Pedro Manuel Dias Neto Domingos
@itqb.unl.pt
Principal Investigator
ITQB-UNL
Positions
July 2015 – present – Principal Investigator, ITQB-UNL, Instituto de Tecnologia Química e Biológica – Universidade Nova de Lisboa, Portugal. Research Group Leader and Head of the Laboratory of Cell Signaling in Drosophila
July 2008 – June 2015 – Assistant Investigator, ITQB-UNL, Instituto de Tecnologia Química e Biológica – Universidade Nova de Lisboa, Portugal. Research Group Leader and Head of the Laboratory of Cell Signaling in Drosophila.
April 2002 – June 2008 - Postdoctoral Associate, The Rockefeller University, New York, USA.
Mentor: Hermann Steller.
Sep. 2001- March 2002 – Postdoctoral Associate, The Rockefeller University, New York, USA.
Mentor: Ali Hemmati-Brivanlou.
Sep. 1997-August 2001 - PhD student, National Institute for Medical Research, Mill Hill, London, UK..
Mentor: Robb Krumlauf.
EDUCATION
University of Lisbon, Portugal Bachelor Honors 1989-1995 Biochemistry
University College London, UK PhD 1997-2001 Developmental Biology
Mentor: Robb Krumlauf
The Rockefeller University, USA Postdoc 2001-2008 Genetics
Mentor: Hermann Steller
RESEARCH, TEACHING, or OTHER INTERESTS
Developmental Biology, Cell Biology, Biochemistry, Genetics and Molecular Biology, Genetics
FUTURE PROJECTS
Structure and dynamics of the Xport-A/Rhodopsin1 interaction at atomic resolution
Rhodopsins are essential for vision and mutations in human rhodopsins that perturb its folding cause autosomal dominant Retinitis Pigmentosa, an incurable disease that leads to blindness. This proposal intends to go beyond the state-of-the-art by gaining access to dynamic structural information on chaperone-client protein interactions in membranes by monitoring dynamic intra- and intermolecular interactions of Xport-A (chaperone) with Rhodopsin-1 (client).
Applications Invited
PhD/MSc students
Scopus Publications
Scopus Publications
Catarina J. Gaspar, Tiago Gomes, Joana C. Martins, Manuel N. Melo, Colin Adrain, Tiago N. Cordeiro, and Pedro M. Domingos
Elsevier BV
Rita Rosado-Ramos, Gonçalo M. Poças, Daniela Marques, Alexandre Foito, David M. Sevillano, Mafalda Lopes-da-Silva, Luís G. Gonçalves, Regina Menezes, Marcel Ottens, Derek Stewart,et al.
Springer Science and Business Media LLC
AbstractParkinson’s Disease (PD) is a common neurodegenerative disorder affecting millions of people worldwide for which there are only symptomatic therapies. Small molecules able to target key pathological processes in PD have emerged as interesting options for modifying disease progression. We have previously shown that a (poly)phenol-enriched fraction (PEF) of Corema album L. leaf extract modulates central events in PD pathogenesis, namely α-synuclein (αSyn) toxicity, aggregation and clearance. PEF was now subjected to a bio-guided fractionation with the aim of identifying the critical bioactive compound. We identified genipin, an iridoid, which relieves αSyn toxicity and aggregation. Furthermore, genipin promotes metabolic alterations and modulates lipid storage and endocytosis. Importantly, genipin was able to prevent the motor deficits caused by the overexpression of αSyn in a Drosophila melanogaster model of PD. These findings widens the possibility for the exploitation of genipin for PD therapeutics.
Abdulbasit Amin, Marina Badenes, Johanna Tüshaus, Érika de Carvalho, Emma Burbridge, Pedro Faísca, Květa Trávníčková, André Barros, Stefania Carobbio, Pedro M. Domingos,et al.
