Coding

Part:BBa_K5177001:Design

Designed by: Francisco Sobral Calça Tavares Correia   Group: iGEM24_Manchester   (2024-09-30)


GsPilA-LRELHLNNN


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

IDT Codon Optimization for E. coli. Peptide tags kept under 9 residues in length due to lack of expression for longer sequences in past work [10][15]


Source

The gene pilA from Geobacter sulfurreducens (NCBI: NC_002939.5) was codon optimised for expression in Escherichia coli and synthesised by IDT. The peptide tag was adapted from Federico et al. (2015) [5]

References

[1]Orgel, J.P.R.O., Eid, A., Antipova, O., Bella, J. and Scott, J.E. (2009). Decorin Core Protein (Decoron) Shape Complements Collagen Fibril Surface Structure and Mediates Its Binding. PLoS ONE, 4(9), p.e7028. doi:https://doi.org/10.1371/journal.pone.0007028.


[2] Bella, J., Hindle, K.L., McEwan, P.A. and Lovell, S.C. (2008). The leucine-rich repeat structure. Cellular and molecular life sciences: CMLS, [online] 65(15), pp.2307–2333. doi:https://doi.org/10.1007/s00018-008-8019-0.


[3]R. Keene , D., D. San Antonio, J., Mayne , R., J. McQuillan, D., Sarris , G., A. Santoro, S. and V. Iozzo, R. (2000). Decorin Binds Near the C Terminus of Type I Collagen. Journal of Biological Chemistry, 275(29), pp.21801–21804. doi:https://doi.org/10.1074/jbc.C000278200.


[4]Wahyudi, H., Reynolds, A.A., Li, Y., Owen, S.C. and Yu, S.M. (2016). Targeting collagen for diagnostic imaging and therapeutic delivery. Journal of Controlled Release, [online] 240, pp.323–331. doi:https://doi.org/10.1016/j.jconrel.2016.01.007.


[5]Federico, S., Pierce, B.F., Piluso, S., Wischke, C., Lendlein, A. and Neffe, A.T. (2015). Design of Decorin-Based Peptides That Bind to Collagen I and their Potential as Adhesion Moieties in Biomaterials. Angewandte Chemie International Edition, 54(37), pp.10980–10984. doi:https://doi.org/10.1002/anie.201505227.


[6] Holmes DE, Dang Y, Walker DJF, Lovley DR. The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer. Microbial Genomics. 2016 Aug 25;2(8).


[7] Vargas M, Malvankar NS, Tremblay PL, Leang C, Smith JA, Patel P, et al. Aromatic Amino Acids Required for Pili Conductivity and Long-Range Extracellular Electron Transport in Geobacter sulfurreducens. Giovannoni SJ, editor. mBio. 2013 May;4(2).


[8] Adhikari RY, Malvankar NS, Tuominen MT, Lovley DR. Conductivity of individual Geobacter pili. RSC Advances. 2016 Jan 19;6(10):8354–7.


[9] Ing NL, Nusca TD, Hochbaum AI. Geobacter sulfurreducens pili support ohmic electronic conduction in aqueous solution. Physical Chemistry Chemical Physics 2017 Jan 1;19(32):21791–9.


[10] Ueki T, Walker DJF, Woodard TL, Nevin KP, Nonnenmann SS, Lovley DR. An Escherichia coli Chassis for Production of Electrically Conductive Protein Nanowires. ACS Synthetic Biology. 2020 Mar 3;9(3):647–54.


[11] Nevin KP, Zhang P, Franks AE, Woodard TL, Lovley DR. Anaerobes unleashed: Aerobic fuel cells of Geobacter sulfurreducens. J Power Sources. 2011;196(18):7514–8.


[12] Dang Y, Walker DJF, Vautour KE, Dixon S, Holmes DE. Arsenic Detoxification by Geobacter Species. Liu SJ, editor. Applied and Environmental Microbiology. 2017 Feb 15;83(4).


[13] Cologgi DL, Speers AM, Bullard BA, Kelly SD, Reguera G. Enhanced Uranium Immobilization and Reduction by Geobacter sulfurreducens Biofilms. Parales RE, editor. Applied and Environmental Microbiology. 2014 Nov;80(21):6638–46


[14] Ueki T, Walker DJF, Tremblay PL, Nevin KP, Ward JE, Woodard TL, et al. Decorating the Outer Surface of Microbially Produced Protein Nanowires with Peptides. ACS Synthetic Biology. 2019 Jul 12;8(8):1809–17.


[15] Eric Szmuc, David J.F. Walker, Dmitry Kireev, Deji Akinwande, Derek R. Lovley, Benjamin Keitz, Andrew Ellington. Engineering Geobacter pili to produce metal:organic filaments, Biosensors and Bioelectronics, Volume 222, 2023.


[16] Liu X, Walker DJF, Nonnenmann SS, Sun D, Lovley DR. Direct Observation of Electrically Conductive Pili Emanating from Geobacter sulfurreducens. Papoutsakis ET, editor. mBio. 2021 Aug 31;12(4).


[17] Malvankar, N.S., Vargas, M., Nevin, K., Tremblay, P.-L., Evans-Lutterodt, K., Nykypanchuk, D., Martz, E., T. Tuominen, M. and R. Lovley, D. (2015). Structural Basis for Metallic-Like Conductivity in Microbial Nanowires. American Society for Microbiology mBio, 6(2). doi:https://doi.org/10.1128/mbio.00084-15.


[18] Grenier, D. (1996). Collagen-binding activity of Prevotella intermedia measured by a microtitre plate adherence assay. Microbiology, 142(6), pp.1537–1541. doi:https://doi.org/10.1099/13500872-142-6-1537.