Biology subjects

Hatin, I.

Publications and source records attributed to Hatin, I..

8 recordsLinked to original sources

bioRxiv2026

Ribo-seq reveals IsrR-mediated translational repression of SAOUHSC_02924 (gabT) during iron limitation in Staphylococcus aureus

Iron is essential for bacterial growth but can be toxic in excess. To maintain iron homeostasis, bacteria employ regulatory mechanisms, including small RNAs (sRNAs). In Staphylococcus aureus, we identified the sRNA IsrR as a critical mediator of the iron-sparing response, enabling bacterial fitness in iron-limited environments such as those encountered during host infection. Here, we use ribosome profiling (Ribo-seq) to define the translational regulatory network of IsrR under iron-limited conditions. Our analysis identifies multiple genes under IsrR control, including SAOUHSC_02924 (gabT), which encodes a putative 4-aminobutyrate aminotransferase. Given that IsrR downregulates iron-dependent TCA cycle enzymes, we propose that repression of gabT prevents the accumulation of TCA cycle precursors under iron depletion, thereby avoiding metabolic imbalances. These findings expand the role of IsrR in metabolic reprogramming and highlight its contribution to S. aureus survival in iron-restricted host niches.

microbiology↗

bioRxiv2026

Non-coding RNA RsaE regulates biofilm thickness, viability and dissemination in methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is a formidable human pathogen responsible for life-threatening infections worldwide. Central to its pathogenic success is the tightly coordinated regulation of virulence factors, including the phenol soluble modulins (PSM), short amphipathic toxins that drive cytolysis, immune evasion and biofilm maturation. We previously identified the conserved non-coding RNA RsaE as a putative regulator of the psm operon, but the biological significance of this interaction remained unclear. Here we show that RsaE and endoribonuclease Y jointly regulate psm transcript abundance at the post-transcriptional and transcriptional levels, the latter primarily through activation of the agr quorum sensing system. We show that the psm transcript is unusually stable and highly structured, with Shine-Dalgarno sequences of individual toxin-coding sequences differentially accessible, providing a mechanism for translational fine-tuning of individual PSM peptides. In vitro biofilm analyses revealed that RsaE deletion produces thinner biofilms with reduced extracellular DNA accumulation on the surface and transiently elevated cell viability. Strikingly, in a murine catheter infection model,{Delta} rsaE biofilms exhibited structural abnormalities and significantly reduced dissemination to kidneys. These findings identify the RsaE non-coding RNA as a key regulator linking central metabolism and quorum sensing to toxin expression, biofilm maturation and infection in MRSA. Author summaryMethicillin-resistant Staphylococcus aureus (MRSA) causes severe, often device-associated infections that are hard to treat. A central reason for its success is tight control over toxins such as the -phenol-soluble modulins (PSM), which help bacteria damage host cells and build/disperse biofilms. Small RNAs (sRNAs) are fast-acting genetic regulators in bacteria, that also regulate toxin production. We show that the conserved sRNA RsaE and the endoribonuclease RNase Y jointly tune the level and lifetime of the psm RNA transcript, which encodes four PSM peptides. The psm RNA is unusually stable and highly structured with its design favouring translation of PSM4 over the other peptides. Removing RsaE or RNase Y increases psm transcription via the agr quorum-sensing system and further stabilises the psm RNA. In biofilms, loss of RsaE reduces the thickness and extracellular DNA layer, while increasing early cell viability. In a mouse catheter model, RsaE deletion leads to structurally altered biofilms and reduced early dissemination to kidneys. These results identify RsaE as a key regulator connecting metabolism and quorum sensing to toxin expression, biofilm maturation and disease progression, and point to RNA-centred strategies to regulate MRSA spread from biofilms.

biochemistry↗

bioRxiv2025

Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis

Ancestrally non-genic sequences are now widely recognized as potential reservoirs for the de novo emergence of new genes. Across clades, some de novo genes were proven to have substantial phenotypic effects, and to contribute to the emergence of novel biological functions. Yet, little is still known about the starting material from which de novo genes emerge, especially in plants. To fill this gap, we generated Ribosome Profiling data from Arabidopsis lyrata and characterized the evolution of translated regions genome-wide across the Arabidopsis genus. Synteny analysis revealed 163 actively translated regions in A. lyrata whose coding potential (Open Reading Frames, ORFs or Coding DNA sequences, CDSs) has emerged de novo within the Arabidopsis genus. Most of these de novo translated regions were species- and even accession-specific, indicating their transient nature, with patterns of polymorphism consistent with neutral evolution in natural populations. They were also significantly shorter and less expressed than conserved protein-coding genes, and their GC content increased with phylogenetic conservation. Twenty-one of them belonged to previously annotated CDSs, and are therefore promising putative de novo genes, while most were located in intergenic regions and are thus newly discovered. Our results demonstrate the abundance of translation events outside of conserved CDSs, and their role as starting material for the emergence of novel genes in plants. Significance statementA central open question in genome evolution is how novel protein-coding genes arise from noncoding nucleotide DNA sequences and eventually contribute to the stable repertoires of "canonical" genes. Here, we focused specifically on the early stages of this important evolutionary process, whereby previously non-coding intergenic nucleotide sequences eventually acquire open reading frames carrying signatures of active translation. This phenomenon has been crucially under-studied so far, especially in plants. By combining ribosome profiling data and a careful genome comparison strategy among closely related Arabidopsis species, our results demonstrate the pervasive translation and de novo origin of a large number of small intergenic ORFs and illustrate their role as starting material for the emergence of novel genes in plants. Key-words: de novo genes, Arabidopsis, pervasive translation, intergenic ORFs, ribosome profiling

