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Identification of phage recombinase function unit in genus Corynebacterium

  • Applied Genetics and Molecular Biotechnology
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Abstract

Phage recombinase function unit (PRFU) plays a key role in the life cycle of phage. Repurposing this system such as lambda-Redαβ or Rac-RecET for recombineering has gained success in Escherichia coli. Previous studies have showed that most PRFUs only worked well in its native hosts but poorly in the distant species. Thus, identification of new PRFUs in specific species is necessary for the development of its corresponding genetic engineering tools. Here, we present a thorough study of PRFUs in the genomes of genus Corynebacterium. We first used a database to database searching method to facilitate accurate prediction of novel PRFUs in 423 genomes. A total number of 60 sets of unique PRFUs were identified and divided into 8 types based on evolution affinities. Recombineering ability of the 8 representative PRFUs was experimentally verified in the Corynebacterium glutamicum ATCC 13032 strain. In particular, PRFU from C. aurimucosum achieved highest efficiency in both ssDNA and dsDNA mediated recombineering, which is expected to greatly facilitate genome engineering in genus Corynebacterium. These results will provide new insights for the study and application of PRFUs.

Key points

• First report of bioinformatic mining and systematic analysis of Phage recombinase function unit (PRFU) in Corynebacterium genomes.

• Recombineering ability of the representative PRFUs was experimentally verified in Corynebacterium glutamicum ATCC 13032 strain.

• PRFU with the highest recombineering efficiency at 10-2 magnitude was identified from Corynebacterium aurimucosum.

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Data Availability

1. Genomes: ftp://ftp.ncbi.nlm.nih.gov/genomes/all

2. Conserved domain: https://www.ncbi.nlm.nih.gov/cdd/

3. Genome information: https://www.ncbi.nlm.nih.gov/genome/, the Genome Assembly and Annotation report section

4. Protein structure: https://www.rcsb.org/

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Acknowledgements

We thank Haiying Jin for her help in the recombineering with ssDNA experiment. We also thank Qilong Qin for reviewing the manuscript.

Author and contributors

YZ participated in the conceptualization, data curation, formal analysis, investigation, methodology, project administration, software, validation, visualization, and writing process. QS participated in the conceptualization, funding acquisition, project administration, resources, supervision, writing review and editing process. QW participate in the funding acquisition and writing-review and editing process. TY participated in the conceptualization of oligo-mediated recombineering and methodology of oligo-mediated recombineering, resources and writing-review and editing process.

Funding

This work was financially supported by the grant from the National Natural Science Foundation of China (31730003), National Key Research and Development Program of China (2019YFA0904004), Key R&D Program of Shandong Province (2020CXGC010602), and the China Postdoctoral Science Foundation funded project (2019M662341).

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Correspondence to Tianyuan Su or Qingsheng Qi.

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The authors declare that there are no conflicts of interest.

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Chang, Y., Wang, Q., Su, T. et al. Identification of phage recombinase function unit in genus Corynebacterium. Appl Microbiol Biotechnol 105, 5067–5075 (2021). https://doi.org/10.1007/s00253-021-11384-x

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  • DOI: https://doi.org/10.1007/s00253-021-11384-x

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