Biology subjects

Ricci, E.

Publications and source records attributed to Ricci, E..

7 recordsLinked to original sources

bioRxiv2026

Viral Infections Drive Functional Remodeling of Ribosome-Associated Proteins

Viruses hijack host ribosomes to synthesize their proteins and have evolved various strategies to manipulate translation, including the association of numerous non-ribosomal proteins, known as ribosome-associated proteins (RAPs), with the core ribosome. However, current methods of capturing RAPs that associate transiently and/or in small amounts with ribosomes are suboptimal. To address this issue, we developed an enhanced ribosome affinity purification (eRAP) method that enables the capture of over 500 previously unreported RAPs. Using eRAP, we investigated whether the composition of ribosomes changes during infection by two very different viruses: herpes simplex virus 1 (HSV-1) and Sindbis virus (SINV). Our results revealed that viral infection does not substantially alter the composition of core ribosomes but does drive extensive remodeling of RAPs in a virus-specific manner. Functional analyses with SINV showed that several of these RAPs are critical for viral propagation. Additionally, we discovered that the RAP ASCC3 plays a novel role in promoting the expression of secretory proteins, including viral glycoproteins. This occurs independently of ASCC3s canonical function of rescuing ribosome collisions. Together, our findings establish the ribosome as a dynamic regulatory hub that undergoes remodeling to achieve virus-specific translational output, highlighting the functional significance of ribosomal heterogeneity.

molecular biology↗

bioRxiv2025

Enhancement of Prednisolone efficacy and safety in Duchenne muscular dystrophy via neutrophil elastase inhibition

Duchenne muscular dystrophy (DMD) is a genetic disorder characterized by muscle wasting, and leading to premature death. The pathogenesis of DMD is complex. It is triggered by loss of the cytoskeletal protein dystrophin, which causes muscle fiber instability and damage, followed by chronic inflammation and fibrotic replacement of damaged muscle tissue. Here we investigated the hypothesis that inhibition of neutrophil elastase, which is increased in dystrophic mice and impairs myogenesis, could provide a therapeutic effect in DMD. While neutrophil elastase inhibition, via the orally bioavailable compound Alvelestat, enhances myogenesis both in vitro and in vivo and reduces muscle damage and fibrosis, it does not produce a significant beneficial effect on the functional outcomes. However, when co- administered with the standard of care Prednisolone, Alvelestat dramatically enhances Prednisolone efficacy in a mouse model of DMD. In key functional tests, the performance of mice co-dosed with Alvelestat and Prednisolone is almost three times better than that of mice treated with Prednisolone alone. Additionally, co-administration of Alvelestat and Prednisolone reduces Prednisolones negative effects on muscle mass and resistance to fatigue. These findings are consistent with the finding that Prednisolone induces neutrophil elastase expression in patients affected by DMD. Our data support a beneficial role for neutrophil elastase inhibition in a mouse model of DMD that is also treated with Prednisolone, suggesting that a combinatorial therapy for DMD including a corticosteroid and a neutrophil elastase inhibitor could be trialed in humans. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/640472v3_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@f20853org.highwire.dtl.DTLVardef@b7fforg.highwire.dtl.DTLVardef@12fe312org.highwire.dtl.DTLVardef@e4cf0c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

The inflammatory and tumor suppressor SAMD9L acts through a Schlafen-like box to restrict HIV and inhibit cell translation in SAAD/ATXPC

