Final Report Summary - UBSPECIFIC (Specificity in the ubiquitin system)
Most proteins are altered after their generation, and these so-called post-translational modifications (PTMs) change a proteins half-life, localisation, activity and function. Perhaps the most complex modification exists when proteins are ubiquitinated. Ubiquitin is a small protein itself, and as such can get further modified - polyubiquitin chains exist, and ubiquitin is also modified by other PTMs, such as phosphorylation and acetylation. It is now clear that a huge variety of ubiquitination events exist, and are exploited by cells to regulate their intrinsic processes.
The Komander lab aims to unravel the complexity in ubiquitin signalling, and to characterise the specificity in the associated proteins and enzymes. We approach the system from the modification itself, and try to work backwards with the goal to eventually associate new ubiquitin signals with the cellular pathways they regulate. For this we study the assembly enzymes including E2 enzymes and
We have made considerable progress towards this goal. We have contributed a large number of basic insights, in which we have identified E3 ligases, deubiquitinases and ubiquitin receptors that were highly specific in their activity to target just one or a subset of ubiquitin signals. As such, we have contributed methods and protocols that now allow us to study novel ubiquitin modification, such as K6- or K33-linked ubiquitin chains, for the first time.
Our work has also unveiled novel enzymes in proteins that were not known to be enzymes, such as family of unknown function (FAM) 105b, which we renamed OTULIN. OTULIN is a deubiquitinase for Met1-linked ‘linear’ ubiquitin chains, a chain type highly important in inflammatory signalling. With structural work, we were able to understand in molecular detail how OTULIN achieved its specificity, unravelling a mechanisms of ubiquitin-assisted catalysis, and starting to link it to inflammatory signalling cascades (Keusehotten et al, Cell 2013). Biochemical and cell-biological work associated OTULIN with the Linear ubiquitin chain assembly complex and also revealed how this complex is regulated by an interplay of interacting deubiquitinases (Elliott et al, Mol Cell 2014, 2016). Physiological studies in mice and men showed the importance of OTULIN for the immune system’s health in animals, and even identified a human genetic disease, in which mutations in OTULIN lead to potentially lethal autoinflammation. We named this new disease OTULIN related autoinflammatory syndrome (ORAS)(Damgaard et al, Cell 2016).
In the last few years, we have focussed our efforts to understand molecularly the cellular process of mitophagy, which we and others have revealed in recent works to be regulated by multiple types of ubiquitin chain types including e.g. unstudied K6-linked chains, as well as by phosphorylated ubiquitin. We have contributed molecular and biochemical characterisation of phospho-ubiquitin (Wauer et al, EMBO J 2015, Gladkova et al, EMBO J 2017), Parkin (Wauer et al, EMBO J 2013, Nature 2015), USP30 (Gersch et al, NSMB 2017) and ubiquitin phosphorylation by PINK1 (Schubert et al, Nature 2017), and contributed in our work a large number of functional insights and tools, such as affinity tools for Lys6-linked chains (Michel et al, Mol Cell 2017, Gersch et al NSMB 2017).
It is clear that the PINK1 generated Ser65-phosphorylated ubiquitin is just the tip of an iceberg of novel and potentially important ubiquitin modifications. A deeper understanding of these will emerge from identification of cellular contexts, the associated regulatory machinery, and identification of new ubiquitin receptors. In the next decade, we will focus on gaining these insights, which should eventually lead to a deeper appreciation of the ubiquitin code and its immense power in cellular regulation.
The Komander lab aims to unravel the complexity in ubiquitin signalling, and to characterise the specificity in the associated proteins and enzymes. We approach the system from the modification itself, and try to work backwards with the goal to eventually associate new ubiquitin signals with the cellular pathways they regulate. For this we study the assembly enzymes including E2 enzymes and
We have made considerable progress towards this goal. We have contributed a large number of basic insights, in which we have identified E3 ligases, deubiquitinases and ubiquitin receptors that were highly specific in their activity to target just one or a subset of ubiquitin signals. As such, we have contributed methods and protocols that now allow us to study novel ubiquitin modification, such as K6- or K33-linked ubiquitin chains, for the first time.
Our work has also unveiled novel enzymes in proteins that were not known to be enzymes, such as family of unknown function (FAM) 105b, which we renamed OTULIN. OTULIN is a deubiquitinase for Met1-linked ‘linear’ ubiquitin chains, a chain type highly important in inflammatory signalling. With structural work, we were able to understand in molecular detail how OTULIN achieved its specificity, unravelling a mechanisms of ubiquitin-assisted catalysis, and starting to link it to inflammatory signalling cascades (Keusehotten et al, Cell 2013). Biochemical and cell-biological work associated OTULIN with the Linear ubiquitin chain assembly complex and also revealed how this complex is regulated by an interplay of interacting deubiquitinases (Elliott et al, Mol Cell 2014, 2016). Physiological studies in mice and men showed the importance of OTULIN for the immune system’s health in animals, and even identified a human genetic disease, in which mutations in OTULIN lead to potentially lethal autoinflammation. We named this new disease OTULIN related autoinflammatory syndrome (ORAS)(Damgaard et al, Cell 2016).
In the last few years, we have focussed our efforts to understand molecularly the cellular process of mitophagy, which we and others have revealed in recent works to be regulated by multiple types of ubiquitin chain types including e.g. unstudied K6-linked chains, as well as by phosphorylated ubiquitin. We have contributed molecular and biochemical characterisation of phospho-ubiquitin (Wauer et al, EMBO J 2015, Gladkova et al, EMBO J 2017), Parkin (Wauer et al, EMBO J 2013, Nature 2015), USP30 (Gersch et al, NSMB 2017) and ubiquitin phosphorylation by PINK1 (Schubert et al, Nature 2017), and contributed in our work a large number of functional insights and tools, such as affinity tools for Lys6-linked chains (Michel et al, Mol Cell 2017, Gersch et al NSMB 2017).
It is clear that the PINK1 generated Ser65-phosphorylated ubiquitin is just the tip of an iceberg of novel and potentially important ubiquitin modifications. A deeper understanding of these will emerge from identification of cellular contexts, the associated regulatory machinery, and identification of new ubiquitin receptors. In the next decade, we will focus on gaining these insights, which should eventually lead to a deeper appreciation of the ubiquitin code and its immense power in cellular regulation.