PhD Birol Cabukusta


(1) Role of membrane contacts sites in regulating sphingolipid homeostasis

Membrane contact sites are cellular domains where two organelles come closer to facilitate molecular function and promote functional integration. Among their many functions, membrane contact sites play a key role in controlling intracellular lipid flows and distributions; as lipids cannot diffuse freely in cytosol, their transport must be facilitated. ER-localized highly conserved VAP protein family members mediate membrane contact sites by tethering proteins of the apposing membrane to the ER. These membrane contact sites formed by VAPs are often the sites of lipid exchange between organelles. My research focuses on the role of individual VAPs on specific lipid pipelines between organelles.

(2) New players in MHCII antigen presentation by genome-wide CRISPR/Cas9 activation screen

Proper immune response to pathogenic invasion requires presentation of extracellular antigens by MHC class II on antigen-presenting cells. Processing of antigens, their loading to MHCII and presentation are complex multi-component processes. Although most of the proteins involved in these processes have been identified, many aspects of antigen presentation by MHCII yet to be explored. Using a genome-wide CRISPR/Cas9 over-expression library, we aim to identify the unknown proteins that regulate MHC class II antigen presentation.

Curriculum Vitae:

I completed my Bachelor’s and Master’s degrees in Turkey and the Netherlands, respectively. As a part of the EU-funded Marie Curie ITN SPHINGONET, I moved to Germany for my PhD at University of Osnabrück. During my PhD, I studied an ER-localized enzyme that synthesizes the lipid ceramide phosphoethanolamine and pursued a better understanding of sphingolipid homeostasis in mammalian cells. I obtained my PhD in November 2016 and started my post-doc in Neefjes lab in January 2017. I like coffee.


  • Mechanisms of lysosomal positioning and movement.

    Cabukusta B, Neefjes J.

    Traffic. 2018;19(10):761-769.

  • ER residency of the ceramide phosphoethanolamine synthase SMSr relies on homotypic oligomerization mediated by its SAM domain.

    Cabukusta B, Kol M, Kneller L, Hilderink A, Bickert A, Mina JG, Korneev S, Holthuis JC.

    Sci Rep. 2017;7:41290.

  • Oligomeric State of a Candidate Endoplasmic Reticulum (ER) Ceramide Sensor by Single-molecule Photobleaching

    Cabukusta B, Köhlen JA, Richter CP, You C, Holthuis JC.

    J Biol Chem. 2016;291(47):24735-24746.


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