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Structure-Guided Phylogeny of Tailed Bacteriophages
Doctoral study program
Life Sciences (Faculty of Science, Masaryk University)
Supervisor
Annotation
Tailed phages are a diverse group of viruses abundant in all econiches as revealed by recent metagenomic studies. In the past ten years a substantial effort has been made over an evolutionary sound classification of these viruses. However, due to rapid evolution, the phylogenetic signal, contained in the amino acid sequence of tailed phages, is eroded. As a result, current classification stays fragmented. On the other hand, protein folds remain conserved over greater evolutionary distances. Therefore, phylogenetic inference based on the structure of phage virion proteins may provide a deeper insight into their evolutionary history. Currently, the methods for structure-guided phylogeny are not well developed. The purpose of this project is to optimize the method for maximum likelihood phylogenetic inference on protein structure and use it to reveal new evolutionary connections within tailed phages. The work will involve general bioinformatics methods, including bash-scripting, database search tools, multiple sequence alignment tools and phylogenetic software. The candidate will gain extensive theoretical background and practical skills to work in the field of evolutionary biology.
Recommended literature
- Weinheimer AR, Ha AD, Aylward FO. Towards a unifying phylogenomic framework for tailed phages. PLoS Genet. 2025 Feb 5;21(2):e1011595. doi: 10.1371/journal.pgen.1011595. PMID: 39908317; PMCID: PMC11835377.
- Mifsud JCO, Suchard MA, Holmes EC, Lemey P. Recent advances in the inference of deep viral evolutionary history. J Virol. 2025 Sep 23;99(9):e0029225. doi: 10.1128/jvi.00292-25. Epub 2025 Aug 22. PMID: 40844272; PMCID: PMC12456133.
- Ng WM, Stelfox AJ, Bowden TA. Unraveling virus relationships by structure-based phylogenetic classification. Virus Evol. 2020 Feb 12;6(1):veaa003. doi: 10.1093/ve/veaa003. PMID: 32064119; PMCID: PMC7015158.
- Moi D, Bernard C, Steinegger M, Nevers Y, Langleib M, Dessimoz C. Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses. Nat Struct Mol Biol. 2025 Oct 10. doi: 10.1038/s41594-025-01649-8. Epub ahead of print. PMID: 41073779.
Research area
Structural biology, virology
Keywords
Tailed bacteriophages; Viral evolution; Structural phylogeny; Protein fold conservation; Structure-guided classification
Funding of the PhD candidate
The student will be supported by the ERC consolidator grant Phage infection of bacterial biofilm (101043452).
In the academic year 2026/27 the net income of the CEITEC PhD School student is expected to be at least CZK 29,400 (approx. EUR 1215)
Requirements for candidate
The prospective student should be interested in learning techniques of structural phylogeny. Previous experience with molecular biology, programming, scripting, and data analyses is a plus.
Information about the supervisor
Pavel Plevka is the Research Group Leader and Director of CEITEC Masaryk University in Brno, Czech Republic. Pavel Plevka has determined the structures of several viruses, most notably that of human enterovirus 71 that causes potentially fatal encephalitis in small children. Furthermore, he studied the maturation of the dengue virus. He focuses on cryo-electron microscopy of viruses and other macromolecular complexes. Pavel Plevka studied Molecular Biology and Virology at the Faculty of Science at Charles University in Prague and graduated in 2002, then went on to complete his doctoral studies in Structural Biology in 2009 at Uppsala University in Sweden. For the next four years, he worked as a Postdoctoral Research Associate in Michael Rossmann’s Group at Purdue University in the United States. In 2013, he received an ERC Starting Grant and established his own research group that is focused on Structural Virology at CEITEC Masaryk University in Brno. He is a laureate of the Neuron Prize for Young Scientists and the Werner von Siemens Prize for the most important discovery in basic research. In 2023, he became the Director of CEITEC Masaryk University. In 2022, he was awarded the ERC Consolidator Grant.