The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo- attB sites in the genus Nocardia

Marion Herisse; Jessica L Porter; Romain Guerillot; Takehiro Tomita; Anders Goncalves Da Silva; Torsten Seemann; Benjamin P Howden; Timothy P Stinear; Sacha J Pidot

doi:10.7717/peerj.4784

The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo- attB sites in the genus Nocardia

PeerJ. 2018 May 4:6:e4784. doi: 10.7717/peerj.4784. eCollection 2018.

Authors

Marion Herisse¹, Jessica L Porter¹, Romain Guerillot¹, Takehiro Tomita², Anders Goncalves Da Silva^{1

2}, Torsten Seemann^{1

2}, Benjamin P Howden^{1

2

3}, Timothy P Stinear^{1

2

3}, Sacha J Pidot¹

Affiliations

¹ Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, Australia.
² Microbiological Diagnostic Unit, University of Melbourne, Melbourne, VIC, Australia.
³ Doherty Applied Microbial Genomics, University of Melbourne, Melbourne, VIC, Australia.

Abstract

Plasmid vectors based on bacteriophage integrases are important tools in molecular microbiology for the introduction of foreign DNA, especially into bacterial species where other systems for genetic manipulation are limited. Site specific integrases catalyze recombination between phage and bacterial attachment sites (attP and attB, respectively) and the best studied integrases in the actinomycetes are the serine integrases from the Streptomyces bacteriophages ΦC31 and ΦBT1. As this reaction is unidirectional and highly stable, vectors containing phage integrase systems have been used in a number of genetic engineering applications. Plasmids bearing the ΦBT1 integrase have been used to introduce DNA into Streptomyces and Amycolatopsis strains; however, they have not been widely studied in other actinobacterial genera. Here, we show that vectors based on ΦBT1 integrase can stably integrate into the chromosomes of a range of Nocardia species, and that this integration occurs despite the absence of canonical attB sites in these genomes. Furthermore, we show that a ΦBT1 integrase-based vector can insert at multiple pseudo-attB sites within a single strain and we determine the sequence of a pseudo-attB motif. These data suggest that ΦBT1 integrase-based vectors can be used to readily and semi-randomly introduce foreign DNA into the genomes of a range of Nocardia species. However, the precise site of insertion will likely require empirical determination in each species to avoid unexpected off-target effects.

Keywords: DNA integration; Nocardia; Serine recombinase; Streptomyces; ΦBT1.

Grants and funding

This work was supported by a National Health and Medical Research Council of Australia project grant (No. APP1105522). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.