Sterile alpha motif domain-containing proteins 9 and 9L (SAMD9/9L) are associated with life-threatening genetic diseases and are restriction factors of poxviruses. Yet, their cellular function and the extent of their antiviral role are poorly known. Here, we found that interferon-stimulated SAMD9L, and not SAMD9, restricts HIV-1 replication at the translation step, with a strong inhibition of Transmitted/Founder HIV-1 patient strains. More broadly, SAMD9L restricts primate lentiviruses, but not another retrovirus (MLV) or two ssRNA viruses (MOPV, VSV). Using structural modeling and mutagenesis of SAMD9L, we identified a Schlafen(SLFN)-like active site necessary for HIV-1 restriction. By testing a germline gain-of-function variant from patients with SAMD9L-associated autoinflammatory disease (SAAD) and ataxia-pancytopenia (ATXPC), we determined that SAMD9L cellular and pathogenic functions also depend on the SLFN-like active site. Finally, we propose a model in which SAMD9L translational repression could be dependent on codon-usage, linking its cellular function and the virus-specific innate immunity. The identification of another Achilles heel of HIV, as well as the inflammatory SAMD9L effector and auto-regulatory determinants, provide novel avenues against infectious and genetic diseases. Significance statementThis study identifies SAMD9L as a potent HIV-1 antiviral factor from the interferon immunity and deciphers the host determinants underlying SAMD9L translational repression. The characterization of SAMD9L activity and determinants is also of medical importance for patients with rare genetic diseases bearing deleterious mutations in SAMD9L or with specific cancers. We demonstrate that a pathogenic SAMD9L patients variant is inactivated by the mutation of an identified active site in a SLFN-like box, resulting in an abolished translational shutdown. Furthermore, we describe SAMD9L, but not SAMD9, as an antiviral factor of HIV and lentiviruses, through a translational repression mediated by the SLFN-like box and potentially dependent on codon usage. These findings may have implications to better fight against HIV/AIDS as well as SAAD/ATXPC. Key findings- SAMD9L, but not SAMD9, restricts HIV-1, including Transmitted/Founder patient strains. - SAMD9L broadly restricts primate lentiviruses, but not the retrovirus MLV, nor two ssRNA viruses, the Rhabdovirus VSV and the Arenavirus MOPV. - SAMD9L inhibits viral and cellular translation through an essential E198/D243 active site in a SLFN-like box. - The SAMD9L-associated autoinflammatory disease (SAAD) F886Lfs*11 variant has enhanced HIV translational repression, unveiling an autoregulatory domain of the anti-lentiviral function.

immunology↗

bioRxiv2022

Extensive uORF translation from HIV-1 transcripts conditions DDX3 dependency for expression of main ORFs and elicits specific T cell immune responses in infected individuals

Human immunodeficiency virus type-1 (HIV-1) is a complex retrovirus which relies on alternative splicing, translational and post-translational mechanisms to produce more than 15 functional proteins from its single [~]10kb transcriptional unit. Here, we have applied ribosome profiling and nascent protein labeling at different time points during infection of CD4+ T lymphocytes to characterize the translational landscape of cellular and viral transcripts during the course of infection. Our results indicate a strong impact of viral infection on host cellular transcript levels but a modest impact on global translation rates. Analysis of ribosome profiling reads from viral transcripts reveals extensive and productive non-AUG translation of small peptides from multiple upstream open reading-frames (uORFs) located in the 5 long terminal repeat. Remarkably, these uORFs derived peptides elicit specific T cell responses in HIV-infected individuals. uORFs are conserved among other retroviruses and, together with the TAR sequence, condition the dependency on DDX3 for efficient translation of the main viral open-reading frames.

microbiology↗

bioRxiv2022

Coupling and Heterogeneity Modulate Pacemaking Capability in Healthy and Diseased Two-Dimensional Sinoatrial Node Tissue Models

Both experimental and modeling studies have attempted to determine mechanisms by which a small anatomical region, such as the sinoatrial node (SAN), can robustly drive electrical conduction in the human heart. However, despite important advances from prior research, important questions remain unanswered. This study aimed to investigate, through mathematical modeling, the role of intercellular coupling and cellular heterogeneity in synchronization and pacemaking within the healthy and diseased SAN. In a multicellular computational model of a monolayer of either human or rabbit SAN cells, simulations revealed that heterogenous cells synchronize their discharge frequency into a unique beating rhythm across a wide range of cellular heterogeneity and intercellular coupling. However, an insightful and unanticipated behavior appears in pathological conditions precipitated by perturbations of certain ionic currents (gCaL = 0.5): an intermediate range of intercellular coupling (900-4000 M{Omega}) is beneficial to the human SAN automaticity, enabling a very small portion of tissue (3.4%) to drive propagation, which fails with both lower and higher resistances. This protective effect of intercellular coupling and heterogeneity, seen in both human and rabbit tissues, highlights the remarkable resilience of the SAN. Overall, the model here developed allowed insight into the mechanisms of automaticity of the human sinoatrial node. The simulations suggest that certain degrees of gap junctional expressions protect the SAN from ionic perturbations that might be caused by drugs or mutations.

