Biology subjects

Bujosa, P.

Publications and source records attributed to Bujosa, P..

3 recordsLinked to original sources

bioRxiv2025

Downstream effects of the ''Less, but More'' Fgf signaling in Oikopleura dioica: Fgf receptor expansion and RTK pathway simplification.

Fibroblast growth factor (FGF) signaling is central to chordate development and has been extensively remodeled in tunicates. Recent findings show that appendicularians have massively lost all ancestral chordate Fgf subfamilies except two, the Fgf9/16/20 and Fgf11/12/13/14 subfamilies, which in contrast have undergone a burst of lineage-specific duplications and diversification into novel paralogs, in an evolutionary scenario that we have named "Less, but More". Here, we investigate the downstream effects of the Fgf losses and duplications ion Fgf receptors (FgfRs) and intracellular RTK components in the appendicularian Oikopleura dioica. We show that the single ancestral FgfR gene has expanded into three paralogs (FgfRa-c), which are conserved across cryptic O. dioica species, yet highly divergent from other chordates. Despite strong sequence divergence, structural modeling indicates preservation of canonical FgfR architecture. Expression analyses reveal distinct spatiotemporal patterns: FgfRa and FgfRb are maternally supplied and enriched in mesodermal derivatives, whereas FgfRc is restricted to neural and epithelial tissues. Genome surveys of downstream RTK pathways show conservation of core RAS/MAPK, PLC{gamma}/PKC, and PI3K/AKT cascades, but with losses of classical Ras genes and several adaptors, suggesting a lineage-specific simplification of transduction complexes. Transduction gene expression shifts from broad maternal ubiquity to tissue-specific domains, particularly in brain, notochord, muscle, and gonadal primordia throughout embryonic and larval development. Appendicularians appear as the only non-vertebrate chordate lineage that recapitulate the vertebrate-like FgfR expansion following Fgf ligands diversification. Downstream components, however, evolved more conservatively, tending toward simplification, reinforcing the view that appendicularians generate signaling innovation despite extensive gene loss.

evolutionary biology↗

bioRxiv2024

Less, but more: new insights from appendicularians on chordate Fgf evolution and the divergence of tunicate lifestyles.

The impact of gene loss on the divergence of taxa and the generation of evolutionary innovations is a fundamental aspect of Evolutionary Biology that remains unclear. Here, using the evolution of the Fibroblast Growth Factors (FGFs) in appendicularians as a case study, we investigate how gene losses have influenced the evolution of chordates, especially the divergence among tunicates. Our work reveals an unprecedented case of massive losses of all Fgf gene subfamilies, except for the Fgf9/16/20 and Fgf11/12/13/14, which in turn suffered two bursts of gene duplications. Phylogenetic inferences and genomic analyses of gene synteny conservation, gene architecture, alternative splicing and protein 3D-structure have allowed us to reconstruct the history of appendicularian Fgf genes in the context of chordate evolution, providing compelling evidence supporting the paracrine secreting functions and the intracellular functions of the Fgf9/16/20 and Fgf11/12/13/14 subfamilies, respectively. Exhaustive analysis of developmental Fgf expression in Oikopleura dioica as a model for appendicularians reveals a paradigmatic case of what could be referred as "less, but more", providing a conceptual evolutionary framework characterized by four associated evolutionary patterns: conservation of ancestral Fgf expression domains; function shuffling between paralogs upon gene loss; innovation of new expression domains after the bursts of Fgf duplications; and the extinction of Fgf functions linked to gene losses. The findings of this work allow us to formulate novel hypotheses about the potential impact of losses and duplications of Fgf genes on the transition from an ancestral ascidian-like biphasic lifestyle to a fully free-living style of appendicularians. These hypotheses include the massive co-option of Fgf genes for the patterning of the oikoblast responsible of the house architecture, and for the development of the tail fin; the recruitment of Fgf11/12/13/14 genes into the evolution of a new mouth, and their role modulating neuronal excitability; the evolutionary innovation of an "anterior tail" FGF signaling mesodermal source upon the loss of retinoic acid signaling; and the potential link between the loss of Fgf7/10/22 and Fgf8/17/18 and the loss of drastic metamorphosis, mesenchymal cells and lack of tail absorption in appendicularians, in contrast to ascidians.

evolutionary biology↗

bioRxiv2023

Somatic chromosome pairing has a determinant impact on 3D 1 chromatin organization

In the nucleus, chromatin is intricately structured into multiple layers of 3D organization important for genome activity. How distinct layers influence each other is not well understood. In particular, the contribution of chromosome pairing to 3D chromatin organization has been largely neglected. Here, we address this question in Drosophila, an organism that shows robust chromosome pairing in interphasic somatic cells. The extent of chromosome pairing depends on the balance between pairing and anti-pairing factors, with the anti-pairing activity of the CAP-H2 condensin II subunit being the best documented. Here, we identify the zinc-finger protein Z4 as a strong anti-pairer that interacts with and mediates the chromatin binding of CAP-H2. We also report that hyperosmotic cellular stress induces fast and reversible chromosome unpairing that depends on Z4/CAP-H2. And, most important, by combining Z4 depletion and osmostress, we show that chromosome pairing reinforces intrachromosomal 3D interactions. On the one hand, pairing facilitates RNAPII occupancy that correlates with enhanced intragenic gene-loop interactions. In addition, acting at a distance, pairing reinforces chromatin-loop interactions mediated by Polycomb (Pc). In contrast, chromosome pairing does not affect which genomic intervals segregate to active (A) and inactive (B) compartments, with only minimal effects on the strength of A-A compartmental interactions. Altogether, our results unveil the intimate interplay between inter-chromosomal and intra-chromosomal 3D interactions, unraveling the interwoven relationship between different layers of chromatin organization and the essential contribution of chromosome pairing.

genomics↗