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Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family

Delia Casas-Pastor, Raphael Rene Müller, Anke Becker, Mark Buttner, Carol Gross, Thorsten Mascher, Alexander Goesmann, View ORCID ProfileGeorg Fritz
doi: https://doi.org/10.1101/2019.12.11.873521
Delia Casas-Pastor
1Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Germany
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Raphael Rene Müller
2Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
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Anke Becker
1Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Germany
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Mark Buttner
3Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Carol Gross
4Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
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Thorsten Mascher
5Institute of Microbiology, Technische Universität Dresden, Germany
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Alexander Goesmann
2Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
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Georg Fritz
1Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Germany
6School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
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  • ORCID record for Georg Fritz
  • For correspondence: georg.fritz@uwa.edu.au
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Abstract

Extracytoplasmic function σ factors (ECFs) represent one of the major bacterial signal transduction mechanisms in terms of abundance, diversity and importance, particularly in mediating stress responses. Here, we performed a comprehensive phylogenetic analysis of this protein family by scrutinizing all proteins in the NCBI database. As result, we identified ∼10 ECFs per bacterial genome on average and classified them into 157 phylogenetic ECF groups that feature a conserved genetic neighborhood and a similar regulation mechanism. Our analysis expands the number of unique ECF sequences ∼50-fold relative to previous classification efforts, enriches many original ECF groups with previously unclassified proteins and identifies 22 entirely new ECF groups. The ECF groups are hierarchically related to each other and are further composed of subgroups with closely related sequences. This two-tiered classification allows for the accurate prediction of common promoter motifs and the inference of putative regulatory mechanisms across subgroups composing an ECF group. This comprehensive, high-resolution description of the phylogenetic distribution of the ECF family, together with the massive expansion of classified ECF sequences, enables the application of in silico tools for the prediction of important functional residues, and serves as a powerful hypothesis-generator to guide future research in the field.

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Posted December 12, 2019.
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Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family
Delia Casas-Pastor, Raphael Rene Müller, Anke Becker, Mark Buttner, Carol Gross, Thorsten Mascher, Alexander Goesmann, Georg Fritz
bioRxiv 2019.12.11.873521; doi: https://doi.org/10.1101/2019.12.11.873521
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Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family
Delia Casas-Pastor, Raphael Rene Müller, Anke Becker, Mark Buttner, Carol Gross, Thorsten Mascher, Alexander Goesmann, Georg Fritz
bioRxiv 2019.12.11.873521; doi: https://doi.org/10.1101/2019.12.11.873521

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