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Soberanes-Gutiérrez CV, Castillo-Jiménez A, Pérez-Rueda E, Galán-Vásquez E. Construction and analysis of gene co-expression network in the pathogenic fungus Ustilago maydis. Front Microbiol 2022; 13:1048694. [PMID: 36569046 PMCID: PMC9767968 DOI: 10.3389/fmicb.2022.1048694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Biological systems respond to environmental disturbances and a wide range of compounds through complex gene interaction networks. The enormous growth of experimental information obtained using large-scale genomic techniques such as microarrays and RNA sequencing led to the construction of a wide variety of gene co-expression networks in recent years. These networks allow the discovery of clusters of co-expressed genes that potentially work in the same process linking them to biological processes often of interest to industrial, medicinal, and academic research. Methods In this study, we built the gene co-expression network of Ustilago maydis from the gene expression data of 168 samples belonging to 19 series, which correspond to the GPL3681 platform deposited in the NCBI using WGCNA software. This network was analyzed to identify clusters of co-expressed genes, gene hubs and Gene Ontology terms. Additionally, we identified relevant modules through a hypergeometric approach based on a predicted set of transcription factors and virulence genes. Results and Discussion We identified 13 modules in the gene co-expression network of U. maydis. The TFs enriched in the modules of interest belong to the superfamilies of Nucleic acid-binding proteins, Winged helix DNA-binding, and Zn2/Cys6 DNA-binding. On the other hand, the modules enriched with virulence genes were classified into diseases related to corn smut, Invasive candidiasis, among others. Finally, a large number of hypothetical, a large number of hypothetical genes were identified as highly co-expressed with virulence genes, making them possible experimental targets.
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Affiliation(s)
- Cinthia V. Soberanes-Gutiérrez
- Laboratorio de Ciencias Agrogenómicas, de la Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, León, Guanajuato, Mexico
| | - Alfredo Castillo-Jiménez
- Licenciatura en Biología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Ernesto Pérez-Rueda
- Unidad Académica Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mérida, Mexico
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigación en Matemáticas Aplicadas y en Sistemas. Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico,*Correspondence: Edgardo Galán-Vásquez,
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Galán-Vásquez E, Gómez-García MDC, Pérez-Rueda E. A landscape of gene regulation in the parasitic amoebozoa Entamoeba spp. PLoS One 2022; 17:e0271640. [PMID: 35913975 PMCID: PMC9342746 DOI: 10.1371/journal.pone.0271640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/05/2022] [Indexed: 11/27/2022] Open
Abstract
Entamoeba are amoeboid extracellular parasites that represent an important group of organisms for which the regulatory networks must be examined to better understand how genes and functional processes are interrelated. In this work, we inferred the gene regulatory networks (GRNs) in four Entamoeba species, E. histolytica, E. dispar, E. nuttalli, and E. invadens, and the GRN topological properties and the corresponding biological functions were evaluated. From these analyses, we determined that transcription factors (TFs) of E. histolytica, E. dispar, and E. nuttalli are associated mainly with the LIM family, while the TFs in E. invadens are associated with the RRM_1 family. In addition, we identified that EHI_044890 regulates 121 genes in E. histolytica, EDI_297980 regulates 284 genes in E. dispar, ENU1_120230 regulates 195 genes in E. nuttalli, and EIN_249270 regulates 257 genes in E. invadens. Finally, we identified that three types of processes, Macromolecule metabolic process, Cellular macromolecule metabolic process, and Cellular nitrogen compound metabolic process, are the main biological processes for each network. The results described in this work can be used as a basis for the study of gene regulation in these organisms.
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Affiliation(s)
- Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
- * E-mail: (EG-V); (EP-R)
| | - María del Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México
| | - Ernesto Pérez-Rueda
- Unidad Académica Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mérida, Yucatán, México
- * E-mail: (EG-V); (EP-R)
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Romero L, Contreras-Riquelme S, Lira M, Martin AJM, Perez-Rueda E. Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. Front Microbiol 2022; 13:923105. [PMID: 35928164 PMCID: PMC9344073 DOI: 10.3389/fmicb.2022.923105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Gene regulation is a key process for all microorganisms, as it allows them to adapt to different environmental stimuli. However, despite the relevance of gene expression control, for only a handful of organisms is there related information about genome regulation. In this work, we inferred the gene regulatory networks (GRNs) of bacterial and archaeal genomes by comparisons with six organisms with well-known regulatory interactions. The references we used are: Escherichia coli K-12 MG1655, Bacillus subtilis 168, Mycobacterium tuberculosis, Pseudomonas aeruginosa PAO1, Salmonella enterica subsp. enterica serovar typhimurium LT2, and Staphylococcus aureus N315. To this end, the inferences were achieved in two steps. First, the six model organisms were contrasted in an all-vs-all comparison of known interactions based on Transcription Factor (TF)-Target Gene (TG) orthology relationships and Transcription Unit (TU) assignments. In the second step, we used a guilt-by-association approach to infer the GRNs for 12,230 bacterial and 649 archaeal genomes based on TF-TG orthology relationships of the six bacterial models determined in the first step. Finally, we discuss examples to show the most relevant results obtained from these inferences. A web server with all the predicted GRNs is available at https://regulatorynetworks.unam.mx/ or http://132.247.46.6/.
