Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes.

Georgy Smyshlyaev, Alex Bateman, Orsolya Barabas

Molecular systems biology 2021 May

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Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) proteins drive MGE mobilization and could provide markers for MGE detection, but they constitute a diverse family also involved in housekeeping functions. Here, we conducted a comprehensive survey of YRs from bacterial, archaeal, and phage genomes and developed a sequence-based classification system that dissects the characteristics of MGE-borne YRs. We revealed that MGE-related YRs evolved from non-mobile YRs by acquisition of a regulatory arm-binding domain that is essential for their mobility function. Based on these results, we further identified numerous unknown MGEs. This work provides a resource for comparative analysis and functional annotation of YRs and aids the development of computational tools for MGE annotation. Additionally, we reveal how YRs adapted to drive gene transfer across species and provide a tool to better characterize antibiotic resistance dissemination. © 2021 The Authors. Published under the terms of the CC BY 4.0 license.

Citation

Georgy Smyshlyaev, Alex Bateman, Orsolya Barabas. Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes. Molecular systems biology. 2021 May;17(5):e9880