Overview

Doctoral study program
Life Sciences (Faculty of Science, Masaryk University)

Supervisor
Pavel Plevka

Annotation
Despite decades of study, important aspects of phage replication cycles, such as the mechanism of genome delivery, initiation of head assembly, and genome packaging, are poorly understood. We propose to use cryo-electron microscopy and tomography to characterize replication intermediates of phage LE3 infecting Leptospira. The in situ data collection will be enabled by the dimensions of leptospira cells, which are 100 nm thin. Analysis of the infection intermediates will focus on genome delivery, initiation of head assembly, and genome packaging. These processes cannot be studied in vitro because of the challenges of preparing the corresponding complexes in functional form in sufficient amounts.

Recommended literature
Characterization of LE3 and LE4, the only lytic phages known to infect the spirochete Leptospira. Schiettekatte O, Vincent AT, Malosse C, Lechat P, Chamot-Rooke J, Veyrier FJ, Picardeau M, Bourhy P. Sci Rep. 2018 Aug 6;8(1):11781. doi: 10.1038/s41598-018-29983-6.
Molecular architecture of tailed double-stranded DNA phages. Fokine A, Rossmann MG. Bacteriophage. 2014 Jan 1;4(1):e28281. doi: 10.4161/bact.28281. Epub 2014 Feb 21. PMID: 24616838
A century of the phage: past, present and future. Salmond GP, Fineran PC. Nat Rev Microbiol. 2015 Dec;13(12):777-86. doi: 10.1038/nrmicro3564. Epub 2015 Nov 9. PMID: 26548913
Viral genome packaging machines: Structure and enzymology. Catalano CE, Morais MC. Enzymes. 2021;50:369-413. doi: 10.1016/bs.enz.2021.09.006. Epub 2021 Nov 10. PMID: 34861943
Casjens, S. R. (2011). The DNA-packaging nanomotor of tailed bacteriophages. Nature Reviews Microbiology, 9(9), 647–657. doi:10.1038/nrmicro2632
Research area
Structural biology, virology

Keywords
Phage, structure, cryo-EM, genome, delivery, packaging, assembly, molecular motors

Funding of the PhD candidate
The student will be supported by the ERC consolidator grant Phage infection of bacterial biofilm (101043452).

Requirements for candidate
The prospective student should be interested in learning cryo-EM and structure determination approaches. Previous experience with molecular biology, programming, scripting, and data analyses is a plus.

Information about the supervisor
Pavel Plevka is 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.

Information about the application process
https://www.ceitec.eu/ls-mm-phd/

Application webpage
https://www.ceitec.eu/structural-characterization-of-leptophage-replication-cycle/t11450