(r5) ProceduresCompetenceAssays < Lab

---+Competence Assays

A competence assay quantifies the ability of bacterial strains to uptake DNA in culture. The protocol below utilizes genomic DNA extracts obtained using a PureLink genomic DNA minikit (Life Technologies). The DNA should come from a strain with a genome-encoded antibiotic resistance gene against an antibiotic the recipient strain is not resistant to. For transformation into _Acinetobacter baylyi_ ADP1 or IS-x an ADP1 strain with a tdk-KanR cassette inserted into the genome ("AB-KAN") is routinely used with kanamycin for selection as described below.

---+++Materials (for n samples)<br>
   * 13n+9 sterile tubes<br>
   * n+1 sterile 50mL flasks<br>
   * 18n+12 mL sterile LB broth<br>
   * Antibiotic stock solution<br>
   * 100n ng genomic DNA extract<br>
   * 3n+2 Antibiotic LB plates<br>
   * 3n+2 LB plates<br>

---+++Day 0: Inoculation
1. Prepare n+1 tubes with 5ml LB (n samples and 1 uninoculated control)<br>
2. Inoculate sample tubes with either 2uL of liquid culture, a pipette tip with frozen culture, or an isolated colony<br>
3. Incubate overnight at 30°C and 140 RPM

---+++Day 1: Preconditioning
1. Prepare n+1 flasks with 10mL LB (n samples and 1 uninoculated control)<br>
2. Inoculate each flask with 10uL of their respective culture<br>
3. Incubate all flasks overnight at 30°C and 140 RPM<br>

---+++Day 2: Transformation
1. Prepare 3n+2 test tubes with 1mL LB for three replicates per strain, as well as an uninoculated control and –DNA control <br>
2. Add the selected antibiotic stock to each tube to its final working concentration<br>
3. Put 100ng of antibiotic resistant _A. baylyi_ gDNA ("AB-KAN") into all tubes except the two designated for the blank and the –DNA control<br>
4. For each preconditioned flask from Day 1, transfer 70uL of each flask into three separate tubes containing 1mL of LB and the DNA (this gives three trials for each strain we are measuring competence for)<br>
5. Add 70uL of one of the strains to the –DNA control tube (this ensures that the antibiotic is effective, and can be determined the day after plating)<br>
6. Incubate overnight at 30°C and 140 RPM<br>

---+++Day 3: Dilutions and Plating
1. Prepare 9n+6 test tubes containing 10mL of sterile saline solution (3x per tube incubated overnight)<br>
2. Create a dilution series of 1:100, 1:10000, and 1:1000000 (this is done by transferring 100uL of the transformed culture to the first saline tube, vortexing, transferring 100uL of this into the second saline tube, vortexing again, then transferring 100uL of this into the third saline tube, and vortexing)<br>
3. Plate 100uL of each 1:100 dilution onto LB + Antibiotic plates<br>
4. Plate 100uL of each 1:1000000 dilution onto LB plates (without antibiotics)<br>
5. Incubate overnight at 30°C<br>

---+++Day 4: Plate counting
1. Start by ensuring that the antibiotic is effective (there should be no growth on the –DNA control plate that contains LB+Kan, but growth on the LB only plate is expected)<br>
2. If antibiotic effectiveness is confirmed, count all colonies on each plate and record the results<br>
3. Transformation frequencies can be calculated by dividing the number of CFUs on selective media by the number of CFUs on non-selective media<br>

---+++References<br>
Renda BA, Dasgupta A, Leon D, Barrick JE. (2015) Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution. J. Bacteriol. 197: 872-881.<br>
Renda BA, Chan C, Parent KN, and Barrick JE. (2016) Emergence of a competence reducing filamentous phage from the genome of Acinetobacter baylyi ADP1. J. Bacteriol. 198: 3209-3219.<br>

-- Main.AurkoDasgupta - 06 Aug 2012<br>
-- Edited by IsaacGifford - 08 Apr 2020
Barrick Lab > ProtocolList > ProceduresCompetenceAssays
Topic revision: r5 - 2020-04-08 - 15:50:16 - Main.IsaacGifford