Team:Stanford/Design

Stanford iGEM Team Wiki

Design

Overview

Throughout the cloning process for our respective subprojects, our team focused on designing constructs that could be modularly used for future experiments. For example, for DiCE in vitro and in vivo DNA designs we included restriction enzyme cut sites so future users could swap out the target protein and easily adapt our system for their own novel DiCE applications. Furthermore, the cloning work for both the PREDCEL+

DiCE in vivo

During the beginning stages of our team’s project, we branched out our resources and designed several wet-lab and technical projects simultaneously to allot ourselves options. In these early stages, an initial construct design for Qβ was used for proof-of-concept work on the functionality of the beta subunit of Qβ replicase within our host organism, Escherichia Coli. Upon finding initially promising results, our group convened and chose to keep Qβ. In order to prove our hypotheses, we required, however, to optimize our construct design and implementation strategy to appease our goals and allow for a concrete proof-of-concept of directed evolution.

  1. Initial construct design

    In the very early stages of the DiCE leg of the project, the design of the initial vector plasmid was created. Our initial desire was to create a schema to test for the evolutionary capabilities of Qβ in vivo, on a target gene of an antibiotic selection marker. To do so, the intended construct desired extensive cloning. The steps taken to successfully clone the construct are outlined below:

    Step 1: A pET28a+ vector was ordered from New England Biolabs (NEB), while our part inserts Qβ replicase and MDV were ordered from Integrated DNA Technologies (IDT).

    Step 2: The pET28a+ vector was opened up between the T7 promoter and terminator region using a high-fidelity Q5 Polymerase. The linearized vector was then cloned using Gibson Assembly to have an MDV fragment insert.

    Step 3: The cloned vector was then reopened as before in the middle of the MDV region to create MDV-1 and MDV-2 flanking regions, allowing for a gene(s) of choice to be replicated by Qβ by acting as recognition sites on the mRNA.6, 7 One of these genes being that which encodes Qβ replicase itself, which was ligated into the vector via Gibson Assembly.

    Step 4: For a third time, Gibson Assembly cloning was used to insert a chloramphenicol resistance gene, whose DNA fragment was PCRed from an in-house construct supplied by our host student group, BIOME.

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    Step 5: Our construct was, after each cycle of cloning, grown and selected for on kanamycin plates. After the final round of cloning and antibiotic selection, picked colonies were grown in kanamycin, mini-prepped, and then sequence-verified at our local sequencing facility: PAN.

  2. Optimized Design

    In order to refine the original design to better match our ultimate goals, the vector plasmid design was refined to account for concerns with the dynamics and mutagenesis kinetics of the mechanism. Early questions and critics of the original system raised by advisors, interviewees, and ourselves included: how are we to account for the mutagenesis of the Qβ protein itself (Qβ replicase was originally expressed in the mutagenized mRNA)? How might the exponential proliferation of protein account for resistance rather than an optimized protein? And how might the exponential kinetics of the system impact the longevity of the cells? We tackled these problems among others with creating the constructs outlined below:

    Step 1: Using the original pRNA construct as the template plasmid vector, the high fidelity Q5 polymerase was utilized to linearize backbones for both Qβ and No Qβ constructs. The former’s backbone was PCRed with Gibson overhangs from the T7 promoter and terminator in opposing directions. The latter, was PCRed similarly, except with the addition to include the MDV-1 and MDV-2 regions.

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    Our 2019 iGEM team, with three high school interns front and center :)

    Step 2:The Qβ fragment was also PCRed with Gibson overhangs from the original pRNA construct to prepare for Gibson Assembly. Other genes, such as chloramphenicol and ampicillin resistance markers (CMR and AmpR respectively), intended to undergo mutagenesis for proof-of-concept experimentation underwent additional preparatory steps. Another caveat is that when PCR-ing these particular DNA fragments, the Gibson overhangs were designed such that the gene would be ligated into the vector backbone in a reverse complimentary orientation. This would allow us the ability to definitively prove Qβ’s replicative functionality through protein synthesis of antisense mRNA, which can not be created by typical RNA polymerases found in E. coli.

