motivating | |
| − | + | us | |
| − | + | to try it ourselves. | |
| − | + | ||
| − | <i>S. elongatus</i> | + | We made sure to follow the protocol in the above mentioned paper, transforming pRL443 and pRL623 into E. |
| − | + | coli | |
| − | + | HB101 and pSII-trc-pilN into HB101. Overnight cultures of these cells were inoculated and grown to | |
| − | + | OD600≈0.5. | |
| − | + | After washing and incubating them together for half an hour, they were mixed with a exponentially growing | |
| − | + | <i>S. elongatus</i> culture and incubated for 30 minutes again. Thereafter the mixture was blotted on | |
| − | + | sterile filters and | |
| − | + | incubated on BG11 plates for 24h before being transferred onto BG11 plates containing kanamycin | |
| − | + | <a href=https://doi.org/10.1016/j.ymben.2018.06.002> Li et al., 2018 </a> It is important to add, that we | |
| + | also went with another approach for conjugation: Martina Carrillo Camacho from the working group of | ||
| + | Prof. Dr. Tobias Erb provided us with the pRK2013 plasmid, mentioning that she uses it for conjugation. | ||
| + | So we transformed the plasmid into <i> E. coli </i> DH5ɑ and pSII-trc-pilN into HB101, performing the | ||
| + | same | ||
| + | procedure with them as stated above. | ||
| + | <br> | ||
| + | After a whole week we could actually see growing colonies, though they were only from attempts with the | ||
| + | pRK2013 plasmid | ||
| + | <figure Style="text-align:center"> | ||
| + | <img style="height: 50ex; width: 60ex" | ||
| + | src=https://static.igem.org/mediawiki/2019/e/e5/T--Marburg--Trafo-pilN-NSII-UDAR.jpg alt="map"> | ||
| + | <figcaption> | ||
| + | Fig.3 : Pictures of Agarplates with colonies received from the triparental conjugation with the | ||
| + | Helperstrain pRK2013 and HB101, haboring the pSII-trc-pilN Vector. | ||
| + | </figcaption> | ||
</figure> | </figure> | ||
| − | + | ||
| − | + | We were still excited, directly starting liquid cultures and | |
| − | to | + | running |
| − | + | colony PCRs in hope to find our desired result. Although trying a wide variety of primer combinations, | |
| − | + | we were | |
| − | + | not able to find any successful integrations, but as the strain was growing on kanamycin and colony PCR | |
| − | + | does not | |
| − | + | always work right, we wanted to make sure and tried an actual transformation: a YFP construct was | |
| − | + | transformed | |
| − | <i>S. elongatus</i> | + | into our seemingly competent strain, allowing for easy selection afterwards. <b>4 Bilder hiernoch rein |
| − | + | !</b> | |
| − | + | Disappointingly we could not transform the strain. This was in accordance to the results of Petra | |
| − | <a href=https:// | + | Wurmser, who |
| − | + | was also not able to reintroduce natural competence into <i>S. elongatus</i> UTEX 2973 through this | |
| − | + | method. | |
| − | + | <br> | |
| − | + | In hope of better results we decided to try and revert the point mutation in the <i> pilN </i> gene with | |
| − | + | a CRISPR/Cas system.While still working on the system itself as described in the design section | |
| − | < | + | <b>[links to design]</b>, we used |
| − | + | the pSL2680 plasmid <a href=https://www.nature.com/articles/srep39681> Ungerer and Pakrasi, 2016 </a> to | |
| − | + | engineer our strain. We followed their protocol <a href=https://www.addgene.org/85581/>(available | |
| + | here on Addgene)</a> to construct a guiding crRNA, leading the Cas12a enzyme to the mutated <i> | ||
| + | pilN </i> gene and cloned it together with the enzyme and a repair template to revert the point | ||
| + | mutation. Sequencing results of all parts needed were correct, so the final construct could be | ||
| + | transformed into our cyanobacteria .<b>[Fig.XX Seq results nicht da ?]</b> | ||
| + | In this approach triparental conjugation was performed slightly differently, as we wanted to exactly | ||
| + | follow the provided protocol: | ||
| + | In contrary to the other method, a HB101 strain harboring pRL623 was again transformed with the | ||
| + | plasmid | ||
| + | of interest, in this case the fully assembled pSL2680 and the other HB101 strain just contained | ||
| + | pRL443. | ||
