Bioinformatic Investigation of Nuclear Transport

Student: Maddie Davis

Major: Biology and International Studies 

Mentor: Dr. Christine Byrum

Department: Biology

Bioinformatic Investigation of Nuclear Transport

The transport of cellular products between the cytosol and nucleus is critical for many cellular processes. It is generally accepted that products less than 40 kDa easily cross the nuclear membrane independently; however, molecules larger than this must interact with nuclear transport receptors, such as karyopherins, to overcome the energetic barrier for entrance into or exit from the nucleus. Karyopherins are classified into three groups - importins, exportins, and transportins - based on whether they transfer cargo into, out of, or bi-directionally across the nuclear membrane. Each nuclear transport receptor is specialized to interact with specific cargo types and identifies these cargo through nuclear localization signals (NLSs). The Byrum lab has shown that during sea urchin development some karyopherins are differentially expressed. By influencing nucleocytoplasmic distribution of the cargo, karyopherins may impact progression of specific developmental processes (e.g. endomesoderm formation or neurogenesis). Recent mammalian cell line studies have focused on recognizing corresponding cargo for different karyopherin forms and identifying which cargo NLSs correspond to which nuclear transport receptor. We have performed a metadata review to discern which karyopherins likely transfer different transcription factor cargo needed for developmental processes. Current efforts focus on writing a bioinformatic program to identify NLSs in transcription factors that act in sea urchin gene regulatory networks. We hope to use this data in combination with wholemount in situ hybridization data to make informed predictions about roles of individual karyopherins in sea urchin embryogenesis.