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Open AccessArticle
Expanded Gene Regulatory Network Reveals Potential Light-Responsive Transcription Factors and Target Genes in Cordyceps militaris
by
Paradee Buradam
Paradee Buradam 1,2,
Roypim Thananusak
Roypim Thananusak 3,
Mattheos Koffas
Mattheos Koffas 4,5,
Pramote Chumnanpuen
Pramote Chumnanpuen 1,2,3,* and
Wanwipa Vongsangnak
Wanwipa Vongsangnak 1,3,*
1
Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
2
Kasetsart University International College (KUIC), Kasetsart University, Bangkok 10900, Thailand
3
Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
4
Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
5
Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(19), 10516; https://doi.org/10.3390/ijms251910516 (registering DOI)
Submission received: 19 August 2024
/
Revised: 17 September 2024
/
Accepted: 26 September 2024
/
Published: 29 September 2024
Abstract
Cordyceps militaris, a fungus widely used in traditional Chinese medicine and pharmacology, is recognized for its abundant bioactive compounds, including cordycepin and carotenoids. The growth, development, and metabolite production in various fungi are influenced by the complex interactions between regulatory cascades and light-signaling pathways. However, the mechanisms of gene regulation in response to light exposure in C. militaris remain largely unexplored. This study aimed to identify light-responsive genes and potential transcription factors (TFs) in C. militaris through an integrative transcriptome analysis. To achieve this, we reconstructed an expanded gene regulatory network (eGRN) comprising 507 TFs and 8,662 regulated genes using both interolog-based and homolog-based methods to build the protein–protein interaction network. Aspergillus nidulans and Neurospora crassa were chosen as templates due to their relevance as fungal models and the extensive study of their light-responsive mechanisms. By utilizing the eGRN as a framework for comparing transcriptomic responses between light-exposure and dark conditions, we identified five key TFs—homeobox TF (CCM_07504), FlbC (CCM_04849), FlbB (CCM_01128), C6 zinc finger TF (CCM_05172), and mcrA (CCM_06477)—along with ten regulated genes within the light-responsive subnetwork. These TFs and regulated genes are likely crucial for the growth, development, and secondary metabolite production in C. militaris. Moreover, molecular docking analysis revealed that two novel TFs, CCM_05727 and CCM_06992, exhibit strong binding affinities and favorable docking scores with the primary light-responsive protein CmWC-1, suggesting their potential roles in light signaling pathways. This information provides an important functional interactive network for future studies on global transcriptional regulation in C. militaris and related fungi.
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MDPI and ACS Style
Buradam, P.; Thananusak, R.; Koffas, M.; Chumnanpuen, P.; Vongsangnak, W.
Expanded Gene Regulatory Network Reveals Potential Light-Responsive Transcription Factors and Target Genes in Cordyceps militaris. Int. J. Mol. Sci. 2024, 25, 10516.
https://doi.org/10.3390/ijms251910516
AMA Style
Buradam P, Thananusak R, Koffas M, Chumnanpuen P, Vongsangnak W.
Expanded Gene Regulatory Network Reveals Potential Light-Responsive Transcription Factors and Target Genes in Cordyceps militaris. International Journal of Molecular Sciences. 2024; 25(19):10516.
https://doi.org/10.3390/ijms251910516
Chicago/Turabian Style
Buradam, Paradee, Roypim Thananusak, Mattheos Koffas, Pramote Chumnanpuen, and Wanwipa Vongsangnak.
2024. "Expanded Gene Regulatory Network Reveals Potential Light-Responsive Transcription Factors and Target Genes in Cordyceps militaris" International Journal of Molecular Sciences 25, no. 19: 10516.
https://doi.org/10.3390/ijms251910516
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