physiology↗

bioRxiv2019

Global ribosome profiling reveals that mutant huntingtin stalls ribosomes and represses protein synthesis independent of fragile X mental retardation protein

The regulators that stall ribosome translocation are poorly understood. We find that polyglutamine-expanded mutant Huntingtin (mHtt), the Huntingtons disease (HD) causing protein, promotes ribosome stalling and physiologically suppresses protein synthesis. A comprehensive, genome-wide analysis of ribosome footprint profiling (Ribo-Seq) revealed widespread ribosome stalling on mRNA transcripts and a shift in the distribution of ribosomes toward the 5 end, with single-codon unique pauses on selected mRNAs in HD cells. In Ribo-Seq, we found fragile X mental retardation protein (FMRP), a known regulator of ribosome stalling, translationally upregulated and it co-immunoprecipitated with mHtt in HD cells and postmortem brain. Depletion of FMRP gene, Fmr1, however, did not affect the mHtt-mediated suppression of protein synthesis or ribosome stalling in HD cells. Consistent with this, heterozygous deletion of Fmr1 in Q175FDN-Het mouse model, Q175FDN-Het; Fmr1+/-, showed no discernable phenotype, but a subtle deficit in motor skill learning. On the other hand, depletion of mHtt, which binds directly to ribosomes in an RNase-sensitive manner, enhanced global protein synthesis, increased ribosome translocation and decreased stalling. This mechanistic knowledge advances our understanding of the inhibitory role of mHtt in ribosome translocation and may lead to novel target(s) identification and therapeutic approaches that modulate ribosome stalling in HD.\n\nOne Sentence SummaryHuntingtons disease (HD) protein, mHtt, binds to ribosomes and affects their translocation and promotes stalling independent of the fragile X mental retardation protein.

neuroscience↗

bioRxiv2017

Cellular reductase activity in uncultivated Thiomargarita spp. assayed using a redox-sensitive dye

The largest known bacteria, Thiomargarita spp., have yet to be isolated in pure culture, but their large size allows for individual cells to be followed in time course experiments, or to be individually sorted for omics-based investigations. Here we report a novel application of a tetrazolium-based dye that measures the flux of reductase production from catabolic pathways to investigate the metabolic activity of individual cells of Thiomargarita spp. When coupled to microscopy, staining of the cells with a tetrazolium-formazan dye allows for metabolic responses in Thiomargarita spp. to be to be tracked in the absence of observable cell division. Additionally, the metabolic activity of Thiomargarita spp. cells can be differentiated from the metabolism of other microbes in specimens that contain adherent bacteria. The results of our redox-dye-based assay suggests that Thiomargarita is the most metabolically versatile under anoxic conditions where it appears to express cellular reductase activity in response to the electron donors succinate, acetate, citrate, formate, thiosulfate, H2, and H2S. Under hypoxic conditions, formazan staining results suggest the metabolism of succinate, and likely acetate, citrate, and H2S. Cells incubated under oxic conditions showed the weakest formazan staining response, and then only to H2S, citrate, and perhaps succinate. These results provide experimental validation of recent genomic studies of Ca. Thiomargarita nelsonii that suggest metabolic plasticity and mixotrophic metabolism. The cellular reductase response of bacteria attached to the exteriors of Thiomargarita also supports the possibility of trophic interactions between these largest of known bacteria and attached epibionts.\n\nIMPORTANCEThe metabolic potentials of many microorganisms that cannot be grown in the laboratory are known only from genomic data. Genomes of Thiomargarita spp. suggest that these largest of known bacteria are mixotrophs, combining lithotrophic metabolisms with organic carbon degradation. Our use of a redox-sensitive tetrazolium dye to query the metabolism of these bacteria provides an independent line of evidence that corroborates the apparent metabolic plasticity of Thiomargarita observed in recently produced genomes. Finding new cultivation- independent means of testing genomic results is critical to testing genome-derived hypotheses on the metabolic potentials of uncultivated microorganisms.

microbiology↗