Part:BBa_K3841035

Repair template for ADH2 knockout

This repair template is used in combination with BBa_K3841031 or BBa_K3841032 to knock out the adh2 gene in Komagataella phaffii GS115 (previously denoted Pichia pastoris GS115).

Target

The DNA fusion construct is complementary to the upstream region of the adh2 gene on chromosome 2 (position 875148-875192) and the downstream region (position 876246-876290) within the assembled genome ofK. phaffii GS115 strain [1] (Accession number FN392320).

Usage
Co-transformation with a CRISPR-Cas9 plasmid and this repair oligo will mediate homology directed repair (HDR) [2]. For scarless deletion of the adh2 gene, co-transform the repair template with a CRISPR-Cas9 plasmid with crRNA BBa_K3841031 or BBa_K3841032 to aid the HDR. The crRNA should be correctly inserted into a CRISPR-Cas9 plasmid system after a gRNA backbone (we used BBa_K3841003) to induce a double-stranded DNA break. For confidential matters, the CRISPR-Cas9 plasmids sequence cannot be added to the iGEM registry before it has been published. A conceptual map of the CRISPR-Cas9 plasmid system used is seen below.

Conceptual map of CRISPR-Cas9 plasmid system assembled using USER cloning [3]. The crRNA should be placed in front of the gRNA backbone to make the complete sgRNA. The plasmid contains features for being replicated in both bacteria and yeast and appropriate resistance markers. For more information of the assembly of the plasmid, visit 2021 DTU-Denmark’s experimental page

Theoretical expectation
The adh2 gene encodes alcohol dehydrogenase 2, which catalyzes interconversion between alcohols and aldehydes or ketones with the reduction of nicotinamide adenine dinucleotide (NAD+) to NADH. ADH2 has been shown to be promiscuous with regards to the alcohols it can interconvert into aldehydes and ketones. ADH2 can for instance interconvert methanol into formaldehyde [4]. Deletion of the gene was expected to impair the growth of Komagataella phaffii GS115 on methanol.

Functionality
The sgRNA and repair template efficiency was examined using the technique to assess protospacer efficiency (TAPE) [4] in a GS115 Δku70 strain. Highly efficient sgRNA will result in no colonies, while less efficient sgRNA will show a reduced number of colonies as compared to the wildtype or a GS115 Δku70 strain provided with a repair template.

Results
Below is a picture showing K. phaffii GS115 Δku70 transformed with pDIV153_adh2_KO and this repair oligo .

Transformed *K. phaffii* GS115 Δku70 with respective gRNAs and repair templates, if provided. Each gRNA had two candidates (C1 & C2). C1 seems to more efficient than C2. The negative control consists of *K. phaffii* GS115 Δku70 electroporated with water to check for contamination. The other control was *K. phaffii* GS115 Δku70 strain transformed without a repair template (RT)(BBa K3841033). The Triple knockout refers to an experiment were all three knockout plasmids were co-electroporated into *K. phaffii* GS115 Δku70 with respective repair templates. Since it only relies on taking up one plasmid to obtain resistance to NTC, a different approach is recommended to do multiple knockouts.

To see if the knockout was successful, colony PCRs were performed. By the amplification of specific primers, upstream and downstream of the gene, it can be verified if the gene has successfully been knocked out. If the gene has been knocked out the primers are going to be closer to each other resulting in a smaller band in the colony PCR. However if the gene is still present in the genome, the band will include its whole length as seen in the table below.

Expected length of the knockouts

Targeted gene	Expected gene length after knockout	Control lenght
Δaox1	500 bp	2500 bp
Δaox2	500 bp	2500 bp
Δadh2	500 bp	1550 bp

Colony PCRs performed on *Δaox1*, *Δaox2*, and *Δaox2*. Each band corresponds to a unique colony picked from a plate of transformed *K. phaffii* GS115 Δku70. 16 colony PCRs were loaded to the gel on the left, eight *aox1* and eight *aox2* knockout colony PCRs, respectively. Eight *adh2* knockout colonies were loaded the gel on the right. The gel pictures have been cut to fit both in one figure. One band was observed for *aox1* and *aox2* while two bands were observed for *adh2*.

To validate the scarless deletion of adh2 we sent the colony PCRs for Sanger Sequencing. The results we received were inconclusive, and due to time constraints we did not have a chance to repeat the sequencing.

The colony PCR indicated correct deletion of the adh2 gene.
To validate the scarless deletion of adh2 we sent the colony PCRs for Sanger Sequencing. The results showed that we did indeed knock out adh2 as shown below.

Sanger Sequencing confirmation of knockout of *adh2*.

The results above confirms that this part can be used to sucssesfully knock out adh2 in K. phaffii GS115 Δku70.

Due to the assumed knockout of the aox1 and the confirmed knockout of adh2 we suspected the double knockout mutant to be more susceptible to methanol than the K. phaffii GS115 Δku70 mutant strain.

Thus, we conducted a methanol kill curve experiment where the two mutants were grown in increasing amounts of methanol in a BioLector. For a detailed description of the results, visit our result page 2021 DTU-Denmark’s result page.

The results below confirm that knocking out the aox1 and adh2 genes makes the double knockout mutant more susceptible to methanol.

BioLector growth curves of *aox1* and *adh2* double knockout mutant and the *K. phaffii* GS115 Δku70 mutant strain. It is evident that the increasing methanol concentrations affects the growth of the double mutant more than the *K. phaffii* GS115 Δku70 mutant strain, proving that the double knockout mutant is more susceptible to methanol.