| + | Again, both strains were mixed together and then inoculated before being blotted on filters on BG11 | ||
| + | plates. This time, after only 6h the filters were transferred on BG11 plates with kanamycin. | ||
| + | During our first run a few colonies were visible after just three days, but getting cultures to grow | ||
| + | in | ||
| + | liquid media did not work as expected and the colonies did not look as healthy as hoped. | ||
| + | As we have had this kind of issue several times during our project and saw that in literature the | ||
| + | colonies growing on the plates looked differently, we decided to reach out to experienced | ||
| + | researchers | ||
| + | working with the same Synechococcus elongatus strain. We contacted Prof. Dr. James W. Golden from | ||
| + | the | ||
| + | University of California, San Diego to ask for advice <b>[link to golden skype call]</b> and were | ||
| + | able to | ||
| + | discover a crucial difference in the way we work with our strain: while in our own lab this is not | ||
| + | commonly done, the researchers from the Golden lab put Na2S2O3 (sodium thiosulfate) in their BG11 | ||
| + | plates | ||
| + | and we could find literature to support this advice (Thiel et al., 1989). This might seem like a | ||
| + | small | ||
| + | addition, but it proved to be an essential factor, as after adding this ingredient to our own plates | ||
| + | we | ||
| + | were able to grow way better looking colonies, and not just that - the colonies started coming up | ||
| + | after | ||
| + | just one day in our incubator | ||
<figure Style="text-align:center"> | <figure Style="text-align:center"> | ||
| + | <img style="height: 50ex; width: 60ex" src=alt=" [Fig.XX n3w pl4t35 fr0m burg1]!"> | ||
| + | <figcaption> | ||
| + | Fig.4 : [Fig.XX n3w pl4t35 fr0m burg1]! | ||
| + | </figcaption> | ||
| + | </figure> | ||
| + | The reason is simple: When autoclaving agar that contains phosphates, reactive oxygen species such | ||
| + | as | ||
| + | H2O2 can be formed, which can drastically hinder bacterial growth | ||
| + | <a href=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249246/>(Tanaka et al., 2014)</a>. The | ||
| + | thiosulfate from Na2S2O3 is oxidized as H2O2 is reduced to 2 H2O - so clearly thiosulfate can | ||
| + | act as a reducing agent, eliminating reactive oxygen species from the medium. Presumably the | ||
| + | missing sodium thiosulfate in our BG11 agar was not the sole reason we did not get the desired | ||
| + | results on our plate, but in combination with the toxicity of Cas12a (though less toxic than | ||
| + | Cas9, it still exhibits nuclease activity, cutting the DNA of the bacteria) the pressure was too | ||
| + | high for most of the cells. With our new found ingredient we were certain to get it right this | ||
| + | time and set the whole process in motion, this time with BG11 plates including sodium | ||
| + | thiosulfate. In one huge experiment we tried a wide variety of different conjugation approaches, | ||
| + | following the instructions of multiple papers ( <a | ||
| + | href=https://www.nature.com/articles/srep39681> Ungerer and Pakrasi, 2016 </a>, <a | ||
| + | href=https://www.nature.com/articles/srep08132>Yu et al., 2015</a> , <a | ||
| + | href=https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-016-0514-7> Wendt | ||
| + | et al., 2016</a> ). We are currently screening for correct edits and are certain to hold a | ||
| + | naturally competent strain in our hands in a matter of days [Fig.XX new plates from Vincas | ||
| + | conj]. <figure Style="text-align:center"> | ||
<img style="height: 50ex; width: 60ex" | <img style="height: 50ex; width: 60ex" | ||
| − | src=https://static.igem.org/mediawiki/2019/ | + | src=https://static.igem.org/mediawiki/2019/f/ff/T--Marburg--Conjugation_UTEX2973_pSL2680.png |
| + | alt="latest conjugation of UTEX2973 with the plasmid pSL2680."> | ||
<figcaption> | <figcaption> | ||
| − | Fig. | + | Fig.5 : Latest conjugation of UTEX2973 with the plasmid pSL2680. |
| − | + | ||
</figcaption> | </figcaption> | ||
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</figure> | </figure> | ||
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| − | + | </p> | |
