Our lab aims at understanding how protein sequences can become toxic upon mutation.
We are particularly interested in amino acid sequences that can adopt different conformations and undergo a process of self-assembly which results in distinct physical states.
The concept of protein aggregation has mainly been associated to the formation of insoluble amyloid fibrils, best known for their implication in the pathogenesis of a number of neurodegenerative conditions, such as Parkinson’s disease or Amyotrophic Lateral Sclerosis. However, examples of functional amyloid are also widespread, especially across bacteria and fungi. Recently, it has become clear that proteins can assemble also into a more dynamic and reversible state through a process of liquid de-mixing.
Liquid condensates are frequently formed by proteins containing intrinsically disordered regions.The self-assembly of these protein regions results in a distinct liquid phase and it’s key to the formation of many membrane-less organelles, hence contributing to the organisation of the intracellular space. However, also for proteins undergoing liquid de-mixing, the balance between function and dysfunction is far from clear. It is also unknown if, in vivo, liquid de-mixed states are precursors of insoluble amyloid-like states, and to which extent proteins are structured once in the liquid state.
How we do it
In order to understand how mutations affect these delicate equilibria and to elucidate when and why a sequence becomes toxic for the cell, our lab integrates experimental and computational approaches in different model systems. Recently, we developed a Deep Mutational Scanning (DMS) strategy that allows to quantify the toxicity of thousands of mutations in a disordered protein sequence . The idea behind this type of approach is that by portraying the full landscape of the effects of mutations in a specific protein domain we can reach a more systematic and comprehensive understanding of the determinants of toxicity. Besides developing high-throughput methods to measure the toxicity of thousands of mutations in parallel, we are also interested in developing similar strategies to measure in vivo the effect of mutations on the physical state the proteins acquire upon mutation (diffuse, liquid de-mixed, insoluble) and on their ability to nucleate amyloid fibrils. Overall, we aim at generating exhaustive datasets that will give insights into the specific conformations and mechanisms leading to toxicity.
We focus on classical amyloids, such as the amyloid-beta peptide, the main component of the plaques found in Alzheimer’s disease patients, but also on functional yeast prions and on a less characterised part of the human proteome: prion-like domains. Just like most disordered protein regions, prion-like domains are particularly difficult to study in vitro. In this perspective, in vivo approaches such as the ones we develop, can provide a unique opportunity to investigate these sequences in a systematic way.
Map of the effect of mutations on toxicity of the TDP-43 Prion-like Domain.
Average effect of mutations on nucleation, visualised on the cross-section of an amyloid-beta fibril (PDB:5KK3)
|MUTANOMICS · Determining in vivo protein structures and understanding genetic interactions using deep mutagenesis (2021-2025)||European Commission / Proyectos I+D||Benedetta Bolognesi|
|Poly-STOP · Developing modulators of protein aggregation in polyglutamine diseases by deep mutational scanning (2021-2022)||BIST · Barcelona Institute of Science and Technology||Benedetta Bolognesi|
|DeepAmyloids · Massively parallel mutagenesis to understand, predict and prevent amyloid nucleation in neurodegenerative diseases (2021-2024)||Obra Social La Caixa||Benedetta Bolognesi|
|PRIOMUT · Escaneado exhaustivo de mutaciones en un dominio priónico para entender la toxicidad inducida por proteínas (2019-2021)||MICIU / Retos investigación: Proyectos I+D||Benedetta Bolognesi|
- Thermo MaxQ 8000
- Ben Lehner
- Sofia Giorgetti
University of Pavia, Italy
- Xavier Salvatella
- Priyanka Narayan
NIDDK-NIH, Washington D.C
- Broder Schmidt
University of Stanford
The start of the autumn semester finds a new face in IBEC’s research community, with Dr. Benedetta Bolognesi joining the institute as junior group leader. Benedetta has come from Barcelona’s Centre for Genomic Regulation, where she was a postdoc in Ben Lehner’s and Gian Gaetano Tartaglia’s groups. At IBEC she will launch and lead the Protein Phase Transitions in Health and Disease group. During her postdoc, Benedetta focused on why certain genes are toxic when over-expressed. She found that, in some cases, they cause toxicity because the proteins they code for end up forming a different liquid phase in the cytoplasm.