We study function and regulation of proteins related to ubiquitin in cellular processes of pre-messenger RNA splicing and signaling. For these studies we perform experiments in molecular cell biology, genetics, and biochemistry in the budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe. We use mammalian cell cultures and multi-cellular organisms through collaborations to highlight functional conservations of the findings made in these organisms and their potential applications to humans.
Ubiquitin and ubiquitin-like modifiers, for example, Hub1, SUMO, NEDD8, Sde2 etc., are a group of small proteins harboring ubiquitin fold, and function as central regulators for a large number of processes in the cell. The covalent attachment of ubiquitin to target proteins, termed ubiquitination, requires a set of dedicated enzymes. The process of ubiquitination is key for determining fate of target proteins through their degradation in the proteasome. The process also diversifies functions of its targets by modulating their properties in non-proteolytic ways. Other ubiquitin-like modifiers also attach to target proteins as modules or tags, both covalently and non-covalently, and play regulatory roles a similar large number of processes. These modifiers often operate as molecular switch in processes such DNA repair, signal transduction, protein sorting etc.
The ubiquitin-like protein Hub1 is conserved from budding yeast to humans. It binds to splicing factors non-covalently, and functions in pre-mRNA splicing in a unique way, for efficient splicing of a subset of introns and to promote alternative splicing. The ubiquitin-fold harboring Sde2 is conserved in intron-rich eukaryotes from fission yeast to humans. The protein gets incorporated in the splicing machinery, spliceosome, for intron-specific pre-mRNA splicing after cleavage of its ubiquitin fold by specific deubiquitinating enzymes. Defects in heterochromatin silencing and genome stability are known to be hallmarks of many diseases including cancer. Our recent discoveries suggest that the process of intron-specific pre-mRNA splicing becomes critical for heterochromatin silencing and genome stability.
Thakran, P., Pandit, P.A., Datta, S., Kolathur, K.K., Pleiss, J.A., and Mishra, S.K. (2018). Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing. The EMBO Journal 37: 89-101. DOI 10.15252/embj.201796751. Link: http://emboj.embopress.org/content/37/1/89.long
- Mishra, S.K. and Thakran, P. (2018). Intron specificity in pre-mRNA splicing. Current Genetics. DOI: https://doi.org/10.1007/s00294-017-0802-8. Link:https://link.springer.com/article/10.1007%2Fs00294-017-0802-8.
- Ammon, T., Mishra, S.K., Kowalska, K., Popowicz, G.M., Holak, T., and Jentsch, S. (2014). The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells. Journal of Molecular Cell Biology 6: 312-323. Link: https://academic.oup.com/jmcb/article/6/4/312/2886285
- Mishra, S.K., Ammon, T., Popowicz, G.M., Krajewski, M., Nagel, R.J., Ares, M., Holak, T., and Jentsch, S. (2011). Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Nature 474: 173-178. Link: http://www.nature.com/articles/nature10143
- Mishra, S.K., Tripp, J., Winkelhaus, S., Tschiersch, B., Theres, K., Nover, L., and Scharf, K.D. (2002). In the complex family of heat stress transcription factors, HsfA1 has a unique role as master regulator of thermo tolerance in tomato. Genes & Development 16: 1555-1567. Link: http://genesdev.cshlp.org/content/16/12/1555.long