Elsevier BV
Marina Badenes, Emma Burbridge, Ioanna Oikonomidi, Abdulbasit Amin, Érika de Carvalho, Lindsay Kosack, Camila Mariano, Pedro Domingos, Pedro Faísca, and Colin Adrain
Life Science Alliance, LLC
The metalloprotease ADAM17 is a sheddase of key molecules, including TNF and epidermal growth factor receptor ligands. ADAM17 exists within an assemblage, the “sheddase complex,” containing a rhomboid pseudoprotease (iRhom1 or iRhom2). iRhoms control multiple aspects of ADAM17 biology. The FERM domain–containing protein iTAP/Frmd8 is an iRhom-binding protein that prevents the precocious shunting of ADAM17 and iRhom2 to lysosomes and their consequent degradation. As pathophysiological role(s) of iTAP/Frmd8 have not been addressed, we characterized the impact of iTAP/Frmd8 loss on ADAM17-associated phenotypes in mice. We show that iTAP/Frmd8 KO mice exhibit defects in inflammatory and intestinal epithelial barrier repair functions, but not the collateral defects associated with global ADAM17 loss. Furthermore, we show that iTAP/Frmd8 regulates cancer cell growth in a cell-autonomous manner and by modulating the tumor microenvironment. Our work suggests that pharmacological intervention at the level of iTAP/Frmd8 may be beneficial to target ADAM17 activity in specific compartments during chronic inflammatory diseases or cancer, while avoiding the collateral impact on the vital functions associated with the widespread inhibition of ADAM17.
Fátima Cairrão, Cristiana C. Santos, Adrien Le Thomas, Scot Marsters, Avi Ashkenazi, and Pedro M. Domingos
Springer Science and Business Media LLC
AbstractThe unfolded protein response (UPR) maintains homeostasis of the endoplasmic reticulum (ER). Residing in the ER membrane, the UPR mediator Ire1 deploys its cytoplasmic kinase-endoribonuclease domain to activate the key UPR transcription factor Xbp1 through non-conventional splicing of Xbp1 mRNA. Ire1 also degrades diverse ER-targeted mRNAs through regulated Ire1-dependent decay (RIDD), but how it spares Xbp1 mRNA from this decay is unknown. Here, we identify binding sites for the RNA-binding protein Pumilio in the 3′UTR Drosophila Xbp1. In the developing Drosophila eye, Pumilio binds both the Xbp1unspliced and Xbp1spliced mRNAs, but only Xbp1spliced is stabilized by Pumilio. Furthermore, Pumilio displays Ire1 kinase-dependent phosphorylation during ER stress, which is required for its stabilization of Xbp1spliced. hIRE1 can phosphorylate Pumilio directly, and phosphorylated Pumilio protects Xbp1spliced mRNA against RIDD. Thus, Ire1-mediated phosphorylation enables Pumilio to shield Xbp1spliced from RIDD. These results uncover an unexpected regulatory link between an RNA-binding protein and the UPR.
Catarina J Gaspar, Lígia C Vieira, Cristiana C Santos, John C Christianson, David Jakubec, Kvido Strisovsky, Colin Adrain, and Pedro M Domingos
Springer Science and Business Media LLC
The ER membrane protein complex (EMC) is required for the biogenesis of a subset of tail anchored (TA) and polytopic membrane proteins, including Rhodopsin‐1 (Rh1) and the TRP channel. To understand the physiological implications of EMC‐dependent membrane protein biogenesis, we perform a bioinformatic identification of Drosophila TA proteins. From 254 predicted TA proteins, screening in larval eye discs identified two proteins that require EMC for their biogenesis: fan and Xport‐A. Fan is required for male fertility in Drosophila and we show that EMC is also required for this process. Xport‐A is essential for the biogenesis of both Rh1 and TRP, raising the possibility that disruption of Rh1 and TRP biogenesis in EMC mutants is secondary to the Xport‐A defect. We show that EMC is required for Xport‐A TMD membrane insertion and that EMC‐independent Xport‐A mutants rescue Rh1 and TRP biogenesis in EMC mutants. Finally, our work also reveals a role for Xport‐A in a glycosylation‐dependent triage mechanism during Rh1 biogenesis in the endoplasmic reticulum.
