Biology subjects

Aguilar, G.

Publications and source records attributed to Aguilar, G..

12 recordsLinked to original sources

bioRxiv2026

Tag-stabilized fluorescent protein binders for endogenous cell type-specific protein labelling

Protein labelling using genetically encoded fluorescent protein fusions has revolutionized the study of protein localization and function. However, visualizing endogenous proteins in specific cell types remains challenging, as existing approaches often require overexpression or laborious genetic engineering. To address these limitations, we developed a library of fluorescent protein binders using existing nanobodies and single-chain variable fragments that recognize fluorescent proteins and short peptide tags, allowing for modular, cell type-specific labelling of genetically tagged endogenous proteins. We found that fluorescent protein binders generate background fluorescence in the absence of the target protein, reducing signal specificity. To overcome this limitation, we generated destabilized fluorescent protein binders directed against GFP, ALFA, GCN4 peptide and V5. These binders display increased antigen-dependent stability and reduced background fluorescence, thereby improving the signal-to-noise ratio of endogenous protein visualization. We demonstrate the detection of endogenous proteins in drosophila larvae and embryos, zebrafish embryos, as well as in specific neuronal populations of the adult drosophila brain. In the brain, tissue-specific labelling revealed previously unknown protein expression and subcellular localization in sleep-regulatory neurons. Together, our panel of tag-stabilized fluorescent protein binders provides a versatile, ready-to-use toolkit for background-free, cell type-specific visualization of endogenous proteins.

cell biology↗

bioRxiv2025

Direct cell-to-cell transport of Hedgehog morphogen is aided by the diffusible carrier Shifted/DmWif1

The establishment of morphogen gradients is fundamental during embryonic patterning. Yet, the mechanisms by which morphogens disperse remain highly controversial. In a paradigmatic example, the dispersal of the morphogen Hedgehog (Hh) is both limited by and dependent on its lipid modifications. To address this paradox, several competing transport models have been proposed, ranging from lipid-shielding solubilizing factors to transport via specialized filopodia called cytonemes. In this study, we uncover that the lipid-shielding protein DmWif1/Shifted (Shf) participates in the contact-dependent cell transfer of Hh. Using nanobody-based immobilization, we demonstrate the tight association of Shf and Hh to cytoneme membranes. We show that Shf is anchored to membranes by the Hh co-receptor Interference Hedgehog (Ihog) and that the Ihog-Shf complex is required for Hh dispersal and signaling. Together, our results unify cytoneme-mediated transport and membrane release into a single dispersal model, in which local solubilization is required for cytonemes to exchange Hh-bound Shf at cell-cell contacts between presenting and receiving cytonemes.

developmental biology↗

bioRxiv2024

In vivo regulation of an endogenously-tagged protein by a light-regulated kinase

Post-translational modifications (PTMs) are indispensable modulators of protein activity. Most cellular behaviours, from cell division to cytoskeletal organization, are controlled by PTMs, their miss-regulation being associated with a plethora of human diseases. Traditionally, the role of PTMs has been studied employing biochemical techniques. However, these approaches fall short when studying PTM dynamics in vivo. In recent years, functionalized protein binders have allowed the post-translational modification of endogenous proteins by bringing an enzymatic domain in close proximity to the protein they recognize. To date, most of these methods lack the temporal control necessary to understand the complex effects triggered by PTMs. In this study, we have developed a method to phosphorylate endogenous Myosin in a light-inducible manner. The method relies both on nanobody-targeting and light-inducible activation in order to achieve both tight specificity and temporal control. We demonstrate that this technology is able to disrupt cytoskeletal dynamics during Drosophila embryonic development. Together, our results highlight the potential of combining optogenetics and protein binders for the study of the proteome in multicellular systems.

developmental biology↗

bioRxiv2023

Transcriptional control of compartmental boundary positioning during Drosophila wing development

The establishment of tissue axes is fundamental during embryonic development. In the Drosophila wing, the anterior/posterior (AP) and the dorsal/ventral (DV) compartment boundaries provide the basic coordinates around which the tissue develops. These boundaries arise as a result of two lineage decisions, the acquisition of posterior fate by the selector gene engrailed (en) and dorsal fate by the selector gene apterous (ap). While the en expression domain is set up during embryogenesis, ap expression begins only during early wing development. Thus, the correct establishment of the ap expression pattern relative to en must be tightly controlled. Here, we functionally investigate the transcriptional inputs integrated by the early ap enhancer (apE) and their requirement for correct boundary formation. Detailed mutational analyses using CRISPR/Cas revealed a role for apE in positioning the DV boundary relative to the AP boundary, with apE mutants often displaying mirror-image anterior wing duplications. We then designed and applied methods to accomplish tissue-specific enhancer disruption via dCas9 expression. This approach allowed us to dissect the spatiotemporal requirement for apE function, clarifying the mechanism by which apE misregulation leads to AP defects. Base-pair-resolution analyses of apE uncovered a single HOX binding site essential for wing development that, when mutated, led to wingless flies. We demonstrated that the transcription factors Pointed (Pnt), Homothorax (Hth), and Grain (Grn) are required for apE function, and the HOX gene Antennapedia (Antp) contributes to early wing development. Together, our results provide a comprehensive molecular basis of early ap activation and the developmental consequences of its misregulation, shedding light on how compartmental boundaries are set up during development.