genomics↗

bioRxiv2024

Unveiling novel conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling.

The development of ribosomal profiling (Riboseq) revealed the immense coding capacity of human and viral genomes. Here, we used Riboseq to delineate the first translatome of HIV-1 in infected CD4+ T cells. In addition to canonical viral protein coding sequences (CDSs), we identify 98 alternative open reading frames (ARFs), corresponding to small Open Reading Frames (sORFs) that are distributed across the HIV genome including the UTR regions. Using a database of HIV genomes, we observed that most ARF amino-acid sequences are likely conserved among clade B and C of HIV-1, with 8 ARF-encoded amino-acid sequences being more conserved than the overlapping CDSs. Using T cell-based assays and mass spectrometry-based immunopeptidomics, we demonstrate that ARFs encode viral polypeptides. In the blood of HIV-infected individuals, ARF-derived peptides elicit potent poly-functional T cell responses mediated by both CD4+ and CD8+ T cells. Our discovery expands the list of conserved viral polypeptides that are targets for vaccination strategies and might reveal the existence of viral microproteins or pseudogenes.

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↗

bioRxiv2021

2-Guanidino-quinazoline promotes the readthrough of nonsense mutations underlying human genetic diseases

Premature termination codons (PTCs) account for 10% to 20% of genetic diseases in humans. The gene inactivation resulting from PTC can be counteracted by the use of drugs stimulating PTC readthrough, thereby restoring production of the full-length protein. However, a greater chemical variety of readthrough inducers is required to broaden the medical applications of this therapeutic strategy. In this study, we developed a new reporter cell line and performed high-throughput screening (HTS) to identify potential new readthrough inducers. After three successive assays, we isolated 2-guanidino-quinazoline (TLN468). We assessed the clinical potential of this drug as a potent readthrough inducer on the 40 PTCs most frequently responsible for Duchenne muscular dystrophy. We found that TLN468 was more efficient than gentamicin, and acted on a broader range of sequences, without inducing the readthrough of natural stop codons.

molecular biology↗

bioRxiv2021

Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

The noncoding genome plays an important role in de novo gene birth and in the emergence of genetic novelty. Nevertheless, how noncoding sequences properties could promote the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic ORFs (Open Reading Frames) of S. cerevisiae with the aim of (i) exploring whether the large structural diversity observed in proteomes is already present in noncoding sequences, and (ii) estimating the potential of the noncoding genome to produce novel protein bricks that can either give rise to novel genes or be integrated into pre-existing proteins, thus participating in protein structure diversity and evolution. We showed that amino acid sequences encoded by most yeast intergenic ORFs contain the elementary building blocks of protein structures. Moreover, they encompass the large structural diversity of canonical proteins with strikingly the majority predicted as foldable. Then, we investigated the early stages of de novo gene birth by identifying intergenic ORFs with a strong translation signal in ribosome profiling experiments and by reconstructing the ancestral sequences of 70 yeast de novo genes. This enabled us to highlight sequence and structural factors determining de novo gene emergence. Finally, we showed a strong correlation between the fold potential of de novo proteins and the one of their ancestral amino acid sequences, reflecting the relationship between the noncoding genome and the protein structure universe.

evolutionary biology↗

bioRxiv2018

The high turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

Little is known about the rate of emergence of genes de novo, how they spread in populations and what their initial properties are. We examined wild yeast (Saccharomyces paradoxus) populations to characterize the diversity and turnover of intergenic ORFs over short evolutionary time-scales. With ~34,000 intergenic ORFs per individual genome for a total of ~64,000 orthogroups identified, we found de novo ORF formation to have a lower estimated turnover rate than gene duplication. Hundreds of intergenic ORFs show translation signatures similar to canonical genes. However, they have lower translation efficiency, which could reflect a mechanism to reduce their production cost or simply a lack of optimization. We experimentally confirmed the translation of many of these ORFs in laboratory conditions using a reporter assay. Translated intergenic ORFs tend to display low expression levels with sequence properties that generally are close to expectations based on intergenic sequences. However, some of the very recent translated intergenic ORFs, which appeared less than 110 Kya ago, already show gene- like characteristics, suggesting that the raw material for functional innovations could appear over short evolutionary time-scales.

evolutionary biology↗