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bioRxiv · 10.1101/598011

New logic facilitated identification of novel phage recombinase function units

Chang, Y.·Wang, Q.·Su, T.·Qi, Q.
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Abstract

Phage recombinase function unit (PRFU) contains one single strand annealing protein (SSAP) and one 5-3 exonuclease (EXO). Well-known PRFU such as lambda-Red or Rac RecET has been proved to be useful tool in the recombineering of Escherichia coli but had limited efficiency in distant species. Therefore, PRFUs from closely related species were often searched and developed as specific genetic tools. However, there are still many bacteria with few PRFU identified. Here, we hypothesised that the occurrence of PRFU might be related to specific strains. Based on this assumption, we managed to identify 59 unique sets of PRFUs in over 23 species of the genus Corynebacterium, a taxonomic group that were reported to be lacking in such system. The identified PRFUs were then classified to show their similarities and relation to species based on both sequential and structural information. Representative PRFUs were verified to be highly effective in mediating recombineering using ssDNA or dsDNA substrates. Analysis of the functional PRFUs indicated that they share similar local genome contexts, which might suggest their common origin. Our findings reveal the relation of PRFUs, species and strains and provide novel candidate genetic manipulation tools in genus Corynebacterium.\n\nAuthor SummaryGenus Corynebacterium is a taxonomic group with highly diversified species that are of medical, veterinary, or biotechnological relevance. However, being lack of genetic tools limits the study of these species. Our new verified phage recombinase function units (PRFUs) in this genus that are highly effective in mediating recombineering will provide new candidate genetic tools in this genus. Besides, reference genomes were often used for genome study and data mining. While for the mobile genetic elements, their transferable characteristic may affect their occurrence among genomes. Here we provide evidence for this idea by showing that the occurrence of PRFU is strain related but not species related. This may be helpful for the functional genomics study of mobile genetic elements among genomes.

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Chang, Y., Wang, Q., Su, T., Qi, Q.. 2019-04-10. New logic facilitated identification of novel phage recombinase function units. https://doi.org/10.1101/598011

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