Dr. Shravan Kumar Mishra
Associate Professor, Biological Sciences

Wellcome Trust/DBT India Alliance Intermediate Fellow

My webpage

Research Topics
Ubiquitin-Like Modifiers and Control of Pre-mRNA Splicing

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 relevance of our findings in humans.

Ubiquitin and ubiquitin-like modifiers, including Hub1, SUMO, NEDD8, Sde2, are a family of small proteins harboring ubiquitin fold. They function as central regulators for a large number of processes in the cell. The covalent attachment of ubiquitin to target proteins by the process known as ubiquitination requires a set of dedicated enzymes. Ubiquitination is the key for determining fate of target proteins through degradation in the proteasome. This process also diversifies functions of the targets by modulating their properties in non-proteolytic ways. Other ubiquitin-like modifiers also attach to their targets for regulatory activities, both covalently and non-covalently. Ubiquitin-like modifiers thereby act as molecular switches in processes such as DNA repair, signal transduction, protein sorting etc.

The ubiquitin-like proteins Hub1 and Sde2 promote efficient excision of a subset of introns. They bind to targets only non-covalently and function in pre-mRNA splicing in unique ways. Hub1-modified spliceosomes are able to recognize suboptimal introns and promote alternative splicing. Whereas Hub1 is conserved from budding yeast to humans, the ubiquitin-fold-harboring Sde2 protein is found only in intron-rich eukaryotes, from fission yeast to humans. After removal of its ubiquitin fold by specific deubiquitinating enzymes, Sde2 gets incorporated into the spliceosome for intron-specific splicing. Thus, both Hub1 and Sde2 appear to relax spliceosomes’ fidelity on a subset of pre-mRNAs.

The hallmarks of many diseases in humans, including cancer, are the defects in heterochromatin silencing and genome stability. Our findings reveal that the process of intron-specific pre-mRNA splicing induced by ubiquitin-like proteins is critical for heterochromatin silencing and genome stability.

• Anil AT, Choudhary K, Pandian R, Gupta P, Thakran P, Singh A, Sharma M, Mishra SK (2022). Splicing of branchpoint-distant exons is promoted by Cactin, Tls1 and the ubiquitin-fold-activated Sde2. Nucleic Acids Research 50: 10000-10014. https://academic.oup.com/nar/article/50/17/10000/6696354
• Chanarat S, Mishra SK (2018). Emerging Roles of Ubiquitin-like Proteins in Pre-mRNA Splicing. Trends in Biochemical Sciences 43: 896-907. https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(18)30162-2
• Thakran P, Pandit PA, Datta S, Kolathur KK, Pleiss JA, Mishra SK (2018). Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing. The EMBO Journal 37: 89-101. http://emboj.embopress.org/content/37/1/89.long
• Mishra SK, Ammon T, Popowicz GM, Krajewski M, Nagel RJ, Ares M, Holak T, Jentsch S (2011). Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Nature 474: 173-178. http://www.nature.com/articles/nature10143
• Mishra SK, Tripp J, Winkelhaus S, Tschiersch B, Theres K, Nover L, Scharf KD (2002). In the complex family of heat stress transcription factors, HsfA1 has a unique role as master regulator of thermotolerance in tomato. Genes & Development 16: 1555-1567. http://genesdev.cshlp.org/content/16/12/1555.long