Difference between revisions of "Part:BBa K3046008"

Latest revision as of 03:21, 14 December 2019

PLEAPhfbD_1

This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project

Usage and Biology

This is a strong promoter for Aspergillus niger that has high activity in the stationary growth phase.

Characterization

This is a synthetic stationary phase promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the hfbD promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. [1] This is a consensus promoter and are expected to have high expression in the stationary phase.

This promoter was characterised using an mCherry test device,BBa_K3046009, inserted into an AMA1-based test plasmid, BBa_K3046021, and characterisation was done in a microbioreactor (BioLector, m2p-labs) for microtiter scale.
The microtiter scale cultures were made by inoculating 10⁷ spores in 1.5 mL minimal media, and cultures were grown at 30 °C with mixing at 1000 rpm for 78 hours. Both biomass (measured in light scattering units) and fluorescence (at Ex/Emi wavelengths 580 nm/625 nm) was measured continuously.
The predicted behavior of this promoter, is described by the model, which is summarized by the figure below. PLEAPhfbD_1 is expected to show high expression in the stationary growth phase.

Figure 1: The figure shows RNA-seq data for Aspergillus niger in both exponential and stationary phase with the hfbD gene marked in red. The x-axis is the promoter activity in the stationary phase and the y-axis is the promoter activity in the exponential phase, both axes are depicted on a log scale. Here we see that the promoter should be active in stationary phase with a high expression.

For the microtiter scale, the promoter was evaluated in a biolector, producing the following results with regards to growth, fluorescence and dynamic promoter activity.

Figure 2: When analyzed in the microtiter scale on a biolector, the red fluorescence and biomass has been measured and the Dynamic Promoter Activity has been calculated. On the graph Dynamic Promoter Activity (DPA) is green, the biomass is measured in Light Scattering Units (LSU) is in blue, and red fluorescence (RFP) is shown in red. The graphs have been normalized for LSU. Here it is seen that the promoter has a relatively high dynamic promoter activity starting around 35 hours where the biomass curve start to slow down.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 14
Illegal NheI site found at 676
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 436
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

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-<img src="https://static.igem.org/mediawiki/parts/4/45/T--DTU-Denmark--RNASEQhfbD_1.png" style="width: 80%; padding: 15px;" >
+<img src="https://2019.igem.org/wiki/images/thumb/1/13/T--DTU-Denmark--hfbDwikiRNA.png/650px-T--DTU-Denmark--hfbDwikiRNA.png" style="width: 80%; padding: 15px;" >
 <figure>
 <figcaption> Figure 1: The figure shows RNA-seq data for <i>Aspergillus niger</i> in both exponential and stationary phase with the hfbD gene marked in red. The x-axis is the promoter activity in the stationary phase and the y-axis is the promoter activity in the exponential phase, both axes are depicted on a log scale. Here we see that the promoter should be active in stationary phase with a high expression.