Summary

Aim: To characterise PhlF and SrpR repressors and their respective repressible promoters for submission to the iGEM registry.


Results Overview: K1725000 and K1725020 successfully drive expression of GFP in E. coli. K1725042 represses K1725001 GFP expression 83-fold.


Basic Parts submitted:
• BBa_K1725000 – PhlF repressible promoter
• BBa_K1725020 – SrpR repressible promoter
• BBa_K1725040 – phlF encoding PhlF repressor
• BBa_K1725060 – srpR encoding SrpR repressor
• BBa_K1725080 – Promoter (lacI regulated, lambda pL hybrid) with extra NheI site

Introduction

Our genetic circuit needed an inverter, as our UVA sensor turns on transcription, but our circuit needed to turn off transcription when UVA was present. There are several repressor protein/repressible promoter pairs in the iGEM registry suitable for with function such as TetR or LacI, however, it was decided to characterise and submit two new repressors to the registry. Stanton et al., (2014) have recently identified sixteen prokaryotic TetR-like repressors by genomic mining and designed synthetic repressible promoters, as shown in Figure 1A. To understand how they were able to design synthetic repressible promoters, it is important to understand how promoters and repressors work.


Transcription is the process where RNA polymerase binds to DNA to make mRNA; a promoter tells RNA polymerase where to bind to the DNA, so a promoter is found upstream of a gene. Promoters have -10 and -35 sites that RNA polymerase recognises and, as shown in Figure1B, transcription starts at +1. If one or both of these sites are bound by another protein, RNA polymerase cannot recognise the promoter, and transcription does not take place. Transcriptional repressors are proteins that bind to DNA at a specific sequence; this is called the operator sequence. Stanton et al., (2014) overlapped the operator sequence for each repressor over the -10 and/or -35 sites of BBa_J23119, a strong, constitutive Anderson family promoter, meaning when the repressor binds to its operator sequence RNA polymerase cannot recognise the promoter and transcription cannot start, as shown in Figure 1B. This is how the synthetic repressible promoters work.


Figure 1 Synthetic Repressible Promoter Design. A – Synthetic repressible promoters with PhlF and SrpR operator sequences, with -35 and -10 sites shown relative to BBa_J23119, and operator sequence in red capital letters. BioBricks of these promoters include sequence from 5’ end to 3’ end of operator sequence. Image reproduced from (Stanton et al., 2014) B – schematic of RNA polymerase and repressor protein binding to promoter sequence. Altered from (Alberts et al, 2008)


For a repressor to be useful in a genetic circuit, is must be specific so as not to interfere with another part of the circuit or have unwanted interactions within the cell. Repressors that do this are called orthogonal. Repressor A binds to promoter A; repressor B binds to promoter B; but repressor A cannot bind to promoter B, and vice versa. The sixteen prokaryotic TetR-like repressors Stanton et al., (2014) identified are orthogonal, as shown in Figure 2. In particular, TetR, PhlF, and SrpR do not show significant repression of the other’s repressible promoters.


Figure 2 Orthogonal Repressors. Most orthogonal starting top left corner, decreasing towards bottom right corner. Image reproduced from (Stanton et al., 2014)


It was decided to make BioBricks of two of the sixteen repressors and characterise them for the iGEM registry. The first repressor we decided to submit as a BioBrick was the PhlF repressor from Pseudomonas protegens Pf-5. In P. protegens PhlF is involved in regulation of the phlACBD operon which synthesises an antifungal metabolite 2,4-diacetylphloroglucinol (PHL). (Sheehan et al., 2000, Abbas et al., 2002) The second repressor was the SrpR repressor from Pseudomonas putida S12. In P. putida SrpR is involved in regulation of the srpABC operon which is involved in organic solvent tolerance. (Wery et al., 2001, Sun et al., 2011) The aim was to submit and characterise both phlF and srpR and their respective repressible promoters.

Methods

E. coli strains used: TOP10, DH5α, and DS941. Plasmids in Table 1 constructed by BioBrick assembly, and checked by digest before confirming by sequencing.

Table 1 Composite Parts Assembled. K1725041, K1725061, and R0011.B0032 (for assembly into K1725083) construct synthesised by IDT. K1725062 sequencing showed a deletion in K1725080.


Protocols for CaCl2 competent cells, transformation, miniprep, restriction digest, gel electrophoresis, ethidium bromide staining, Azure A staining, gel extraction, oligo annealing, and ligation available on our Protocols page. Fluorescence measurements taken as documented on our Interlab Study page.

Results

GFP fluorescence of K1725001, K1725002, K1725021, K1725022, K1725082, and E5504 was measured to compare the relative strengths of promoters K1725000 and K1725020 to a promoter already well documented in the registry, R0040. Figure 3 shows the fluorescence scan image and a graph of approximate molecules of GFP per cell.

Conclusion

References

Abbas, A., Morrissey, J.P., Marquez, P.C., Sheehan, M.M., Delany, I.R., and O’Gara, F. (2002). Characterization of Interactions between the Transcriptional Repressor PhlF and Its Binding Site at the phlA Promoter in Pseudomonas fluorescens F113. J. Bacteriol. 184, 3008–3016.

Alberts et al (2008). Molecular Biology of the Cell (Garland Science, Taylor and Francis Group). Chapter 7, p337-434

Sheehan, M.M., Delany, I., Fenton, A., Bardin, S., O’Gara, F., and Aarons, S. (2000). Regulation of production of the antifungal metabolite 2,4-diacetylphloroglucinol in Pseudomonas fluorescens F113: genetic analysis of phlF as a transcriptional repressor. Microbiology 146, 537–546.

Stanton, B.C., Nielsen, A.A.K., Tamsir, A., Clancy, K., Peterson, T., and Voigt, C.A. (2014). Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat. Chem. Biol. 10, 99–105.

Sun, X., Zahir, Z., Lynch, K.H., and Dennis, J.J. (2011). An Antirepressor, SrpR, Is Involved in Transcriptional Regulation of the SrpABC Solvent Tolerance Efflux Pump of Pseudomonas putida S12. J. Bacteriol. 193, 2717–2725.

Wery, J., Hidayat, B., Kieboom, J., and Bont, J.A.M. de (2001). An Insertion Sequence Prepares Pseudomonas putida S12 for Severe Solvent Stress. J. Biol. Chem. 276, 5700–5706.

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