    Step 3: Target genes would not only be utilized as is within the DiCE system but as a proof-of-concept for the mutagenic capabilities of Qβ, single nucleotide polymorphisms (SNPs) were introduced to the genes (e.g. CMR and AmpR) using the Quick Change Mutagenesis Kit.

    Step 4: Fragments were then ligated into their respective backbones using Gibson Assembly.

    Step 5: No Qβ as a plasmid is not pragmatically useful as the vector backbone is the same as that of Qβ’s. Rather, this construct serves to propagate a target gene in its original form for practical reasons. This gene within the MDV flanks is then selectively amplified in vitro, using a T7 High-Scribe Kit to prep for transfection and subsequent evolution. In other words, the mRNA itself, serves as the applied construct.

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  3. Mechanism

    Working towards our goal of developing a successful in vivo directed evolution system using Qβ replicase, we attempted to optimize initial constructs to create a streamlined process for set-up, mutagenesis, and selection. The envisioned process is depicted below:

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Above, an in vitro transcribed candidate target gene expressed between the MDV-1 and MDV-2 flanking regions is transfected into the host organism via electroporation. The host organism was made electrocompetent with our own protocol after the transformation of the plasmid vector Qβ.
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At this stage of the DiCE system, transfected mRNAs are replicated by Qβ replicase and the respective protein is translated. Under each replication cycle, variation is increased due to Qβ being error-prone and occurs in tandem with the growth phase below.
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During this phase of the DiCE system, selective pressure is incrementally added, which allows for self-selection of the best mutants by creating an environment, where bacteria must increasingly be closer to having the desired phenotype (i.e. correct genotype) in order to live. Bacteria without functional consensus mutants die and can no longer propagate, whereas successful mutants are propagated.
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Once survival is observed within a given environment, correlating with an observed desired phenotype (e.g. efficient enzymatic activity at higher temperatures or extreme antibiotic resistance). At this point, RNA can simply be extracted out of the culture and synthesized into cDNA to be sequenced and analyzed for consensus mutants.

DiCE in vitro

We envision a workflow where researchers can create selection schema using PCR-amplified linear DNA fragments that link desired behavior to Qß synthesis. The ability to deploy PCR products directly into the directed evolution workflow will allow greatly improved and faster rapid prototyping, as well as dramatically expand accessibility to directed evolution techniques. Within the directed evolution process, the individual mutants are compartmentalized in individual water-in-oil droplets, creating the genotype to phenotype linkage necessary for selection-based directed evolution, ensuring the same self selective power as cellular directed evolution technique analogs.

When creating our constructs, we developed them via PCR amplification directly off our plasmid backbone, generating linear DNA fragments that were transcribed into RNA with the T7 HiScribe Quick Transcription kit, and then directly input into reactions.

Program Outreach

A common pitfall of outreach is to selectively reach out to those who are already well-connected to such opportunities. For our team, being situated in the Bay Area made this all the more pertinent: it would be all too easy to get ample applicants by simply contacting one or two private high schools with already well-established internship programs. We wanted to reach beyond this, however. Thus, we made it our goal to spread the word to people who may not otherwise have the opportunity to get engaged with lab research.

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Email outreach to bioengineering graduate students
To accomplish this we:
  1. Had each Stanford iGEM member contact 2-3 local biology teachers from a variety of high schools.
  2. Had a departmental-wide announcement to graduate students advertising the program and encouraging them to forward our program information widely.
  3. Did in-person outreach to spread the word to local high school students.

We put together and distributed the following informational packet to these different outlets. Note that this is a version prior to the expansion of the program to include minors: https://tinyurl.com/Stanford-iGEM2019-18program

More recently, we improved the cover page to the following (see right). An editable version of this template can be downloaded here for teams interested in building upon this handout to use for their teams

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Updated iGEM Info Handout (template available to download)

Application Process

The goal of the application process was to identify candidates that have demonstrated interest in pursuing science beyond the classroom and that would be committed to the team for the duration of their internships. We emphasized that prior lab experience was not required or expected, and we encourage applicants to highlight other skills and experiences outside of the classroom that may have given them applicable skills to working with a team on a long-term project.

