Transcriptomic adaptations of Clostridium thermocellum strains evolved to grow on xylose

A strain of Acetivibrio thermocellus (colloquially, Clostridium thermocellum) DSM 1313 capable of growing in xylose was created by both rational engineering and adaptive laboratory evolution (ALE) approaches. This RNA-seq experiment compares the transcriptomes of the pre-ALE strain on native substrate with the pre-ALE and post-ALE strains growing in xylose (or xylose plus xylan). These data show the progression of the initially engineered strain from normal growth with a native substrate, to debilitated growth in the new engeered substrate, to improved growth on the engineered substrate after ALE. Genes of various biological functions are found to undergo coordinated changes at various stages of the engineering & ALE campaign. These correlations shed light on the state of the cell at each stage. All together, these data paint a picture of the strain initially undergoing a stress state, which is eventually overcome through ALE. Many of these changes dissipate in the fast growing strain, leaving only permanent changes that enable growth on xylose. Strain KJC355 is A. thermocellus DSM 1313 Δhpt with xylA and xylB genes integrated into the hpt locus. KJC335 was subjected to ALE producing strains KJC19-9 and KJCXn4 which were adaped to growth on xylose or xylose plus xylan, respectively. GSE137509 includes data for KJC355 in cellobiose (native substrate) and xylose (engineered substrate). This submission includes data for KJC19-9 grown in xylose, KJCXn4 grown in xylose + xylan, and KJCXn4 grown in xylose alone.