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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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D’Alessio S, Buckley KM, Kraev I, Hayes P, Lange S. Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin ( Strongylocentrotus purpuratus) Coelomic Fluid-Novel Insights into Echinodermata Biology. BIOLOGY 2021; 10:866. [PMID: 34571743 PMCID: PMC8464700 DOI: 10.3390/biology10090866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
The purple sea urchin (Strongylocentrotus purpuratus) is a marine invertebrate of the class Echinoidea that serves as an important research model for developmental biology, cell biology, and immunology, as well as for understanding regenerative responses and ageing. Peptidylarginine deiminases (PADs) are calcium-dependent enzymes that mediate post-translational protein deimination/citrullination. These alterations affect protein function and may also play roles in protein moonlighting. Extracellular vesicles (EVs) are membrane-bound vesicles that are released from cells as a means of cellular communication. Their cargo includes a range of protein and RNA molecules. EVs can be isolated from many body fluids and are therefore used as biomarkers in physiological and pathological responses. This study assessed EVs present in the coelomic fluid of the purple sea urchin (Strongylocentrotus purpuratus), and identified both total protein cargo as well as the deiminated protein cargo. Deiminated proteins in coelomic fluid EVs were compared with the total deiminated proteins identified in coelomic fluid to assess putative differences in deiminated protein targets. Functional protein network analysis for deiminated proteins revealed pathways for immune, metabolic, and gene regulatory functions within both total coelomic fluid and EVs. Key KEGG and GO pathways for total EV protein cargo furthermore showed some overlap with deimination-enriched pathways. The findings presented in this study add to current understanding of how post-translational deimination may shape immunity across the phylogeny tree, including possibly via PAD activity from microbiota symbionts. Furthermore, this study provides a platform for research on EVs as biomarkers in sea urchin models.
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Affiliation(s)
- Stefania D’Alessio
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
| | | | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Polly Hayes
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
- UCL EGA Institute for Women’s Health, Maternal and Fetal Medicine, London WC1E 6AU, UK
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Masullo T, Biondo G, Natale MD, Tagliavia M, Bennici CD, Musco M, Ragusa MA, Costa S, Cuttitta A, Nicosia A. Gene Expression Changes after Parental Exposure to Metals in the Sea Urchin Affect Timing of Genetic Programme of Embryo Development. BIOLOGY 2021; 10:biology10020103. [PMID: 33535713 PMCID: PMC7912929 DOI: 10.3390/biology10020103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/20/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022]
Abstract
It is widely accepted that phenotypic traits can be modulated at the epigenetic level so that some conditions can affect the progeny of exposed individuals. To assess if the exposure of adult animals could result in effects on the offspring, the Mediterranean sea urchin and its well-characterized gene regulatory networks (GRNs) was chosen as a model. Adult animals were exposed to known concentrations of zinc and cadmium (both individually and in combination) for 10 days, and the resulting embryos were followed during the development. The oxidative stress occurring in parental gonads, embryo phenotypes and mortality, and the expression level of a set of selected genes, including members of the skeletogenic and endodermal GRNs, were evaluated. Increased oxidative stress at F0, high rates of developmental aberration with impaired gastrulation, in association to deregulation of genes involved in skeletogenesis (dri, hex, sm50, p16, p19, msp130), endodermal specification (foxa, hox11/13b, wnt8) and epigenetic regulation (kat2A, hdac1, ehmt2, phf8 and UBE2a) occurred either at 24 or 48 hpf. Results strongly indicate that exposure to environmental pollutants can affect not only directly challenged animals but also their progeny (at least F1), influencing optimal timing of genetic programme of embryo development, resulting in an overall impairment of developmental success.
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Affiliation(s)
- Tiziana Masullo
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
| | - Girolama Biondo
- Institute for Anthropic Impacts and Sustainability in Marine Environment-National Research Council (IAS-CNR), Detached Unit of Capo Granitola, Via del mare 3, 91021 Campobello di Mazara, Italy;
| | - Marilena Di Natale
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
- Department of Earth and Marine Science (DiSTeM), University of Palermo, Via Archirafi 20, 90123 Palermo, Italy
| | - Marcello Tagliavia
- Institute for Biomedical Research and Innovation-National Research Council-(IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy;
| | - Carmelo Daniele Bennici
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
| | - Marianna Musco
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
| | - Maria Antonietta Ragusa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy; (M.A.R.); (S.C.)
| | - Salvatore Costa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy; (M.A.R.); (S.C.)
| | - Angela Cuttitta
- Institute for Studies on the Mediterranean-National Research Council (ISMED-CNR), Detached Unit of Palermo, Via Filippo Parlatore 65, 90145 Palermo, Italy; (T.M.); (M.D.N.); (C.D.B.); (M.M.)
