Difference between revisions of "Part:BBa K4260111"

Revision as of 21:32, 10 October 2022

RecA mini intein mediated ESR1 protein with OmpA signal peptide, linker and AmilCP.

This part encodes an intein mediated biosensor, consisting of a divided AmilCP chromoprotein gene, a mutated intein RecA N-terminal and C-terminal domains and a ESR1 Ligand Binding Domain. The RecA intein comes from Mycobacterium tuberculosis (Mtu) which has been mutated with the purpose of making it more stable.

The usage of an intein mediated biosensor allows for protein post traductional modification in presence of a ligand, in this case an EDC, through a process known as protein splicing, consisting of a multi-step biochemical reaction comprised as a cleavage and the formation of a peptide bond. A change in coloration depending on the EDC concentration offers a visual indicator due to the union of the two N and C extein, being a AmilCP chromoprotein [BBa_K592009]. The expected result being a blue coloration in the final media or after the protein centrifugation.

Sequence and Features

Design

[[File:RecA_intein_biosensor_animated_gif.gif|300px|thumb|right|Fig.1:RecA intein mediated biosensor behavior in the presence endocrine disrupting chemicals (EDCs).]]

RecA intein ESR1 biosensor consists of two inteins capable joining two protein fragments and separating from them. The ESR1 biosensor gene coding for the hERalpha protein was introduced with its respective linker, with the purpose of separating the N-terminal and C-terminal RecA inteins in the presence of EDCs; when the ESR1 biosensor binds to an EDC, the inteins may carry protein spicing, ligate the two N and C exteins and separate the ESR1 biosensor, ESR1 linker and the two N and C extein complex. The two endogenous fragments encode the chromoprotein AmilCP [BBa_K592009].

RecA intein was build from the first 111 and last 58 amino acids from the wild type RecA full-lenght intein [1]. Moreover a mutation was carried (Val67Leu) to make the RecA intein a stable protein [2]. The functionality of the Barcelona 2020 team's inteins from the biobrick [BBa_K348400] was verified to check the functibility of the HERα protein to be used in the biosensor as a biological receptor for EDCs.

The whole coding sequence consists of the OmpA solubility tag for better interaction between the biosensor and EDCs, the first 100 amino acids from the AmilCP blue chromoprotein [BBa_K592009], the N-terminal RecA mini intein consisting of the first 111 amino acids from Mycobacterium tuberculosis (Mtu) RecA intein with optimized codons for E. coli with a mutation (V67L) for stabilizing the structure that had been perturbed without a central endonuclease domain [6], the ESR1 linker to avoid interactions between proteins, the ESR1 biosensor, the C-terminal RecA mini intein consisting of the last 58 amino acids of Mtu RecA intein, and the rest of the AmilCP blue chromoprotein.

Fig.2:Coding sequence for RecA intein ESR1 biosensor.

Usage and Biology

Biology

The RecA mini intein ESR1 biosensor was synthesized in two fragments: the first 533 bases as the first fragment and the last 2764 bases as the second fragment by IDT. An Overlapping PCR was carried, where two homologous sequences get overlapped and amplified with the objective of getting a single DNA strand [7]. Immediately the overlapping PCR was done, a normal amplification PCR was carried. The final PCR product was run into an agarose gel through electrophoresis and purified. The vector used to add the RecA intein biosensor was pJET 1.2/blunt and cloned into ''E.coli'' DH5-alpha strain [8]. After cloning, the plasmid was extracted and cloned into BL21 and HMS174 E. coli strains for protein expression.

Usage

Two protein expression plans were made with the purpose of exploring different types of protein expression, the first one was a Cell Free System, which does not require living cells to perform this expression, instead the cell machinery is used to express the wanted protein; the second one is a living cell system with solid and liquid media with different concentrations of EDCs.

Fig.3:Cell Free System samples 1) Extract (800 µL) + PCR sequence amplification (50 µL) + BPA (50 µL) + R1 buffer (100 µL), 2) Extract (800 µL) + (50 µL) + BPA (50 µL) + R1 buffer, 3) Extract (800 µL) + PCR sequence amplification (50 µL) + R1 buffer.

Plan 1: Cell Free System

Firstly, the BL21 strain was inoculated and incubated overnight in 100 mL of LB+Amp media, when the cells were at an optical density of 0.6, they were induced with IPTG and left overnight; then the cells were centrifuged, and the biomass was resuspended with R1 buffer, lysed with the help of the polytron homogenizer, and the supernatant was recovered containing protein remains and ribosomes. The resulting supernatant can be used to carry protein expression without the need for any transformed living cells since all the machinery needed to express protein such as ribosomes and protein remains are all present in the supernatant. After the cell “extract” was obtained, the RecA mini intein biosensor amplified sequence through PCR was added to the extract for its proper translation and expression, along with EDCs: three solutions were made, one with cell extract, PCR amplified sequence and EDCs, the second without the PCR amplified sequence, and the third without EDCs. The expected result is a change in coloration observed in the first solution, in contrast with the other two, that may serve as negative controls.

