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eIF4B mRNA Translation Contributes to Cleavage Dynamics in Early Sea Urchin Embryos. BIOLOGY 2022; 11:biology11101408. [PMID: 36290313 PMCID: PMC9598784 DOI: 10.3390/biology11101408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Cell division, also known as mitosis, relies on a complex cascade of molecular events that orchestrates the whole process and decides when cells can start dividing. A key factor in this process is protein synthesis, which is carefully regulated inside the cell to assure the timely production of all the proteins required for mitosis. The embryos of sea urchins divide rapidly after fertilization and represent an informative model to analyze the role of protein synthesis regulation during cell cycle progression. For example, the analysis in the 1980s of sea urchin embryos fostered the discovery of Cyclin B, the first representative of a family of proteins that plays a universal role in controlling cell division. This finding was awarded in 2001 with the Nobel Prize in Physiology and Medicine. However, much remains to be learned, and how protein synthesis controls the time and speed of mitosis in a developing embryo is still unclear. For instance, discovering whether the translation of other mRNAs than mitotic cyclins is required to finely regulate the rate of embryonic cleavage has never been tested. In this work, we investigated the role of the translation of an mRNA encoding a protein called eIF4B in the dynamics of embryonic cell division. We showed that newly synthesized eIF4B directly impacts cell division rates in two sea urchin species. Cell divisions are delayed when the production of eIF4B is inhibited in a fertilized egg. Conversely, increased production of eIF4B accelerates mitosis. Therefore, eIF4B mRNA translation represents a new means to regulate the pace of embryonic cleavages. Moreover, since eIF4B is a translational regulator, our findings suggest that the function of its mRNA translation is boosting the production of other proteins essential for mitosis. The cells of the sea urchin embryos seem thus equipped with a controlling device capable of modulating cell division rates, a molecular switch that could contribute to coordinating the first steps of development in other animals as well. Abstract During the first steps of sea urchin development, fertilization elicits a marked increase in protein synthesis essential for subsequent cell divisions. While the translation of mitotic cyclin mRNAs is crucial, we hypothesized that additional mRNAs must be translated to finely regulate the onset into mitosis. One of the maternal mRNAs recruited onto active polysomes at this stage codes for the initiation factor eIF4B. Here, we show that the sea urchin eIF4B orthologs present the four specific domains essential for eIF4B function and that Paracentrotus lividus eIF4B copurifies with eIF4E in a heterologous system. In addition, we investigated the role of eIF4B mRNA de novo translation during the two first embryonic divisions of two species, P. lividus and Sphaerechinus granularis. Our results show that injection of a morpholino directed against eIF4B mRNA results in a downregulation of translational activity and delays cell division in these two echinoids. Conversely, injection of an mRNA encoding for P. lividus eIF4B stimulates translation and significantly accelerates cleavage rates. Taken together, our findings suggest that eIF4B mRNA de novo translation participates in a conserved regulatory loop that contributes to orchestrating protein synthesis and modulates cell division rhythm during early sea urchin development.