- Correspondence: (A.C.); (A.N.)
| | - Aldo Nicosia
- Institute for Biomedical Research and Innovation-National Research Council-(IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy;
- Correspondence: (A.C.); (A.N.)
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Russo R, Chiaramonte M, Lampiasi N, Zito F. MITF: an evolutionarily conserved transcription factor in the sea urchin Paracentrotus lividus. Genetica 2019; 147:369-379. [PMID: 31625006 DOI: 10.1007/s10709-019-00077-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/09/2019] [Indexed: 11/28/2022]
Abstract
Microphthalmia-associated transcription factor (MITF) is a member of MYC superfamily, associated with melanocyte cells, as it was discovered in depigmented mice. However, over the last years it was found to be involved in many cellular signaling pathways, among which oncogenesis, osteoclast differentiation, and stress response. In mammals, Mitf gene mutations can cause diverse syndromes affecting pigmentation of eyes or skin, bone defects and melanomas. As MITF protein homologs were also found in some invertebrates, we have isolated and characterized the MITF cDNAs from the sea urchin Paracentrotus lividus, referred to as Pl-Mitf. The in silico study of the secondary and tertiary structure of Pl-Mitf protein showed high conserved regions mostly lying in the DNA binding domain. To understand the degree of evolutionary conservation of MITF, a phylogenetic analysis was performed comparing the Pl-Mitf deduced protein with proteins from different animal species. Moreover, the analysis of temporal and spatial expression pattern of Pl-Mitf mRNA showed that it was expressed from the onset of gastrulation of the sea urchin embryo to the pluteus larva, specifically in primary mesenchymes cells (PMCs), the sea urchin skeletogenic cells, and in the forming archenteron, the larval gut precursor. In silico protein-protein interactions analysis was used to understand the association of MITF with other proteins. Our results put in evidence the conservation of the MITF protein among vertebrates and invertebrates and may provide new perspectives on the pathways underlying sea urchin development, even if further functional analyses are needed.
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Affiliation(s)
- Roberta Russo
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l'Innovazione Biomedica, Via Ugo La Malfa 153, 90146, Palermo, Italy.
| | - Marco Chiaramonte
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l'Innovazione Biomedica, Via Ugo La Malfa 153, 90146, Palermo, Italy
| | - Nadia Lampiasi
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l'Innovazione Biomedica, Via Ugo La Malfa 153, 90146, Palermo, Italy
| | - Francesca Zito
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l'Innovazione Biomedica, Via Ugo La Malfa 153, 90146, Palermo, Italy.
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Vibrio Proteases for Biomedical Applications: Modulating the Proteolytic Secretome of V. alginolyticus and V. parahaemolyticus for Improved Enzymes Production. Microorganisms 2019; 7:microorganisms7100387. [PMID: 31554228 PMCID: PMC6843219 DOI: 10.3390/microorganisms7100387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 01/03/2023] Open
Abstract
Proteolytic enzymes are of great interest for biotechnological purposes, and their large-scale production, as well as the discovery of strains producing new molecules, is a relevant issue. Collagenases are employed for biomedical and pharmaceutical purposes. The high specificity of collagenase-based preparations toward the substrate strongly relies on the enzyme purity. However, the overall activity may depend on the cooperation with other proteases, the presence of which may be essential for the overall enzymatic activity, but potentially harmful for cells and tissues. Vibrios produce some of the most promising bacterial proteases (including collagenases), and their exo-proteome includes several enzymes with different substrate specificities, the production and relative abundances of which strongly depend on growth conditions. We evaluated the effects of different media compositions on the proteolytic exo-proteome of Vibrio alginolyticus and its closely relative Vibrio parahaemolyticus, in order to improve the overall proteases production, as well as the yield of the desired enzymes subset. Substantial biological responses were achieved with all media, which allowed defining culture conditions for targeted improvement of selected enzyme classes, besides giving insights in possible regulatory mechanisms. In particular, we focused our efforts on collagenases production, because of the growing biotechnological interest due to their pharmaceutical/biomedical applications.
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