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| − | + | <h2>CRISPR gene editing</h2> | |
| − | + | <p>CRISPR gene editing | |
| − | + | Although CRISPR/Cas systems have been discussed as incredibly powerful tools in genetic engineering, they have | |
| − | + | not yet been widely used in cyanobacterial research, which is why we set out to implement such a system, based | |
| − | + | on CRISPR/Cas12a, into our Green Expansion of the Marburg Collection <b>[Link to MarburgCollection]</b>. | |
| − | + | <br> | |
| − | + | As CRISPR/Cas12a has already been reported to work in <i> S.elongatus</i> UTEX 2973 <a | |
| − | + | href=https://www.nature.com/articles/srep39681> Ungerer and Pakrasi, 2016 </a>, we were sure that it could | |
| − | + | be transformed into a Golden Gate Assembly compatible version, allowing for more flexible design | |
| − | + | considerations <b></b>[Link to Design of CRISPR ]</b>. | |
| − | + | While we started the cloning processes needed to change the existing vector into the phytobrick standard, we | |
| − | + | tried the vector at hand ourselves, in order to assess its usefulness. | |
| − | + | Following the given protocols we constructed a CRISPR/Cas12a vector harboring a crRNA and repair template | |
| − | + | designed to revert the point mutation in the <i> pilN </i> gene of our <i> S.elongatus</i> strain. After a | |
| − | + | few | |
| − | + | initial problems we were able to get conjugants and are currently screening for those containing the desired | |
| − | + | edit - more on this approach can be found in the Natural Competence section of our results. | |
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<br> | <br> | ||
| − | + | In order to modularize this system we built different parts for our genetic toolbox. First of all we created | |
| − | + | a | |
| − | + | lvl 0 part of the Cas12a protein by amplifying the sequence from the pSL2680 plasmid, including overhangs | |
| − | + | that | |
| − | + | enabled us to clone the PCR product into a lvl 0 acceptor vector | |
| − | + | ||
| − | + | <figure Style="text-align:center"> | |
| − | + | <img style="height: 45ex; width: 55ex" | |
| − | + | src=https://static.igem.org/mediawiki/2019/a/ae/T--Marburg--Cas12a_CDS_lvl0.png alt="map"> | |
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<figcaption> | <figcaption> | ||
| − | Fig. | + | Fig. 6: The plasmid map for the coding sequence of the lvl0 construct. |
</figcaption> | </figcaption> | ||
</figure> | </figure> | ||
| − | + | ||
| − | + | Sequencing results proved, that this crucial part was correctly assembled, ready to be used in lvl 1 | |
| − | + | constructs | |
| − | + | - which we promptly did, using the following lvl 0 parts: | |
| − | + | pMC0_1_03 + pMC0_2_03 + pMC0_3_07 + pMC0_4_33 + pMC0_5_07 + pMC0_6_17 | |
| − | + | <figure Style="text-align:center"> | |
| − | + | <img style="height: 45ex; width: 55ex" | |
| − | + | src=https://static.igem.org/mediawiki/2019/a/ae/T--Marburg--Cas12a_CDS_lvl0.png alt="map"> | |
| − | + | <figcaption> | |
| − | + | Fig. 7: caption: sequencing result of the coding sequence of the Cas12a protein. | |
| − | + | </figcaption> | |
| − | + | ||
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| − | + | ||
| − | + | ||
| − | <img style="height: | + | |
| − | src= | + | |
| − | + | ||
| − | <figcaption> Fig. | + | |
| − | + | ||
</figure> | </figure> | ||
| − | + | The chosen promoter is a rather weak one, so that overproduction of Cas12a is prevented, leading to less | |
| − | + | toxicity in the cells | |
| − | + | <figure Style="text-align:center"> | |
| − | + | <img style="height: 45ex; width: 55ex" | |
| − | + | src=https://static.igem.org/mediawiki/2019/7/74/T--Marburg--Cas12a_CDS_lvl1.png alt="map"> | |
| − | + | <figcaption> | |
| − | + | Fig. 8: The lvl1 construct of the Cas12a protein was built with a weaker promoter to reduce toxic | |
| − | <img style="height: | + | effects. |
| − | src= | + | </figcaption> |
| − | + | ||
| − | <figcaption> Fig. | + | |
| − | + | ||
</figure> | </figure> | ||
| − | + | <br> | |
| − | + | ||
| − | + | Having built this construct, we continued to build the other missing part: the crRNA. | |