developmental biology↗

bioRxiv2023

Characterization of the RBM15 protein binding with XCI-escaping long noncoding RNAs

The RNA binding motif 15 protein (RBM15) plays a critical role in post-transcriptional regulation. Its role in facilitating N6-methyladenosine (m6A) modification, specifically through guiding the writer complex (WTAP METTL13 METTL14) to DRACH sequence motifs, has been demonstrated for several classes of RNA, including long noncoding RNAs (lncRNAs). The structural mechanism that underlies how RBM15 interacts with RNA has yet to be elucidated. In this study, we mined and bioinformatically assessed publicly available genome-wide RNA 2D structural probing and RBP cross-linking and immunoprecipitation data to investigate how RBM15 interacts with RNA, with a focus on lncRNA transcripts. RBM15, which possesses three RNA recognition motifs (RRMs), primarily interacts with stem-loop structured RNA motifs. Structural modeling reveals RRMs 2 and 3 are coaxially stacked in solution; these two RRMs are responsible for driving RBM15s interaction with RNA. We further demonstrate this experimentally with two RNA hairpins, revealing low micromolar binding affinities. Altogether, this work provides insight into the structural mechanism by which RBM15 interacts with RNAs to govern biological function.

biochemistry↗

bioRxiv2023

Shaping and interpretation of Dpp morphogen gradient by endocytic trafficking

Dpp/BMP is a morphogen that controls patterning and growth in the Drosophila wing disc. Endocytic trafficking has been proposed to control extracellular Dpp spreading or removal, and Dpp signaling. However, how Dpp morphogen gradient is shaped and interpreted by endocytic trafficking remains unclear due to the lack of tools to visualize Dpp distribution at the physiological level. Here we generate functional fluorescent protein tagged dpp alleles to visualize both extracellular and intracellular Dpp distribution. Using these alleles, we found that, while Dynamin-mediated internalization of Dpp is required for Dpp signal activation, Rab5-mediated trafficking is not required for Dpp spreading or signaling as proposed before but for shutting off Dpp signaling through downregulating activated receptors. We provide evidence that Dpp signaling is terminated at Multivesicular body (MVB) likely through sorting activated receptors into intraluminal vesicles (ILVs) rather than Rab7-mediated lysosomal degradation. We further found that blocking MVB formation expanded Dpp signaling gradient without affecting extracellular Dpp gradient, thus compromising extracellular Dpp gradient interpretation. These results indicate that extracellular Dpp gradient is shaped by Dynamin-mediated internalization of Dpp and interpreted by duration of Dpp signaling.

developmental biology↗

bioRxiv2022

Heterodimerization-dependent secretion of BMPs in Drosophila

Combinatorial signaling is key to instruct context-dependent cell behaviors. During embryonic development, adult homeostasis and disease, Bone Morphogenetic Proteins (BMPs) act as dimers to instruct specific cellular responses. BMP ligands can form both homo- or heterodimers; however, obtaining direct evidence of the endogenous localization and function of each form has proven challenging. Here, we make use of precise genome editing and direct protein manipulation via protein binders to dissect the existence and functional relevance of BMP homo- and heterodimers in the Drosophila wing imaginal disc. This approach revealed in situ the existence of Dpp (BMP2/4)/Gbb (BMP5/6/7/8) heterodimers. We found that Gbb, despite being produced by all the cells of the wing imaginal disc, is only secreted by the cells in which Dpp is expressed. Dpp and Gbb form a gradient of heterodimers whereas neither Dpp nor Gbb homodimers are evident under endogenous physiological conditions. We find that the formation of heterodimers is critical for obtaining optimal signaling and long-range BMP distribution in the developing wing. These results indicate that Dpp/Gbb heterodimers are the active signal required for epithelial patterning and growth.

developmental biology↗

bioRxiv2022

In vivo seamless genetic engineering via CRISPR-triggered single-strand annealing

Precise genome engineering is essential for both basic and applied research. CRISPR/Cas accelerated the speed and ease by which defined exogenous sequences are integrated into specific loci. Nevertheless, knock-in generation in multicellular animals remains challenging, partially due to the complexity of insertion screening. Even when achieved, the analysis of protein localization can still be unfeasible in highly packed tissues, where spatial and temporal control of gene labeling would be ideal. Here, we describe SEED/Harvest, an efficient knock-in method based on homology-directed (HDR) and single-strand annealing (SSA) repair pathways. HDR mediates the integration of a switchable cassette. Upon a subsequent CRISPR-triggered repair event, resolved by SSA, the cassette is seamlessly removed. Germline excision of SEED cassettes allows for fast and robust knock-in generation with both fluorescent proteins and short protein tags in tandem. Tissue-specific expression of Cas9 results in somatic cassette excision, conferring spatio-temporal control of protein labelling and the conditional rescue of mutants. Finally, to achieve conditional protein labeling and manipulation of short tag knock-ins, we have developed a toolbox based on rational engineering and functionalization of the ALFA nanobody.