Jessika C Bridi, Erika Bereczki, Saffron K Smith, Gonçalo M Poças, Benjamin Kottler, Pedro M Domingos, Christopher J Elliott, Dag Aarsland, and Frank Hirth
Oxford University Press (OUP)
Abstract Alpha-synuclein (α-syn) mislocalization and accumulation in intracellular inclusions is the major pathological hallmark of degenerative synucleinopathies, including Parkinson’s disease, Parkinson’s disease with dementia and dementia with Lewy bodies. Typical symptoms are behavioural abnormalities including motor deficits that mark disease progression, while non-motor symptoms and synaptic deficits are already apparent during the early stages of disease. Synucleinopathies have therefore been considered synaptopathies that exhibit synaptic dysfunction prior to neurodegeneration. However, the mechanisms and events underlying synaptopathy are largely unknown. Here we investigated the cascade of pathological events underlying α-syn accumulation and toxicity in a Drosophila model of synucleinopathy by employing a combination of histological, biochemical, behavioural and electrophysiological assays. Our findings demonstrate that targeted expression of human α-syn leads to its accumulation in presynaptic terminals that caused downregulation of synaptic proteins, cysteine string protein, synapsin, and syntaxin 1A, and a reduction in the number of Bruchpilot puncta, the core component of the presynaptic active zone essential for its structural integrity and function. These α-syn-mediated presynaptic alterations resulted in impaired neuronal function, which triggered behavioural deficits in ageing Drosophila that occurred prior to progressive degeneration of dopaminergic neurons. Comparable alterations in presynaptic active zone protein were found in patient brain samples of dementia with Lewy bodies. Together, these findings demonstrate that presynaptic accumulation of α-syn impairs the active zone and neuronal function, which together cause synaptopathy that results in behavioural deficits and the progressive loss of dopaminergic neurons. This sequence of events resembles the cytological and behavioural phenotypes that characterise the onset and progression of synucleinopathies, suggesting that α-syn-mediated synaptopathy is an initiating cause of age-related neurodegeneration.
Estefanie Dufey, José Manuel Bravo-San Pedro, Cristian Eggers, Matías González-Quiroz, Hery Urra, Alfredo I. Sagredo, Denisse Sepulveda, Philippe Pihán, Amado Carreras-Sureda, Younis Hazari,et al.
Springer Science and Business Media LLC
AbstractThe molecular connections between homeostatic systems that maintain both genome integrity and proteostasis are poorly understood. Here we identify the selective activation of the unfolded protein response transducer IRE1α under genotoxic stress to modulate repair programs and sustain cell survival. DNA damage engages IRE1α signaling in the absence of an endoplasmic reticulum (ER) stress signature, leading to the exclusive activation of regulated IRE1α-dependent decay (RIDD) without activating its canonical output mediated by the transcription factor XBP1. IRE1α endoribonuclease activity controls the stability of mRNAs involved in the DNA damage response, impacting DNA repair, cell cycle arrest and apoptosis. The activation of the c-Abl kinase by DNA damage triggers the oligomerization of IRE1α to catalyze RIDD. The protective role of IRE1α under genotoxic stress is conserved in fly and mouse. Altogether, our results uncover an important intersection between the molecular pathways that sustain genome stability and proteostasis.
