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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.

ORGANISM(S): Acetivibrio thermocellus 27405

PROVIDER: GSE87407 | GEO | 2016/09/28

SECONDARY ACCESSION(S): PRJNA344675

REPOSITORIES: GEO

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Project description:Background (Pseudo)Bacteroides cellulosolvens is a cellulolytic bacterium producing the most extensive and intricate cellulosomal system known in nature. Recently, an elaborate architecture of B. cellulosolvens cellulosomal system was revealed from its genome sequence analysis, and first evidence on the interactions between its structural and enzymatic components were detected in vitro. Yet, the cellulolytic potential of the bacterium in carbohydrate deconstruction may reside only within complete high-molecular weight protein complexes, which are secreted from the bacterium. Results The current proteome-wide work reveals patterns of protein expression of various cellulosomal components, and explores the differential expression signature upon bacterial growth two carbon sources, either cellobiose or microcrystalline cellulose. Mass spectrometry analysis of the bacterial secretome fraction revealed the expression of 24 scaffoldin structural units and 166 dockerin-bearing enzymes, in addition to free enzymatic subunits. All these components comprise cell-free and cell-bound cellulosomes for more efficient carbohydrate degradation. Various glycoside hydrolase (GH) family memebers were represented among 102 carbohydrate-degrading enzymes, including the most abundant GH48 exoglucanase. Specific cellulosomal components were associatred with different carbon sources, in cellulosomal fractions of different molecular weights. Overall, microcrystalline cellulose-derived cellulosomes showed higher expression levels of the structural and enzymatic components, and exhibited the highest degradation activity on five different carbohydrates. The cellulosomal activity of B. cellulosolvens showed high degradation rates that are very promising in biotechnological terms and were compatible with the activity levels exhibited by C. thermocellum purified cellulosomes. Conclusions The current research demonstrates the involvement of key cellulosomal factors participating in the mechanism of carbohydrate degradation by B. cellulosolvens. The powerful ability of the bacterium to exhibit different degradation strategies of various carbon sourcesis revealed. Thus, a novel components reservoir of degradation machineries that may serve for subsequent cellulosomal research, as a pool for designing new cellulolytic cocktails for biotechnological purposes.

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

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