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Genomic Insights into Evolution of AdpA Family Master Regulators of Morphological Differentiation and Secondary Metabolism in Streptomyces

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Abstract

The AdpA protein from a streptomycin producer Streptomyces griseus is a founding member of the AdpA family of pleiotropic regulators, known to be ubiquitously present in streptomycetes. Functional genomic approaches revealed a huge number of AdpA targets, leading to the claim that the AdpA regulon is the largest one in bacteria. The expression of adpA is limited at the level of translation of the rare leucyl UUA codon. All known properties of AdpA regulators were discovered on a few streptomycete strains. There are open questions about the true abundance and diversity of AdpA across actinobacterial taxa (and beyond) and about the possible evolutionary forces that shape the AdpA orthologous group in Streptomyces. Here we show that, with respect to the TTA codon, streptomycete adpA is more diverse than has been previously thought, as the genes differ in presence/position of this codon. Reciprocal best hits to AdpA can be found in many actinobacterial orders, with a domain organization resembling that of the prototypical AdpA, but other configurations also exist. Diversifying positive selection was detected within the DNA-binding (AraC) domain in adpA of Streptomyces origin, most likely affecting residues enabling AdpA to recognize a degenerate operator. Sequence coding for putative glutamine amidotransferase (GATase-1) domain also shows signs of positive selection. The two-domain organization of AdpA most likely arose from a fusion of genes encoding separate GATase-1 and AraC domains. Indeed, we show that the AraC domain retains a biological function in the absence of the GATase-1 part. We suggest that acquisition of the regulatory role by TTA codon is a relatively recent event in the evolution of AdpA, which coincided with the rise of the Streptomycetales clade and, at present, is under relaxed selective constraints. Further experimental scrutiny of our findings is invited, which should provide new insights into the evolution and prospects for engineering of an AdpA-centered regulatory network.

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Acknowledgements

The work was supported by grant BG-41Nr from the Ministry of Education and Science of Ukraine (to B.O.).

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  1. Mariia Rabyk and Oleksandr Yushchuk have contributed equally to the work.

Authors and Affiliations

  1. Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine

    Mariia Rabyk, Oleksandr Yushchuk, Ihor Rokytskyy & Bohdan Ostash

  2. Institute of Applied Simulations, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Einsiedlerstrasse 31a, 8820, Wädenswil, Switzerland

    Maria Anisimova

  3. Swiss Institute of Bioinformatics, Lausanne, Switzerland

    Maria Anisimova

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  1. Mariia Rabyk
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  2. Oleksandr Yushchuk
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Correspondence to Bohdan Ostash.

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Rabyk, M., Yushchuk, O., Rokytskyy, I. et al. Genomic Insights into Evolution of AdpA Family Master Regulators of Morphological Differentiation and Secondary Metabolism in Streptomyces. J Mol Evol 86, 204–215 (2018). https://doi.org/10.1007/s00239-018-9834-z

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