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A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis

Nature Microbiology volume 4, pages 226–233 (2019)Cite this article

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Abstract

Steroids are essential triterpenoid molecules that are present in all eukaryotes and modulate the fluidity and flexibility of cell membranes. Steroids also serve as signalling molecules that are crucial for growth, development and differentiation of multicellular organisms1,2,3. The steroid biosynthetic pathway is highly conserved and is key in eukaryote evolution4,5,6,7. The flavoprotein squalene epoxidase (SQE) catalyses the first oxygenation reaction in this pathway and is rate limiting. However, despite its conservation in animals, plants and fungi, several phylogenetically widely distributed eukaryote genomes lack an SQE-encoding gene7,8. Here, we discovered and characterized an alternative SQE (AltSQE) belonging to the fatty acid hydroxylase superfamily. AltSQE was identified through screening of a gene library of the diatom Phaeodactylum tricornutum in a SQE-deficient yeast. In accordance with its divergent protein structure and need for cofactors, we found that AltSQE is insensitive to the conventional SQE inhibitor terbinafine. AltSQE is present in many eukaryotic lineages but is mutually exclusive with SQE and shows a patchy distribution within monophyletic clades. Our discovery provides an alternative element for the conserved steroid biosynthesis pathway, raises questions about eukaryote metabolic evolution and opens routes to develop selective SQE inhibitors to control hazardous organisms.

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Fig. 1: Identification of an AltSQE from P. tricornutum.
Fig. 2: Distribution of SQE across the tree of life.
Fig. 3: Characterization of AltSQEs from various species.

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Data availability

Gene sequences used in this study were deposited in GenBank under the accession numbers MH422131 to MH422144. All other data that support the findings of this study are available from the corresponding author upon request.

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Acknowledgements

We thank R. De Clercq and T. Lapshina for technical assistance, Y. Bai, M. Johnson and R. Abbriano-Burke for support with confocal microscopy and M. Huysman and L. De Veylder for providing the P. tricornutum cDNA library. J.P. is a postdoctoral fellow of the Research Foundation-Flanders. E.V. is funded by the BOF project GOA01G01715. M.F. is supported by a CSIRO Synthetic Biology Future Science Fellowship, co-funded by CSIRO and the University of Technology Sydney.

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Authors and Affiliations

  1. Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium

    Jacob Pollier, Emmelien Vancaester, Klaas Vandepoele & Alain Goossens

  2. VIB Center for Plant Systems Biology, Ghent, Belgium

    Jacob Pollier, Emmelien Vancaester, Klaas Vandepoele & Alain Goossens

  3. Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia

    Unnikrishnan Kuzhiumparambil & Michele Fabris

  4. CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland, Australia

    Claudia E. Vickers & Michele Fabris

  5. Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland, Australia

    Claudia E. Vickers

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Contributions

J.P., E.V., U.K. and M.F. carried out the experiments. J.P., K.V., A.G. and M.F. designed the experiments. All authors contributed to writing of the manuscript.

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Correspondence to Alain Goossens.

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Supplementary information

Supplementary Information

Supplementary Figures 1–8, Supplementary Table 1.

Reporting Summary

Supplementary Dataset 1

Overview of all detected alternative and conventional SQE protein sequences in all queried organisms.

Supplementary Dataset 2

Maximum-likelihood phylogeny of eukaryotic and viral AltSQE proteins constructed from an alignment of homologues from 202 organisms and 403 informative aligned sites, rooted with ERG3. Proteins are coloured based on their phylogenetic affiliations and bootstrap values are mentioned at the right of every node.

Supplementary Dataset 3

Maximum-likelihood phylogeny of eukaryotic conventional SQE proteins constructed from an alignment of homologues from 235 organisms and 624 informative aligned sites, rooted with UbiH. Proteins are coloured based on their phylogenetic affiliations and bootstrap values are mentioned at the right of every node.

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Pollier, J., Vancaester, E., Kuzhiumparambil, U. et al. A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis. Nat Microbiol 4, 226–233 (2019). https://doi.org/10.1038/s41564-018-0305-5

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