Part:BBa_K5416000
HRT2trunc
This part is designed by Imperial_College 2024, a rubber synthase enzyme engineered to work in their composite parts to form artifical rubber-producing organelles.
HRT2trunc (Rubber cis-1,4-polyprenyltransferase HRT2, truncated)
This part encodes the truncated version of rubber producing prenyltransferase HRT2 from the rubber tree H brasiliensis (K1088024). HRT2 uses isopentenyl diphosphate (IPP) as substrates to produce cis-1,4-polyisoprene natural rubber[1][2]. This enzyme has a unique unit consisting of a hydrophobic channel, where allows the polymerization of the IPP precursors to occur at the entrance and eject the polymerized natural rubber chain through the exit.
Design
Protein Engineering
Too Long Didn’t Read: Here is our proposed workflow for redesigning this part where the HRT2 is edited into the HRT2trunc tested in our project.
Inspired by HRT2 parts designed by SDU_Denmark (K1088024), we applied several major modifications on protein structure of HRT2. These generate with new HRT2 with higher solubility; and prevent the formation of HRT2 dimer during expression. This modified HRT2 is coupled with multiple strategies (detailed below) during our project for higher rubber yield.
The protein engineering process to design this part begins with identify the function of each protein domains according to the literature and protein structure database. Whereby we have identified the several domains from the original amino acid sequence of this HRT2 [2][3].
Fig 1: Structure and domains of HRT2 from H. brasiliensis.
Fig 2: Strunctural alignment of HRT2 (blue) with cis-prenyltransferase from Homo sapiens.
Fig.3 (a): The illustration of the engineering on HRT2 domains to produce HRT2trunc. (b) molecular surface of HRT2trunc structure predicted by Alphafold, where a channel for polyisoprene is retained (indicated with red arrows) after truncation. (c)(d): Structure of HsCPT, and the molecular surface.
Fig.4 (a): Final structure of HRT2trunc, predicted by Alphafold2.
Expression
Fig.5 SDS-PAGE, lane L Precison Plus Dual Color protein ladder marker (Bio-rad); lane 4 overnight culture of E. coli BL21 strain expressing this part. Where a band around 22kDa is vaguely identified.
Burden
Fig.6 The growth assay of this part in its E. coli BL21 transformant,under 1mM IPTG induction at 37C
Variants of This Part
Through the path of modular engineering, Imperial-College 2024 have also designed the variants of this parts for the formation of artifical organelles.
Fig.7 The variants of this part
Reference:
1. Asawatreratanakul, K., Zhang, Y.-W., Wititsuwannakul, D., Wititsuwannakul, R., Takahashi, S., Rattanapittayaporn, A. and Koyama, T. (2003). Molecular cloning, expression and characterization of cDNA encoding cis-prenyltransferases from Hevea brasiliensis. European Journal of Biochemistry, 270(23), pp.4671–4680. doi: https://doi.org/10.1046/j.1432-1033.2003.03863.x.
2. Yamashita, S. and Takahashi, S. (2020). Molecular Mechanisms of Natural Rubber Biosynthesis. Annual Review of Biochemistry, 89(1), pp.821–851. doi: https://doi.org/10.1146/annurev-biochem-013118-111107.
3. Takahashi S, Koyama T. Structure and function of cis‐prenyl chain elongating enzymes. The Chemical Record. 2006;6(4):194-205.
4. Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nature methods. 2022 Jun;19(6):679-82.
5. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic acids research. 2003 Jul 1;31(13):3381-5.
6. Maree HJ, van der Walt E, Tiedt FA, Hanzlik TN, Appel M. Surface display of an internal His-tag on virus-like particles of Nudaurelia capensis ω virus (NωV) produced in a baculovirus expression system. Journal of virological methods. 2006 Sep 1;136(1-2):283-8.
Index
MIPTHIAFIL DGNGRFAKKH KLPEGGGHKA GFLALLNVLT YCYELGVKYA TIYAFSIDNF RRKPHEVQYV MNLMLEKIEG MIMEESIINA YDICVRFVGN LKLLDEPLKT AADKIMRATA KNSKFVLLLA VCYTSTDEPH HHHHHPYINP YPDVLIRTSG ETRLSNYLLW QTTNCILYSP HALWPEIGLR HVVWAVQ
The sequnence above is the amino acid sequenc of this part. Displayed here to make codon optimization and protein engineering easier. The sequence in deep green (html#003300) codes for the truncated major enzyme unit of the HRT2 and HRT2trunc. The sequence in pink is the 6xHis-tag introduced to this part (#ff99cc).
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
None |