Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum
Genes involved in cellular processes undergo environment-dependent co-regulation, but the co-expression patterns of fungal cellulase and xylanase-encoding genes remain unclear. Here, we identified two novel carbon sources, methylcellulose and 2-hydroxyethyl cellulose, which efficiently induced the s...
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doaj-80c69d2fc7124bbc9d1bb12e5d6b99eb2020-11-25T00:45:24ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-03-011110.3389/fmicb.2020.00520525297Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicumCheng-Xi LiShuai ZhaoXue-Mei LuoJia-Xun FengGenes involved in cellular processes undergo environment-dependent co-regulation, but the co-expression patterns of fungal cellulase and xylanase-encoding genes remain unclear. Here, we identified two novel carbon sources, methylcellulose and 2-hydroxyethyl cellulose, which efficiently induced the secretion of cellulases and xylanases in Penicillium oxalicum. Comparative transcriptomic analyses identified carbon source-specific transcriptional patterns, mainly including major cellulase and xylanase-encoding genes, genes involved in glycolysis/gluconeogenesis and the tricarboxylic acid cycle, and genes encoding transcription factors, transporters and G protein-coupled receptors. Moreover, the weighted correlation network analysis of time-course transcriptomes, generated 17 highly connected modules. Module MEivory, comprising 120 members, included major cellulase and xylanase-encoding genes, genes encoding the key regulators PoxClrB and PoxXlnR, and a cellodextrin transporter POX06051/CdtC, which were tightly correlated with the filter-paper cellulase, carboxymethylcellulase and xylanase activities in P. oxalicum. An expression kinetic analysis indicated that members in MEivory were activated integrally by carbon sources, but their expressional levels were carbon source- and/or induction duration-dependent. Three uncharacterized regulatory genes in MEivory were identified, which regulate the production of cellulases and xylanases in P. oxalicum. These findings provide insights into the mechanisms associated with the synthesis and secretion of fungal cellulases and xylanases, and a guide for P. oxalicum application in biotechnology.https://www.frontiersin.org/article/10.3389/fmicb.2020.00520/fullco-expression networkcellulasexylanasetime-course transcriptomePenicillium oxalicum |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Cheng-Xi Li Shuai Zhao Xue-Mei Luo Jia-Xun Feng |
spellingShingle |
Cheng-Xi Li Shuai Zhao Xue-Mei Luo Jia-Xun Feng Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum Frontiers in Microbiology co-expression network cellulase xylanase time-course transcriptome Penicillium oxalicum |
author_facet |
Cheng-Xi Li Shuai Zhao Xue-Mei Luo Jia-Xun Feng |
author_sort |
Cheng-Xi Li |
title |
Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum |
title_short |
Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum |
title_full |
Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum |
title_fullStr |
Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum |
title_full_unstemmed |
Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum |
title_sort |
weighted gene co-expression network analysis identifies critical genes for the production of cellulase and xylanase in penicillium oxalicum |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2020-03-01 |
description |
Genes involved in cellular processes undergo environment-dependent co-regulation, but the co-expression patterns of fungal cellulase and xylanase-encoding genes remain unclear. Here, we identified two novel carbon sources, methylcellulose and 2-hydroxyethyl cellulose, which efficiently induced the secretion of cellulases and xylanases in Penicillium oxalicum. Comparative transcriptomic analyses identified carbon source-specific transcriptional patterns, mainly including major cellulase and xylanase-encoding genes, genes involved in glycolysis/gluconeogenesis and the tricarboxylic acid cycle, and genes encoding transcription factors, transporters and G protein-coupled receptors. Moreover, the weighted correlation network analysis of time-course transcriptomes, generated 17 highly connected modules. Module MEivory, comprising 120 members, included major cellulase and xylanase-encoding genes, genes encoding the key regulators PoxClrB and PoxXlnR, and a cellodextrin transporter POX06051/CdtC, which were tightly correlated with the filter-paper cellulase, carboxymethylcellulase and xylanase activities in P. oxalicum. An expression kinetic analysis indicated that members in MEivory were activated integrally by carbon sources, but their expressional levels were carbon source- and/or induction duration-dependent. Three uncharacterized regulatory genes in MEivory were identified, which regulate the production of cellulases and xylanases in P. oxalicum. These findings provide insights into the mechanisms associated with the synthesis and secretion of fungal cellulases and xylanases, and a guide for P. oxalicum application in biotechnology. |
topic |
co-expression network cellulase xylanase time-course transcriptome Penicillium oxalicum |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2020.00520/full |
work_keys_str_mv |
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