Gonçalo M. Poças, Pedro M. Domingos, and Christen K. Mirth
MyJove Corporation
Foraging and feeding behaviors allow animals to access sources of energy and nutrients essential for their development, health, and fitness. Investigating the neuronal regulation of these behaviors is essential for the understanding of the physiological and molecular mechanisms underlying nutritional homeostasis. The use of genetically tractable animal models such as worms, flies, and fish greatly facilitates these types of studies. In the last decade, the fruit fly Drosophila melanogaster has been used as a powerful animal model by neurobiologists investigating the neuronal control of feeding and foraging behaviors. While undoubtedly valuable, most studies examine adult flies. Here, we describe a protocol that takes advantage of the simpler larval nervous system to investigate neuronal substrates controlling feeding behaviors when larvae are exposed to diets differing in their protein and carbohydrates content. Our methods are based on a quantitative colorimetric no-choice feeding assay, performed in the context of a neuronal thermogenetic-activation screen. As a read-out, the amount of food eaten by larvae over a 1 h interval was used when exposed to one of the three dye-labeled diets that differ in their protein to carbohydrates (P:C) ratios. The efficacy of this protocol is demonstrated in the context of a neurogenetic screen in larval Drosophila, by identifying candidate neuronal populations regulating the amount of food eaten in diets of different macronutrient quality. We were also able to classify and group the genotypes tested into phenotypic classes. Besides a brief review of the currently available methods in the literature, the advantages and limitations of these methods are discussed and, also, some suggestions are provided about how this protocol might be adapted to other specific experiments.
Pedro M. Domingos, Andreas Jenny, Keon F. Combie, David del Alamo, Marek Mlodzik, Hermann Steller, and Bertrand Mollereau
Elsevier BV
Marion Robin, Abdul Raouf Issa, Cristiana C. Santos, Francesco Napoletano, Céline Petitgas, Gilles Chatelain, Mathilde Ruby, Ludivine Walter, Serge Birman, Pedro M. Domingos,et al.
Informa UK Limited
ABSTRACT The tumor suppressor TP53/p53 is a known regulator of apoptosis and macroautophagy/autophagy. However, the molecular mechanism by which TP53 regulates 2 apparently incompatible processes remains unknown. We found that Drosophila lacking p53 displayed impaired autophagic flux, higher caspase activation and mortality in response to oxidative stress compared with wild-type flies. Moreover, autophagy and apoptosis were differentially regulated by the p53 (p53B) and ΔNp53 (p53A) isoforms: while the former induced autophagy in differentiated neurons, which protected against cell death, the latter inhibited autophagy by activating the caspases Dronc, Drice, and Dcp-1. Our results demonstrate that the differential use of p53 isoforms combined with the antagonism between apoptosis and autophagy ensures the generation of an appropriate p53 biological response to stress.
Colin Adrain, Sivan Henis-Korenblit, and Pedro M. Domingos
The Company of Biologists
ABSTRACT It was a sunny Ericeira, in Portugal, that received the participants of the EMBO Workshop on Proteostasis, from 17 to 21 November 2017. Most participants gave talks or presented posters concerning their most recent research results, and lively scientific discussions occurred against the backdrop of the beautiful Atlantic Ocean. Proteostasis is the portmanteau of the words protein and homeostasis, and it refers to the biological mechanisms controlling the biogenesis, folding, trafficking and degradation of proteins in cells. An imbalance in proteostasis can lead to the accumulation of misfolded proteins or excessive protein degradation, and is associated with many human diseases. A wide variety of research approaches are used to identify the mechanisms that regulate proteostasis, typically involving different model organisms (yeast, invertebrates or mammalian systems) and different methodologies (genetics, biochemistry, biophysics, structural biology, cell biology and organismal biology). Around 140 researchers in the proteostasis field met in the Hotel Vila Galé, Ericeira, Portugal for the EMBO Workshop in Proteostasis, organized by Pedro Domingos (ITQB-NOVA, Oeiras, Portugal) and Colin Adrain (IGC, Oeiras, Portugal). In this report, we attempt to review and integrate the ideas that emerged at the workshop. Owing to space restrictions, we could not cover all talks or posters and we apologize to the colleagues whose presentations could not be discussed.
Huai-Wei Huang, Brian Brown, Jaehoon Chung, Pedro M. Domingos, and Hyung Don Ryoo
Elsevier BV
Miguel Cavadas, Ioanna Oikonomidi, Catarina J. Gaspar, Emma Burbridge, Marina Badenes, Inês Félix, Alfonso Bolado, Tianyi Hu, Andrea Bileck, Christopher Gerner,et al.
