Difference between revisions of "Part:BBa K3046002"

Latest revision as of 03:14, 14 December 2019

PLEAPsonB_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 medium strength constitutive promoter for Aspergillus niger.

Characterization

This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the sonB promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. [1] This version is a consensus sequence of the sonB promoters in Aspergillus and is expected to have a medium strength expression.

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 multiple scales using a confocal microscope, a microbioreactor (BioLector, m2p-labs) for microtiter scale, in shake flasks for medium scale and in a 1 liter bioreactor for large 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. In the medium scale, cultures were grown in 200 mL minimal media in 500 mL shake flasks with baffles at 30 °C and 250 rpm. Here samples were taken with regular intervals. The promoter was also tested at 1 liter bioreactor scale and grown in 1 L minimal media, pH 5, 800 rpm, and samples were taken with regular intervals. Additionally, the off-gas was measured for CO₂ content to determine the growth.
The data for the shake flask- and bioreactor-scale experiments wea generated by purifying protein from the sampled biomass and computing the TexasRed equivalent fluorescence per protein. A Bradford assay was used to determine the protein concentration after extraction, and fluorescence was measured in a plate reader at Ex/Emi wavelengths 580 nm/625 nm
The predicted behavior of this promoter, is described by the model, which is summarized by the figure below. PLEAPsonB_1 is expected to show constitutive expression with medium promoter strength.

Figure 1: The figure shows RNA-seq data for Aspergillus niger in both exponential and stationary phase with the glaA 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 relatively constitutive.

For microscopy, the samples were analyzed under a confocal microscope for red fluorescence as seen in the following picture. We see that mCherry is clearly produced, which shows that the promoter works in A. niger.

Figure 2: Pictures from confocal microscopy of A. niger producing mCherry using the promoter PLEAPsonB_1.

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 3: 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 starts expression of mCherry around 35 hours.

In the medium scale, the promoters were analyzed in duplicate and the TexasRed equivalent fluorescence per protein was graphed, as seen below.

Figure 4: This figure shows 5 different promoters , run in two duplicates. The top row is replicate one and the bottom row is replicate two. From left to right, the columns are: Negative control, Positive control, PLAEPglaA_1, PLEAPglaA_2, PLEAPsonB_1, and PLEAPunk_1. The y-axis is showing mmol TexasRed/µg protein, x-axis is showing time in hours. Here, a distinct difference from the negative control is seen for PLEAPsonB_1.

Lastly, the promoter was analyzed in a 1 liter bioreactor.

Figure 5: Graphs show data from 1 L bioreactors. The top row shows equivalents of TexasRed per protein and the bottom row shows accumulated CO₂, which is correlated to biomass growth. From left to right is seen following samples : Negative control, Positive control, PLEAPsonB_1 run 2, PLEAPsonB_1 run 1, and PLEAPglaA_2. Here it can be seen that both PLEAPsonB_1 duplicates are distinct from the negative control with regards to fluorescence.

Sequence and Features

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal XbaI site found at 602
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 694
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 343
Illegal BglII site found at 654
23
INCOMPATIBLE WITH RFC[23]
Illegal XbaI site found at 602
25
INCOMPATIBLE WITH RFC[25]
Illegal XbaI site found at 602
1000
COMPATIBLE WITH RFC[1000]

@@ Line 12: / Line 12: @@
 ===Characterization===
 <html>
-This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the sonB promoter from different <i>Aspergillus</i> spp., and the gene was chosen based on RNA-seq data from <i>Aspergillus niger</i>. This version is a consensus sequence of the sonB promoters in <i>Aspergillus</i> and is expected to have a medium strength expression.
+This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the sonB promoter from different <i>Aspergillus</i> spp., and the gene was chosen based on RNA-seq data from <i>Aspergillus niger</i>. [1] This version is a consensus sequence of the sonB promoters in <i>Aspergillus</i> and is expected to have a medium strength expression.
 <br><br>
 This promoter was characterised using an mCherry test device,<a href=”https://parts.igem.org/wiki/index.php?title=Part:BBa_K3046009” target=”_blank”>BBa_K3046009</a>, inserted into an AMA1-based test plasmid, <a href=”https://parts.igem.org/wiki/index.php?title=Part:BBa_K3046021” target=”_blank_”>BBa_K3046021</a>, and characterisation was done in multiple scales using a confocal microscope, a microbioreactor (BioLector, m2p-labs) for microtiter scale, in shake flasks for medium scale and in a 1 liter bioreactor for large scale.
@@ Line 24: / Line 24: @@
 The predicted behavior of this promoter, is described by the model, which is summarized by the figure below. PLEAPsonB_1 is expected to show constitutive expression with medium promoter strength.
-<img src="https://parts.igem.org/wiki/images/b/be/T--DTU-Denmark--RNASEQsonB_1.png" style="width: 80%; padding: 15px;" >
+<img src="https://2019.igem.org/wiki/images/thumb/c/cd/T--DTU-Denmark--RNA_SonB.png/650px-T--DTU-Denmark--RNA_SonB.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 glaA 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 relatively constitutive.