Revision as of 03:04, 11 October 2023

P_Tet* promoter + RBS

Introduction

The 2023 UT Austin iGEM Team’s modular microcin expression parts collection includes parts necessary for engineering a bacterial chassis to secrete microcins, a type of small antimicrobial peptide. Our team has specifically designed parts to engineer a modular two-plasmid system that facilitates extracellular secretion of microcins by the chassis. One plasmid contains the microcin with a signal peptide sequence that indicates to the cell that the microcin is to be secreted. The other plasmid (pSK01) is from the literature (Kim et al., 2023) and contains genes for the proteins CvaA and CvaB, which are necessary to secrete small peptides using the E. coli microcin V (MccV) type I secretion system (T1SS) shown in Figure 2 of our Project Description.

Our parts collection includes a a selection of promoter (Type 2), coding sequence (Type 3), and terminator/regulatory gene (Type 4) parts that can be easily assembled to express microcins either constitutively or under inducible control. This allows for the modular engineering of microcin expression plasmids containing various microcins that can undergo extracellular secretion when used in conjunction with the secretion system plasmid pSK01.

Our basic and composite parts follow the Bee Toolkit/Yeast Toolkit standard of Golden Gate assembly (Lee et al., 2015; Leonard et al., 2018). This standard includes type-specific prefix and suffix overhangs for each part, but these overhangs are NOT included in their sequences in the registry unless they include a section of the part—as seen in the Type 3 part prefix which includes the ATG start codon of the coding sequence. For reference, part type-specific prefix and suffix overhangs are listed in Figure 2 on our Parts page.

Categorization

Basic parts

• Promoters (Type 2) – Seven inducible promoters selected due to their relatively high dynamic range (Meyer et al., 2019) and apparent functionality in a variety of Proteobacteria (Schuster & Reisch, 2021), and one constitutive CP25 promoter (Leonard et al., 2018).
• Coding Sequences (Type 3) – Signal peptide + microcin fusion coding sequences, a green fluorescent protein gene, and secretion system genes cvaAB.
• Terminators/Regulatory Genes (Type 4) – An rpoC terminator plus a collection of seven regulatory genes, each associated with one of our seven inducible promoters.

Composite parts

• Constitutive Microcin Expression Assemblies - Assemblies of microcins (some with immunity proteins) with a constitutive CP25 promoter and rpoC terminator. These function alongside pSK01 in a two-plasmid secretion system, and we use these two-plasmid systems to assess if our novel microcins are effective inhibitors of pathogenic targets.
• Inducible Promoter GFP Assemblies – Assemblies of GFP under the control of various inducible promoter systems. These were used to assess the dynamic range of our inducible promoter systems.
• Inducible Microcin Expression Assemblies – Assemblies of select microcins under the control of an inducible promoter system.

Usage and Biology

This part consists of the P_tet* promoter upstream of a ribosome binding site, with a hammerhead ribozyme (HHRz) sequence included in the intervening 5' untranslated region to insulate gene expression levels from coding sequence effects on mRNA structure. This promoter can be bound by TetR (BBa_K4579026), a transcriptional repressor that can be removed from the promoter when bound by anhydrotetracycline (aTc), allowing for the selective induction of transcription in cells containing both P_tet* and the tetR gene. This part can be used as a Type 2 part in the BTK/YTK standard.

Design Notes

When creating our inducible promoter parts, we used the YFP-expressing individual sensor plasmids from the E. coli ‘Marionette’ paper as PCR templates (Meyer et al., 2019), as these include inducible promoters and their regulatory transcription factors on a standardized backbone. Due to the homology of the backbone between these plasmids, we created universal primers that allowed us to amplify the promoter from any one of the sensor plasmids. One big design complication in this process was the fact that the YFP-expressing sensor plasmids all contained a BsaI site in the region just upstream of the promoter where one of the universal primers would bind. We designed our primers to create a single point mutation in order to mutate out this illegal BsaI site.

Characterization

Source

This promoter was amplified from pAJM.011 using PCR before being integrated into a part plasmid for our assemblies. This part was sourced from pAJM.011 on AddGene (https://www.addgene.org/108529/) (Meyer et al., 2018). pAJM.011 contains YFP under inducible control by pTet and TetR.

References

1. Cole, T. J., Parker, J. K., Feller, A. L., Wilke, C. O., & Davies, B. W. (2022). Evidence for widespread class II microcins in Enterobacterales Genomes. Applied and Environmental Microbiology, 88(23), e01486-22.
2. Kim, S. Y., Parker, J. K., Gonzalez-Magaldi, M., Telford, M. S., Leahy, D. J., & Davies, B. W. (2023). Export of Diverse and Bioactive Small Proteins through a Type I Secretion System. Applied and Environmental Microbiology, 89(5), e00335-23.
3. Lee, M. E., DeLoache, W. C., Cervantes, B., & Dueber, J. E. (2015). A highly characterized yeast toolkit for modular, multipart assembly. ACS Synthetic Biology, 4(9), 975-986.
4. Leonard, S. P., Perutka, J., Powell, J. E., Geng, P., Richhart, D. D., Byrom, M., Kar, S., Davies, B. W., Ellington, D. E., Moran, N. A., & Barrick, J. E. (2018). Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids. ACS Synthetic Biology, 7(5), 1279-1290.
5. Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J., & Voigt, C. A. (2019). Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Nature Chemical Biology, 15(2), 196-204.
6. Schuster, L. A., & Reisch, C. R. (2021). A plasmid toolbox for controlled gene expression across the Proteobacteria. Nucleic Acids Research, 49(12), 7189-7202.

Sequence and Features