| − | + | The design of the pSL2680 plasmid was mostly kept the same, but in order to have an easy and cheap selection | |
| − | + | method we switched the lacZ cassette with a GFP cassette | |
| − | + | <figure Style="text-align:center"> | |
| − | + | <img style="height: 40ex; width: 65ex" | |
| − | + | src=https://static.igem.org/mediawiki/2019/7/7e/T--Marburg--Cas12a_crRNA_lvl0.png | |
| − | + | alt="m[Fig XX plasmid map of crRNA lvl0]. Through sequencingap"> | |
| − | <img style="height: | + | <figcaption> |
| − | src= | + | Fig. 9: lvl0 design for the crRNA. The spacer can be exchanged with even more gRNAs to allow for |
| − | alt=" | + | multiplex genome editing. |
| − | <figcaption> Fig. | + | </figcaption> |
| − | + | </figure> | |
| + | <br> | ||
| + | |||
| + | |||
| + | we could show the correct assembly of this part - everything was as we planned in our design | ||
| + | <b>[Link to design of CRISPR]</b> meaning that we had all the parts in our MoClo standard. | ||
| + | <figure Style="text-align:center"> | ||
| + | <img style="height: 40ex; width: 80ex" | ||
| + | src=https://static.igem.org/mediawiki/2019/3/30/T--Marburg--Cas12a_crRNA_lvl0_seq.png | ||
| + | alt="[Fig XX seq results of crRNA lvl0],"> | ||
| + | <figcaption> | ||
| + | Fig. 10: sequencing result of the lvl0 construct of the crRNA | ||
| + | </figcaption> | ||
</figure> | </figure> | ||
| − | + | <br> | |
| + | As the whole system is built for modular cloning in the PhytoBrick syntax, it is possible to freely exchange | ||
| + | the | ||
| + | parts around the Cas12a and crRNA parts. This enables the use of different promoters, allowing for easy | ||
| + | screening: Constructs with weaker promoters in front of the cas12a gene would lead to less gene expression | ||
| + | and | ||
| + | therefore lower toxicity of the whole system. The free exchange of these promoter parts can consequently be | ||
| + | used | ||
| + | for the creation of a library in order to look for the perfectly fitting promoter for this system | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | Successfully creating these invaluable parts, we were able to establish a workflow for faster cloning in <i> | ||
| + | S.elongatus</i>. | ||
| + | As our system is modularized, it is possible to easily exchange the GFP cassette for the desired crRNA, | ||
| + | which | ||
| + | can be done in a single reaction, further simplifying the cloning process of CRISPR/Cas12a constructs. | ||
| + | As shown before <b>[Link to design of Natural Competence]</b>, the cloning process with the pSL2680 can take | ||
| + | over a | ||
| + | week, is tedious work and is accompanied by another couple of days waiting for colonies. In comparison, our | ||
| + | system enables for efficient cloning in only four days: On the first day the construct is assembled in a | ||
| + | Golden | ||
| + | Gate reaction, which is thereafter transformed into E.coli. The next day colonies can be picked, inoculated | ||
| + | and | ||
| + | the construct can be extracted in the evening. On the third day it can be transformed into <i> | ||
| + | S.elongatus</i> - | ||
| + | and on the fourth day colonies can be screened. | ||
| + | The missing piece to apply an edit is the repair template. Skimming through literature, we noticed that | ||
| + | transformation of linear DNA fragments into <i> S.elongatus</i> is supposedly more efficient than the | ||
| + | transformation of whole plasmids <a href=https://doi.org/10.1016/j.biori.2017.09.001> (Almeida et al., | ||
| + | 2017)</a> - and we were able to verify this fact in our own experiments [Fig XX linear transformation | ||
| + | plate pic]. This further simplifies our above mentioned workflow, as we are able to simply PCR the | ||
| + | needed repair template from a DNA sequence and use the PCR product for transformation into <i> | ||
| + | S.elongatus</i>. Our toolbox has a | ||
| + | special feature that can be used for exactly this workflow: a NotI cutting site can be found in our | ||
| + | constructs, | ||
| + | which is used to linearize them, so that they can be more efficiently transformed. | ||
| + | <br> | ||
| + | We are more than certain that our modular CRISPR/Cas12a proves to be an invaluable contribution to the | ||
