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Prediction of biological functions of Shewanella-like protein phosphatases (Shelphs) across different domains of life

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Abstract

PPP protein phosphatases are an important enzyme family involved in a variety of aspects of cellular signalling and metabolism. PPPs are ubiquitous in eukaryotes, and are also present in many bacteria. Canonical eukaryotic PPP phosphotases are represented by five major subfamilies (PP1, PP2A, calcineurin, PP5 and PPEF/PP7). We previously reported that three “bacterial-like” PPP groups span the prokaryote–eukaryote boundary, including “Shewanella-like” phosphatases (Shelphs), which are in the focus of this study. Here we predict possible biological functions and functional partners of Shelphs by examining composition of bacterial operons and expression data for eukaryotes available in public databases. In Arabidopsis thaliana, the predicted possible roles include light-dependent regulation of chloroplast functions, signalling between the nucleus and the chloroplast, and defence responses. In Plasmodium falciparum, Shelphs are predicted to be associated with host cell invasion. One isoform has been located in the apical complex, essential for the interaction with the host cell. This makes P. falciparum Shelphs obvious potential candidates for therapeutic targets. Shelphs are also present in bacteria that constitute a considerable proportion of symbiotic microflora in humans. The predicted involvement of bacterial Shelphs in sensing and import of nutrients and extrusion of toxins may be relevant to the links between physiology of humans and our symbionts. Thus, despite the absence of Shelphs in animals, including humans, they may have a direct relationship to human health. Some predicted biological processes and potential functional partners of Shelphs are common between different bacterial and/or eukaryotic lineages, suggesting evolutionary conservation of some Shelph regulatory modules.

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Acknowledgements

The authors are indebted to all researchers who have deposited their primary data into open access repositories, and who have made their software freely available. This work would have been impossible without these contributions. We are also grateful to Jonathan Goldberg for critical reading of the manuscript and valuable comments.

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  1. Mikhail A. Kutuzov & Alexandra V. Andreeva

    Present address: Department of Medicine, Northwestern University, Chicago, IL, 60611, USA

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  1. Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, 60612, USA

    Mikhail A. Kutuzov & Alexandra V. Andreeva

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  1. Mikhail A. Kutuzov
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Correspondence to Mikhail A. Kutuzov or Alexandra V. Andreeva.

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This work is dedicated to the memory of Nelly Bennett, our collaborator and friend.

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Kutuzov, M.A., Andreeva, A.V. Prediction of biological functions of Shewanella-like protein phosphatases (Shelphs) across different domains of life. Funct Integr Genomics 12, 11–23 (2012). https://doi.org/10.1007/s10142-011-0254-z

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  • DOI: https://doi.org/10.1007/s10142-011-0254-z

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