Elsevier BV
Joana Branco-Santos, Federico Herrera, Gonçalo M. Poças, Yolanda Pires-Afonso, Flaviano Giorgini, Pedro M. Domingos, and Tiago F. Outeiro
Oxford University Press (OUP)
Huntington’s disease (HD) is neurodegenerative disorder caused by a polyglutamine expansion in the N-terminal region of the huntingtin protein (N17). Here, we analysed the relative contribution of each phosphorylatable residue in the N17 region (T3, S13 and S16) towards huntingtin exon 1 (HTTex1) oligomerization, aggregation and toxicity in human cells and Drosophila neurons. We used bimolecular fluorescence complementation (BiFC) to show that expression of single phosphomimic mutations completely abolished HTTex1 aggregation in human cells. In Drosophila, Mimicking phosphorylation at T3 decreased HTTex1 aggregation both in larvae and adult flies. Interestingly, pharmacological or genetic inhibition of protein phosphatase 1 (PP1) prevented HTTex1 aggregation in both human cells and Drosophila while increasing neurotoxicity in flies. Our findings suggest that PP1 modulates HTTex1 aggregation by regulating phosphorylation on T3. In summary, our study suggests that modulation of HTTex1 single phosphorylation events by PP1 could constitute an efficient and direct molecular target for therapeutic interventions in HD.
B. Mollereau, N.M. Rzechorzek, B.D. Roussel, M. Sedru, D.M. Van den Brink, B. Bailly-Maitre, F. Palladino, D.B. Medinas, P.M. Domingos, S. Hunot,et al.
Elsevier BV
G. M. Pocas, J. Branco-Santos, F. Herrera, T. F. Outeiro, and P. M. Domingos
Oxford University Press (OUP)
Protein misfolding and aggregation is a major hallmark of neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's disease (PD) and Huntington's disease (HD). Until recently, the consensus was that each aggregation-prone protein was characteristic of each disorder [α-synuclein (α-syn)/PD, mutant huntingtin (Htt)/HD, Tau and amyloid beta peptide/AD]. However, growing evidence indicates that aggregation-prone proteins can actually co-aggregate and modify each other's behavior and toxicity, suggesting that this process may also contribute to the overlap in clinical symptoms across different diseases. Here, we show that α-syn and mutant Htt co-aggregate in vivo when co-expressed in Drosophila and produce a synergistic age-dependent increase in neurotoxicity associated to a decline in motor function and life span. Altogether, our results suggest that the co-existence of α-syn and Htt in the same neuronal cells worsens aggregation-related neuropathologies and accelerates disease progression.
Dina S. Coelho, Catarina J. Gaspar, and Pedro M. Domingos
Public Library of Science (PLoS)
The Unfolded Protein Response is a homeostatic mechanism that permits eukaryotic cells to cope with Endoplasmic Reticulum (ER) stress caused by excessive accumulation of misfolded proteins in the ER lumen. The more conserved branch of the UPR relies on an ER transmembrane enzyme, Ire1, which, upon ER stress, promotes the unconventional splicing of a small intron from the mRNA encoding the transcription factor Xbp1. In mammals, two specific regions (the hydrophobic region 2 - HR2 - and the C-terminal translational pausing site) present in the Xbp1unspliced protein mediate the recruitment of the Xbp1 mRNA-ribosome-nascent chain complex to the ER membrane, so that Xbp1 mRNA can be spliced by Ire1. Here, we generated a Drosophila Xbp1 deletion mutant (Excision101) lacking both HR2 and C-terminal region, but not the Ire1 splicing site. We show that Ire1-dependent splicing of Xbp1 mRNA is reduced, but not abolished in Excision101. Our results suggest the existence of additional mechanisms for ER membrane targeting of Xbp1 mRNA that are independent of the C-terminal domain of Drosophila Xbp1unspliced.
