Characterization

Two fungal promoters have been characterized by both a qualitative and a quantitative analysis. The initial plan was to characterize all our fungal promoters; PgpdA a strong constitutive promoter, DMKP-P6 a medium strength constitutive promoter, and PalcA an inducible promoter. However, it was not possible for us to amplify PgpdA with the linkers matching the USER cassette of plasmid p68, which might have been due to the quality of the template. The promoters DMKP-P6 and PalcA were succesfully obtained and characterized. A simple way of analyzing promoters is by measuring its efficiency in front of a reporter gene. This was done by performing the widely used β-galactosidase assay (1) with the modifications described here.

Genetics and USER cloning

Aspergillus nidulans can integrate DNA fragments into its genome based on repair of double stranded breaks in two ways, either by non-homologous end joining (NHEJ) or homologous recombination (HR). Integration by NHEJ will occur randomly, which means that DNA fragments will be integrated at a random site in a random number of copies, with little or no end processing. HR uses widespread homology search to repair breaks and does this without loosing any of the sequence around the break (3, 4). For characterization of the promoters it was important only to have one copy integrated in the genome. The host strain used for transformation, nkuAΔ, was therefore a NHEJ deficient strain, meaning that integration was done by HR (2).

p68 is a plasmid that contains a lacZ gene, terminator, and a USER cassette. It also contains up- and down stream regions for targeting to a specific site called IS1 situated 202 bp downstream of AN6638 and 245 bp upstream of AN6639 (5). For HR to occur gene-targeting substrates have to contain these large homologous sequences around 1500 bp to ensure the targeted integration (5).

p68 was digested with AsiSi for 2 hours and afterwards nicked with Nb.bstI for 1 hour. The vector and each of the promoters were then mixed in a USER reaction. Prior to transformation of A. nidulans the plasmids were linearized with NotI to increase transformation efficiency. The nkuAΔ transformants containing PalcA::lacZ and the nkuAΔ transformants containing DMKP-P6::lacZ will be referred to as nkuAΔ-IS1::PalcA::lacZ::TtrpC::argB and nkuAΔ-IS1::DMKP-P6::lacZ::TtrpC::argB, respectively.

Qualitative analysis

First, the promoters were evaluated qualitatively by stabbing nkuAΔ-IS1::PalcA::lacZ::TtrpC::argB and nkuAΔ-IS1::DMKP-P6::lacZ::TtrpC::argB on 5-bromo-4-chloro-3-indolyl-D-galactoside (X-gal) plates. A functional promoter allows the expression of the lacZ gene and thereby β-galactosidase production, which results in blue colonies on X-gal plates. The blue color is produced because β-galactosidase cleaves X-gal into 5- bromo-4-chloro-3-indolyl (blue) and D-galactose. Thus, blue colonies indicate that the transcription of the lacZ gene has occurred. It should be noted that the X-gal plates used for the PalcA transformants contained glycerol as carbon source and ethanol and threonine to induce the PalcA promoter.

The plates contain two positive controls that express lacZ from the constitutive promoters PgpdA 0.5kb and PgpdA 1.0kb (nkuAΔ-IS1::PgpdA 0.5kb::lacZ::TtrpC::argB and nkuAΔ-IS1::PgpdA 1.0kb::lacZ::TtrpC::argB) that are used for comparison of the intensity of the blue color. Moreover, the reference strain nkuAΔ-IS1::DMKP-P6::TtrpC::argB (without the lacZ gene) was also placed on the plates. The PgpdA 0.5kb promoter on both plates appeared to endorse the strongest expression. When comparing the intensities of the two transformants with the DMKP-P6 promoter it is clear that the expression of lacZ is more similar to the expression of PgpdA 1.0kb. The same observation is made for the PalcA-2 promoter, however the expression of the lacZ gene in the PalcA transformants differ, since the color intensity for PalcA-1 is the lower than for PalcA-2. Thus, the qualitative analysis indicates that both promoters DMKP-P6 and PalcA are of medium strength. This is in accordance with previous data for the DMKP-P6 promoter, but PalcA is known to be a strong promoter and we would have expected to see the same color intensity of the PalcA transformants as we did for the nkuAΔ-IS1::PgpdA 0.5kb::lacZ::TtrpC::argB strain. A reason for this could be a sub-optimalt level of inducer in the X-gal plates.

Quantitative analysis

The level of protein production was examined by performing a β-galactosidase assay. Firstly conidia from a three-point stab of two of each type of transformant were grown in minimal media for 48 hours and then proteins were extracted from the cultures. The protein extracts were used for the β-galactosidase and Bradford assays described below and all measurements were performed in triplicates.

Measuring the optical density of fungi can be very difficult because fungi grow in complex structures, are heavy and not single celled like bacteria. Therefore the OD measurement that is usually performed would not be accurate enough. Instead the protein concentration of the sample was determined by a Bradford assay. For the Bradford assay it was necessary to make a standard with known concentrations of bovine serum albumin (BSA) in order to determine the protein concentrations. The protein samples and BSA standards were mixed with Bradford reagent. The procedure is based on the dye, Brilliant Blue G (Sigma-Aldrich) forming a complex with the proteins in solution. This dye-protein complex results in a shift of the absorption maximum of the dye from 465nm to 595nm, where the absorption is proportional to protein present.

For the β-galactosidase assay a solution of o–nitrophenyl-β–D–galactoside (ONPG) was used to measure the β-galactosidase activity. β-galactosidase hydrolyses ONPG to o–nitrophenol resulting in a yellow color at a linear rate until total degradation of ONPG. In other words, the amount of o-nitrophenol produced is proportional to the amount of β-galactosidase present in the sample (6).
Protein extracts were mixed with z-buffer in a microtiter plate, ONPG was added and OD420 was measured every minute for 20 minutes. The specific activities were calculated using the equation below.