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

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.

Identification and Expression Analysis of Sugar Transporter Gene Family in Aspergillus oryzae

“…Above, it is not hard to conclude the variations in the distribution and number of SUT genes among filamentous fungi; this difference may be caused by the evolution of different strains in adapting to distinct external environments. Coincidentally, beyond comparative genomics, researchers identified 85 SUTs in C. militaris , which is closed to A. niger , clustering into nine subfamilies [ 14 ]. Moreover, 100 sugar transporter genes in the silkworm Bombyx mori genome (categorized into 11 distinct groups in the phylogenetic tree) and 20 SUT genes were identified from the cassava ( Manihot esculenta ) genome, which were further divided into four clades [ 17 , 23 ].…”

“…For example, different SUT families in Aspergillus niger ( A. niger ) have a dynamic expression pattern during growth on distinct carbon sources and hence enable the organism to adapt to an extremely broad range of environments [ 13 ]. Contrary to A. niger , in response to different carbon sources, Cordyceps militaris ( C. militaris ) SUT genes within each subfamily harbor an analogous expression pattern with the exception of those involved in the pentose subfamily, which were highly expressed in the xylose culture [ 14 ]. Vankuyk et al reported that regulators CreA regulated the expression of SUT genes in A. niger in response to extracellular pH changes [ 15 ].…”

“…These approaches have become a primary strategy in characterizing gene expression profiles and elucidating the genetic networks in all fields, such as animals [ 17 , 18 ], plants [ 21 – 23 ], and fungi [ 13 , 24 – 26 ]. However, just a few of the SUTs have been reported in fungi, such as trehalose transporter in Beauveria bassiana (BbAGT1), putative pentose transporter in C. militaris (CCM_06358), and raffinose transporter in Metarhizium robertsii (Mrt) [ 14 , 27 , 28 ]. Nonetheless, there is no systematic analysis and characterization of SUT family genes in A. oryzae .…”

Metabolic Responses of Carotenoid and Cordycepin Biosynthetic Pathways in Cordyceps militaris under Light-Programming Exposure through Genome-Wide Transcriptional Analysis

“…To uncover the reporter metabolites, the previous genome-scale metabolic network (GSMN) of C. militaris ( i NR1329) [ 15 ] was improved by introducing the genes and their associated metabolites and biochemical reactions involved in carotenoid biosynthetic pathway and sugar transport system, as previously reported [ 7 , 14 , 30 ]. The additional genes identified from the first GSMN of C. militaris ( i WV1170) [ 31 ] together with extensive data mining from different databases were newly added into i NR1329, thereby enhancing the gene content of the improved GSMN in this study.…”

Dissecting Mutational Allosteric Effects in Alkaline Phosphatases Associated with Different Hypophosphatasia Phenotypes: An Integrative Computational Investigation

“…[25] Structural modeling combined with network theory has been widely exploited in studying protein topology and dynamics. [26, 27] The description of protein structure as a structural network provides an efficient tool to dissect complex protein functions. [28] Based on protein structural network model, different topological parameters and algorithms have been developed to describe structural changes associated with mutations.…”