| + | tools | ||
| + | available in cyanobacterial research, especially for the Golden Gate community, which is growing bigger | ||
| + | and | ||
| + | bigger every year - also thanks to the iGEM headquarters finally integrating the TypeIIS standard into | ||
| + | the | ||
| + | competition! | ||
| + | </p> | ||
| + | |||
| + | <h4>Cyanobacterial shuttle vectors </h4> | ||
| + | |||
| + | As we have already clarified in the description part, self replicating shuttle vectors are essential for many | ||
| + | workflows, as the gene expression levels are higher and non of the tedious selection processes that come with | ||
| + | genomic integrations have to be done. <br> | ||
| + | |||
| + | On our road to the modular vector we were seeking, we firstly cured our own S. elongatus UTEX 2973 strain of its | ||
| + | pANS plasmid. This was done by transforming the pAM4787 vector, which holds a spectinomycin resistance as well as a | ||
| + | YFP cassette | ||
| + | <a href= https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000377> (Chen et al., 2016)</a>. | ||
| + | Due to plasmid incompatibility - explained here in our design section <b>[Link to shuttle vector design]</b> - and because antibiotic pressure is applied, the pANS plasmid was over time cured from the | ||
| + | strain, which then just kept the pAM4787 plasmid. Transformation was done by conjugation with the pRK2013 plasmid in | ||
| + | DH5ɑ and the pAM4787 in HB101. Both were grown to an OD600≈0.5, washed in LB and mixed with S. elongatus which was | ||
| + | grown to late exponential phase and then washed in BG11. | ||
| + | We could clearly show, that the conjugant strain bears the pAM4787 plasmid if selective pressure is held up. | ||
| + | <figure Style="text-align:center"> | ||
| + | <img style="height: 65ex; width: 50ex" | ||
| + | src= https://static.igem.org/mediawiki/2019/e/eb/T--Marburg--YFPconstructConjugantFACS.png | ||
| + | alt=" https://static.igem.org/mediawiki/2019/e/eb/T--Marburg--YFPconstructConjugantFACS.png"> | ||
| + | <figcaption> | ||
| + | Fig. 11: Cell counts of conjugant strain. The y axis shows relative YFP fluorescence and the x axis relative autofluorescence. | ||
| + | </figcaption> | ||
| + | </figure> | ||
| + | This was followed by us starting to culture the pAM4787 bearing strain without | ||
| + | antibiotics again, slowly removing selective pressure from the cells. As the plasmid does not give them any other | ||
| + | advantage and is probably just more metabolic burden due to the constantly produced YFP proteins it is slowly being | ||
| + | lost. | ||
| + | We could prove this in multiple setups: with the flow cytometry device we were kindly granted access to we could | ||
| + | clearly show the missing YFP signal in the cured <i>S. elongatus </i>strain and | ||
| + | logically this could also be observed over our UV table | ||
| − | + | <figure Style="text-align:center"> | |
| − | + | <img style="height: 65ex; width: 50ex" | |
| − | + | src= https://static.igem.org/mediawiki/2019/c/c4/T--Marburg--CuredStrainsFACS.png | |
| − | + | alt="https://static.igem.org/mediawiki/2019/c/c4/T--Marburg--CuredStrainsFACS.png "> | |
<img style="height: 65ex; width: 50ex" | <img style="height: 65ex; width: 50ex" | ||
| − | + | src= https://static.igem.org/mediawiki/2019/d/da/T--Marburg--CuredStrainUV.png | |
| − | + | alt="https://static.igem.org/mediawiki/2019/d/da/T--Marburg--CuredStrainUV.png"> | |
| − | <figcaption> | + | <figcaption> |
| − | </ | + | a) Cell counts of cured strain. The y axis shows relative YFP fluorescence and the x axis relative autofluorescence |
| − | + | b) Comparison of the fluorescence signal of the transformed (left) and cured (right) strain. | |
| − | + | </figcaption> </figure> | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | Furthermore we performed colony PCRs as a test. We sent our plasmid-free strain to Next Generation Sequencing in order to ensure that the strain really has lost the | |
| − | . | + | pANS plasmid. |
| − | + | <figure Style="text-align:center"> | |
| − | + | <img style="height: 65ex; width: 50ex" | |
