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Title: Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells

Clostridium thermocellum forms biofilms adherent to lignocellulosic feedstock in a typical continuous cell-monolayer to efficiently break down and uptake cellulose hydrolysates. The sessile cells of biofilms may revert to non-adherent planktonic cells through generation of offspring cells or microenvironment constraints such as limited surface area. These interdependent cell populations co-exist and have different contributions to culture activity and growth. Here, 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. Furthermore, 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 DNAmore » by nucleotide excision repair and removal of terminal proteins by proteases. Our knowledge of these cellular adaptations will aid the engineering of industrially relevant strains for consolidated bioprocessing of solid lignocellulosic biomass« less
Authors:
 [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [2] ;  [1] ;  [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC) and Biosciences Division
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC) and Chemical Sciences Division
Publication Date:
Grant/Contract Number:
AC05-00OR22725
Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Clostridium thermocellum; biofilm; transcriptomics; proteomics; RNA-seq; gene expression analysis; metabolic engineering
OSTI Identifier:
1361314

Dumitrache, Alexandru, Klingeman, Dawn M., Natzke, Jace, Rodriguez Jr, Miguel, Giannone, Richard J., Hettich, Robert L., Davison, Brian H., and Brown, Steven D.. Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells. United States: N. p., Web. doi:10.1038/srep43583.
Dumitrache, Alexandru, Klingeman, Dawn M., Natzke, Jace, Rodriguez Jr, Miguel, Giannone, Richard J., Hettich, Robert L., Davison, Brian H., & Brown, Steven D.. Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells. United States. doi:10.1038/srep43583.
Dumitrache, Alexandru, Klingeman, Dawn M., Natzke, Jace, Rodriguez Jr, Miguel, Giannone, Richard J., Hettich, Robert L., Davison, Brian H., and Brown, Steven D.. 2017. "Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells". United States. doi:10.1038/srep43583. https://www.osti.gov/servlets/purl/1361314.
@article{osti_1361314,
title = {Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells},
author = {Dumitrache, Alexandru and Klingeman, Dawn M. and Natzke, Jace and Rodriguez Jr, Miguel and Giannone, Richard J. and Hettich, Robert L. and Davison, Brian H. and Brown, Steven D.},
abstractNote = {Clostridium thermocellum forms biofilms adherent to lignocellulosic feedstock in a typical continuous cell-monolayer to efficiently break down and uptake cellulose hydrolysates. The sessile cells of biofilms may revert to non-adherent planktonic cells through generation of offspring cells or microenvironment constraints such as limited surface area. These interdependent cell populations co-exist and have different contributions to culture activity and growth. Here, 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. Furthermore, 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. Our knowledge of these cellular adaptations will aid the engineering of industrially relevant strains for consolidated bioprocessing of solid lignocellulosic biomass},
doi = {10.1038/srep43583},
journal = {Scientific Reports},
number = ,
volume = 7,
place = {United States},
year = {2017},
month = {2}
}