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    Gene Regulatory Networks of Penicillium echinulatum 2HH and Penicillium oxalicum 114-2 Inferred by a Computational Biology Approach

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    Date
    2020-10
    Author

    Lenz, Alexandre Rafael

    Galán-Vásquez, Edgardo

    Balbinot, Eduardo

    de Abreu, Fernanda Pessi

    Souza de Oliveira, Nikael

    da Rosa, Leticia Osorio

    de Avila e Silva, Scheila

    Camassola, Marli

    Dillon, Aldo Jose Pinheiro

    Pérez-Rueda, Ernesto [Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Chile]

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    Abstract
    Penicillium echinulatum 2HH and Penicillium oxalicum 114-2 are well-known cellulase fungal producers. However, few studies addressing global mechanisms for gene regulation of these two important organisms are available so far. A recent finding that the 2HH wild-type is closely related to P. oxalicum leads to a combined study of these two species. Firstly, we provide a global gene regulatory network for P. echinulatum 2HH and P. oxalicum 114-2, based on TF-TG orthology relationships, considering three related species with well-known regulatory interactions combined with TFBSs prediction. The network was then analyzed in terms of topology, identifying TFs as hubs, and modules. Based on this approach, we explore numerous identified modules, such as the expression of cellulolytic and xylanolytic systems, where XlnR plays a key role in positive regulation of the xylanolytic system. It also regulates positively the cellulolytic system by acting indirectly through the cellodextrin induction system. This remarkable finding suggests that the XlnR-dependent cellulolytic and xylanolytic regulatory systems are probably conserved in both P. echinulatum and P. oxalicum. Finally, we explore the functional congruency on the genes clustered in terms of communities, where the genes related to cellular nitrogen, compound metabolic process and macromolecule metabolic process were the most abundant. Therefore, our approach allows us to confer a degree of accuracy regarding the existence of each inferred interaction.
    URI
    http://repositorio.umayor.cl/xmlui/handle/sibum/8411
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652724/pdf/fmicb-11-588263.pdf
    https://dx.doi.org/10.3389%2Ffmicb.2020.588263
    https://www.frontiersin.org/articles/10.3389/fmicb.2020.588263/pdf
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    Modificado por: Sistema de Bibliotecas Universidad Mayor - SIBUM
    DSpace software copyright © 2002-2018  DuraSpace