Switch Contrast

Trentini Lab

Our Research

Virtually all cellular functions are executed by proteins. The synthesis of a functional protein encompasses many complex processes: translation, folding into an appropriate three-dimensional structure, (in many cases) assembly into a macromolecular complex, and localization to a specific cellular compartment. Mistakes can occur during any of these steps, resulting in a myriad of different defective protein species. Moreover, many proteins are susceptible to damage by endogenous and environmental stresses, given the dynamic and often unstable nature of protein structures. It is therefore no wonder that roughly 10% of the proteome mass is dedicated to the life cycle of proteins. The proteostasis network is estimated to comprise ∼2,000 factors that act in concert to maintain the fitness of the proteome, including molecular chaperones and their regulatory co-factors, quality-control factors such as E3 ubiquitin ligases, and degradation machineries such as the ubiquitin–proteasome and autophagy–lysosome systems. Importantly, maintaining the correct protein fold is important not only to avoid loss-of-function effects, but also the formation of potentially toxic protein aggregates that represent a hallmark of many aging-associated neurodegenerative diseases. 

Our group is broadly interested in the following questions:

  • How do protein quality control players distinguish between functional and defective proteins, despite the huge diversity of the proteome?
  • Protein degradation is performed by hundreds of different pathways belonging to the ubiquitin–proteasome or autophagy–lysosome systems. How is the division of labor achieved, and how redundant are these pathways?
  • How does proteotoxic stress and/or loss of fidelity in the DNA>RNA>Protein flow of information affect the fitness of the proteome? What are the adaptive mechanisms engaged in specific proteostasis perturbations?

Topic: Ribosome-associated quality control

Ribosome-associated quality control (RQC) is a conserved eukaryotic pathway that removes nascent polypeptide chains from ribosomes that stalled during translation. The key component of this pathway, the E3 Ubiquitin ligase Listerin/Ltn1, first came into attention when a mouse genetic screen showed that a partial loss-of-function mutation in the LTN1 gene causes a profound neurodegenerative phenotype. Since then, considerable advances been made towards mechanistically characterizing the components of the RQC pathway. Interestingly, it has been shown that stalled nascent chains can be extended with non-templated c-terminal Alanine and Threonine residues (CAT tails). These extensions have been suggested to promote stalled nascent chain degradation by two mechanisms: increasing chances of Listerin-mediated ubiquitination by exposing Lysine residues initially buried in the ribosomal exit tunnel, or by assuming a “degron” function, i.e., marking proteins for proteasomal degradation once they are released from the ribosome. However, CAT tails can also self-associate and form insoluble aggregates that can disrupt the proteostasis network, highlighting the importance of proper clearance of stalled nascent chains.  

Most insights into RQC came from the analysis of artificial model substrates containing specific ribosomal-stalling sequences. The most potent stalling sequence characterized so far consists in long stretches of AAA codons (circa 20 or more), which encode for poly(Lys) chains. Translation of these sequence can naturally occur when the mRNA’s poly(A) tail is erroneously inserted inside the coding sequence, rather than at the 3’ UTR. Apart from this situation, little is known about the natural causes of ribosomal stalling and RQC-mediated degradation. 

Some of the questions we want to address:

  • What are the major triggers of RQC-mediated degradation in vivo?
  • In which situations RQC becomes essential?
  • How does RQC communicate with mRNA and other protein quality control pathways?

? For further info check out our review paper "Ending a bad start: Triggers and mechanisms of co-translational protein degradation"

Multi-pass transmembrane proteins are a new class of RQC substrates

Figure, RQC

In a previous study, we obtained the first dataset of endogenous targets of the RQC pathway in human cells via a serendipitous method: using MHC-I antigen presentation as a proxy for protein degradation (Trentini et al. PNAS 2020). Unexpectedly, from the circa 100 substrates we identified as constitutive targets of RQC in HeLa cells, 5 proteins belonged to the SLC family of transmembrane transporters. Closer inspection of our immunopeptidomics dataset revealed that proteins containing 10 or more transmembrane segments are more likely to be targeted by the RQC than soluble proteins of a similar size. Of notice, this tendency was not observed for secretory, ER-resident, or mono-pass transmembrane proteins. This suggests that it is the intrinsic challenges of synthesizing transmembrane segments that renders these proteins prone to RQC-mediated degradation, rather than their site of translation at the ER surface.

We are currently investigating what are the causes and quality control mechanisms involved in RQC-mediated degradation of complex transmembrane proteins. Key questions include:

  • What are the causes of terminal ribosomal stalling during transmembrane protein synthesis?
  • Can defective membrane insertase complexes impair ribosome elongation?
  • Does co-translational protein folding influence RQC-mediated protein quality control?
  • Is there an interplay between regulators of translation dynamics and RQC activation?
  • How does proteotoxic ER stress impact the incidence of RQC activation?
  • What are the quality control factors involved in RQC recruitment and degradation of transmembrane proteins?

? For further reading check out our pre-print: “Principles of ribosome-associated protein quality control during the synthesis of CFTR”

Research environment

We are based at the Center for Molecular Medicine Cologne (CMMC), a central autonomous research and educational center located at the heart of the Life Science Campus at the University of Cologne (UoC), Germany. The institute provides administrative infrastructure, modern laboratories, as well as access to a number of core facilities (https://www.cmmc-uni-koeln.de/core-facilities/overview) that offer not only state-of-the-art equipment, but also training and support with data analysis. Research on campus encompasses a wide range of molecular, genetic and "omics" approaches using various model organisms and unique disease models. Therefore, our team has all the tools and the support needed to pursue any scientific question that becomes of interest. Moreover, one of CMMC’s strengths is to bring together research scientists and clinicians in order to foster interdisciplinary collaboration from the laboratory to the clinic, creating unique opportunities for translational research.

The CMMC building is located within walking reach to many internationally recognized institutes, such as the Cologne Center for Genomics, Max Planck Institute for Metabolism Research, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD), and the Max-Planck Institute for Biology of Ageing. Notably, Cologne is one of the world-leading places for aging research. Since our main topic of investigation – proteostasis – represents one of the pillars of aging, we are well integrated in this environment. This means not only numerous possibilities for collaboration, but also a thriving scientific environment with an abundant offer of lectures in our interest range.

PhD students in our lab will have the opportunity to join a structured graduate program, such as the Interdisciplinary Program Molecular Medicine (IPMM) and the Graduate School for Biological Sciences (GsfBS). These programs foster career development through scientific and soft skills training, advanced method courses, networking opportunities, systematic guidance, and administrative support. We are happy to provide our students with a solid platform to advance their careers.

Last but not least, Cologne is a vibrant, cosmopolitan city located at the heart of Europe. It is the fourth-most populous city in Germany, having more than 30% of its residents coming from abroad. Moreover, Cologne has numerous cultural opportunities, strong visual arts and cinema, theatre, opera, orchestra, jazz and live music scene. It is truly a fun-loving city, epitomized by its world famous Carnival festivities. Our English-speaking lab is eager to get into the spirit of the city and to welcome scientists from any nationality.

For further information, please visit www.cmmc-uni-koeln.de