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Cells. 2020 Feb 10;9(2). pii: E401. doi: 10.3390/cells9020401.

Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and Protein Structural Analysis.

Author information

1
Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China.
2
Genetic Engineering and Bioinformatics Program, Graduate School, Kasetsart University, Bangkok 10900, Thailand.
3
Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
4
Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand.
5
Omics Center for Agriculture, Bioresources, Food, and Health, Faculty of Science, Kasetsart University (OmiKU), Bangkok 10900, Thailand.

Abstract

Beyond comparative genomics, we identified 85 sugar transporter genes in Cordyceps militaris, clustering into nine subfamilies as sequence- and phylogenetic-based functional classification, presuming the versatile capability of the fungal growths on a range of sugars. Further analysis of the global gene expression patterns of C. militaris showed 123 genes were significantly expressed across the sucrose, glucose, and xylose cultures. The sugar transporters specific for pentose were then identified by gene-set enrichment analysis. Of them, the putative pentose transporter, CCM_06358 gene, was highest expressed in the xylose culture, and its functional role in xylose transport was discovered by the analysis of conserved structural motifs. In addition, a battery of molecular modeling methods, including homology modeling, transport pathway analysis, residue interaction network combined with molecular mechanics Poisson-Boltzmann surface area simulation (MM-PBSA), was implemented for probing the structure and function of the selected pentose transporter (CCM_06358) as a representative of sugar transportome in C. militaris. Considering the network bottlenecks and structural organizations, we further identified key amino acids (Phe38 and Trp441) and their interactions with other residues, contributing the xylose transport function, as verified by binding free energy calculation. The strategy used herein generated remarkably valuable biological information, which is applicable for the study of sugar transportome and the structure engineering of targeted transporter proteins that might link to the production of bioactive compounds derived from xylose metabolism, such as cordycepin.

KEYWORDS:

carbon metabolism; comparative genomics; cordyceps militaris; network analysis; protein structure; sugar transporter

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