Model of cap‐dependent translation initiation in sea urchin: A step towards the eukaryotic translation regulation network

Bellé, Robert; Prigent, Sylvain; Siegel, Anne

doi:10.1002/mrd.21142

Cited by 7 publications

(9 citation statements)

References 43 publications

(49 reference statements)

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“…A model for cap-dependent translation initiation in sea urchin has been proposed (Belle et al, 2010) based on the systemic environment of BIOCHAM software (Calzone et al, 2006). The Biocham model contains too many reactions and undetermined parameters to allow quantitative simulations of dynamic changes occurring at fertilization.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2014

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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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Section: Resultsmentioning

confidence: 99%

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

et al. 2014

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“…To study early development of the brown algal model E. siliculosus , Billoud et al [139] developed a stochastic 1D nearest-neighbor automaton that was further implemented to characterize an artificial mutant altered in its pattern of development [140]. At the cellular scale, and for sea urchin, gene regulatory networks [141], and translational regulation networks [142] were developed a few years ago. Regarding metabolic processes, relevant networks have been reconstructed for marine microorganisms such as Thermotoga maritima [143], Vibrio vulnificus [144], and Phaeodactylum tricornutum [118].…”

Section: Metabolite Profiling For Integrative and Systems Biologymentioning

confidence: 99%

Mass Spectrometry-Based Metabolomics to Elucidate Functions in Marine Organisms and Ecosystems

2012

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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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“…Many tools we reviewed have only been used by their developers. Two relevant exceptions, however, are Biocham, used e.g., by Bellé et al (2010) and GNA, used e.g., by Viretta and Fussenegger (2004) and Sepulchre et al (2007). …”

Section: Discussionmentioning

confidence: 99%

“…Moreover, Biocham has been used by biologists working independently from Biocham's developers. Bellé et al (2010), for instance, has used Biocham to model the cap-dependent translation initiation in sea urchin.…”

Section: Specialized Toolsmentioning

confidence: 99%

An overview of existing modeling tools making use of model checking in the analysis of biochemical networks

Carrillo¹,

Góngora²,

Rosenblueth³

2012

Front. Plant Sci.

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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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Model of cap‐dependent translation initiation in sea urchin: A step towards the eukaryotic translation regulation network

Cited by 7 publications

References 43 publications

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

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

Mass Spectrometry-Based Metabolomics to Elucidate Functions in Marine Organisms and Ecosystems

An overview of existing modeling tools making use of model checking in the analysis of biochemical networks

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