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Team:Macquarie Australia/Results
From 2012.igem.org
Results and Characterisation
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Heme Oxygenase |
Bacteriophytochromes |
Heme Oxygenase |
Bacteriophytochromes |
Heme Oxygenase |
Bacteriophytochromes |
The Switch |
Heme Oxygenase Results
We produced a Heme Oxygenase BioBrick that was codon optimized for E. coli. The Gibson assembly of the T7 promoter containing Heme Oxygenase was successful. The transformation was successful with numerous colonies grown using Chloramphenicol as the selecting agent. Six colonies were selected and then they were sequenced before digestion with EcoR1 and Spe1. The sequencing showed that all of the colonies contained the plasmid with a Heme oxygenase identical to the original protein sequence. The gel containing the digested Heme Oxygenase bearing plasmid can be seen in Figure 1.
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Figure 1: The restriction digest showing the linearised plasmid backbone (Black Box) and the heme oxygenese gene (Green Box). We used a 1kb ladder. |
The sequencing results for the six plasmids above can be seen below.
Heme Oxygenase Sequencing Results
The plasmids from the gel seen above was sequenced using the forward and reverse primers for the BioBricks. We performed Blastx pipeline to determine if there was a significant change in the protein sequence.
| Sample | Proposed Identity | e-value | MaxID |
| 1C-6F | Heme Oxygenase (Synechocystic sp. PCC603) | 7e-176 | 99% |
| 1C-6R | Heme Oxygenase (Synechocystic sp. PCC603) | 1e-171 | 99% |
| 1C-4F | Heme Oxygenase (Synechocystic sp. PCC603) | 4e-176 | 99% |
| 1C-4R | Heme Oxygenase (Synechocystic sp. PCC603) | 6e-172 | 99% |
| 1C-5F | Heme Oxygenase (Synechocystic sp. PCC603) | 1e-23 | 92% |
| 1C-5F | Heme Oxygenase (Synechocystic sp. PCC603) | 6e-172 | 99% |
Given that this was the source of our gene the sequencing result was accurate. We then compared to the original gBlock sequence and determined that the sequencing was accurate and confirmed the identity of the plasmid. The Blastn pipeline indicated that there was no significant change from the theoretical sequence. With this data we would assume that the protein would be functional and performed assays to determine if this was the case.
Characterisation of Heme Oxygenase
The T7 bearing Heme Oxygenase produced was characterised to determine if it was functional. BL21 E. coli was transformed with the plasmid, selected for using chloramphenicol and a culture was inoculated. The culture was then induced with ALA (d-aminolevulinic acid) for the heme pathway and IPTG to promote protein production. They were incubated overnight and the cells were spun down. We observed a functional Heme Oxygenase and the cells appeared a vibrant green after induction by ALA and IPTG. We observed this as well in our assembled switch. The image below demonstrates the green produced compared to uninduced Heme Oxygenase and the Bacteriophytochrome. Need to insert image
Bacteriophytochromes Results
Like the Heme Oxygenase, the bacteriophytochromes from Deinococcus radiodurans and Agrobacterium tumefaciens were codon optimised for use in E. Coli. The identity of the plasmid was determined by sequencing and by digestion.
The digest above shows only show one band for the Agro + T7 digest. The length of the vector and the bacteriophytochrome are similar and make it difficult to resolve the two bands. Only the digested plasmid can be seen which indicates that the bacteriophytochrome component was synthesised correctly based on the length of the fragments.
The first Agro with no T7 lane (asterixed lane) shows incomplete digestion of a BioBrick part.
Bacteriophytochrome Sequencing
| Sequence | Proposed Identity | E value | Max ID |
| F3CE1 | Chain A, Crystal Structure Of A Monomeric Infrared Fluorescent Deinococcus Radiodurans Bacteriophytochrome Chromophore Binding Domain | 3.00E-160 | 99% |
| R3CE1 | photoreceptor [Deinococcus radiodurans R1] Full=Bacteriophytochrome | 9.00E-65 | 85% |
| F3CE2 | Chain A, Crystal Structure Of A Monomeric Infrared Fluorescent Deinococcus Radiodurans Bacteriophytochrome Chromophore Binding Domain | 2.00E-161 | 99% |
| F3CE3 | Chain A, Crystal Structure Of A Monomeric Infrared Fluorescent Deinococcus Radiodurans Bacteriophytochrome Chromophore Binding Domain | 8.00E-163 | 99% |
| R4KE2 | bacteriophytochrome protein [Agrobacterium tumefaciens str. C58] | 0 | 99% |
| R5CE1 | bacteriophytochrome protein [Agrobacterium tumefaciens str. C58] | 0 | 99% |
| R5CE3 | bacteriophytochrome protein [Agrobacterium tumefaciens str. C58] | 0 | 99% |
- We successfully produced our bacteriophytochromes with protein sequences matching the theoretical sequence.
- The difference in identity is due to the codon optimisation performed. It was also affected by short sequencing reads.
The The Blastx pipeline showed that there was an identical match to the orginal source for the sequencing performed. Blastn were run to determine the deviance from the theoretical sequence. The Blastn searches produced indicated that the sequences were nearly identical. The changed bases were examined on the sequencing output and determined to be possible misreads.
Bacteriophytochrome Characterisation
The Switch
Two of the BioBricks produced were ligated together to produce the light switch. We demonstrated that the switch was produced by inspecting a gel following ligation and then digestion. The gel can be seen below.
Gel 1: We have run against a Heme Oxygenase standard (Lane 1). The gel contains digested fragments from our composite BioBrick (Heme Oxygenase and Agro). The upper band (Black Box) is the Heme Oxygenase with the bacteriophytochrome and the bottom band (blue) is the plasmid backbone.
This provided the evidence that the product had been successfully ligated.
The Infrared Gel
An SDS page gel was run of the ligation products to observe if the heme oxygenase was able to produce biliverdin and then to determine if it was binding with the bacteriophytochrome. The biliverdin binds to a specific site in the bacteriophytochrome. As biliverdin is IR active this coupling can be ovbserved under infrared (IR) light.
A positive result for the self assembly of our switch would be an IR active band in the SDS PAGE gel, this was observed at the expected molecular weight,
