Team:Stanford-Brown/Projects/EuCROPIS

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Revision as of 19:45, 27 September 2013

1 Introduction
2 Construct Assembly
3 Protocols
4 Lab Notebook
5 Data
6 BioBricks
7 Acknowledgements

Introduction

In 2016, the German Aerospace Center will be launching the Euglena: Combined Regenerative Organic-Food Production In Space (EuCROPIS) satellite mission into low-earth orbit. While the mission's main objective is to study food production, the Germans have invited several other researchers, including astrobiology researchers from NASA, to participate in the study by sending their own experiments along as secondary payloads. As a result, we are proud to announce that we will be using the EuCROPIS mission as a way to test synthetic biology in space for the first time!

In 2011, the Brown-Stanford iGEM team built PowerCell, a photosynthetic and nitrogen-fixing cyanobacterium engineered to secrete sucrose. The project addressed one of NASA's key concerns regarding the future of terraforming Mars, the need for in-situ resource utilization. Since sending materials into space is very expensive, engineering an organism that could be used as an energy source was key. Through the secretion of its naturally-generated sucrose, PowerCell addressed this need effectively by providing other bacterial cultures with a rich carbon source that can ideally be used to produce biomass such as food or drugs.

Despite the results generated by the 2011 team in the lab, however, the need to assess PowerCell's effectiveness in space arose, which is where we come in.

The goal of our EuCROPIS project was to find a way to assess the efficacy of PowerCell while aboard the German satellite mission. Due to the constraints provided by the mission - such as the need for the experimental organisms to survive harsh conditions in outer space in addition to months or years waiting on the launchpad, the fact that the satellite can only measure data via a spectrophotometer, and the experimental constraints posed by using Pharmasat microfluidic cards - we decided to validate PowerCell by building a chromogenic biosensor in Bacillus subtilis.

We chose to work with the bacterium B. subtilis in developing our biosensor because it is a hardy organism that forms endospores in nutrient-depleted conditions and can survive for years in the environmental extremes found in space (cold, desiccation, pressure, low gravity, etc.). When it is exposed to nutrients, however, such as sucrose, the bacterium undergoes germination. As a result, we've characterized promoters associated with sucrose induction (sacY) and sporulation (spo0A) with chromoproteins in varying colors. By linking colorimetric proteins to these genes, we will be able to monitor the state our biosensor is in and see whether it is able to make use of the sucrose being provided by the PowerCell that it is cultured with within the wells of the microfluidics card. The color changes associated with the change in states can be picked up by the spectrophotometer and reported back to us here on earth, thereby letting us know how the first synthetically biological organism to be sent up into space is faring!

Construct Assembly

We began by researching and identifying genes associated with sporulation, germination, and sucrose induction in Bacillus subtilis. We decided to focus on sacY, a gene the regulates sucrose induction and is itself induced by the presence of sucrose, and spo0A, a gene that regulates sporulation by influencing more than 500 genes related to sporulation. We attempted to isolate the genes from the genome using PCR with mixed results. We decided instead to construct the two promoters by annealing complimentary oligos from Elim, and using PCR to add the BioBrick ends.

We used 3A assembly to add a ribosome binding site from the registry (BBa_B0034) directly downstream of our sucrose inducer promoter (see Figure A). After an E/P digestion, we proceeded to another 3A assembly to add a red chromoprotein (eForRed: BBa_K592012) downstream of the sucrose inducer promoter and ribosome binding site (Figure B). Likewise we did another assembly in parallel to add a red fluorescent protein (BBa_E1010) downstream of the sucrose inducer promoter and ribosome binding site. We then used primers from Elim and PCR to add the restriction sites BamHI and HindIII to either side of our two constructs. In addition, we ordered two constructs from DNA 2.0: the sucrose inducing promoter linked to eForRed and the sporulation regulator promoter linked to a blue chromoprotein (BBa_K864401). We designed the constructs such that they were flanked with the restriction sites BamHI and HindIII. These two restriction sites allowed us to ligate each of our constructs into Bacillus subtilis integration vectors (BGSC: ECE115). Finally, we used electroporation to transform into electrocompetent Bacillus subtilis cells.

