Transcriptomic Analysis of a Clostridium thermocellum Strain Engineered to Utilize Xylose: Responses to Xylose versus Cellobiose Feeding

Albert Tafur Rangel, Trevor Croft, Andres Gonzalez Barrios, Luis Reyes, Pin-Ching Maness, Katherine Chou

Research output: Contribution to journalArticlepeer-review

6 Scopus Citations


Clostridium (Ruminiclostridium) thermocellum is recognized for its ability to ferment cellulosic biomass directly, but it cannot naturally grow on xylose. Recently, C. thermocellum (KJC335) was engineered to utilize xylose through expressing a heterologous xylose catabolizing pathway. Here, we compared KJC335′s transcriptomic responses to xylose versus cellobiose as the primary carbon source and assessed how the bacteria adapted to utilize xylose. Our analyses revealed 417 differentially expressed genes (DEGs) with log2 fold change (FC) >|1| and 106 highly DEGs (log2 FC >|2|). Among the DEGs, two putative sugar transporters, cbpC and cbpD, were up-regulated, suggesting their contribution to xylose transport and assimilation. Moreover, the up-regulation of specific transketolase genes (tktAB) suggests the importance of this enzyme for xylose metabolism. Results also showed remarkable up-regulation of chemotaxis and motility associated genes responding to xylose feeding, as well as widely varying gene expression in those encoding cellulosomal enzymes. For the down-regulated genes, several were categorized in gene ontology terms oxidation–reduction processes, ATP binding and ATPase activity, and integral components of the membrane. This study informs potentially critical, enabling mechanisms to realize the conceptually attractive Next-Generation Consolidated BioProcessing approach where a single species is sufficient for the co-fermentation of cellulose and hemicellulose.

Original languageAmerican English
Article number14517
Number of pages15
JournalScientific Reports
Issue number1
StatePublished - 2020

Bibliographical note

Publisher Copyright:
© 2020, The Author(s).

NREL Publication Number

  • NREL/JA-2700-77374


  • biohydrogen
  • biomass conversion
  • Clostridium thermocellum
  • consolidated bioprocessing
  • transcriptomic analyses
  • xylose


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