| − | + | src= https://static.igem.org/mediawiki/2019/e/e9/T--Marburg--ColonyPCRcuredStrain.jpg | |
| − | + | alt="gel pcr"> | |
| − | + | <figcaption> Fig. 12: Colony PCR of the wild type, the conjugated and the cured strain. | |
| − | + | </figcaption> | |
| + | </figure> | ||
| + | |||
| + | Our next step was the characterization of the cyanobacterial shuttle vector mentioned in our design section <b>[Link to | ||
| + | design]</b>. | ||
| + | In an extensive flow cytometry experiment we assessed the fluorescence of a transformed YFP-construct in our cured | ||
| + | strain, showing that the shuttle vector with the minimal replication element can be maintained in<i>S. elongatus </i> UTEX | ||
| + | 2973 . | ||
| + | <figure Style="text-align:center"> | ||
| + | <img style="height: 65ex; width: 50ex" | ||
| + | src= | ||
| + | alt="hier kommen noch 3 bilder von FACS Messung aber no time"> | ||
| + | <figcaption> Fig. 13: hier kommen noch 3 bilder von FACS Messung aber no time. | ||
| + | </figcaption> | ||
| + | </figure> | ||
| + | After another four weeks of cultivation we looked at our | ||
| + | cultures again on the UV table to check if fluorescence was still present and the high intensity of the fluorescence | ||
| + | proved to us, that the plasmid is still stably replicated in our strain, showing us, that the minimal replication | ||
| + | element does indeed work in our strain. | ||
| + | For further analysis we performed qPCR with this transformed strain, in order to check the copy number of the | ||
| + | vector. We used the copy number of pANL as a reference, which is supposedly at ~2,6 copies per chromosome | ||
| + | <a href= https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000377> (Chen et al., 2016)</a>. Our data shows a ~4,5 times higher copy number relative to pANL, meaning that the construct is | ||
| + | maintained with approximately 11,7 copies per chromosome. | ||
| + | <figure Style="text-align:center"> | ||
| + | <img style="height: 65ex; width: 50ex" | ||
| + | src= | ||
| + | alt="hier kommen noch 3 bilder [FigXX Honrok qPCR data? diagramm biddeeeeeeeeeeeeeee] aber no time"> | ||
| + | <figcaption> Fig. 14: hier kommen noch 3 bilder [FigXX Honrok qPCR data? diagramm biddeeeeeeeeeeeeeee] aber no time. | ||
| + | </figcaption> | ||
| + | </figure> | ||
| + | |||
| + | |||
| + | Additionally we measured the fluorescence signals in a plate reader at different optical densities and could again | ||
| + | confirm high fluorescence signals, indicating strong gene expression in constructs built around this replication | ||
| + | element. | ||
| + | <figure Style="text-align:center"> | ||
| + | <img style="height: 65ex; width: 50ex" | ||
| + | src= https://static.igem.org/mediawiki/2019/f/f0/T--Marburg--results_yfp_pam_4787_6_replicates.jpg | ||
| + | alt="diagramm"> | ||
| + | <figcaption> Fig. 15:YFP fluorescence at different optical densities. </figcaption> | ||
| + | </figure> | ||
| + | |||
| − | + | All this data confirms that the construct actually works and can be reliably used as a cyanobacterial shuttle | |
| − | </ | + | vector, proving that BBa_K3228069 works as intended, thus functioning as our validated part. |
| − | + | This assumption is solidified by all our sequence data, showing that the shuttle vectors were completely assembled | |
| − | + | as planned in our design section <b>[Link to design of shuttle vectors]</b> | |
| − | + | . | |
| − | + | <figure Style="text-align:center"> | |
| − | </p> | + | <img style="height: 65ex; width: 50ex" |
| + | src= xyz | ||
| + | alt="disgramm"> | ||
| + | <figcaption> Fig. 16: [FigXX seq results of lvl1 and lvl2 ori] </figcaption> | ||
| + | </figure> | ||
| + | </p> | ||
| + | |||
| + | </p> | ||
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Revision as of 01:31, 22 October 2019
R E S U L T S
The way to the results we demonstrate here was full of success and failure. Therefore, it was necessary to compare and revise our theoretical plans with the practical work and the associated results. After trying our best to implement our plans, we would like to show you on this page that we have managed to realize some of our goals and are able to show some achievements for every sub-group.