Figure A

Figure B

Protocols

Protocols used for this project can be found here

Lab Notebook

The EuCROPIS lab notebook can be accessed here.

Data


Figure 1. Cluster of WT bacillus (phase contrast)	Figure 2. Spores + Vegetative bacillus


Figure 3. Dense culture of SacY-eforRed bacillus DIC	Figure 4. Figure 3 in fluorescence mode


Figure 5. Same as 209 but with shorter exposure (Fluoresence)	Figure 6. SacY + RPF (Fluoresence)


Figure 7. Exact same imaging area as 212-214, but with phase. (PH

BioBricks

[http://parts.igem.org/Part:BBa_K1218001 BBa_K1218001 (pSB1C3)]: This part is the sacY promoter; sacY is a gene that regulates sucrose induction in Bacillus subtilis.

[http://parts.igem.org/Part:BBa_K1218020 BBa_K1218020 (pSB1K3)]: This is a compound part containing the sacY promoter (BBa_K1218001: a sucrose inducer in Bacillus subtilis) and a ribosome binding site (BBa_B0034).

[http://parts.igem.org/Part:BBa_K1218021 BBa_K1218021 (pSB1C3)]: This part is the spo0A promoter; spo0A regulates sporulation in Bacillus subtilis.

[http://parts.igem.org/Part:BBa_K1218023 BBa_K1218023 (pJ201)]: This composite part contains sacY (BBa_K1218001: a sucrose inducer in Bacillus subtilis), a ribosome binding site (BBa_B0034), and eForRed, a red chromoprotein developed by Uppsala (BBa_K592012). We intend to use it as a chromogenic reporter induced by sucrose.

[http://parts.igem.org/Part:BBa_K1218025 BBa_K1218025 (pSB1K3)]: This composite part contains sacY (BBa_K1218001: a sucrose inducer in Bacillus subtilis), a ribosome binding site (BBa_B0034), and a red fluorescent protein (BBa_E1010). We intend to use it as a chromogenic reporter induced by sucrose.

Acknowledgements

We would like to thank:

Ryan Kent, Dr. Lynn Rothschild, Dr. Joe Shih, and Dr. Kosuke Fujisima -- Primary advisors
Dr. Gary Wessel -- Advice on testing construct
Dr. Rocco Mancinelli -- Feedback on our presentation, papers about the EuCROPIS mission
Dr. Lilah Rahn-Lee -- Advice on choosing B. subtilis genes
Dr. Daniel R. Zeigler, BGSC Director and the Bacillus Genetic Stock Center -- Free strains of Bacillus integration vectors
Dr. Elwood Agasid -- Explanation of EuCROPIS mission from an engineering perspective

Retrieved from "http://2013.igem.org/Team:Stanford-Brown/Projects/EuCROPIS"

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-== Discussion ==
-We successfully built constructs linking our two promoters of interest with chromoproteins and fluorescent proteins of varying colors. Using an integration vector, we transformed our constructs into <i>B. subtilis</i>. Microscopy reveals that some of our <i>B. subtilis</i> cells were transformed successfully, specifically for the construct that links the sucrose inducer promoter with a red chromoprotein that has fluorescent properties (Figure 4) and the construct that links the sucrose inducer promoter with a red fluorescent protein (Figure 6). The controls which contain the integration vector but no construct did not fluoresce. We believe that the red fluorescence is being induced by the sucrose found in LB, but we have several obstacles to overcome before we can prove this to be true and further characterize our promoters.
-First, we are testing minimal media solutions to prove that the <i>B. subtilis</i> does not fluoresce except in the presence of sucrose. Second, comparing Figures 3 and 4 illustrates that many of the cells are not <i>B. subtilis</i> cells containing our constructs. This is in part due to an unknown contaminant. The contaminant and the unusual lawn-like morphology of our <i>B. subtilis</i> transformant when grown on a plate (Figure x) make it impossible for us to find and pick individual colonies containing the proper construct. We are in the process of solving this problem, and when we do, we will be able to qualitatively and quantitatively test color change and fluorescence in response to sucrose and sporulation medium.
 == '''BioBricks''' ==