Transcriptomics,Genomics

Dataset Information

144

Significant gene expression differences between sessile biofilms and planktonic cells of Clostridium thermocellum


ABSTRACT: Clostridium thermocellum forms adherent biofilms on lignocellulosic feedstock in a typical continuous cell-monolayer to efficiently break down and uptake cellulose hydrolysates. The adherent biofilm (i.e., sessile cells) may freely revert to the non-adherent form (i.e., planktonic cells) through generation of offspring cells or microenvironment constraints such as limited surface area. The two interdependent cell populations co-exist and have different contributions to culture activity and growth. We developed a novel bioreactor design to rapidly harvest sessile and planktonic cell populations for omics studies. In RNA-seq analyses, within 3299 protein coding genes, 59% (or 1958 genes) were differentially expressed with a minimum two-fold change between the two cell populations isolated simultaneously at high culture activity. Sessile cells had definitive greater expression of genes involved in catabolism of carbohydrates by glycolysis and pyruvate fermentation, ATP generation by proton gradient, the anabolism of proteins and lipids and cellular functions critical for cell division; planktonic cells had notably higher gene expression for flagellar motility and chemotaxis, cellulosomal cellulases and anchoring scaffoldins, and a range of stress induced homeostasis mechanisms such as oxidative stress protection by antioxidants and flavoprotein co-factors, methionine repair, Fe-S cluster assembly and repair in redox proteins, cell growth control through tRNA thiolation, recovery of damaged DNA by nucleotide excision repair and removal of terminal proteins by proteases. Knowledge of these cellular adaptations will aid the engineering of industrially relevant strains for consolidated bioprocessing of solid lignocellulosic biomass. Overall design: Differential RNA-Seq analyses to investigate sessile and planktonic cell populations for omics studies

INSTRUMENT(S): Illumina MiSeq (Ruminiclostridium thermocellum 27405)

SUBMITTER: Dawn Marie Klingeman  

PROVIDER: GSE87407 | GEO | 2016-09-28

SECONDARY ACCESSION(S): PRJNA344675

REPOSITORIES: GEO

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Publications

Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells.

Dumitrache Alexandru A   Klingeman Dawn M DM   Natzke Jace J   Rodriguez Miguel M   Giannone Richard J RJ   Hettich Robert L RL   Davison Brian H BH   Brown Steven D SD  

Scientific reports 20170227


Clostridium (Ruminiclostridium) thermocellum is a model organism for its ability to deconstruct plant biomass and convert the cellulose into ethanol. The bacterium forms biofilms adherent to lignocellulosic feedstocks in a continuous cell-monolayer in order to efficiently break down and uptake cellulose hydrolysates. We developed a novel bioreactor design to generate separate sessile and planktonic cell populations for omics studies. Sessile cells had significantly greater expression of genes in  ...[more]

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