Dina S. Coelho and Pedro M. Domingos
Frontiers Media SA
Inositol-requiring enzyme 1 (Ire1) is an important transducer of the unfolded protein response (UPR) that is activated by the accumulation of misfolded proteins in the endoplamic reticulum (ER stress). Activated Ire1 mediates the splicing of an intron from the mRNA of Xbp1, causing a frame-shift during translation and introducing a new carboxyl domain in the Xbp1 protein, which only then becomes a fully functional transcription factor. Studies using cell culture systems demonstrated that Ire1 also promotes the degradation of mRNAs encoding mostly ER-targeted proteins, to reduce the load of incoming ER “client” proteins during ER stress. This process was called RIDD (regulated Ire1-dependent decay), but its physiological significance remained poorly characterized beyond cell culture systems. Here we review several recent studies that have highlighted the physiological roles of RIDD in specific biological paradigms, such as photoreceptor differentiation in Drosophila or mammalian liver and endocrine pancreas function. These studies demonstrate the importance of RIDD in tissues undergoing intense secretory function and highlight the physiologic role of RIDD during UPR activation in cells and organisms.
Dina S. Coelho, Fatima Cairrão, Xiaomei Zeng, Elisabete Pires, Ana V. Coelho, David Ron, Hyung Don Ryoo, and Pedro M. Domingos
Elsevier BV
Vanya I. Rasheva and Pedro M. Domingos
Springer Science and Business Media LLC
Pedro M Domingos and Hermann Steller
Elsevier BV
Hyung Don Ryoo, Pedro M Domingos, Min-Ji Kang, and Hermann Steller
Springer Science and Business Media LLC
Bertrand Mollereau and Pedro M. Domingos
Wiley
AbstractHow a pool of equipotent cells acquires a multitude of distinct fates is a major question in developmental biology. The study of photoreceptor (PR) cell differentiation in Drosophila has been used to address this question. PR differentiation is a process that extends over a period of 5 days: It begins in the larval eye imaginal disc when PRs are recruited and commit to particular PR fates, and it culminates in the pupal eye disc with the morphogenesis of the rhabdomeres and the initiation of rhodopsin expression. Several models for PR specification agree that the Ras and Notch signaling pathways are important for the specification of different PR subtypes (Freeman [1997] Development 124:261–270; Cooper and Bray [2000] Curr. Biol. 10:1507–1510; Tomlinson and Struhl [2001] Mol. Cell. 7:487–495). In the first part of this review, we briefly describe the different signaling pathways and transcription factors required for the specification and differentiation of the different PR subtypes in the larval eye disc. In the second part, we review the roles of several transcription factors, which are required for the terminal photoreceptor differentiation and rhodopsin expression. Developmental Dynamics 232:585–592, 2005. © 2005 Wiley‐Liss, Inc.
Pedro M. Domingos, Marek Mlodzik, César S. Mendes, Samara Brown, Hermann Steller, and Bertrand Mollereau
The Company of Biologists
The establishment of planar cell polarity in the Drosophila eye requires correct specification of the R3/R4 pair of photoreceptor cells. In response to a polarizing factor, Frizzled signaling specifies R3 and induces Delta, which activates Notch in the neighboring cell, specifying it as R4. Here, we show that the spalt zinc-finger transcription factors(spalt major and spalt-related) are part of the molecular mechanisms regulating R3/R4 specification and planar cell polarity establishment. In mosaic analysis, we find that the spalt genes are specifically required in R3 for the establishment of correct ommatidial polarity. In addition, we show that spalt genes are required for proper localization of Flamingo in the equatorial side of R3 and R4, and for the upregulation of Delta in R3. These requirements are very similar to those of frizzled during R3/R4 specification. We show that spalt genes are required cell-autonomously for the expression of seven-up in R3 and R4, and that seven-up is downstream of spalt genes in the genetic hierarchy of R3/R4 specification. Thus, spalt and seven-up are necessary for the correct interpretation of the Frizzled-mediated polarity signal in R3. Finally, we show that, posterior to row seven, seven-up represses spaltin R3/R4 in order to maintain the R3/R4 identity and to inhibit the transformation of these cells to the R7 cell fate.