Team
Team manager: Henry Yves & Henras Anthony
Presentation
Our research aims to understand how ribosomes are assembled in eukaryotic cells from the nascent ribosomal RNAs (rRNAs) transcribed by RNA polymerases I and III (RNA Pol I and III) and ribosomal proteins (RPs).
A large number of ribosome assembly factors (AFs) play a central role in the assembly and maturation of precursor particles. These assembly and maturation steps involve the progressive folding of the rRNAs and incorporation of RPs to yield the mature ribosomal subunits.
Our niches in the field are:
PROJECT 1 : to study the molecular functions of AFs involved in the least understood stages of this process, namely the early, co-transcriptional events in the nucleolus, that are not amenable to structure determination by cryo-EM approaches;
PROJECT 2 : to investigate how the activity of AFs is regulated by signaling pathways during growth and proliferation, which is a poorly explored area;
PROJECT 3 : to determine how the early-acting AFs, many of which contain intrinsically disordered domains, participate to the organization of the nucleolus in physiological and stress conditions.
Project 1
The catalytic activity of ribosomes is carried by the rRNAs. Hence one the most important aspects of ribosome synthesis is the processing and stepwise folding of rRNA precursors to obtain properly structured and therefore active rRNAs. The general aim of PROJECT 1 is to decipher the molecular events at play during the earliest stages of the production of the large ribosomal subunit, with a particular emphasis on the initial compaction and folding steps of the pre-rRNAs. The first precursor to the large ribosomal subunit, termed the primordial pre-60S particle, is assembled both co- and post-transcriptionnally. During these very ill-defined early assembly steps, pre-rRNA folding and modification are initiated. The primordial pre-60S particle contains more than 30 AFs, several of which belong to RNA helicase families. Moreover, scores of box C/D and box H/ACA snoRNPs transiently associate with the primordial pre-60S particle, in particular the box H/ACA snR37 snoRNP and the box C/D snR190 snoRNP. AFs and snoRNPs contribute, directly and indirectly, to pre-rRNA modification and folding. We are analysing how AFs and snoRNPs interact with the pre-rRNA component of the primordial pre-60S particle and with each other and how they collaborate to promote pre-rRNA modification and folding. We are particularly interested in a complex of five AFs, the Npa1 complex, which contains the Dbp6 helicase, and in its physical and functional interactions with the snR190 snoRNP (Jaafar et al., 2021; Khreiss et al., 2023; Hamze et al., 2025). For our analyses, we are using state of the art approaches, alone or in collaboration, such as in vivo cross-linking (CRAC), affinity purifications (including using antisense RNAs), SHAPE-map (collaboration with Bruno Sargueil, Paris), RiboMethSeq and HydraPsySeq (collaboration with Yuri Motorin, Nancy) and cryo-EM (collaboration with Célia Plisson-Chastang, MCD).
Project 2
Eukaryotic cell physiology is shaped by various extracellular signals such as nutrients, hormones, and growth factors. Key to this signaling are the mammalian Target of Rapamycin (mTOR) and Ras/Mitogen-Activated Protein Kinase (MAPK) pathways, which regulate cellular growth, proliferation, and differentiation. These pathways play crucial roles in protein synthesis, particularly ribosome biogenesis, a highly energy-demanding process, especially in rapidly dividing cells. Ribosome production must be finely tuned to ensure optimal protein translation during favorable growth conditions while avoiding energy waste in restrictive environments. Research over the past decades has established the significant role of mTOR and MAPK pathways in regulating the initial stages of ribosome biogenesis, specifically the transcription by RNA Pol I. In addition to increasing rRNA transcription, mTOR and MAPK pathways drive the translation of mRNAs encoding RPs and AFs in the cytoplasm, thus coordinating the synthesis of ribosomal subunit components and ribosome biogenesis factors. Despite this established coordination, the involvement of mTOR and MAPK in regulating the co- and post-transcriptional steps of ribosome assembly and maturation remains unclear. PROJECT 2 seeks to investigate the contribution of the mTOR and MAPK pathways to the co- and post-transcriptional stages of ribosome biogenesis, utilizing cutting-edge and widely used techniques for analyzing cellular signaling, including phospho mass spectrometry (Cerezo et al., 2021). This work is carried out in collaboration with Philippe Roux’s team at the Institute for Research in Immunology and Cancer (IRIC) in Montreal, Canada. By examining these processes, we aim to bridge the gap between the well-known roles of these pathways in transcription and translation, providing a more complete understanding of their impact on ribosome production in human cells.
