RIBOSOME AND RNA HOMEOSTASIS
Sébastien Ferreira-Cerca's team aims to characterize the conserved and specific molecular principles involved in RNA metabolism across the different domains of life and is particularly interested in those involved in the ribosome life cycle.
To this end, we use a combination of approaches, such as genetic, biochemical, molecular, cellular and structural biology approaches, as well as a wide range of model organisms, including the model archaea: H. volcanii and S. acidocaldarius.
Our research is structured around 3 main axes:
Axis I: Conserved and specific molecular principles involved in the ribosome life cycle
Ribosomes are large, universally conserved ribonucleoprotein particles that ensure protein synthesis in every cell. The universal conservation of ribosome function and structure provides a unique paradigm to understand how RNP assembly mechanisms and functions have evolved. Our research aims to contribute to a better characterization of the conserved and specific molecular principles involved in the ribosome life cycle and to define the key principles of archaeal ribosome homeostasis.
Accordingly, we study ribosome synthesis, assembly, function, degradation, the subcellular organization of these processes, and the underlying regulatory mechanisms that control them. Furthermore, to better understand the functional conservation of these molecular principles, we use a functional comparative analysis between different archaeal model organisms such as H. volcanii and S. acidocaldarius (e.g., Knüppel et al., 2018; Jüttner et al., 2020; Knüppel et al., 2021), but we also exploit other model organisms across the tree of life, such as E. coli (e.g., Knüppel et al., 2021) and/or S. cerevisiae (e.g., Knüppel et al., 2018).
In recent years, our studies have provided additional in vivo insights into the ribosomal RNA maturation process in archaea (Grünberger et al., 2022 BioRxiv) and into the biogenesis of archaeal small ribosomal subunits. Notably, our work has provided functional evidence for similarities between late steps of archaeal and eukaryotic small ribosomal subunit biogenesis in vivo (Knüppel et al., 2018), as well as functional specificities of archaeal ribosome biogenesis (Jüttner et al., 2020; Schwarz et al., 2020; Knüppel et al., 2021; Vayssières et al., 2023).
Axis II: Defining the full spectrum of RNA-protein and protein-protein interactions in archaea
Systematic identification of RNA-binding proteins and protein-protein interactions, as well as determination of their respective functional contribution to cellular metabolism have been applied in bacterial and eukaryotic model organisms. However, such a comprehensive view has not been obtained for any archaeal organism.
Using RNA interactome capture strategies and systematic analysis of protein-protein interactions, we aim to contribute to:
1) defining the full range of archaeal protein/RNA and protein-protein interactions and their dynamics,
2) functionally characterizing conserved and specific features of archaeal RNA metabolism, and
3) exploring structural and functional innovations of archaeal RNPs.
Axis III: Expanding the Archaea Toolbox
Partly due to their late discovery and specific growth conditions, many key methodological tools for gene expression analysis have not been applied or adapted to the study of archaeal biology. To fill some of these technological gaps, we are continuously adapting various methodologies facilitating the analysis of (r)RNA metabolism and gene expression in archaea.
In recent years, we have optimized the use of nucleotide and amino acid analogues (Knüppel et al., 2017; Knüppel et al., 2021, Braun et al., 2022, Kern & Ferreira-Cerca 2022) as well as in vivo RNA structure analysis using SHAPE reagents (Knüppel et al., 2020; Knüppel et al., 2021), in the model archaea Haloferax volcanii and/or Sulfolobus acidocaldarius.
Recently, we have also explored Nanopore sequencing technology to analyze ribosomal RNA maturation and modifications (Grünberger et al., 2023).
