In order to detect the presence of the specific non-natural amino acid (nnAA) in vivo the concecpt of amber suppression is used [1]. This means that the occurrence of the amber stop codon (UAG) in an ORF does not stop the protein translation but codes for a specific nnAA, in our case O-methyl-l-tyrosine (OMT). However, the incorporation requires the presence of the nnAA in the medium, otherwise the translation stops. The mechanism requires a tRNA with an anticodon complementary to the amber stop codon and an aminoacyl RNA synthetase (aaRS) loading the tRNA with the specific nnAA. The tRNA and aaRS combination is called an 'orthogonal pair'.
Orthogonal Pair
The recognition of the amber stop codon requires a tRNA with an anticodon complementary to the amber stop codon and an aaRS specifically loading the tRNA with the nnAA. In order to ensure the nnAA is not incorporated for other codons except the amber stop codon, the tRNA and the aaRS have to be orthogonal to the natural aaRS's and tRNAs. This means the aaRS must not load any other tRNA and the tRNA must not be loaded by any other aaRS. Therefore, Wang et. al originally used the tyrosyl-tRNA and tyrosyl-RS from the methanogenic archaeon Methanocaldococcus jannaschii : The anticodon of the tRNA was replaced by the amber anticodon and the aaRS was optimized for the recognition of OMT in place of tyrosine via directed evolution. Introduced into Escherichia coli, this pair is orthogonal to every natural pair due to the genetic distance between E. coli and M. jannaschii. Nowadays, over 70 different aaRS [3] have been designed, each one capable of incorporating a specific amino acid, many of them with special chemical characteristics, allowing e.g. 'click' chemistry or photoactivation.
In our project, we use an orthogonal pair from the "Expanded Genetic Code Measurement Kit" as template, specifically the one used for incorporation of ONBY (BBa_SomeBrick), and replaced the ORF with an E. coli codon optimized ORF for OMT-RS. Furthermore we placed the OMT-RS coding region behind a RBS (BBa_B0034) and a strong constitutive Anderson promotor (BBa_J23101). A successful expression of the OMT-RS gene in this construct was observed (Fig. 1).
Usage of amber codon
The incorporation of an amber codon causes the complete translation of the respective protein in presence of the nnAA and cancels the translation in absence. In our implementation the amber codon is replacing a codon in the beginning of the ORFs of the Colicin E2 Immunity protein (Y8OMT) and the Zif23-GCN4 repressor (F4OMT). In consequence, both proteins are functionally produced only if the nnAA is available in sufficient concentration in the medium.
The non-natural amino acid
We decided to use O-methyl-l-tyrosine for our nnAA due to its multiple advantageous properties:
Low costs
Nontoxic
Unproblematic import into cells
No further biochemical activity
Feasible chemical synthesis
Stable in water
Unavailable in nature
Well documented
Low interference with protein activity
An institute or company could choose its own specific nnAA with the corresponding orthogonal pair. This enables a reliable protection against corporate espionage or bioterrorism, since the opposing party does normally not know which nnAA is used in the respective application. However, using the same nnAA like OMT in every application should prevent the biological and genetic spread of the respective microorganism in the environment.
REPORTER
ABSTRACT [...]
[...]
bildunterschrift: igem team darmstadt 2016
KILL(switch)
ABSTRACT [...]
[...]
GENOMIC INTEGRATION
ABSTRACT
Abstract
Artificial plasmids, which we transform into cells during the year on iGEM all the time,
are a significant burden to the host. The design of our pathways, for example the combination of a promoter and RBS,
result in different amounts of product. The measurement of the metabolic burden is the key for a quantitative optimization
in metabolic engineering. Hereby, the measurement of the hosts' optical density, which should give you a feedback on the
growth rate, shows you a very inaccurate value of the metabolic burden and even that just after a long time. F. Ceronie, R. Algar,
G.B. Stan, T. Ellis thought about the need of a highly quantitative accurate measurement and found a solution in the measurement of
a fluorophore, which the host expresses constitutively. They demonstrate, that the measurement of GFP has great advantages
over the measurement of OD, because it is much faster and more precise. Using this method, it is now possible to measure the
impact of transformed plasmid live and with high accuracy. This new approach is of economical interest, because it enables
scientist to test a lot of different pathways at once in a short time, just by using a fluoreader.
Our main project aims
on developing a safety plasmid. To measure the metabolic burden caused by the safety plasmid, but also every plasmid that we
design now and in the future, we want to build a meausurement strain based on the model of F. Ceronie et al. To achieve the
most sensitive results, we used the λ‑Integrase Site‑specific Recombination Pathway, described by A. Landy
in 2015, to integrate exactly one copy of GFP into E. coli K12 JM109. Therfore we designed two plasmids, based on
BBa_I11020 and BBa_I11023. We measured our strain using single cell measurement as well as measurements with a fluoreader.
Metabolic burden
.......
Genomic integration
The λ‑integrase, originally derived from the λ‑Phage, catalyzes in combination with several assisting proteins the excessive and integrative recombination of the phage's genome with the chromosomal genome of a host. For this, two attachment sites are needed: one located on the bacterial genome (attB) and the other located on the λ‑genome, which also contains several binding sites for regulatory proteins. The attachment sites contain homologous recognition sequences, called BOB' Region (attB) and COC' Region (attP). These can be connected by the λ‑integrase and the bacterial integration host factor (IHF) via Holliday junction forming an intasome, a DNA‑protein‑complex, producing hybrid attachment sites attL and attR.
For the integration of a gene of interest (GOI) into the chromosomal genome of E. coli there are two plasmids needed. One, called integration plasmid, contains the constitutively expressed GOI GFP with a LVA degradation tag, which, as previously mentioned, is also the reporter that is necessary for the measurement of the metabolic burden and should be integrated into the E. coli genome. It also contains the attP site that enables the integration. There are two bidirectional terminators located on each side of the attP to protect the GFP Operon from the transcription of the other neighbouring genes. The antibiotic resistance will also be integrated into the genome if the genomical integration succeeds, so we decided to use a Kanamycin resistance, as it is less commonly used in iGEM than Ampicillin or Chloramphenicol. Therefore, we chose the backbone pSB3K3, which also possesses a low copy ori and eases the later performed plasmid curing. The second plasmid is a helper plasmid and is necessary for transposing the GFP into the chromosomal genome as it contains the protein λ‑integrase with a ribosomal binding site (RBS). To verify whether the recombination was successful one can perform a PCR with primers binding to the attB site of the E. coli and the VR Primer, which binds on every BioBrick compliant plasmid. As the one primer binds on the genome and the other on a plasmid, there can only be a PCR amplicon if the integration has succeeded.
Integration strains
A suitable genomic integration strain needs to carry the attB sequence needed for λ‑integrase mediated recombination, which can be troublesome because many commonly used E. Coli strains already have the λ‑phage integrated into its genome. Also, the attB site needed for the integration is blocked in λ (DE3) phage.
For our integration strain we chose the E. Coli JM109 strain because it matched all our demands and was also freely and easily available to us.