Plan 2: IntAssay

The quantity of blue chromoprotein is expected to vary increasingly as the concentration of BPA grows. This variation will be measured by a spectrophotometer, with LB medium as blank and the sample analysis of triplicated E. coli culture exposed to BPA concentrations after induction with IPTG. There were four different BPA concentrations managed in this assay, 1.69 mg/L, 1 mg/L, 5.5 mg/L, 11 mg/L, the range of the concentrations included the ones obtain in analysis of wastewater [9] and the concentration at which the mitochondrial complex I decreases [10]. The assay divided in three ways to expose the cell to the solution BPA/ethanol, the first being plating 100 L of the solutions in petri dishes, doing triplicates and three negative controls containing ethanol, IPTG and bacteria alone. The second method was the solutions being added to 10 mL liquid LB medium with HMS174-BBa_K4260111 induced by IPTG and to observe the results. It was proposed to measure the variations of the intensity of the blue chromoprotein by absorbances at 588 nm and then treat them by ANOVA analysis to determine if the BPA concentration is relevant to the blue chromoprotein concentration in the media.

Fig.4:Plan 2: IntAssay diagram.

Results

Overlapping PCR

The overlapping PCR was carried to ligate two RecA mini intein ESR1 biosensor sequences. With a successful ligation and amplification of the resulting ligated DNA sequence. The two initial sequences had a homologous region required to carry the overlapping PCR protocol; the first sequence (RecA seq. 1) had a length of 533 bp and the second one (RecA seq 2.) had 2764 bp, resulting on an expected 3297 bp ligated DNA sequence.

Fig.4:Plan 2: IntAssay diagram.

pJET1.2/blunt vector ligation Future of this part

References

[1] Wood, D. W., Wu, W., Belfort, G., Derbyshire, V., & Belfort, M. (1999). A genetic system yields self-cleaving inteins for bioseparations. Nature biotechnology, 17(9), 889-892.

[2] Gierach, I., Li, J., Wu, W. Y., Grover, G. J., & Wood, D. W. (2012). Bacterial biosensors for screening isoform-selective ligands for human thyroid receptors α-1 and β-1. FEBS open bio, 2, 247-253.

[3] Van Roey, P., Pereira, B., Li, Z., Hiraga, K., Belfort, M., & Derbyshire, V. (2007). Crystallographic and mutational studies of Mycobacterium tuberculosis recA mini-inteins suggest a pivotal role for a highly conserved aspartate residue. Journal of molecular biology, 367(1), 162-173.

[4] TecCEM 2021 https://2021.igem.org/Team:TecCEM

[5] Joshua S. Klein, Siduo Jiang, Rachel P. Galimidi, Jennifer R. Keeffe, Pamela J. Bjorkman. (2014) Design and characterization of structured protein linkers with differing flexibilities. Protein Engineering, Design and Selection, Volume 27, Issue 10, Pages 325–330. https://doi.org/10.1093/protein/gzu043

[6] Chen, X., Zaro, J. L., & Shen, W.-C. (2013). Fusion protein linkers: Property, design and functionality. Advanced Drug Delivery Reviews, 65(10), 1357–1369. doi:10.1016/j.addr.2012.09.039

[7] Anna Bahle. (2019). Overlap extension PCR. CEPLAS, Heinrich Heine University. Institute for Synthetic Microbiology. Protocols.io. https://dx.doi.org/10.17504/protocols.io.psndnde

[8] pJET 1.2/blunt vector: https://www.snapgene.com/resources/plasmid-files/?set=basic_cloning_vectors&plasmid=pJET1.2

[9] Fukazawa, H., Hoshino, K., Shiozawa, T., Matsushita, H., & Terao, Y. (2001). Identification and quantification of chlorinated bisphenol A in wastewater from wastepaper recycling plants. Chemosphere, 44(5), 973-979.

[10] Ooe H., Taira T., Iguchi-Ariga S. M. and Ariga H. (2005) Induction of reactive oxygen species by bisphenol A and abrogation of bisphenol A-induced cell injury by DJ-1. Toxicol Sci 88, 114-26.

Costa, S., Almeida, A., Castro, A., & Domingues, L. (2014). Fusion tags for protein solubility, purification and immunogenicity in Escherichia coli: the novel Fh8 system. Frontiers in microbiology, 5, 63.

Shah, N. H., & Muir, T. W. (2014). Inteins: nature's gift to protein chemists. Chemical science, 5(2), 446-461.

Shingledecker, K., Jiang, S. Q., & Paulus, H. (1998). Molecular dissection of the Mycobacterium tuberculosis RecA intein: design of a minimal intein and of a trans-splicing system involving two intein fragments. Gene, 207(2), 187-195.

Davis, E. O., Sedgwick, S. G., & Colston, M. J. (1991). Novel structure of the recA locus of Mycobacterium tuberculosis implies processing of the gene product. Journal of bacteriology, 173(18), 5653-5662.