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

Journal of Biological Engineering

Nynke H. Dekker¹  Anne S. Meyer¹  Theo van Laar¹  M. Charl Moolman¹  Sriram Tiruvadi Krishnan¹ 

[1] Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, Delft 2628 CJ, The Netherlands

关键词: Cell shape analysis;    Growth curve analysis;    EBU plate assay;    Strain validation;    P1 phage transduction;    Recombineering;    Escherichia coli;    Chromosome engineering;   

Others  :  1219593
DOI  :  10.1186/s13036-015-0008-x

 received in 2015-02-11, accepted in 2015-06-02,  发布年份 2015

【 摘 要 】

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, λ-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.

【 授权许可】

   
2015 Tiruvadi Krishnan et al.

【 图 表 】

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