S T R A I N
E N G I N E E R I N G
At this passage we show how to do genetic modifications to regain the natural competence of Synechococcus elongatus UTEX 2973. With these methods we succeed the natural transformation of plasmids in UTEX2973.
Colony pictures
The Colony picture Collaboration
Results
Natural competence
Reintroducing natural competence into our S. elongatus strain was an important goal for us. To make sure
that
our S. elongatus UTEX 2973 actually holds the point mutation in the pilN gene we thought it has,
we sequenced
this region - and the results showed the expected mutation
Although not our favorite method, we tried integrating an intact copy of the pilN gene into neutral site
II of
S. elongatus UTEX 2973 following the example of Li
et al., 2018 . We received pSII-trc-pilN, the same plasmid used by Li et al., as a gift from Petra
Wurmser from the research group of Prof. Kaldenhoff in Darmstadt and conjugated it into our strain via
triparental conjugation. 
After a whole week we could actually see growing colonies, though they were only from attempts with the
pRK2013 plasmid
In hope of better results we decided to try and revert the point mutation in the pilN gene with
a CRISPR/Cas system.While still working on the system itself as described in the design section
[links to design], we used
the pSL2680 plasmid Ungerer and Pakrasi, 2016 to
engineer our strain. We followed their protocol (available
here on Addgene) to construct a guiding crRNA, leading the Cas12a enzyme to the mutated
pilN gene and cloned it together with the enzyme and a repair template to revert the point
mutation. Sequencing results of all parts needed were correct, so the final construct could be
transformed into our cyanobacteria .[Fig.XX Seq results nicht da ?]
In this approach triparental conjugation was performed slightly differently, as we wanted to exactly
follow the provided protocol:
In contrary to the other method, a HB101 strain harboring pRL623 was again transformed with the
plasmid
of interest, in this case the fully assembled pSL2680 and the other HB101 strain just contained
pRL443.
Again, both strains were mixed together and then inoculated before being blotted on filters on BG11
plates. This time, after only 6h the filters were transferred on BG11 plates with kanamycin.
During our first run a few colonies were visible after just three days, but getting cultures to grow
in
liquid media did not work as expected and the colonies did not look as healthy as hoped.
As we have had this kind of issue several times during our project and saw that in literature the
colonies growing on the plates looked differently, we decided to reach out to experienced
researchers
working with the same Synechococcus elongatus strain. We contacted Prof. Dr. James W. Golden from
the
University of California, San Diego to ask for advice [link to golden skype call] and were
able to
discover a crucial difference in the way we work with our strain: while in our own lab this is not
commonly done, the researchers from the Golden lab put Na2S2O3 (sodium thiosulfate) in their BG11
plates
and we could find literature to support this advice (Thiel et al., 1989). This might seem like a
small
addition, but it proved to be an essential factor, as after adding this ingredient to our own plates
we
were able to grow way better looking colonies, and not just that - the colonies started coming up
after
just one day in our incubator
CRISPR gene editing
CRISPR gene editing
Although CRISPR/Cas systems have been discussed as incredibly powerful tools in genetic engineering, they have
not yet been widely used in cyanobacterial research, which is why we set out to implement such a system, based
on CRISPR/Cas12a, into our Green Expansion of the Marburg Collection [Link to MarburgCollection].
As CRISPR/Cas12a has already been reported to work in S.elongatus UTEX 2973 Ungerer and Pakrasi, 2016 , we were sure that it could
be transformed into a Golden Gate Assembly compatible version, allowing for more flexible design
considerations [Link to Design of CRISPR ].
While we started the cloning processes needed to change the existing vector into the phytobrick standard, we
tried the vector at hand ourselves, in order to assess its usefulness.
Following the given protocols we constructed a CRISPR/Cas12a vector harboring a crRNA and repair template
designed to revert the point mutation in the pilN gene of our S.elongatus strain. After a
few
initial problems we were able to get conjugants and are currently screening for those containing the desired
edit - more on this approach can be found in the Natural Competence section of our results.