We designed an application process with two phases: a written application with a letter of recommendation from a teacher or mentor, followed by a face-to-face interview with two to three members of the iGEM team.

For the application we asked for a one-page cover letter addressing the following four questions:

  1. Why would you like to work on the Stanford iGEM team this summer?
  2. What level of commitment can you have this summer?
  3. What prior experiences have you had that may be relevant to your experience this summer?
  4. How have your prior experiences uniquely prepared you to contribute to iGEM?

They could submit this cover letter along with basic information at this google form. As an additional resource, here are email templates that our team used throughout the process. Although teams may need to modify these documents to to tailor them for their respective programs, we encourage teams to use them as starting points for their program and to reach out to us if they have any questions.

Gaining Departmental Support

Having minors work supervised exclusively by undergraduates in a lab with a variety of safety hazards creates significant liability. Thus, getting support for a program such as this is inherently political and can be a time-intensive and bureaucratic process—get started well-before summer to leave time for outreach and a substantive application process!

Our first recommendation is to reach out to immediate mentors that know the larger system within which your iGEM team is operating. For us, this was the teaching lab’s Lab Manager. She knew what entity would ultimately need to approve such a program (the BioE Department Chair), she had recommendations for putting together a proposal, she knew some of the safety training requirements and pointed us to resources for minor-specific requirements, and finally she could connect us to the intermediate faculty from which we would need to garner support before proceeding to the department chair.

Our final proposal was a modified version of the aforementioned informational handout, but with an additional letter of support from our lab manager.

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Take the time to build relationships across your department

My final more personal recommendation here is to balance being both professional and personal as you build relationships with those across the department. Though it may at times seem like a bureaucratic web of rules, building mutual trust with all those you come across can go much further than you may expect.

Safety

Safety was at the forefront, tail-end, and just about every step of the internship program. Before entering lab we had a comprehensive list of required safety trainings and documentation to complete, as well as a detailed list of requirements while working in lab.

In addition to the usual lab safety standards, working with minors poses a few additional hurdles. While these are unique for each university, beyond parental consent and liability forms from parental guardians Stanford also required that all of the undergraduates on our team completed additional “Working with Minors” online trainings, got official background checks, and were fingerprinted.

In addition to the safety checklist, we documented the expected types of lab work in which high school students may participate, and also outlined off-limit work (such as tissue culture and chemical room access). For all time in lab, we ensured high school students would always be paired with at least one undergraduate at all times.

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18+ Safety Contract

Mentorship Structure

We approached the mentorship structure with intention: we aimed to create a program that efficiently used both undergraduate and high school students’ time, that would expose interns to a variety of types of work, and that would allow interns to take ownership over part of the project.

We encouraged interns to commit to 6-8 weeks (four week minimum), working in lab 4 hours per day Monday to Friday. Our team quickly realized that it was most effective to have the mornings reserved for the undergrads to do logistical work, long-term project planning, and initial lab work, then to have the interns join us in lab at 1:00PM for the remainder of the day.

We set aside the first 2 weeks for interns to shadow a variety of the sub-projects our team were working on in order to maximize exposure to different lab techniques. We put together a document with descriptions and links to protocols for common lab techniques (including basic instructions for using Benchling), and had interns print and annotate the procedures.

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The interns' first assignment: Gaining familiarity with protocols fundamentals

Following this initial phase, we then decided the interns were ready to take on their own sub-project: AcrIIA4 Directed Evolution. With assistance when needed, we let them design primers, submit sequencing data, and ultimately plan their own lab work timeline.

For the final phase we helped the interns write up the content of their sub-project for the website (check out “AcrIIA4 Evolution”!). While recognizing that research is never complete, this final push was critical for pulling together the work they had completed thus far, for recognizing and contextualizing the motivations for the work they were doing, and for ultimately sharing their findings with the larger scientific community.

Gathering and Implementing Program Feedback

From the get-go, we were up front with the interns that the program was a novel one. We highly encouraged open communication and constructive feedback on both positive and negative aspects of the experience so that we could continue to improve.

