Coding

Part:BBa_K3629006

Designed by: Sravya Kakumanu   Group: iGEM20_Calgary   (2020-10-11)


Neurospora crassa CBHI with Myc Tag

Cellobiohydrolase I coding sequence from Neurospora crassa with Myc tag.

Usage and Biology

Yarrowia lipolytica is an emerging chassis in the molecular biology community. Its unique metabolic properties and efficient protein production and secretion mechanisms make it a desirable chassis for heterologous protein expression/secretion. In fact, it has been shown to have better secretory mechanisms than Saccharomyces cerevisiae (1). Therefore, using this chassis to secrete cellulase enzymes- which are enzymes that require high levels of secretion, is well suited.

Fully functional cellulase is composed of:

  1. Endoglucanases (EG) which randomly cleave internal beta-bonds of cellulose polymers to make them shorter
  2. Cellobiohydrolases (CBH or exoglucanases) which cleave the shorter polymers to make cellobiose
    • CBHI= Acts on reducing end of sugar molecule
    • CBHII= Acts on non-reducing end of sugar molecule
  3. Beta-glucosidases (BGS) which cleave the cellobiose disaccharide to free glucose units

These proteins must be in the correct proportions to each other to efficiently degrade cellulose.

CBHs provide the bulk of cellulose degradation by directionally degrading the polymers into cellobiose disaccharide units (2) While EGs enhance the ability of CBHs to act by producing more active sites for them, CBHs can still function at the ends of long cellulose polymers. Specifically, CBHI acts on the reducing ends of sugar polymers, whereas CBHII acts on the non-reducing ends. Together, these CBHs can efficiently degrade cellulose polymers from both directions.

In addition to providing the P. funiculosum derived CBHI (BBa_K3629005) this CBHI has also been proven to have high efficiency in Y. lipolytica due to its superior activity on amorphous cellulose substrate (3).

Design

The native signal peptide from N. crassa was removed so it would not interfere with fused secretion tags native to Y. lipolytica

This coding sequence was attached to the Lip2 signal peptide (BBa_K1592000), the TEFin promoter (BBa_K3629001), and the XRP2 terminator (BBa_K3629004) in creation of the expression construct for this part (BBa_K3629014). We provided the fully functional expression construct in our collection for teams who want to transform and use this protein directly in Y. lipolytica, however just the coding sequence is provided here in case teams want to use different promoters and/or signal peptides.

The expression constructs in our collection that can be assembled together to form a Y. lipolytica strain(s) that can fully degrade cellulose are:


A Myc affinity tag was included in this part, however not for the purpose of purification in our project, but for use in ELISA and western blot detection by using antibodies specific to the tag. This presents a cheaper and more accessible option rather than acquiring an antibody specific to the entire protein. However, future teams may choose to use this tag in purification which may be necessary in further characterization experiments. A spacer with a thrombin cleavage site was included in case the tag interferes with the protein function. Furthermore, in case this protein is expressed in tandem with the other two CBHs provided in our collection, we made all three CBHs have different affinity tags so they can be individually purified and detected as they have similar molecular weights.

  1. BBa_K3629005= Modified P. funiculosum CBHI with 6x His tag
  2. BBa_K3629006= N. crassa CBHI with Myc tag
  3. BBa_K3629007= T. reesei CBHII with FLAG tag

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 585
    Illegal BglII site found at 945
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 1453
  • 1000
    COMPATIBLE WITH RFC[1000]

Codon optimized for expression and function in Y. lipolytica.

References

1. Celińska, E., Borkowska, M., Białas, W., Korpys, P., & Nicaud, J. (2018, June). Robust signal peptides for protein secretion in Yarrowia lipolytica: Identification and characterization of novel secretory tags. Retrieved October 28, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5959983/

2. Taylor, L., Knott, B., Baker, J., Alahuhta, P., Hobdey, S., Linger, J., . . . Beckham, G. (2018, March 22). Engineering enhanced cellobiohydrolase activity. Retrieved October 28, 2020, from https://www.nature.com/articles/s41467-018-03501-8_

3. Guo Z-P, Duquesne S, Bozonnet S, Cioci G, Nicaud J-M, Marty A, O’Donohue MJ. Conferring cellulose-degrading ability to Yarrowia lipolytica to facilitate a consolidated bioprocessing approach. Biotechnology for Biofuels. 2017;10(1). doi:10.1186/s13068-017-0819-8


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