DNA

Part:BBa_K4342031

Designed by: Samer Salman   Group: iGEM22_Austin_UTexas   (2022-10-12)
Revision as of 15:36, 12 October 2022 by NeilTian (Talk | contribs)


nptII Detector Rescue Cassette

Introduction

Intro-part-figure.png


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).


Usage and Biology

ACIAD2049 is a nonessential gene in Acinetobacter baylyi ADP1. Knocking out this gene allows for the integration of other DNA sequences in its chromosomal location. Cooper et al. and colleagues have taken advantage of the ACIAD2049 gene deletion to create ADP1-based biosensors capable of detecting diseases within the human body [1]. Using this part, we demonstrate that deleting ACIAD2049 can be used to detect antibiotic resistance genes using ADP1 as a chassis organism.

The nptII gene in Acinetobacter baylyi ADP1 codes for kanamycin antibiotic resistance. Deleting a section of this gene prevents ADP1 from growing on kanamycin antibiotic, making ADP1 susceptible to this antibiotic. This allows for the detection of homologous recombination/transformation of the correct nptII antibiotic resistance gene by ADP1.


Design

The nptII detector construct composite part consists of the ACIAD2049 Upstream Homology (BBa_4342001) + nptII broken gene (BBa_4342015) + ACIAD2049 Upstream Homology (BBa_4342002). This composite part deletes the nptII gene in ADP1, making ADP1 susceptible to kanamycin antibiotic. This allows for the selection of functional nptII gene transformants when grown on kanamycin.

References

[1] De Vries, J., Wackernagel, W. (1998). Detection of nptII (kanamycin resistance) genes in genomes of transgenic plants by marker-rescue transformation. Molecular and General Genetics, 257, 606-613. https://doi.org/10.1007/s004380050688

[2] Kong, K., Schneper, L., Mathee, K. (2010). Beta-lactam Antibiotics: From Antibiosis to Resistance and Bacteriology. APMIS, 118(1), 1-36. https://doi.org/10.1111/j.1600-0463.2009.02463.x

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 1040
    Illegal EcoRI site found at 3493
    Illegal XbaI site found at 180
    Illegal XbaI site found at 1325
    Illegal XbaI site found at 2537
    Illegal XbaI site found at 3413
    Illegal SpeI site found at 3091
    Illegal PstI site found at 645
    Illegal PstI site found at 1303
    Illegal PstI site found at 1890
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 1040
    Illegal EcoRI site found at 3493
    Illegal NheI site found at 4032
    Illegal SpeI site found at 3091
    Illegal PstI site found at 645
    Illegal PstI site found at 1303
    Illegal PstI site found at 1890
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 1040
    Illegal EcoRI site found at 3493
    Illegal BglII site found at 1677
    Illegal BglII site found at 3251
    Illegal BglII site found at 3749
    Illegal BamHI site found at 1291
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 1040
    Illegal EcoRI site found at 3493
    Illegal XbaI site found at 180
    Illegal XbaI site found at 1325
    Illegal XbaI site found at 2537
    Illegal XbaI site found at 3413
    Illegal SpeI site found at 3091
    Illegal PstI site found at 645
    Illegal PstI site found at 1303
    Illegal PstI site found at 1890
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 1040
    Illegal EcoRI site found at 3493
    Illegal XbaI site found at 180
    Illegal XbaI site found at 1325
    Illegal XbaI site found at 2537
    Illegal XbaI site found at 3413
    Illegal SpeI site found at 3091
    Illegal PstI site found at 645
    Illegal PstI site found at 1303
    Illegal PstI site found at 1890
    Illegal NgoMIV site found at 2331
  • 1000
    COMPATIBLE WITH RFC[1000]


[edit]
Categories
Parameters
None