To further encourage and formalize this process, we had interns fill out an anonymous satisfaction and feedback survey both midway and at the end of the program. We included an input field for a random number the intern could put so we could track performance longitudinally while still maintaining anonymity. We tracked some metrics quantitatively such as overall satisfaction and whether the interns felt their time was being used effectively, and we also gave space for more qualitative feedback such as “What aspects of the program would you like continued” and “Please provide 1 to 3 areas where we could improve to maximize your experience this summer.”

These survey results both helped us to make tweaks to the program midway through the summer, and it also gave us concrete areas to work on for next year (see data below!).

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Interns feedback and satisfaction survey

Closing Out the Program

Though it may seem a small detail, we’re strong advocates of a fun last day :) On one of the last days of summer, we invited the three interns back for one last celebration of all the hard work we completed over the summer. We put together personalized certificates of completion for the high schoolers, we got some ice cream, and had a relaxing afternoon enjoying a picnic out on the oval.

Novel Selection Schema

PREDCEL+

Like PACE, PREDCEL+ relies on M13 bacteriophage to carry a library of mutant genes. The replication of these viruses is tied to the fitness of the mutant gene such that the most fit gene mutants produce more offspring, which eventually become the majority of the viral population. Conventional PACE and PREDCEL creates this linkage by creating a biocircuit whose output is M13 gene III (gIII), which encodes a phage protein (pIII) involved with phage entry into the cell9. However, even low amounts of gIII expression render cells resistant to phage infection10, complicating matters. We decided to use a different phage protein involved in mediating phage entry, pVI (encoded by gVI), for our selection based on findings that it does not render cells resistance to further infection, is unstable in the absence of pIII, and leads to higher phage production when expressed at higher rates8.

One roadblock encountered early-on when using PACE was that phage may not be able to propagate in culture if they all encode mutants poor at performing the task to be evolved. This leads to ‘phage washout,’ where evolution halts due to the inability of the phage to replicate. This issue was solved by using a genetic element termed a ‘drift cassette,’ which can inducibly express gIII or gVI when needed10. Typically, drift is induced earlier in the evolution and reduced gradually to zero as the evolution progresses. However, it is unclear how much or when drift should be induced without periodically conducting plaque assays to visualize the amount of phage at any given moment. The Stanford 2019 iGEM team thus developed an ‘infection reporter’ based on GFP fluorescence output to report on what fraction of cells at any given moment in time are infected with phage. GFP expression is driven by the phage shock promoter (Ppsp), which responds to filamentous phage infection (specifically, expression of M13 gIV, which causes pores in the E. coli membrane that allow phage progeny to leave the cell10) in addition to osmotic shock, organic solvents, and blockage of secA machinery used for protein export11. We used two sequences for Ppsp in our designs - one described by the 2018 FSU iGEM team11 (part BBa_K2832003) and the other the wild-type Ppsp in plasmid pDB023f1 from Prof. David Liu’s lab12 (part BBa_K3258000).

To further simplify the cloning of PREDCEL+ and limit the possibility of phages containing mutant proteins propagating outside of engineered host cells, we split our system into three plasmids, which we term the helper plasmid (HP), accessory and mutagenesis plasmid (APMP), and the selection plasmid (SP). The components of each are detailed in the figure below:

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Figure 1.

To test our designed PREDCEL+ architecture, we decided to recapitulate the evolution done on the T7 RNA Polymerase to allow it to recognize the T3 RNA polymerase promoter conducted in the seminal PACE paper1. We thus used a more specific APMP and SP. All plasmids used are outlined below:

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Figure 2.

Novel Selection Schema Using PREDCEL+

Once validated, we aimed to use PREDCEL+ to test out a standardized selection schema for biosensor evolution. Making use of the discretized nature of PREDCEL, we thought it easy to transfer between multiple populations of bacteria in such a way that the gene to evolve is selected to be fit in all of them. We thought we could make use of this advantage to select for biosensors by negatively and positively selecting for and against binding, respectively, in the presence and absence of the desired molecule to sense13. As a proof of concept, we decided to evolve the lacI repressor to respond to new substrates and to adjust the dynamic range of the lacI IPTG dose response. To this end, we developed two APMPs - one for positive selection and the other for negative selection. All plasmids used for the evolution are presented below:

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Figure 3.

