Project 5

Research Project 5:
Ubiquitination in regulation of lysosome functions




Project Summary

Ubiquitination is a reversible post-translational modification involved in the regulation of most cellular processes. Modification of a substrate protein with ubiquitin controls either protein turnover by providing proteasomal or lysosomal targeting signals, or cellular signal transduction by regulating protein interactions and activities. We proposed that ubiquitination of lysosome-resident and -associated proteins can play important physiological roles in controlling the various aspects of lysosome function. Critical contributions of the first funding period were the improvement of proteomic technologies and biochemical and cell biological studies on E3 ubiquitin ligases and deubiquitinases (DUBs) that enabled us to reveal novel aspects of ubiquitin signaling in the context of lysosomes. In the framework of the second funding period we plan to expand our studies to further investigate functional roles of ubiquitin regulatory networks at the lysosome and explore if disruption of these networks contributes to the pathogenesis observed in lysosomal storage diseases or bacterial infection. Specifically, our project aims to characterize (i) the functional role of ubiquitination of TRPML1 and LAPTM4B in regulation of lysosome biogenesis and calcium signaling, (ii) the ubiquitinome of lysosomes isolated from Cln3 KI, a model of Batten Disease, and knockout of TMEM55B, a critical regulator of lysosome positioning, (iii) serine ubiquitination of SNARE proteins (STX17 and Snap29) and their impacts on lysosome and associated vesicle fission and fusion events, and (iv) to study the physiological consequences of non-proteolytic ubiquitination of the Ragulator complex. To this end, we will employ various biochemical and cell biological approaches together with state-of-the-art mass spectrometry techniques, as well as fluorescent and super-resolution microscopy. In summary, this collaborative project has a potential to better understand how ubiquitination affects the fate and function of individual lysosomal proteins, which in turn control critical aspects of lysosome function. Further, we expect to gain new insight into the signaling events underlying pathophysiological changes in lysosomal storage diseases and Legionella pneumophila infection.



Mader J, Huber J, Bonn F, Dötsch V, Rogov VV, Bremm A. Oxygen-dependent asparagine hydroxylation of the ubiquitin-associated (UBA) domain in Cezanne regulates ubiquitin binding. J Biol Chem 2020; 295:2160-74.

Akutsu M, Dikic I, Bremm A. Ubiquitin chain diversity at a glance. J Cell Sci 2016; 129:875-80.

Shin D, Mukherjee R, Liu Y, Gonzalez A, Bonn F, Liu Y, Rogov VV, Heinz M, Stolz A, Hummer G, Dötsch V, Luo ZQ, Bhogaraju S, Dikic I. Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Mol Cell 2020; 77:164-79.

Bhogaraju S, Bonn F, Mukherjee R, Adams M, Pfleiderer MM, Galej WP, Matkovic V, Lopez-Mosqueda J, Kalayil S, Shin D, Dikic I. Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin-catalysed glutamylation. Nature 2019; 572:382-6.