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Russo R, Ragusa MA, Arancio W, Zito F. Gene, Protein, and in Silico Analyses of FoxO, an Evolutionary Conserved Transcription Factor in the Sea Urchin Paracentrotus lividus. Genes (Basel) 2024; 15:1078. [PMID: 39202438 PMCID: PMC11353378 DOI: 10.3390/genes15081078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
FoxO is a member of the evolutionary conserved family of transcription factors containing a Forkhead box, involved in many signaling pathways of physiological and pathological processes. In mammals, mutations or dysfunctions of the FoxO gene have been implicated in diverse diseases. FoxO homologs have been found in some invertebrates, including echinoderms. We have isolated the FoxO cDNA from the sea urchin Paracentrotus lividus (Pl-foxo) and characterized the corresponding gene and mRNA. In silico studies showed that secondary and tertiary structures of Pl-foxo protein corresponded to the vertebrate FoxO3 isoform, with highly conserved regions, especially in the DNA-binding domain. A phylogenetic analysis compared the Pl-foxo deduced protein with proteins from different animal species and confirmed its evolutionary conservation between vertebrates and invertebrates. The increased expression of Pl-foxo mRNA following the inhibition of the PI3K signaling pathway paralleled the upregulation of Pl-foxo target genes involved in apoptosis or cell-cycle arrest events (BI-1, Bax, MnSod). In silico studies comparing molecular data from sea urchins and other organisms predicted a network of Pl-foxo protein-protein interactions, as well as identified potential miRNAs involved in Pl-foxo gene regulation. Our data may provide new perspectives on the knowledge of the signaling pathways underlying sea urchin development.
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Affiliation(s)
- Roberta Russo
- Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy; (W.A.); (F.Z.)
| | - Maria Antonietta Ragusa
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy;
| | - Walter Arancio
- Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy; (W.A.); (F.Z.)
| | - Francesca Zito
- Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy; (W.A.); (F.Z.)
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Telmer CA, Karimi K, Chess MM, Agalakov S, Arshinoff BI, Lotay V, Wang DZ, Chu S, Pells TJ, Vize PD, Hinman VF, Ettensohn CA. Echinobase: a resource to support the echinoderm research community. Genetics 2024; 227:iyae002. [PMID: 38262680 PMCID: PMC11075573 DOI: 10.1093/genetics/iyae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024] Open
Abstract
Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein-protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community.
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Affiliation(s)
- Cheryl A Telmer
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Macie M Chess
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sergei Agalakov
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Bradley I Arshinoff
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Vaneet Lotay
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Dong Zhuo Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Stanley Chu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Troy J Pells
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Zito F, Bonaventura R, Costa C, Russo R. Carbonic anhydrases in development: morphological observations and gene expression profiling in sea urchin embryos exposed to acetazolamide. Open Biol 2023; 13:220254. [PMID: 36597694 PMCID: PMC9811153 DOI: 10.1098/rsob.220254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Carbonic anhydrases (CANs) are conserved metalloenzymes catalysing the reversible hydration of carbon dioxide into protons and bicarbonate, with important roles in cells physiology. Some CAN-coding genes were found in sea urchin genome, although only one involved in embryonic skeletogenesis was described in Paracentrotus lividus. Here, we investigated gene expression patterns of P. lividus embryos cultured in the presence of acetazolamide (AZ), a CAN inhibitor, to combine morphological defects with their molecular underpinning. CAN inhibition blocked skeletogenesis, affected the spatial/temporal expression of some biomineralization-related genes, inhibited embryos swimming. A comparative analysis on the expression of 127 genes in control and 3 h/24 h AZ-treated embryos, using NanoString technology, showed the differential expression of genes encoding for structural/regulatory proteins, with different embryonic roles: biomineralization, transcriptional regulation, signalling, development and defence response. The study of the differentially expressed genes and the signalling pathways affected, besides in silico analyses and a speculative 'interactomic model', leads to predicting the presence of various CAN isoforms, possibly involved in different physiological processes/activities in sea urchin embryo, and their potential target genes/proteins. Our findings provide new valuable molecular data for further studies in several biological fields: developmental biology (biomineralization, axes patterning), cell differentiation (neural development) and drug toxicology (AZ effects on embryos/tissues).