In order to modularize this system we built different parts for our genetic toolbox. First of all we created
a
lvl 0 part of the Cas12a protein by amplifying the sequence from the pSL2680 plasmid, including overhangs
that
enabled us to clone the PCR product into a lvl 0 acceptor vector
Having built this construct, we continued to build the other missing part: the crRNA.
The design of the pSL2680 plasmid was mostly kept the same, but in order to have an easy and cheap selection
method we switched the lacZ cassette with a GFP cassette
![m[Fig XX plasmid map of crRNA lvl0]. Through sequencingap](https://static.igem.org/mediawiki/2019/7/7e/T--Marburg--Cas12a_crRNA_lvl0.png)
we could show the correct assembly of this part - everything was as we planned in our design
[Link to design of CRISPR] meaning that we had all the parts in our MoClo standard.
![[Fig XX seq results of crRNA lvl0],](https://static.igem.org/mediawiki/2019/3/30/T--Marburg--Cas12a_crRNA_lvl0_seq.png)
As the whole system is built for modular cloning in the PhytoBrick syntax, it is possible to freely exchange
the
parts around the Cas12a and crRNA parts. This enables the use of different promoters, allowing for easy
screening: Constructs with weaker promoters in front of the cas12a gene would lead to less gene expression
and
therefore lower toxicity of the whole system. The free exchange of these promoter parts can consequently be
used
for the creation of a library in order to look for the perfectly fitting promoter for this system
Successfully creating these invaluable parts, we were able to establish a workflow for faster cloning in
S.elongatus.
As our system is modularized, it is possible to easily exchange the GFP cassette for the desired crRNA,
which
can be done in a single reaction, further simplifying the cloning process of CRISPR/Cas12a constructs.
As shown before [Link to design of Natural Competence], the cloning process with the pSL2680 can take
over a
week, is tedious work and is accompanied by another couple of days waiting for colonies. In comparison, our
system enables for efficient cloning in only four days: On the first day the construct is assembled in a
Golden
Gate reaction, which is thereafter transformed into E.coli. The next day colonies can be picked, inoculated
and
the construct can be extracted in the evening. On the third day it can be transformed into
S.elongatus -
and on the fourth day colonies can be screened.
The missing piece to apply an edit is the repair template. Skimming through literature, we noticed that
transformation of linear DNA fragments into S.elongatus is supposedly more efficient than the
transformation of whole plasmids (Almeida et al.,
2017) - and we were able to verify this fact in our own experiments [Fig XX linear transformation
plate pic]. This further simplifies our above mentioned workflow, as we are able to simply PCR the
needed repair template from a DNA sequence and use the PCR product for transformation into
S.elongatus. Our toolbox has a
special feature that can be used for exactly this workflow: a NotI cutting site can be found in our
constructs,
which is used to linearize them, so that they can be more efficiently transformed.
We are more than certain that our modular CRISPR/Cas12a proves to be an invaluable contribution to the
tools
available in cyanobacterial research, especially for the Golden Gate community, which is growing bigger
and
bigger every year - also thanks to the iGEM headquarters finally integrating the TypeIIS standard into
the
competition!
Cyanobacterial shuttle vectors
As we have already clarified in the description part, self replicating shuttle vectors are essential for many workflows, as the gene expression levels are higher and non of the tedious selection processes that come with genomic integrations have to be done.On our road to the modular vector we were seeking, we firstly cured our own S. elongatus UTEX 2973 strain of its pANS plasmid. This was done by transforming the pAM4787 vector, which holds a spectinomycin resistance as well as a YFP cassette (Chen et al., 2016). Due to plasmid incompatibility - explained here in our design section [Link to shuttle vector design] - and because antibiotic pressure is applied, the pANS plasmid was over time cured from the strain, which then just kept the pAM4787 plasmid. Transformation was done by conjugation with the pRK2013 plasmid in DH5ɑ and the pAM4787 in HB101. Both were grown to an OD600≈0.5, washed in LB and mixed with S. elongatus which was grown to late exponential phase and then washed in BG11. We could clearly show, that the conjugant strain bears the pAM4787 plasmid if selective pressure is held up.
The Golden Gate
collaboration
The Golden Gate collaboration
TEXT HERE