Essential validation methods for E. coli strains created by chromosome engineering

Essential validation methods for E. coli strains created by chromosome engineering

Krishnan, S.T.
Moolman, M.C.
Van Laar, T.
Meyer, A.S.
Dekker, N.H.

Applied Sciences

BN/Bionanoscience

2015-07-01

Background Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used in both fundamental and industrial research to introduce multiple insertions in the same Escherichia coli strain. To date, ?-Red recombination (also known as recombineering) and P1 phage transduction are the most successfully implemented chromosome engineering techniques in E. coli. However, due to errors that can occur during the strain creation process, reliable validation methods are essential upon alteration of a strain’s chromosome. Results and discussion Polymerase chain reaction (PCR)-based methods and DNA sequence analysis are rapid and powerful methods to verify successful integration of DNA sequences into a chromosome. Even though these verification methods are necessary, they may not be sufficient in detecting all errors, imposing the requirement of additional validation methods. For example, as extraneous insertions may occur during recombineering, we highlight the use of Southern blotting to detect their presence. These unwanted mutations can be removed via transducing the region of interest into the wild type chromosome using P1 phages. However, in doing so one must verify that both the P1 lysate and the strains utilized are free from contamination with temperate phages, as these can lysogenize inside a cell as a large plasmid. Thus, we illustrate various methods to probe for temperate phage contamination, including cross-streak agar and Evans Blue-Uranine (EBU) plate assays, whereby the latter is a newly reported technique for this purpose in E. coli. Lastly, we discuss methodologies for detecting defects in cell growth and shape characteristics, which should be employed as an additional check. Conclusion The simple, yet crucial validation techniques discussed here can be used to reliably verify any chromosomally engineered E. coli strains for errors such as non-specific insertions in the chromosome, temperate phage contamination, and defects in growth and cell shape. While techniques such as PCR and DNA sequence verification should standardly be performed, we illustrate the necessity of performing these additional assays. The discussed techniques are highly generic and can be easily applied to any type of chromosome engineering.

chromosome engineering
Escherichia coli
recombineering
P1 phage transduction
strain validation
EBU plate assay
growth curve analysis
cell shape analysis
OA-Fund TU Delft

http://resolver.tudelft.nl/uuid:af1dcff9-1617-4835-a3a0-0469e1581337

https://doi.org/10.1186/s13036-015-0008-x

BioMed Central

1754-1611

http://www.jbioleng.org/content/9/1/11

Journal of Biological Engineering, 9, 2015

Institutional Repository

journal article

© 2015 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)