genetics↗

bioRxiv2020

Glypicans specifically regulate Hedgehog signaling through their interaction with Ihog in cytonemes

The conserved family of Hedgehog (Hh) signaling proteins plays a key role in cell-cell communication in development, tissue repair and cancer progression. These proteins can act as morphogens, inducing responses dependent on the ligand concentration in target cells located at a distance. Hh proteins are lipid modified and thereby have high affinity for membranes, which hinders the understanding of their spreading across tissues. Direct contact between cell membranes by filopodia-like structures (also known as cytonemes) could be the simplest explanation for Hh dispersal. To better understand this signaling mechanism, we have analyzed in Drosophila the interaction between the glypicans that, besides for other pathways, are necessary for Hh signaling, plus the adhesion molecules and Hh coreceptors Ihog and Boi. We describe that glypicans (Dally and Dally-like protein) are required to maintain Ihog, but not Boi, protein levels. We also show that ectopic Ihog stabilizes cytonemes through its interaction with glypicans, and we determine that two Ihog fibronectin III domains are essential for this interaction. Our data suggest that this interaction with Ihog in cytonemes confers the specificity of glypicans for Hh signaling.

developmental biology↗

bioRxiv2020

A new perspective on the evolution of the interaction between the Vg/VGLL1-3 proteins and the TEAD transcription factors

The most downstream elements of the Hippo pathway, the TEAD transcription factors, are regulated by several cofactors, such as Vg/VGLL1-3. Earlier findings on human VGLL1 and here on human VGLL3 show that these proteins interact with TEAD via a conserved amino acid motif called the TONDU domain. Surprisingly, our studies reveal that the TEAD-binding domain of Drosophila Vg and of human VGLL2 is more complex and contains an additional structural element, an {Omega}-loop, that contributes to TEAD binding and in vivo function. To explain this unexpected structural difference between proteins from the same family, we propose that, after the genome-wide duplications at the origin of vertebrates, the {Omega}-loop present in an ancestral VGLL gene has been lost in some VGLL variants. These findings illustrate how structural and functional constraints can guide the evolution of transcriptional cofactors to preserve their ability to compete with other cofactors for binding to transcription factors.

biochemistry↗

bioRxiv2020

Protein manipulation using single copies of short peptide tags in cultured cells and in Drosophila melanogaster

Cellular development and specialized cellular functions are regulated processes which rely on highly dynamic molecular interactions among proteins, distributed in all cell compartments. Analysis of these interactions and their mechanisms of action has been one of the main topics in cellular and developmental research over the last fifty years. Studying and understanding the functions of proteins of interest (POIs) has been mostly achieved by their alteration at the genetic level and the analysis of the phenotypic changes generated by these alterations. Although genetic and reverse genetic technologies contributed to the vast majority of information and knowledge we have gathered so far, targeting specific interactions of POIs in a time- and space-controlled manner or analyzing the role of POIs in dynamic cellular processes such as cell migration or cell division would require more direct approaches. The recent development of specific protein binders, which can be expressed and function intracellularly, together with several improvements in synthetic biology techniques, have contributed to the creation of a new toolbox for direct protein manipulations. We selected a number of short tag epitopes for which protein binders from different scaffolds have been developed and tested whether these tags can be bound by the corresponding protein binders in living cells when they are inserted in a single copy in a POI. We indeed find that in all cases, a single copy of a short tag allows protein binding and manipulation. Using Drosophila, we also find that single short tags can be recognized and allow degradation and relocalization of POIs in vivo.

cell biology↗

bioRxiv2019

Theranostic cranial implant for hyperspectral light delivery and microcirculation imaging without scalp removal

Light based techniques for imaging, diagnosing and treating the brain have become widespread clinical tools, but application of these techniques is limited by optical attenuation in the scalp and skull. This optical attenuation reduces the achievable spatial resolution, precluding the visualization of small features such as brain microvessels. The goal of this study was to assess a strategy for providing ongoing optical access to the brain without the need for repeated craniectomy or retraction of the scalp. This strategy involves the use of a transparent cranial implant and skin optical clearing agents, and was tested in mice to assess improvements in optical access which could be achieved for laser speckle imaging of cerebral microvasculature. Combined transmittance of the optically cleared scalp overlying the transparent cranial implant was as high as 89% in the NIR range, 50% in red range, 24% in green range, and 20% in blue range. In vivo laser speckle imaging experiments of mouse cerebral blood vessels showed that the proposed optical access increased signal-to-noise ratio and image resolution, allowing for visualization of microvessels through the transparent implant, which was not possible through the uncleared scalp and intact skull.

bioengineering↗