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Moundoyi H, Demouy J, Le Panse S, Morales J, Sarels B, Cormier P. Toward Multiscale Modeling of Molecular and Biochemical Events Occurring at Fertilization Time in Sea Urchins. Results Probl Cell Differ 2018; 65:69-89. [DOI: 10.1007/978-3-319-92486-1_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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Picard V, Mulner-Lorillon O, Bourdon J, Morales J, Cormier P, Siegel A, Bellé R. Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization. Mol Reprod Dev 2016; 83:1070-1082. [PMID: 27699901 DOI: 10.1002/mrd.22746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/01/2016] [Indexed: 01/24/2023]
Abstract
Sea urchin eggs exhibit a cap-dependent increase in protein synthesis within minutes after fertilization. This rise in protein synthesis occurs at a constant rate for a great number of proteins translated from the different available mRNAs. Surprisingly, we found that cyclin B, a major cell-cycle regulator, follows a synthesis pattern that is distinct from the global protein population, so we developed a mathematical model to analyze this dissimilarity in biosynthesis kinetic patterns. The model includes two pathways for cyclin B mRNA entry into the translational machinery: one from immediately available mRNA (mRNAcyclinB) and one from mRNA activated solely after fertilization (XXmRNAcyclinB). Two coefficients, α and β, were added to fit the measured scales of global protein and cyclin B synthesis, respectively. The model was simplified to identify the synthesis parameters and to allow its simulation. The calculated parameters for activation of the specific cyclin B synthesis pathway after fertilization included a kinetic constant (ka ) of 0.024 sec-1 , for the activation of XXmRNAcyclinB, and a critical time interval (t2 ) of 42 min. The proportion of XXmRNAcyclinB form was also calculated to be largely dominant over the mRNAcyclinB form. Regulation of cyclin B biosynthesis is an example of a select protein whose translation is controlled by pathways that are distinct from housekeeping proteins, even though both involve the same cap-dependent initiation pathway. Therefore, this model should help provide insight to the signaling utilized for the biosynthesis of cyclin B and other select proteins. Mol. Reprod. Dev. 83: 1070-1082, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vincent Picard
- CNRS UMR 6241, Laboratoire LINA, Université de Nantes, Nantes, France.,CNRS, IRISA-UMR 6074, Campus de Beaulieu, Rennes, France.,INRIA, Centre Rennes-Bretagne Atlantique, Symbiose, Campus de Beaulieu, Rennes, France
| | - Odile Mulner-Lorillon
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, Roscoff Cedex, France.,CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, Roscoff Cedex, France
| | - Jérémie Bourdon
- CNRS UMR 6241, Laboratoire LINA, Université de Nantes, Nantes, France
| | - Julia Morales
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, Roscoff Cedex, France.,CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, Roscoff Cedex, France
| | - Patrick Cormier
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, Roscoff Cedex, France.,CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, Roscoff Cedex, France
| | - Anne Siegel
- CNRS, IRISA-UMR 6074, Campus de Beaulieu, Rennes, France.,INRIA, Centre Rennes-Bretagne Atlantique, Symbiose, Campus de Beaulieu, Rennes, France
| | - Robert Bellé
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, Roscoff Cedex, France.,CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, Roscoff Cedex, France
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Laurent S, Richard A, Mulner-Lorillon O, Morales J, Flament D, Glippa V, Bourdon J, Gosselin P, Siegel A, Cormier P, Bellé R. Modelization of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensitive. Front Genet 2014; 5:117. [PMID: 24834072 PMCID: PMC4018528 DOI: 10.3389/fgene.2014.00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/16/2014] [Indexed: 11/13/2022] Open
Abstract
Fertilization of sea urchin eggs involves an increase in protein synthesis associated with a decrease in the amount of the translation initiation inhibitor 4E-BP. A highly simple reaction model for the regulation of protein synthesis was built and was used to simulate the physiological changes in the total 4E-BP amount observed during time after fertilization. Our study evidenced that two changes occurring at fertilization are necessary to fit with experimental data. The first change was an 8-fold increase in the dissociation parameter (koff1) of the eIF4E:4E-BP complex. The second was an important 32.5-fold activation of the degradation mechanism of the protein 4E-BP. Additionally, the changes in both processes should occur in 5 min time interval post-fertilization. To validate the model, we checked that the kinetic of the predicted 4.2-fold increase of eIF4E:eIF4G complex concentration at fertilization matched the increase of protein synthesis experimentally observed after fertilization (6.6-fold, SD = 2.3, n = 8). The minimal model was also used to simulate changes observed after fertilization in the presence of rapamycin, a FRAP/mTOR inhibitor. The model showed that the eIF4E:4E-BP complex destabilization was impacted and surprisingly, that the mechanism of 4E-BP degradation was also strongly affected, therefore suggesting that both processes are controlled by the protein kinase FRAP/mTOR.
