A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities

Deirdre E. Ricaurte, Esteban Martínez-García, Ákos Nyerges, C. Pál, Víctor de Lorenzo, Tomás Aparicio

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Bacterial recombineering typically relies on genomic incorporation of synthetic oligonucleotides as mediated by Escherichia coli λ phage recombinase β – an occurrence largely limited to enterobacterial strains. While a handful of similar recombinases have been documented, recombineering efficiencies usually fall short of expectations for practical use. In this work, we aimed to find an efficient Recβ homologue demonstrating activity in model soil bacterium Pseudomonas putida EM42. To this end, a genus-wide protein survey was conducted to identify putative recombinase candidates for study. Selected novel proteins were assayed in a standardized test to reveal their ability to introduce the K43T substitution into the rpsL gene of P. putida. An ERF superfamily protein, here termed Rec2, exhibited activity eightfold greater than that of the previous leading recombinase. To bolster these results, we demonstrated Rec2 ability to enter a range of mutations into the pyrF gene of P. putida at similar frequencies. Our results not only confirm the utility of Rec2 as a Recβ functional analogue within the P. putida model system, but also set a complete workflow for deploying recombineering in other bacterial strains/species. Implications range from genome editing of P. putida for metabolic engineering to extended applications within other Pseudomonads – and beyond.

Original languageEnglish
Pages (from-to)176-188
Number of pages13
JournalMicrobial Biotechnology
Volume11
Issue number1
DOIs
Publication statusPublished - Jan 1 2018

Fingerprint

Bacterial Genomes
Recombinases
Workflow
Surveying
Genes
Proteins
Metabolic engineering
Bacteriophages
Oligonucleotides
Coliphages
Metabolic Engineering
Escherichia coli
Pseudomonas putida
Bacteria
Substitution reactions
Soils
Soil
Mutation
Gene Editing

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Biochemistry
  • Applied Microbiology and Biotechnology

Cite this

Ricaurte, D. E., Martínez-García, E., Nyerges, Á., Pál, C., de Lorenzo, V., & Aparicio, T. (2018). A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities. Microbial Biotechnology, 11(1), 176-188. https://doi.org/10.1111/1751-7915.12846

A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities. / Ricaurte, Deirdre E.; Martínez-García, Esteban; Nyerges, Ákos; Pál, C.; de Lorenzo, Víctor; Aparicio, Tomás.

In: Microbial Biotechnology, Vol. 11, No. 1, 01.01.2018, p. 176-188.

Research output: Contribution to journalArticle

Ricaurte, DE, Martínez-García, E, Nyerges, Á, Pál, C, de Lorenzo, V & Aparicio, T 2018, 'A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities', Microbial Biotechnology, vol. 11, no. 1, pp. 176-188. https://doi.org/10.1111/1751-7915.12846
Ricaurte, Deirdre E. ; Martínez-García, Esteban ; Nyerges, Ákos ; Pál, C. ; de Lorenzo, Víctor ; Aparicio, Tomás. / A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities. In: Microbial Biotechnology. 2018 ; Vol. 11, No. 1. pp. 176-188.
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