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Affiliation(s)
- Luis Romero
- Licenciatura en Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Sebastian Contreras-Riquelme
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Manuel Lira
- Cómputo Académico, Facultad de Ciencias - UMDI-Sisal, Sede Parque Científico y Tecnológico de Yucatán, Universidad Nacional Autónoma de México, Mérida, Mexico
| | - Alberto J. M. Martin
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Alberto J. M. Martin,
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Mexico
- *Correspondence: Ernesto Perez-Rueda,
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Cano R, Lenz AR, Galan-Vasquez E, Ramirez-Prado JH, Perez-Rueda E. Gene Regulatory Network Inference and Gene Module Regulating Virulence in Fusarium oxysporum. Front Microbiol 2022; 13:861528. [PMID: 35722316 PMCID: PMC9201490 DOI: 10.3389/fmicb.2022.861528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022] Open
Abstract
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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Affiliation(s)
- Regnier Cano
- Centro de Investigaciones Científicas de Yucatán, Mérida, Mexico
| | - Alexandre Rafael Lenz
- Departamento de Ciências Exatas e da Terra, Universidade do Estado da Bahia, Salvador, Brazil
| | - Edgardo Galan-Vasquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico, Mexico
| | | | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica Yucatán Universidad Nacional Autónoma de México, Mérida, Mexico
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Olivares-Yañez C, Sánchez E, Pérez-Lara G, Seguel A, Camejo PY, Larrondo LF, Vidal EA, Canessa P. A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride. Comput Struct Biotechnol J 2021; 19:6212-6228. [PMID: 34900134 PMCID: PMC8637145 DOI: 10.1016/j.csbj.2021.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Botrytis cinerea and Trichoderma atroviride are two relevant fungi in agricultural systems. To gain insights into these organisms' transcriptional gene regulatory networks (GRNs), we generated a manually curated transcription factor (TF) dataset for each of them, followed by a GRN inference utilizing available sequence motifs describing DNA-binding specificity and global gene expression data. As a proof of concept of the usefulness of this resource to pinpoint key transcriptional regulators, we employed publicly available transcriptomics data and a newly generated dual RNA-seq dataset to build context-specific Botrytis and Trichoderma GRNs under two different biological paradigms: exposure to continuous light and Botrytis-Trichoderma confrontation assays. Network analysis of fungal responses to constant light revealed striking differences in the transcriptional landscape of both fungi. On the other hand, we found that the confrontation of both microorganisms elicited a distinct set of differentially expressed genes with changes in T. atroviride exceeding those in B. cinerea. Using our regulatory network data, we were able to determine, in both fungi, central TFs involved in this interaction response, including TFs controlling a large set of extracellular peptidases in the biocontrol agent T. atroviride. In summary, our work provides a comprehensive catalog of transcription factors and regulatory interactions for both organisms. This catalog can now serve as a basis for generating novel hypotheses on transcriptional regulatory circuits in different experimental contexts.
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Affiliation(s)
- Consuelo Olivares-Yañez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Biotecnologia Vegetal, Universidad Andres Bello, Republica 330, Santiago, Chile
| | - Evelyn Sánchez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Genomica y Bioinformatica, Facultad de Ciencias, Universidad Mayor, Camino la Pirámide 5750, Huechuraba, Santiago, Chile
| | - Gabriel Pérez-Lara
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Biotecnologia Vegetal, Universidad Andres Bello, Republica 330, Santiago, Chile
| | - Aldo Seguel
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Pamela Y Camejo
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Luis F Larrondo
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Elena A Vidal
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Genomica y Bioinformatica, Facultad de Ciencias, Universidad Mayor, Camino la Pirámide 5750, Huechuraba, Santiago, Chile.,Escuela de Biotecnologia, Facultad de Ciencias, Universidad Mayor, Camino la Pirámide 5750, Huechuraba, Santiago, Chile
| | - Paulo Canessa
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Biotecnologia Vegetal, Universidad Andres Bello, Republica 330, Santiago, Chile
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