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Affiliation(s)
- Sébastien Laurent
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Adrien Richard
- Université de Nice-Sophia Antipolis, UMR 7271, Laboratoire I3S Sophia, Antipolis, France
| | - Odile Mulner-Lorillon
- Sorbonne Universités, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France
| | - Julia Morales
- Sorbonne Universités, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France
| | - Didier Flament
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Virginie Glippa
- Sorbonne Universités, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France
| | - Jérémie Bourdon
- CNRS UMR 6241, Laboratoire LINA, Université de Nantes Nantes, France
| | - Pauline Gosselin
- Sorbonne Universités, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France
| | - Anne Siegel
- CNRS, IRISA-UMR 6074, Campus de Beaulieu Rennes, France ; INRIA, Centre Rennes - Bretagne Atlantique, Symbiose, Campus de Beaulieu Rennes, France
| | - Patrick Cormier
- Sorbonne Universités, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France
| | - Robert Bellé
- Sorbonne Universités, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development Station Biologique de Roscoff, Roscoff cedex, France
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Carrillo M, Góngora PA, Rosenblueth DA. An overview of existing modeling tools making use of model checking in the analysis of biochemical networks. FRONTIERS IN PLANT SCIENCE 2012; 3:155. [PMID: 22833747 PMCID: PMC3400939 DOI: 10.3389/fpls.2012.00155] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 06/24/2012] [Indexed: 05/24/2023]
Abstract
Model checking is a well-established technique for automatically verifying complex systems. Recently, model checkers have appeared in computer tools for the analysis of biochemical (and gene regulatory) networks. We survey several such tools to assess the potential of model checking in computational biology. Next, our overview focuses on direct applications of existing model checkers, as well as on algorithms for biochemical network analysis influenced by model checking, such as those using binary decision diagrams (BDDs) or Boolean-satisfiability solvers. We conclude with advantages and drawbacks of model checking for the analysis of biochemical networks.
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Affiliation(s)
| | | | - David A. Rosenblueth
- *Correspondence: David A. Rosenblueth, Departamento de Ciencias de la Computación, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Apdo. 20-726, 01000 México D.F., México. e-mail:
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Goulitquer S, Potin P, Tonon T. Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems. Mar Drugs 2012; 10:849-880. [PMID: 22690147 PMCID: PMC3366679 DOI: 10.3390/md10040849] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 03/13/2012] [Accepted: 03/21/2012] [Indexed: 01/01/2023] Open
Abstract
Marine systems are very diverse and recognized as being sources of a wide range of biomolecules. This review provides an overview of metabolite profiling based on mass spectrometry (MS) approaches in marine organisms and their environments, focusing on recent advances in the field. We also point out some of the technical challenges that need to be overcome in order to increase applications of metabolomics in marine systems, including extraction of chemical compounds from different matrices and data management. Metabolites being important links between genotype and phenotype, we describe added value provided by integration of data from metabolite profiling with other layers of omics, as well as their importance for the development of systems biology approaches in marine systems to study several biological processes, and to analyze interactions between organisms within communities. The growing importance of MS-based metabolomics in chemical ecology studies in marine ecosystems is also illustrated.
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Affiliation(s)
- Sophie Goulitquer
- Plate-forme MetaboMER, CNRS & UPMC, FR2424, Station Biologique, 29680 Roscoff, France
| | - Philippe Potin
- UMR 7139 Marine Plants and Biomolecules, UPMC Univ Paris 6, Station Biologique, 29680 Roscoff, France; (P.P.); (T.T.)
- UMR 7139 Marine Plants and Biomolecules, CNRS, Station Biologique, 29680 Roscoff, France
| | - Thierry Tonon
- UMR 7139 Marine Plants and Biomolecules, UPMC Univ Paris 6, Station Biologique, 29680 Roscoff, France; (P.P.); (T.T.)
- UMR 7139 Marine Plants and Biomolecules, CNRS, Station Biologique, 29680 Roscoff, France
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