Part:BBa_K4342000
tdk/kan Cassette
Introduction
The 2022 UT Austin iGEM Team’s Part Collection provides a number of DNA sequences and procedures for genetically engineering Acinetobacter baylyi ADP1. We were able to effectively engineer ADP1's genome using a two-step genetic engineering protocol. See the Engineering Page for more details on how we modified ADP1's genome. On this page, we explain how our part collection can be used alongside this two-step protocol to delete ADP1 genes, insert DNA sequences into any chromosomal location, and engineer an ADP1-based biosensor to detect any DNA sequence of interest.
We hope this part collection guides future iGEM teams in engineering ADP1 and utilizing ADP1’s flexibility to tackle any challenge in synthetic biology.
Categorization
For our parts collection, we categorize our parts into the following categories:
Upstream
An Upstream basic part is a DNA sequence directly upstream of a target gene. These basic parts are homology flanks that are used for ADP1 Genetic Engineering. Examples include the ACIAD2049 Upstream for P. destructans detector (BBa_4342003) and pbpG Upstream (BBa_4342011).
Downstream
A Downstream basic part is a DNA sequence directly downstream of a target gene. These basic parts are homology flanks that are used for ADP1 Genetic Engineering. Examples include ACIAD2049 Downstream for P. destructans detector (BBa_4342004) and pbpG Downstream (BBa_4342012).
Integration Cassettes
An "Integration" cassette is a composite part consisting of an "Upstream" basic part, the tdk/kan basic part (BBa_4342000), and a "Downstream" basic part. These parts are designed to use in the first transformation step in ADP1 Genetic Engineering. Examples include the ACIAD2049 Integration cassette (BBa_4342019) and the acrB Integration cassette (BBa_4342023).
Rescue Cassettes
"Rescue" cassette is a composite part consisting of an "Upstream" basic part, an optional genetic device, and a "Downstream" basic part. These parts are designed to use in the second transformation step in ADP1 Genetic Engineering. Examples include the ACIAD2049 Rescue cassette (BBa_4342020, Upstream + Downstream), the YFP Rescue cassette (BBa_4342030, Upstream + Genetic Device + Downstream), and the nptII Detector Rescue cassette (BBa_4342031, Upstream + Composite Part + Downstream).
Genetic Device
"Genetic Device" is a basic part that can be any DNA sequence to be integrated into ADP1. Examples include the CymR YFP (BBa_4342008) and the nptII Broken Gene (BBa_4342015).
We further categorize each part with a standardized Golden Gate Assembly (GGA) Type 1-8 Overhang [2]. Each type is ligated to a complementary type (ex. Type 2 can be ligated to Type 1 and Type 3). Moreover, some parts contain consecutive GGA Type numbers, such as Type 234. These DNA sequences start with a Type 2 Overhang and end with a Type 4 Overhang (ex. tdk/kan cassette (BBa_4342000).
tdk/kan cassette is categorized as a Type 2-4 Integration cassette in our part collection.
Usage and Biology
The tdk/kan cassette is the keystone of our parts collection. It is a highly versatile sequence used for efficiently and effectively engineering the Acinetobacter baylyi ADP1 genome. This part contains the kanR and tdk genes, which allow for the selection and counterselection of genetically engineered ADP1 cells. tdk confers Azidothymidine (AZT) susceptibility, and kanR confers Kanamycin (Kan) susceptibility.[1].
The 2022 UT Austin iGEM team used the tdk/kan cassette to successfully delete a number of genes, insert DNA sequences into the ADP1 chromosome, and engineer an ADP1-based biosensor for detecting antibiotic resistance genes and P. destructans. Our design process and two-step ADP1 genetic engineering protocol can be found on the Parts, Contribution, and Engineering pages of our Wiki.
Design
The pbpG Integration part comprises the 3695 bp region combining the pbpG Upstream (BBa_4342011), tdk/kan (BBa_4342000) cassette, and pbpG Downstream (BBa_4342012) parts.
- Please note that BsaI restriction sites have been removed to meet RFC[1000] BioBrick Assembly Compatibility. To see in-depth primer design, please see Figure 4 on the Engineering Page for more details on how to design primers containing the correct GGA Type Overhang and restriction sites.
Step 1
The pbpG Integration cassette is designed to allow for successful transformant selection on Kanamycin (Kan) via the kanR gene (Figure 1).
Step 2
The tdk/kan cassette can subsequently be knocked out to create a 4 bp minimal scar deletion of ACIAD2049 via BsmBI digestion. During this reaction, a pbpG Rescue cassette (BBa_4342022) is constructed. We use the pbpG Rescue cassette to select for successful transformants on Azidothymidine (AZT) (Figure 2).
Composite Parts
The composite parts below utilized this part for ADP1 genetic engineering:
Characterization
References
[1] Metzgar, D., Bacher, J. M., Pezo, V., Reader, J., Doring, V., Schimmel, P., Marliere, P., & de Crecy-Lagard, V. (2004). Acinetobacter sp.. ADP1: An ideal model organism for genetic analysis and Genome Engineering. Nucleic Acids Research, 32(19), 5780–5790. https://doi.org/10.1093/nar/gkh881.
[2] Lee, M.E., DeLoache, W.C., Cervantes, B., and Dueber, J.E. (2015). A highly characterized yeast toolkit for modular, multipart assembly. ACS synthetic biology 4, 975–986. 10.1021/sb500366v.
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal XbaI site found at 719
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 713
Illegal XhoI site found at 875 - 23INCOMPATIBLE WITH RFC[23]Illegal XbaI site found at 719
- 25INCOMPATIBLE WITH RFC[25]Illegal XbaI site found at 719
- 1000COMPATIBLE WITH RFC[1000]
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