Biology subjects

Igreja, C.

Publications and source records attributed to Igreja, C..

7 recordsLinked to original sources

bioRxiv2026

Ribosome profiling reveals widespread translational control across developmental stages in the brown alga Ectocarpus

Translation represents a central regulatory layer of gene expression, enabling rapid and dynamic modulation of protein output. While its importance in development is well established, it remains poorly characterized outside animals and land plants. Brown algae, and in particular Ectocarpus, offer a compelling system to investigate translational regulation in development, having evolved multicellularity independently of other major eukaryotic lineages and exhibiting a complex life cycle with distinct haploid and diploid developmental programs. Although transcriptional regulation contributes to Ectocarpus development, the striking similarity of transcriptomes across life cycle stages indicates that transcription alone is insufficient to explain their distinct developmental identities, pointing to a major role for post-transcriptional regulation. Here, we establish ribosome profiling in Ectocarpus and define its translatome across key developmental stages. We uncover widespread stage- and sex-specific translational regulation, with post-transcriptional buffering emerging as the predominant mode of control. Genes subject to translational regulation exhibit optimized codon usage, broader transcriptional profiles and shorter 3' UTRs. These genomic features are associated with variation in translation efficiency. Collectively, these results provide the first comprehensive characterization of the Ectocarpus translatome and highlight a major role for translational regulation in developmental gene expression in an independently evolved multicellular lineage.

developmental biology↗

bioRxiv2026

Plasticity in nonsense-mediated decay and translation initiation regulate polyphenism

Developmental plasticity is increasingly recognised as facilitator of evolutionary novelty. However, how plasticity itself evolves and how variation in plastic trait expression is structured in populations remain unknown1,2. The predatory nematode Pristionchus pacificus exhibits mouth-form plasticity with underlying molecular mechanisms being increasingly identified3. We investigate the temporal scale of natural variation of mouth-form plasticity. An 11-year survey characterised Adoretus beetle-derived isolates from Colorado, La Reunion Island and revealed a gradual shift in mouth-form preference. Quantitative trait locus mapping of mouth-form preferences identified a single peak harbouring the developmental switch gene eud-1. Through CRISPR-engineering and biochemical assays, we show that plasticity in nonsense-mediated decay coupled with alternative start codon selection resulting in different N-terminal proteoforms of EUD-1 are associated with natural variation of mouth-form preference. This work provides molecular explanations for variation in plastic trait expression and links nonsense variants in the major developmental switch locus to ecological and evolutionary processes.

evolutionary biology↗

bioRxiv2025

Poly(UG)-tailed RNAs are involved in the control of thousands of genes predominantly in the germline in Pristionchus pacificus

In the nematode Caenorhabditis elegans, the terminal transferase RDE-3 adds a poly(UG)-tail to the free 3 end of RNA molecules generated by the action of primary siRNAs or piRNAs. The tailed RNA serves as a template for RNA-dependent RNA polymerases (RdRp) to generate secondary siRNAs, thereby reinforcing the RNAi effect. In this iterative process, progressively shorter tailed RNAs are formed. In C. elegans, injection of poly(UG)-tailed single-stranded RNA (ssRNA) leads to RNAi-mediated gene silencing, thereby bypassing the need for the processing of double-stranded RNA into siRNAs. We wondered if poly(UG)-tailed ssRNAs could also be used for experimental gene knockdown in nematodes where long dsRNA-mediated RNAi does not work reliably, such as the satellite model organism Pristionchus pacificus or parasitic nematodes of the genus Strongyloides. Here we show that injection of poly(UG)-tailed RNA leads to gene knock down in P. pacificus and that the injected RNA, as well as the corresponding endogenous RNA, serve as substrate for the formation of new poly(UG)-tailed RNAs. Different from C. elegans, in P. pacificus, the knockdown effect depends on the redundant activity of the three rde-1 paralogs present in this species. We detected endogenously occurring poly(UG)-tailed RNAs derived from thousands of genes, more than half of which belong to germline-specific co-expression clusters. Mutations in Ppa-rde-3, lead to sterility. In contrast, in Strongyloides spp., we found poly(UG)-tailed RNAs to be much less abundant, if not absent. Our results show that poly(UG)-tailed RNAs are not restricted to C. elegans and suggest that they play an important function in the germ line in P. pacificus.

