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

Lenz, Alexandre Rafael; Galán-Vásquez, Edgardo; Balbinot, E.; Abreu, Fernanda Pessi de; Oliveira, Nikael Souza de; Rosa, Letícia Osório da; Silva, Scheila de Ávila e; Camassola, Marli; Dillon, Aldo José Pinheiro; Pérez‐Rueda, Ernesto

doi:10.3389/fmicb.2020.588263

Cited by 13 publications

(10 citation statements)

References 92 publications

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“…Then, each community is considered as a single node on its own, and a subsequent step is repeated until there is only a single node left or when the modularity cannot be increased in a single step (Blondel et al, 2008). These metrics provide information about how connected the elements in a network and their module structure are (Junker and Schreiber, 2011;Lenz et al, 2020).…”

Section: Network Structural Analysismentioning

confidence: 99%

“…Only few GRNs have been experimentally characterized for fungal organisms, such as S. cerevisiae (Monteiro et al, 2020), Aspergillus nidulans and Neurospora crassa (Hu et al, 2018). For this reason, homology-based approaches tend to be a solution for the study of GRNs in other lesser-known organisms (Galán-Vásquez et al, 2016;Lenz et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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Identifying Genes Devoted to the Cell Death Process in the Gene Regulatory Network of Ustilago maydis

et al. 2021

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Cell death is a process that can be divided into three morphological patterns: apoptosis, autophagy and necrosis. In fungi, cell death is induced in response to intracellular and extracellular perturbations, such as plant defense molecules, toxins and fungicides, among others. Ustilago maydis is a dimorphic fungus used as a model for pathogenic fungi of animals, including humans, and plants. Here, we reconstructed the transcriptional regulatory network of U. maydis, through homology inferences by using as templates the well-known gene regulatory networks (GRNs) of Saccharomyces cerevisiae, Aspergillus nidulans and Neurospora crassa. Based on this GRN, we identified transcription factors (TFs) as hubs and functional modules and calculated diverse topological metrics. In addition, we analyzed exhaustively the module related to cell death, with 60 TFs and 108 genes, where diverse cell proliferation, mating-type switching and meiosis, among other functions, were identified. To determine the role of some of these genes, we selected a set of 11 genes for expression analysis by qRT-PCR (sin3, rlm1, aif1, tdh3 [isoform A], tdh3 [isoform B], ald4, mca1, nuc1, tor1, ras1, and atg8) whose homologues in other fungi have been described as central in cell death. These genes were identified as downregulated at 72 h, in agreement with the beginning of the cell death process. Our results can serve as the basis for the study of transcriptional regulation, not only of the cell death process but also of all the cellular processes of U. maydis.

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Section: Network Structural Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identifying Genes Devoted to the Cell Death Process in the Gene Regulatory Network of Ustilago maydis

et al. 2021

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“…This inference is based on the hypothesis that if the sequences corresponding to TFs and TGs are conserved in the model organisms and in F. oxysporum , then regulatory interactions are also conserved. Similar approaches have been proposed for Penicillium echinulatum 2HH, Penicillium oxalicum 114–2, and Ustilago maydis ( Lenz et al, 2020 ; Soberanes-Gutiérrez et al, 2021 ).…”

Section: Resultsmentioning

confidence: 86%

“…In recent years, gene regulatory networks (GRNs) have grown popular as an effective applied biology approach for describing relationships between regulatory components (transcription factors, or TFs) and their target genes, or TGs (e.g., enzymes and structural proteins), key components of cell circuits ( Mercatelli et al, 2020 ). GRNs have been used to understand many global cellular processes, such as diseases, cell growth, and the improvement of omics data interpretation, including single-cell RNA sequencing ( Jackson et al, 2020 ; Lenz et al, 2020 ). In this regard, a GRN is a collection of interactions represented in a graph, where genes or proteins are represented as vertices and their regulatory interactions are represented as edges.…”

Section: Introductionmentioning

confidence: 99%

Gene Regulatory Network Inference and Gene Module Regulating Virulence in Fusarium oxysporum

et al. 2022

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In this work, we inferred the gene regulatory network (GRN) of the fungus Fusarium oxysporum by using the regulatory networks of Aspergillus nidulans FGSC A4, Neurospora crassa OR74A, Saccharomyces cerevisiae S288c, and Fusarium graminearum PH-1 as templates for sequence comparisons. Topological properties to infer the role of transcription factors (TFs) and to identify functional modules were calculated in the GRN. From these analyzes, five TFs were identified as hubs, including FOXG_04688 and FOXG_05432, which regulate 2,404 and 1,864 target genes, respectively. In addition, 16 communities were identified in the GRN, where the largest contains 1,923 genes and the smallest contains 227 genes. Finally, the genes associated with virulence were extracted from the GRN and exhaustively analyzed, and we identified a giant module with ten TFs and 273 target genes, where the most highly connected node corresponds to the transcription factor FOXG_05265, homologous to the putative bZip transcription factor CPTF1 of Claviceps purpurea, which is involved in ergotism disease that affects cereal crops and grasses. The results described in this work can be used for the study of gene regulation in this organism and open the possibility to explore putative genes associated with virulence against their host.

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“…In eukaryotic systems, each gene needs an individual promoter that can be recognized by RNA polymerases and transcription factors to initiate transcription (Curran et al., 2014 ), as well as an individual terminator to control the termination of transcription and mRNA half-life (Kuersten & Goodwin, 2003 ; Wang et al., 2019 ). The gene regulatory divergence between difference species has been reported (Lenz et al., 2020 ; Li & Fay, 2017 ), which demonstrated the complex expression profiles and the difficulties with cross-expression between different species. In this study, we evaluated cross-species expression efficiencies of promoters and terminators from Penicillium to yeast.…”

Section: Discussionmentioning

confidence: 99%

Characterization of cross-species transcription and splicing from Penicillium to Saccharomyces cerevisiae

Lin

Guang

et al. 2021

Journal of Industrial Microbiology and Biotechnology

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Heterologous expression of eukaryotic gene clusters in yeast has been widely used for producing high-value chemicals and bioactive secondary metabolites. However, eukaryotic transcription cis-elements are still under-characterized, and the cross-species expression mechanism remains poorly understood. Here we used the whole expression unit (including original promoter, terminator and open reading frame with introns) of orotidine 5'-monophosphate decarboxylases from fourteen Penicillium species as a showcase, and analyzed their cross-species expression in Saccharomyces cerevisiae. We found that pyrG promoters from the Penicillium species could drive URA3 expression in yeast, and that inefficient cross-species splicing of Penicillium introns might result in weak cross-species expression. Thus, this study demonstrates cross-species expression from Penicillium to yeast, and sheds light on the opportunities and challenges of cross-species expression of fungi expression units and gene clusters in yeast without refactoring for novel natural product discovery.

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

Cited by 13 publications

References 92 publications

Identifying Genes Devoted to the Cell Death Process in the Gene Regulatory Network of Ustilago maydis

Identifying Genes Devoted to the Cell Death Process in the Gene Regulatory Network of Ustilago maydis

Gene Regulatory Network Inference and Gene Module Regulating Virulence in Fusarium oxysporum

Characterization of cross-species transcription and splicing from Penicillium to Saccharomyces cerevisiae

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