A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides

Anna D. Corts, Lynn C. Thomason, Ryan T. Gill, Jeffrey A. Gralnick

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

Shewanella oneidensis MR-1 is an invaluable host for the discovery and engineering of pathways important for bioremediation of toxic and radioactive metals and understanding extracellular electron transfer. However, genetic manipulation is challenging due to the lack of genetic tools. Previously, the only reliable method used for introducing DNA into Shewanella spp. at high efficiency was bacterial conjugation, enabling transposon mutagenesis and targeted knockouts using suicide vectors for gene disruptions. Here, we describe development of a robust and simple electroporation method in S. oneidensis that allows an efficiency of ~4.0 x 106 transformants/µg DNA. High transformation efficiency is maintained when cells are frozen for long term storage. In addition, we report a new prophage-mediated genome engineering (recombineering) system using a λ Red Beta homolog from Shewanella sp. W3-18-1. By targeting two different chromosomal alleles, we demonstrate its application for precise genome editing using single strand DNA oligonucleotides and show that an efficiency of ~5% recombinants among total cells can be obtained. This is the first effective and simple strategy for recombination with markerless mutations in S. oneidensis. Continued development of this recombinant technology will advance high-throughput and genome modification efforts to engineer and investigate S. oneidensis and other environmental bacteria.

Original languageEnglish (US)
Article number39
JournalScientific Reports
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2019

Bibliographical note

Funding Information:
We thank Irene Choi for her contribution during the conduct of this study and Evan D. Brutinel for constructing the S. oneidensis lacZ strain. We also thank Nina Costantino and Donald L. Court for their editorial comments. This work was supported by ONR grant N00014-17-2600 to J.A.G and R.T.G, and by DOE grant DE-SC0018368 to R.T.G. This work was supported, in part, by the Intramural Research Program of the National Institutes of Health, National Cancer Institute, Center for Cancer Research. This project has also been partly funded with federal funds from the National Cancer Institute, National Institutes of Health, under contract no. HHSN261200800001E.

Publisher Copyright:
© 2019, The Author(s).

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