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Affiliation(s)
- Francesca Zito
- Istituto per la Ricerca e l'Innovazione Biomedica, Consiglio Nazionale delle Ricerche, via Ugo La Malfa 153, Palermo 90146, Italy
| | - Rosa Bonaventura
- Istituto per la Ricerca e l'Innovazione Biomedica, Consiglio Nazionale delle Ricerche, via Ugo La Malfa 153, Palermo 90146, Italy
| | - Caterina Costa
- Istituto per la Ricerca e l'Innovazione Biomedica, Consiglio Nazionale delle Ricerche, via Ugo La Malfa 153, Palermo 90146, Italy
| | - Roberta Russo
- Istituto per la Ricerca e l'Innovazione Biomedica, Consiglio Nazionale delle Ricerche, via Ugo La Malfa 153, Palermo 90146, Italy
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Varrella S, Danovaro R, Corinaldesi C. Assessing the eco-compatibility of new generation sunscreen products through a combined microscopic-molecular approach. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120212. [PMID: 36152716 DOI: 10.1016/j.envpol.2022.120212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/31/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
There is now unequivocal evidence that sunscreen can severely affect marine ecosystems. However, so far, most studies have focused on the impact of single sunscreen ingredients rather than on the whole sunscreen products, which are released into the marine environment. In the present work, we investigated the ecological impact of six formulations, which represent the "new generation" organic UV filters such as diethylamino hydroxybenzoyl hexyl benzoate (DHHB), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), ethylhexyl triazone (EHT), and bis-ethylhexyloxyphenol methoxyphenyl triazine (BEMT), which are progressively replacing the "old generation" organic UV filters (e.g., oxybenzone, octinoxate) banned in several countries of the world. The six formulations tested were characterized by a different combination of ingredients, on a model species particularly sensitive to environmental alterations: the sea urchin, Paracentrotus lividus. We investigated the sea urchin responses both in terms of gene expression and anomalies in embryonic development. We found that all sunscreen products containing only MBBT, DHHB, BEMT, and EHT as UV filters, are more eco-compatible than those also containing also ES, or other ingredients such as emollients and texturizing compounds, which may act synergistically causing molecular stress, morphological anomalies, and ultimately possible death. Overall, the results presented here provide new insights on the effects of sunscreen products based on "new generation" UV filters, and highlights the urgency of testing complete formulations, rather than just specific UV filters to ascertain the eco-compatibility of sunscreen products, to effectively minimize their impact on marine ecosystems.
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Affiliation(s)
- Stefano Varrella
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy; Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
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Chiaramonte M, Bonaventura R, Costa C, Zito F, Russo R. [6]-Gingerol dose-dependent toxicity, its role against lipopolysaccharide insult in sea urchin (Paracentrotus lividus Lamarck), and antimicrobial activity. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2020.100833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Changes in the proteome of sea urchin Paracentrotus lividus coelomocytes in response to LPS injection into the body cavity. PLoS One 2020; 15:e0228893. [PMID: 32074628 PMCID: PMC7030939 DOI: 10.1371/journal.pone.0228893] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
Background The immune system of echinoderm sea urchins is characterised by a high degree of complexity that is not completely understood. The Mediterranean sea urchin Paracentrotus lividus coelomocytes mediate immune responses through phagocytosis, encapsulation of non-self particles, and production of diffusible factors including antimicrobial molecules. Details of these processes, and molecular pathways driving these mechanisms, are still to be fully elucidated. Principal findings In the present study we treated the sea urchin P. lividus with the bacterial lipopolysaccharide (LPS) and collected coelomocytes at different time-points (1, 3, 6 and 24 hours). We have shown, using label-free quantitative mass spectrometry, how LPS is able to modulate the coelomocyte proteome and to effect cellular pathways, such as endocytosis and phagocytosis, as soon as the immunomodulating agent is injected. The present study has also shown that treatment can modulate various cellular processes such as cytoskeleton reorganisation, and stress and energetic homeostasis. Conclusions Our data demonstrates, through mass spectrometry and the following functional annotation bioinformatics analysis, how the bacterial wall constituent is sufficient to set off an immune response inducing cytoskeleton reorganisation, the appearance of clusters of heat shock proteins (Hsp) and histone proteins and the activation of the endocytic and phagocytic pathways. Data are available via ProteomeXchange with identifier PXD008439.
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