Abstract
Polysumoylation is a crucial cellular response to stresses against genomic integrity or proteostasis. Like the small ubiquitin-like modifier (SUMO)-targeted ubiquitin ligase RNF4, proteins with clustered SUMO-interacting motifs (SIMs) can be important signal transducers downstream of polysumoylation. To identify novel polySUMO-binding proteins, we conducted a computational string search with a custom Python script. We found clustered SIMs in another RING domain protein Arkadia/RNF111. Detailed biochemical analysis of the Arkadia SIMs revealed that dominant SIMs in a SIM cluster often contain a pentameric VIDLT ((V/I/L/F/Y)(V/I)DLT) core sequence that is also found in the SIMs in PIAS family E3s and is likely the best-fitted structure for SUMO recognition. This idea led to the identification of additional novel SIM clusters in FLASH/CASP8AP2, C5orf25, and SOBP/JXC1. We suggest that the clustered SIMs in these proteins form distinct SUMO binding domains to recognize diverse forms of protein sumoylation.
Highlights
Sumoylation is recognized by proteins with small ubiquitin-like modifier (SUMO)-interacting motifs
As the consensus sequence of a SUMO-interacting motifs (SIMs) would match to a very large number of proteins, we only aimed for proteins with SIM-like sequences resembling those in RNF4
Considering that all known SIM structures are -strands, we have noticed that SIM2, -3, and -4, but not SIM1 in RNF4, favor a -strand conformation as predicted by PELE, a collection of secondary structure prediction algorithms hosted on Biology Workbench
Summary
Sumoylation is recognized by proteins with SUMO-interacting motifs. Results: SUMO-interacting motifs were identified through a computational string search and validated in SUMO binding assays. Conclusion: Arkadia, FLASH, C5orf, and SOBP all contain clustered SIMs. Significance: These proteins contain distinct SUMO binding structures responsible for the recognition of diverse forms of sumoylation. Like the small ubiquitin-like modifier (SUMO)-targeted ubiquitin ligase RNF4, proteins with clustered SUMO-interacting motifs (SIMs) can be important signal transducers downstream of polysumoylation. Detailed biochemical analysis of the Arkadia SIMs revealed that dominant SIMs in a SIM cluster often contain a pentameric VIDLT ((V/I/L/F/Y)(V/I)DLT) core sequence that is found in the SIMs in PIAS family E3s and is likely the bestfitted structure for SUMO recognition. This idea led to the identification of additional novel SIM clusters in FLASH/ CASP8AP2, C5orf, and SOBP/JXC1. We identified four mammalian proteins, Arkadia/RNF111, FLASH/CASP8AP2, C5orf, and SOBP/JXC1, all containing clustered SIMs
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