Dr Mark van Breugel, PhD

Undergraduate Teaching

Essential Skills for Biochemists (BIO101 - Module Organiser)

Biochemistry Communication I (BIO202) 

Biochemistry Communication II (BIO301)

Molecular Basis of Disease (BIO363) 

Enzyme Catalysis (BIO365) 

Protein Structure, Folding & Assemblies (BIO367) 

Project Skills in the Life Sciences (BIO603)

Research Projects (BIO600)

Postgraduate Teaching

AI and Data Science in Biology (BIO720P)

Research

Research Interests:

Assembly mechanisms and functions of centrioles and centrosomes

Utilising protein biochemistry, structural biology and cell biology to unravel the workings of a crucial eukaryotic cell organelle in health and in disease. 

Centrioles are one of the largest protein assemblies found in animal cells. They are barrel-shaped cell organelles, which form the core of centrosomes and influence the organisation of the microtubule cytoskeleton in cells. If too many centrioles are made, extra centrosomes are formed which can cause problems in cell division and lead to diseases such as cancer. Centrioles also have another crucial function. They can dock to the cell membrane and template the outgrowth of hair-like cell projections called cilia and flagella. Cilia/flagella can move in a wave-like manner and thereby move fluid along the cell surface or propel cells, as observed in sperm cells. Other cilia types are immotile and act as sensory devices with which cells perceive their environment, e.g. detect smells, light or signalling molecules. Due to their key role in cilia formation, centriole defects can cause infertility and a class of diseases called ciliopathies.

While many centriole components have been identified, it is largely unknown how exactly they come together, what precise role and mechanism of action these components have and how diseases result from their dysfunction. My lab tries to address these questions using a wide variety of methods ranging from structural techniques such as X-ray crystallography and electron microscopy as well as biochemical and cell biological approaches. Our projects comprise:

Centriole structure and beyond

We have shown how centriole symmetry and diameter is established through the self-association of a single protein into 9-fold symmetric rings. Furthermore we have uncovered the structural basis of several other centriole assembly processes. However, many open questions remain concerning centriole duplication, elongation, maturation and the interfacing of centrioles with the pericentriolar material that surrounds them. Our projects address these questions by identifying the interactions of key players, determining their high-resolution structures and establishing their exact mechanisms in centriole formation and function in vivo through structure-based mutagenesis experiments. 

Centriole proteins in diseases

Through a combination of structural and in vivo approaches we have established that centriole duplication defects are the likely cause of the neuro-developmental disease, microcephaly. Furthermore, we showed that mutations in the core centriole component CEP120 cause two different ciliopathies by destabilising the protein and compromising the distal end structure of centrioles. However, for the vast majority of disease-causing mutations of centriole components, it is unclear what their molecular pathology mechanisms are. Importantly, studying these mutations also provides deep insights into the normal functioning of the intact proteins. Thus, we continue to explore disease mutations in centriole components to establish their exact molecular defects.

Cilia formation (ciliogenesis) mechanisms

Centrioles template cilia, but many aspects of this process are not understood. We are missing high-resolution structural information of key protein complexes involved in cilia formation, information that is necessary to grasp the underlying molecular mechanisms. Our projects aim at establishing suitable purification schemes to obtain these complexes to study them proteomically, biochemically and structurally. Their high-resolution structures will lead to an immediate understanding of how human disease mutations affect them and whether these defects might be rectifiable therapeutically. Importantly, it will allow us to disentangle their diverse cellular roles through engineering site-directed point mutations into them and study the resulting mutants in vivo.

 

Publications

Centriole Publications

Carden S., Vitiello E., Rosa E Silva I., Holder J., Quarantotti V., Kishore K., Roamio Franklin VN., D'Santos C., Ochi T., van Breugel M., Gergely F. 2023. Proteomic profiling of centrosomes across multiple mammalian cell and tissue types by an affinity capture method. Dev Cell. Oct 14:S1534-5807(23)00495-1. doi: 10.1016/j.devcel.2023.09.008. 

van Breugel M., Rosa E Silva I., Andreeva A. 2022. Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes. Commun Biol. Apr 5;5(1):312. doi: 10.1038/s42003-022-03269-0. PMID: 35383272.

Rosa e Silva, I. Binó, L.,  Johnson, C.M., Rutherford, T. J., Neuhaus, D., Andreeva, A., Čajánek, L.,  van Breugel, M. 2021. Molecular mechanisms underlying the role of the centriolar CEP164-TTBK2 complex in ciliopathies. Structure. Sep 7:S0969-2126(21)00302-6

Ochi, T., Quarantotti, V., Lin, H., Jullien, J., Rosa E Silva, I., Boselli, F., Barnabas, D.D., Johnson, C.M., McLaughlin, S.H., Freund, S.M.V., Blackford, A.N., Kimata, Y., Goldstein, R.E., Jackson, S.P., Blundell, T.L., Dutcher, S.K., Gergely, F., van Breugel, M. 2020. CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions. Structure May 5. pii: S0969-2126(20)30131-3

Liu, Y., Kim, J., Philip, R., Sridhar, V., Chandrashekhar, M., Moffat, J., van Breugel, M., Pelletier, L., 2020. Direct Interaction Between CEP85 and STIL Mediates PLK4-driven Directed Cell Migration. Journal of Cell Science 133(8).

Joseph, N., Al-Jassar, C., Johnson, C.M., Andreeva, A., Barnabas, D.D., Freund, S.M.V., Gergely, F., van Breugel, M. 2018. Disease-associated mutations in CEP120 destabilise the protein and impair ciliogenesis. Cell Reports 23(9):2805-2818.

Liu, Y., Gupta, G.D., Barnabas, D.D., Agircan, F.G., Mehmood, S., Wu, D., Coyaud, E., Johnson, C.M., McLaughlin, S.H., Andreeva, A., Freund, S.M.V., Robinson, C.V., Cheung, S.W.T., Raught, B., Pelletier, L., van Breugel, M. 2018. Direct binding of CEP85 to STIL ensures robust PLK4 activation and efficient centriole assembly. Nature Communications 9(1):1731.

Al-Jassar, C., Andreeva, A., Barnabas, D.D., McLaughlin, S.H., Johnson, C.M., Yu, M., van Breugel, M. 2017. The Ciliopathy-Associated Cep104 Protein Interacts with Tubulin and Nek1 Kinase. Structure 25(1):146-156.

van Breugel, M*., Wilcken, R., McLaughlin, S.H., Rutherford, T.J., Johnson, C.M. 2014. Structure of the SAS-6 cartwheel hub from Leishmania major. Elife 3:e01812. (* corresponding author and principal investigator)

Cottee, M.A., Muschalik, N., Wong, Y.L., Johnson, C.M., Johnson, S., Andreeva, A., Oegema, K., Lea, S.M., Raff J.W., van Breugel, M. 2013. Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly. Elife 2:e01071.

van Breugel, M^{^}., Hirono, M., Andreeva, A., Yanagisawa, H.A., Yamaguchi, S., Nakazawa, Y., Morgner, N., Petrovich, M., Ebong, I.O., Robinson, C.V., Johnson, C.M., Veprintsev, D., Zuber, B. 2011. Structures of SAS-6 suggest its organization in centrioles. Science 331(6021):1196-9. (^corresponding author and principal investigator)

 

Supervision

MSc student:

Hannah Tomkinson

Post-doc:

Ifeanyi Enekwa 

Past Lab members:

Ivan Rosa e Silva (Post-doc)
Takashi Ochi (Post-doc)
Caezar al Jassar (Post-doc)
Deepak Barnabas (PhD student)
Marike van Roon (Technician)