Composite

Part:BBa_K4347011

Designed by: Victor Di Donato, Nicoletta de Maat   Group: iGEM22_Queens_Canada   (2022-07-07)
Revision as of 15:58, 21 July 2022 by Victor5688 (Talk | contribs) (→‎Usage and Biology)

Bst fusion with Sac7e and point mutations for enhanced thermal stability codon optimized for E.coli

This fusion protien was designed by linking the N-terminus of a modified Bst polymerase with thermostable DNA binding protien Sac7e using a flexible (GGGGS)4 linker to increase polymerase thermostability and processivity in LAMP reaction.

Usage and Biology

Use point mutation one instead

Bst polymerase Large Fragment is a family I DNA polymerase derived from the thermophilic bacterium Geobacillus stearothermophilus. Bst polymerase Large Fragment is notable for its strong strand displacement activity and thermal stability [1]. Bst also contains a 5' to 3' DNA polymerase activity but lacks 3' to 5' exonuclease activity[2]. These unique features allow Bst polymerase to facilitate isothermal amplification techniques such as LAMP and rt-LAMP.

Bst polymerase derived from thermophilic bacterium Geobacillus stearothermophilus used in LAMP modelled on PyMol.

Sac7e is part of the 7 kDa DNA-binding family and is a highly thermostable and pH resistant protien that aids in the binding of double stranded DNA. Sac7e is thermally stable to 85.5°C and compared to other similar proteins, Sac7e showed the highest affinity for dsDNA (KD = 11 μM), with binding sites ~ 6-8 bases per protein[3].

DNA binding protien "Sac7e" modelled in Pymol.

A more thermally stable and processive polymerase

This final iteration of the new polymerase is an improvement of our previous part; BBa_K4347010, as it is a combination of our more thermally stable polymerase (BBa_K4347007) fused with DNA binding protien Sac7e (BBa_K4347006). The modified Bst polymerase contains three point mutations in the polymerase thumb domain: K549W, K582L and Q584L, which have been proven to improve thermal stability in Bst homologue Taq polymerase[4]. The overall change in Gibbs free energy of wild-type Bst was calculated to be -150.13 kcal/mol, and the overall stability of the mutated Bst was calculated to be -152.03 kcal/mol thus indicative of a more thermally stable protein.

Thermal stability of Bst fusion protien computed from YASARA.

Along with an increased thermal stability, the mutated polymerase was fused to a DNA binding protien Sac7e to increase polymerase processivity during the LAMP reaction. Sac7e is isolated from thermoacidophilic archaeon Sulfolobus acidocaldarius and is part of the 7 kDa DNA-binding family[3]. Sac7e binds to DNA without a strong sequence preference. In complex with DNA, a small beta-barrel is capped by anamphiphilic C-terminal a-helix. The triple-stranded beta-sheet is placed across the DNA minor groove with the intercalation of the Val26 and Met29 side-chains into DNA base-pairs, causing a sharp kink in the DNA duplex[5]. 7 kDa DNA-binging protiens have been shown to increase processivity when fused to polymerases such as Taq[6].

Fully modified Bst polymerase with fusion protien and point mutations modelled in Pymol.




Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 5
    Illegal XhoI site found at 209
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 1015
  • 1000
    COMPATIBLE WITH RFC[1000]


References


1. Ignatov, K. B., Barsova, E. V., Fradkov, A. F., Blagodatskikh, K. A., Kramarova, T. V., & Kramarov, V. M. (2014). A strong strand displacement activity of thermostable DNA polymerase markedly improves the results of DNA amplification. BioTechniques, 57(2), 81–87. https://doi.org/10.2144/000114198

2. Aliotta JM, Pelletier JJ, Ware JL, Moran LS, Benner JS, Kong H (1996). Thermostable Bst DNA polymerase I lacks a 3'-->5' proofreading exonuclease activity. (5-6):185-95. PMID: 8740835

3. Kalichuk, V., Béhar, G., Renodon-Cornière, A., Danovski, G., Obal, G., Barbet, J., Mouratou, B., & Pecorari, F. (2016). The archaeal “7 KDA DNA-binding” proteins: Extended characterization of an old gifted family. Scientific Reports, 6(1). https://doi.org/10.1038/srep37274

4. Xi, L. (2009, December 23). WO2009155464A2 - mutated and chemically modified thermally stable DNA polymerases. Google Patents. Retrieved July 12, 2022, from https://patents.google.com/patent/WO2009155464A2/en

5. Su, S., Gao, Y.-G., Robinson, H., Liaw, Y.-C., Edmondson, S. P., Shriver, J. W., & Wang, A. H.-J. (2000). Crystal structures of the chromosomal proteins SSO7D/sac7d bound to DNA containing T-G mismatched base-pairs. Journal of Molecular Biology, 303(3), 395–403. https://doi.org/10.1006/jmbi.2000.4112

6. Wang, Y. (2004). A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro. Nucleic Acids Research, 32(3), 1197–1207. https://doi.org/10.1093/nar/gkh271

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