molecular biology↗

bioRxiv2024

XRN1 supplies free nucleotides to feed alphavirus replication

Several RNA viruses induce widespread degradation of cellular mRNAs upon infection; however, the biological significance and mechanistic details of this phenomenon remain unknown. Here, we make use of a model alphavirus, Sindbis virus (SINV), to fill this knowledge gap. We found that SINV triggers cellular RNA decay through the exonuclease XRN1 and the 5-to-3 degradation machinery (5-3DM). These proteins accumulate at viral replication organelles (VROs) and interact with the non-structural protein 1 (nsP1), bringing mRNA degradation into proximity with vRNA synthesis. Our data suggest that monophosphate nucleotides released by cellular RNA decay are recycled through the salvage pathway to feed viral replications. Our work thus reveals a fundamental connection between cellular mRNA degradation and viral replication via nucleotides repurposing. Research highlightsO_LI5-3 RNA decay is essential for the replication of a wide range of viruses. C_LIO_LIXRN1 directly interacts with transcripts which are degraded during infection. C_LIO_LIRNA decay factors and salvage pathway members localise to viral factories. C_LIO_LISupplying nucleosides to several 5-3DM deficient cells facilitates SINV infection. C_LI

biochemistry↗

bioRxiv2023

A paradigm for regulation at the effector interface with RNA-binding proteins

RNA-binding proteins (RBPs) are key regulators of gene expression, but how RBPs convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a deeply conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of dual-purpose peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by the recruiting RBP. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface, with implications for the evolution and function of RBP-operated regulatory networks.

molecular biology↗

bioRxiv2021

Molecular basis for GIGYF-TNRC6 complex assembly in miRNA-mediated translational repression

The GIGYF proteins associate with 4EHP and RNA-associated proteins to elicit transcript-specific translational repression. However, the mechanism by which the GIGYF1/2-4EHP complex is recruited to its target transcripts remain unclear. Here we report the crystal structures of the GYF domains from GIGYF1 and GIGYF2 in complex with proline-rich sequences from miRISC-binding proteins TNRC6C and TNRC6A, respectively. The TNRC6 proline-rich motifs bind to a conserved array of aromatic residues on the surface of the GIGYF1/2 GYF domain, bridging 4EHP to Argonaute-miRNA mRNA targets. Our structures also reveal a phenylalanine residue conserved from yeast to human GYF domains that contributes to GIGYF2 thermostability. The molecular details we outline here are likely to be conserved between GIGYF1/2 and other RNA-binding proteins to elicit 4EHP-mediated repression in different biological contexts.

biochemistry↗

bioRxiv2021

DAP5 enables translation re-initiation on structured messenger RNAs

Half of mammalian transcripts contain short upstream open reading frames (uORFs) that potentially regulate translation of the downstream coding sequence (CDS). The molecular mechanisms governing these events remain poorly understood. Here we find that the non-canonical initiation factor Death-associated protein 5 (DAP5 or eIF4G2) is selectively required for re-initiation at the main CDS following uORF translation. Using ribosome profiling and luciferase-based reporters coupled with mutational analysis we show that DAP5-mediated re-initiation occurs on messenger RNAs (mRNAs) with long, structure-prone 5' leader sequences and persistent uORF translation. These mRNAs preferentially code for signalling factors such as kinases and phosphatases. We also report that cap/eIF4F- and eIF4A-dependent recruitment of DAP5 to the mRNA facilitates re-initiation by unrecycled post-termination 40S subunits. Our study reveals important mechanistic insights into how a non-canonical translation initiation factor involved in stem cell fate shapes the synthesis of specific signalling factors.

molecular biology↗