Project 3
In silico analyses revealed that the nucleolar proteome is strongly enriched in Intrinsically Disordered Regions (IDRs) present in N- or C-terminal extensions. The IDR is a domain that lacks a fixed or ordered three-dimensional structure and is present in more than 50% of eukaryotic nucleolar proteins. A variety of roles have been attributed to IDRs due to their ability to establish transient and multivalent interactions, but we still have a poor understanding of the role and mechanism of action of these IDRs in the nucleolus and during ribosome biogenesis. Recently, liquid-liquid phase separation (LLPS) has provided a possible mechanism that remains highly controversial. LLPS is driven by low-energy interactions between specific proteins containing intrinsically disordered regions, resulting in the compartmentalization of macromolecules into coexisting subdomains. PROJECT 3 aims to explore the sequence-function paradigm applied to IDRs, one of the major future challenges to be overcome in molecular biology, especially since Alpha-Fold predictions are not applicable to IDRs. By combining cell biology, electronic and photonic microscopy as well as genetic tools in budding yeast, we aim to identify the molecular grammar of IDRs that contribute both to the regulation of ribosome biogenesis and to the organization of the nucleolus, the largest membrane-less organelle in eukaryotes. Our work has already led to the discovery of a novel regulatory system in eukaryotes, the Ribosome Assembly Stress Response (RASTR), which rapidly adjusts chaperone and RP production in response to perturbations in ribosome biogenesis (Albert et al., 2019). We also recently uncovered the role of an extremely abundant and largely overlooked nucleolar lysine-rich IDR, called the KKE/D domain involved in both rRNA modification and nucleolar compaction during stress (Dominique et al., 2024).
Team members
– Hussein Hamze, Mariam Jaafar, Ali Khreiss, Carine Dominique, Jessie Bourdeaux, Paulo Espirito Santo, Alfonso Méndez-Godoy, Dieter Kressler, Odile Humbert, Célia Plisson-Chastang, Benjamin Albert, Anthony K. Henras, Yves Henry. “The snoRNP chaperone snR190 and the Npa1 complex form a macromomecular assembly required for 60S ribosomal subunit maturation”. Nucleic Acids Res 2025, 53. doi: 10.1093/nar/gkaf134.
– Carine Dominique, Nana Kadidia Maiga, Alfonso Méndez-Godoy, Benjamin Pillet, Hussein Hamze, Isabelle Léger-Silvestre, Yves Henry, Virginie Marchand, Valdir Gomes Neto, Christophe Dez, Yuri Motorin, Dieter Kressler, Olivier Gadal, Anthony K. Henras, Benjamin Albert. “The dual life of disordered lysine-rich domains of snoRNP in rRNA modification and nucleolar compaction”. Nat Commun 2024, 15:9415. doi: 10.1038/s41467-024-53805-1.
– Ali Khreiss, Régine Capeyrou, Simon Lebaron, Benjamin Albert, Katherine E Bohnsack, Markus T Bohnsack, Yves Henry, Anthony K Henras, Odile Humbert. “The DEAD-box protein Dbp6 is an ATPase and RNA annealase interacting with the peptidyl transferase center (PTC) of the ribosome”. Nucleic Acids Res 2023, 51:744-764. doi: 10.1093/nar/gkac1196.
– Mariam Jaafar, Julia Contreras, Carine Dominique, Sara Martín-Villanueva, Régine Capeyrou, Patrice Vitali, Olga Rodríguez-Galán, Carmen Velasco, Odile Humbert, Nicholas J Watkins, Eduardo Villalobo, Katherine E Bohnsack, Markus T Bohnsack, Yves Henry, Raghida Abou Merhi, Jesús de la Cruz, Anthony K Henras. “Association of snR190 snoRNA chaperone with early pre-60S particles is regulated by the RNA helicase Dbp7 in yeast”. Nat Commun 2021, 12:6153. doi: 10.1038/s41467-021-26207-w.
– Emilie L Cerezo, Thibault Houles, Oriane Lié, Marie-Kerguelen Sarthou, Charlotte Audoynaud, Geneviève Lavoie, Maral Halladjian, Sylvain Cantaloube, Carine Froment, Odile Burlet-Schiltz, Yves Henry, Philippe P Roux, Anthony K Henras, Yves Romeo. “RIOK2 phosphorylation by RSK promotes synthesis of the human small ribosomal subunit”. PLoS Genet 2021, 17(6):e1009583. doi: 10.1371/journal.pgen.1009583.
– Saïda Mouffok, Régine Capeyrou, Kamila Belhabich-Baumas, Clément Joret, Anthony K Henras, Odile Humbert, Yves Henry. “The G-patch activators Pfa1 and PINX1 exhibit different modes of interaction with the Prp43 RNA helicase”. RNA Biol 2021, 18:510-522. doi: 10.1080/15476286.2020.1818458.
– Benjamin Albert, Isabelle C Kos-Braun, Anthony K Henras, Christophe Dez, Maria Paula Rueda, Xu Zhang, Olivier Gadal, Martin Kos, David Shore. “A ribosome assembly stress response regulates transcription to maintain proteome homeostasis”. eLife 2019. doi: 10.7554/eLife.45002.
Affiliation