Novel DE Application

For our first step towards our goal of designing AcrIIA4 to be more effective at inhibiting xCas9, we had to determine if AcrIIA4 already has some activity against xCas9. Based on our literature search, AcrIIA4 has never been tested against xCas9. There are ten amino acid differences between Cas9 and xCas9. However, two occurred in the AcrIIA4 binding site, and the other eight could have also potentially resulted in conformational changes to the protein that could affect AcrIIA4’s ability to interact with the xCas9 (see model). Based on this modeling, we suspect that AcrIIA4 may not be effective against xCas9 to the same degree as it was with Cas9.

Video Caption: This model supports our hypothesis that AcrIIA4 likely does not effectively inhibit xCas9. Specifically, it shows Cas9 (blue) in its activated form bound to sgRNA (white) and AcrIIA4 (yellow). The AA changes from Cas9 to xCas9 (of which there are 10) are highlighted in green. Cas9 AAs that are within 5 Aº of the AcrIIA4 are highlighted in red, while AAs in the 5-10 Aº range are highlighted orange. Of the 10 xCas9 AA change, two were in the binding pocket of AcrIIA4 (one within 5 Aº and one between 5 and 10 Aº). These two AA changes could likely interfere with AcrIIA4’s ability to interact with xCas9.

This modeling data justified our next steps: designing a system to test AcrIIA4’s current effectiveness against xCas9. We took two approaches to answer this initial question:

1) In Vitro Construct Design
We first designed a cell-free system to test the efficacy of AcrIIA4 against dxCas9, due to its time-effectiveness. Cell-free reactions involve simply the gene fragments of interest and basic cell machinery. Since each linear fragment can be put into the system independently, there are no plasmid constraints typical of in vivo work, resulting in less cloning work. We obtained dCas9, AcrIIA4, and two sgRNA constructs from the Stanley Qi Lab. The two sgRNA constructs consisted of an “Scr sgRNA” that had a scrambled variable targeting region (negative control), and an “RR1 sgRNA” that could guide dCas9 to the RFP gene and thereby silence it. We designed primers that bound to the start and stop codons of these genes, and then added overhangs with a T7 promoter, RBS, and T7 terminator. Additionally, in this cloning process we created a “dead” version of AcrIIA4 that had a frameshift mutation leading to a premature stop codon. Finally, we used a standard RFP plasmid from our lab that already had a T7 promoter and terminator. This RFP was our target gene for the dCas9 and dxCas9, and could visually indicate knockdown status as well as produce data on our plate reader.

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An abridged version of our AcrIIA4 cell free linear construct in Benchling. The primers we used had heads (highlighted in brown) that bound to the AcrIIA4 gene sequence in the plasmid obtained from the Stanley Qi lab. The overhangs for these primers added the necessary promoter (green), RBS (blue) and terminator (grey) needed for cell free expression with just one simple PCR.

2) In Vivo Construct Design
In addition to pursuing AcrIIA4 testing in cell free, we also wanted to design DNA constructs to test its activity in vivo. For this we ran into the problem of needing to put our four different components (1. dxCas9/dCas9 2. RR1/Scr sgRNA, 3. AcrIIA4/dead AcrIIA4, and 4. RFP) into a three plasmid system. Given the starting plasmids we had to work with, the constraints of origins of replication and antibiotics, and aiming to minimize the number of Gibson Assemblies required, we came up with the following cloning plan.

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Our in vivo cloning strategy to test AcrIIA4’s activity against dCas9 (control) and dxCas9 (test).

Unfortunately, while we successfully cloned AcrIIA4 onto the sgRNA plasmid and sequence verified the result, we struggled with the backbone PCR to swap out the dCas9 for the dxCas9. At this point, due to initial promising results from the cell free testing, we decided to optimize our time by halting the in vivo cloning and focusing on testing in vitro.