PMID- 32050592
OWN - NLM
STAT- MEDLINE
DCOM- 20210210
LR  - 20210210
IS  - 2073-4409 (Electronic)
IS  - 2073-4409 (Linking)
VI  - 9
IP  - 2
DP  - 2020 Feb 10
TI  - Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and 
      Protein Structural Analysis.
LID - 10.3390/cells9020401 [doi]
LID - 401
AB  - 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.
FAU - Sirithep, Kanokwadee
AU  - Sirithep K
AD  - Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow 
      University, Suzhou 215123, China.
AD  - Genetic Engineering and Bioinformatics Program, Graduate School, Kasetsart 
      University, Bangkok 10900, Thailand.
FAU - Xiao, Fei
AU  - Xiao F
AD  - Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow 
      University, Suzhou 215123, China.
FAU - Raethong, Nachon
AU  - Raethong N
AD  - Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, 
      Thailand.
FAU - Zhang, Yuhan
AU  - Zhang Y
AD  - Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow 
      University, Suzhou 215123, China.
FAU - Laoteng, Kobkul
AU  - Laoteng K
AD  - 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.
FAU - Hu, Guang
AU  - Hu G
AD  - Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow 
      University, Suzhou 215123, China.
FAU - Vongsangnak, Wanwipa
AU  - Vongsangnak W
AD  - Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow 
      University, Suzhou 215123, China.
AD  - Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, 
      Thailand.
AD  - Omics Center for Agriculture, Bioresources, Food, and Health, Faculty of Science, 
      Kasetsart University (OmiKU), Bangkok 10900, Thailand.
LA  - eng
GR  - RSA6180001/Thailand Research Fund/International
GR  - -/Kasetsart University/International
GR  - 31872723/National Natural Science Foundation of China/International
GR  - -/Thailand Graduate Institute of Science and Technology/International
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20200210
PL  - Switzerland
TA  - Cells
JT  - Cells
JID - 101600052
RN  - 0 (Fungal Proteins)
RN  - 0 (Membrane Transport Proteins)
RN  - 0 (Sugars)
RN  - 7440-44-0 (Carbon)
RN  - A1TA934AKO (Xylose)
SB  - IM
MH  - Amino Acid Motifs
MH  - Amino Acid Sequence
MH  - Biological Transport
MH  - Carbon/*metabolism
MH  - Cordyceps/genetics/*metabolism
MH  - Fungal Proteins/*chemistry/*metabolism
MH  - Gene Regulatory Networks
MH  - Membrane Transport Proteins/metabolism
MH  - *Metabolome
MH  - Phylogeny
MH  - Sugars/*metabolism
MH  - Thermodynamics
MH  - Transcriptome/genetics
MH  - Xylose/metabolism
PMC - PMC7072658
OTO - NOTNLM
OT  - carbon metabolism
OT  - comparative genomics
OT  - cordyceps militaris
OT  - network analysis
OT  - protein structure
OT  - sugar transporter
COIS- The authors declare that they have no conflicts of interest
EDAT- 2020/02/14 06:00
MHDA- 2021/02/11 06:00
PMCR- 2020/02/01
CRDT- 2020/02/14 06:00
PHST- 2019/12/04 00:00 [received]
PHST- 2020/01/24 00:00 [revised]
PHST- 2020/02/05 00:00 [accepted]
PHST- 2020/02/14 06:00 [entrez]
PHST- 2020/02/14 06:00 [pubmed]
PHST- 2021/02/11 06:00 [medline]
PHST- 2020/02/01 00:00 [pmc-release]
AID - cells9020401 [pii]
AID - cells-09-00401 [pii]
AID - 10.3390/cells9020401 [doi]
PST - epublish
SO  - Cells. 2020 Feb 10;9(2):401. doi: 10.3390/cells9020401.