Biology subjects

Favre, S.

Publications and source records attributed to Favre, S..

8 recordsLinked to original sources

bioRxiv2026

A nucleolar assembly module integrates an ancestral isoaspartylase to safeguard ribosome biogenesis

Eukaryotes inherited the core ribosome biogenesis apparatus from archaea. However, nucleocytoplasmic compartmentalisation and expansion to >200 assembly factors created the challenge of integrating this ancestral machinery into a complex maturation programme. One solution is the formation of transient modules in which newly acquired assembly factors support deeply conserved components. Here, we identify such a module, centred on the ancestral isoaspartylase Fap7, which couples the modification of the ribosomal protein uS11 to its incorporation into pre-ribosomes. Fap7 partners with Krr1 to capture uS11, forming an early checkpoint in which uS11 loading licenses Kri1 engagement and assembly progression. Loss of uS11 modification triggers a late checkpoint, preventing aberrant pre-ribosomes from acquiring translational competence. Integrative structure-function studies reveal how the ancestral isoaspartylase is embedded within a conserved eukaryotic assembly-factor network to safeguard the timing, order, and fidelity of ribosome production.

biochemistry↗

bioRxiv2026

A bifunctional H/ACA snoRNP mediates both pseudouridylation and rRNA scaffolding during ribosome assembly

The early steps of eukaryotic large ribosomal subunit assembly remain poorly understood due to the structural flexibility of pre-60S intermediates, whose rRNA is extensively modified by small nucleolar RNPs (snoRNPs). Some snoRNPs, however, lack any modification function and instead scaffold ribosome assembly through largely unknown mechanisms. Here, we show that the H/ACA snoRNP snR37 integrates both modifying and scaffolding roles. Biochemical and structural analyses reveal a canonical H/ACA core that pseudouridylates a conserved uridine in the A site of the peptidyl transferase center, the catalytic heart of the 60S subunit. Additional RNA helices recruit non-core proteins, the Upa1-Upa2 heterodimer and Rbp95, which mediate stable snR37 association with pre-60S complexes. These proteins cooperate with the Npa1 rRNA chaperone complex to link four rRNA domains, thereby structurally organizing early pre-60S intermediates and promoting proper formation of the PTC. This dual organization establishes a paradigm for snoRNPs combining rRNA modification and scaffolding functions.

biochemistry↗

bioRxiv2025

Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1

In eukaryotes, most newly synthesized ribosomal proteins (r-proteins) need to rapidly and safely get into the nucleus to reach their assembly site on pre-ribosomal particles. However, only for few r-proteins tailored support mechanisms involving so-called dedicated chaperones could so far be revealed. Here, with the primary aim of identifying novel dedicated chaperones, we performed TurboID-based proximity labelling with all 46 large subunit r-proteins of Saccharomyces cerevisiae, which unveiled the fungi-specific Acl1 and the conserved Bcl1 as candidate dedicated chaperones of Rpl1. We show that the functionally cooperating Acl1 and Bcl1 both directly interact with Rpl1, form a trimeric Acl1-Rpl1-Bcl1 complex, and enable the nuclear import of Rpl1. Moreover, our crystal structure of the minimal Acl1-Rpl1 complex reveals how Acl1s ankyrin repeat domain shields a positively charged rRNA-binding surface of Rpl1. Our proximity labelling approach also permitted to establish novel interactions between four r-proteins and distinct importins and to illuminate r-protein neighbourhoods on successive pre-60S particles. Additionally, reciprocal proximity labelling with the known dedicated chaperones indicates that almost all appear to be transiently associated with pre-ribosomal particles. Our study provides for the first time comprehensive insight into the physical proximities of large subunit r-proteins along their entire life cycle. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/677003v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1167c6corg.highwire.dtl.DTLVardef@1429c23org.highwire.dtl.DTLVardef@18f7ecorg.highwire.dtl.DTLVardef@13ccdfb_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT C_FIG

biochemistry↗

bioRxiv2025

Sni445 recruits box C/D snoRNPs snR4 and snR45 to guide ribosomal RNA acetylation by Kre33

Eukaryotic ribosome synthesis is a highly complex, multistep process that is best characterized in the yeast Saccharomyces cerevisiae. It is orchestrated by over 200 ribosome assembly factors and 75 small nucleolar ribonucleoproteins (snoRNPs), which guide site-specific chemical modifications of precursor ribosomal RNA (pre-rRNA). While canonical box C/D snoRNPs direct 2-O-methylation, the atypical box C/D snoRNPs snR4 and snR45 mediate acetylation of 18S rRNA residues C1280 and C1773, respectively, catalyzed by the acetyltransferase Kre33. Here, we identify and characterize Ynl050c/Sni445 as a novel ribosome assembly factor and previously unrecognized auxiliary component of the snR4 and snR45 box C/D snoRNPs. Sni445 associates with snR4 and snR45 in their free form and is required for their stable incorporation into 90S pre-ribosomes. Genetic interactions link Sni445 and the snR4 and snR45 snoRNAs to ribosomal proteins Rps20 (uS10) and Rps14 (uS11), which are positioned near the respective acetylation sites in the 40S subunit. Moreover, Sni445 physically interacts with Kre33 within the 90S pre-ribosome, and its absence abolishes acetylation of C1280 and C1773. Our findings suggest that Sni445 facilitates the recruitment of snR4 and snR45 snoRNPs to 90S particles and might promote their interaction with Kre33, thereby enabling the site-specific acetylation of 18S rRNA by Kre33.

molecular biology↗

bioRxiv2025

Targeting CXCR4-expressing TAMs in muscle-invasive bladder cancer to enhance tumor control after immunotherapy

Bladder cancer (BC) is a prevalent malignancy with poor prognosis in advanced stages. While immune checkpoint blockade has revolutionized immunotherapy, its efficacy remains limited for most advanced BC patients. The detailed characterization of BCs tumor microenvironment (TME) is a prerequisite to understand these mechanisms of resistance and to develop new therapeutic strategies. In this study, we used a genetically engineered BC mouse model resistant to anti-PD1 treatment, and BC patient samples, to investigate the evolution of tumor-associated macrophages (TAMs) during BC progression. We identified a subset of pro-tumor TAMs expressing CXCR4, predominantly found in advanced stages of BC-bearing mice and in half of muscle-invasive BC patients from the studied cohort. Interestingly, CXCR4+ TAM-rich regions were associated with CD8 T cell-excluded areas in both mice and patients. Administration of a small molecule CXCR4 inhibitor significantly reduced the number of pro-tumor TAMs within the tumor and markedly prolonged mouse survival. Incorporating this inhibitor into a tri-immunotherapy regimen further enhanced survival, highlighting the potential of targeting multiple pathways to strongly enhance anti-tumor effects and offering new hope for improving immunotherapy in advanced BC.

immunology↗

bioRxiv2023

The ULK1 effector BAG2 regulates autophagy initiation by modulating AMBRA1 localization

Canonical autophagy is regulated by ULK1, the most proximal protein kinase specifically regulating autophagy initiation. To gain new insights into functions of the ULK1 holo-complex in autophagy regulation, we generated a deep ULK1 complex interactome by combining affinity purification- and proximity labelling-mass spectrometry of all four ULK1 complex members: ULK1, ATG13, ATG101 and RB1CC1/FIP200. Under starvation conditions, the ULK1 complex interacts with several protein and lipid kinases and phosphatases implying the formation of a signalosome. Interestingly, also several selective autophagy receptors interact with ULK1 indicating the activation of selective autophagy pathways by nutrient starvation. One effector of the ULK1 complex is the HSC/HSP70 co-chaperone BAG2, which regulates the subcellular localization of the VPS34 lipid kinase complex member AMBRA1. Depending on the nutritional status, BAG2 has opposing roles. In growth promoting conditions, the unphosphorylated form of BAG2 sequesters AMBRA1, attenuating autophagy induction. In starvation conditions, ULK1 phosphorylates BAG2 on Ser31, supporting its recruitment to the ER membrane and positively affecting autophagy flux.

cell biology↗

bioRxiv2021

Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis

The biogenesis of eukaryotic ribosomes involves the ordered assembly of around 80 ribosomal proteins. Supplying equimolar amounts of assembly-competent ribosomal proteins is complicated by their aggregation propensity and the spatial separation of their location of synthesis and pre-ribosome incorporation. Recent evidence has highlighted that dedicated chaperones protect individual, unassembled ribosomal proteins on their path to the pre-ribosomal assembly site. Here, we show that the co-translational recognition of Rpl3 and Rpl4 by their respective dedicated chaperone, Rrb1 or Acl4, prevents the degradation of the encoding RPL3 and RPL4 mRNAs in the yeast Saccharomyces cerevisiae. In both cases, negative regulation of mRNA levels occurs when the availability of the dedicated chaperone is limited and the nascent ribosomal protein is instead accessible to a regulatory machinery consisting of the nascent-polypeptide associated complex and the Caf130-associated Ccr4-Not complex. Notably, deregulated expression of Rpl3 and Rpl4 leads to their massive aggregation and a perturbation of overall proteostasis in cells lacking the E3 ubiquitin ligase Tom1. Taken together, we have uncovered an unprecedented regulatory mechanism that adjusts the de novo synthesis of Rpl3 and Rpl4 to their actual consumption during ribosome assembly and, thereby, protects cells from the potentially detrimental effects of their surplus production.

cell biology↗

bioRxiv2018

Attenuation of chronic antiviral T cell responses through constitutive COX2-dependent prostanoid synthesis by lymph node fibroblasts

Fibroblastic reticular cells (FRC) of lymphoid T zones actively promote T cell trafficking, homeostasis and expansion, but can also attenuate excessive T cell responses via inducible nitric oxide and constitutive prostanoid release. It has remained unclear under which conditions these FRC-derived mediators can dampen T cell responses and whether this occurs in vivo. Here we confirm that murine lymph node FRC produce prostaglandin E2 (PGE2) in a cyclooxygenase-2 (COX2)-dependent and inflammation-independent fashion. We show that this COX2/PGE2 pathway is active during both strong and weak T cell responses, in contrast to nitric oxide which only comes into play during strong T cell responses. In chronic infections in vivo, PGE2-receptor signaling in virus-specific CD8 T cells was shown by others to suppress T cell survival and function. Using CCL19cre x COX2flox/flox mice we now identify CCL19cre+ FRC as the critical source of this COX2-dependent suppressive factor, suggesting PGE2-expressing FRC within lymphoid tissues are an interesting therapeutic target to improve T cell mediated pathogen control during chronic infection.

immunology↗