Global gene expression patterns in Clostridium thermocellum from microarray analysis of chemostat culture on cellulose or cellobiose
ABSTRACT: Earlier studies pointed to the ability of C. thermocellum to exquisitely control gene expression in response to growth rate and the presence of insoluble cellulose or soluble compounds such as cellobiose. This microarray study was carried out in order to examine expression responses of the entire genome. The use of the chemostat technique allowed the effects of different growth rates to be analyzed separately from the effects of different substrates. An 11-chip study of 11 separate C. thermocellum chemostat cultures grown on cellulose or cellobiose at different dilution rates.
Project description:Transcriptional profiling with next-generation sequencing methods demonstrated that a Neurospora crassa mutant with the three most highly expressed beta-glucosidase genes deleted had a transcriptional response to cellobiose similair to that of wild type N. crassa exposed to cellulose. N. crassa was pregrown in Sucrose and transferred to Avicel (cellulose), Cellobiose, Sucrose or media with no carbon added. Biological triplicates used to identify differentially expressed genes in WT on Avicel. Single libraries for mutant strains identify which genes show similair expression on cellobiose as in the WT on cellulose.
Project description:High throughput “omics technologies” such as transcriptomics and proteomics provide insights into the metabolic potential of an organism and have been used to understand the genetic and the central carbon metabolism mechanisms for the production of desired end products in various cellulolytic clostridia cultured on different substrates In this study, C. termitidis was cultured on lignocellulose derived simple and complex sugars: cellobiose, xylose, xylan and α–cellulose as sole carbon sources. 2D HPLC-MS/MS quantitative Proteomic profiles and RNA seq transcriptome profiles (next generation sequencing to identify and quantify RNA in biological samples) were analyzed to identify the genes involved in substrate degradation, cellodextrin transport and end product synthesis related genes Identification of these genes is important in understanding the metabolic networks of C. termitidis and could be valuable engineering targets for improving biomass to biofuel production. Closridium termitidis was cultured on 2g/L each of α-cellulose, xylan, cellobiose and xylose. Samples were collected from the exponential phase. 2 replicate experiments were conducted under each substrate condition
Project description:Earlier studies pointed to the ability of C. thermocellum to exquisitely control gene expression in response to growth rate and the presence of insoluble cellulose or soluble compounds such as cellobiose. This microarray study was carried out in order to examine expression responses of the entire genome. The use of the chemostat technique allowed the effects of different growth rates to be analyzed separately from the effects of different substrates. Overall design: An 11-chip study of 11 separate C. thermocellum chemostat cultures grown on cellulose or cellobiose at different dilution rates.
Project description:This study compares growth of Ruminococcus flavefaciens FD-1 with cellulose or cellobiose as the carbohydrate substrate. Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application to improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels. These results show that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components. 1 species (Ruminococcus flavefaciens FD_1), 2 conditions (cellulose, cellobiose), 4 biological replicates. Direct design with biological dye swap.
Project description:Streptomyces scabies is a plant pathogen responsible for common scab disease on root and tuber crops. The transport of the cellulose by-products cellobiose and cellotriose into the cell induces the biosynthesis of the main phytotoxin thaxtomin A. These carbohydrates bind to the cis-acting sequences of the cellulose utilization repressor CebR and thereby induce the expression of the thaxtomin activator TxtR. We performed a shotgun proteomic experiment to compare the wild-type S. scabies 87-22 and its cebR null mutant in the absence or presence of cellobiose. The global intracellular response during virulent behaviour of this plant pathogen could be determined during this experiment.
Project description:Investigation of whole genome gene expression level changes in Streptomyces sp. SirexAA-E (ActE) when grown on different carbon sources. The results of this study demonstrate that ActE upregulates a small number of genes specific for the utilization of the avaliable carbon source. Cellulolytic Streptomyces sp. SirexAA-E (ActE), isolated from the pinewood-boring wasp Sirex noctilio, has a genome enriched for biomass utilization. The secreted proteomes obtained from growth on pure polysaccharides catalyzed hydrolysis of cellulose, mannan, and xylan with specific activities comparable to Spezyme CP, a commercial cellulase preparation. During reaction of an ActE secretome with cellulose, reducing sugar release was markedly stimulated in the presence of O2. ActE also expresses and secretes an expanded repertoire of enzymes during growth on natural and pre-treated biomass. These results indicate a new microbial contribution to biomass utilization that is widely distributed in natural environments by insects Streptomyces sp. ActE was grown in minimal medium supplimented with 0.5% carbon source (glucose, sigmacell-20, xylan, chitin, cellobiose, or AFEX). Cells were grown for 7 days and total RNA was extracted from the cell pellet. At least 3 biological replicates were performed for each carbon source (glucose, 3; sigmacell, 3; xylan, 5; chitin, 3; cellobiose 3; AFEX 3). Each biological replicate contained 3 technical replicates. The complete dataset were RMA Background Corrected, quantile normalized, the RMA algorithm was utilized by DNAStar ArrayStar.
Project description:Clostridium thermocellum is a promising CBP candidate organism capable of directly converting lignocellulosic biomass to ethanol. Low yields, productivities and growth inhibition prevent industrial deployment of this organism for commodity fuel production. Symptoms of potential redox imbalance such as incomplete substrate utilization, and fermentation products characteristic of overflow metabolism, have been observed during growth. This perceived redox imbalance may be in part responsible for the mentioned bioproductivity limitations. Toward better understanding the redox metabolism of C. thermocellum, we analyzed gene expression, using microarrays, during addition of two stress chemicals (methyl viologen and hydrogen peroxide) which we observed to change fermentation redox potential. High quality RNA was extracted from C. thermocellum grown on cellobiose in chemostat culture and exposed, separately, to methyl viologen and hydrogen peroxide. Transcriptome profiles were obtained at seven time points during actively growing fermentations, 3 minutes, 15 minutes, 35 minutes, 7 hours, 14 hours, 50 hours, and 60 hours after beginning exposure to each stressor. Exposure treatments were carried out in duplicate and reference/untreated samples were taken before and between treatments, after flushing of stressor chemicals and re-equilibration of growth conditions.
Project description:Clostridium thermocellum is a candidate for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Understanding how this organism regulates gene expression is of importance for developing a better fundamental understanding of this industrial relevant bacterium. We are primarily interested in gene regulation by three predicted LacI regulators. A previous report of one LacI regulator in C. thermocellum ATCC27405 (Cthe_2808) indicated this was a transcriptional repressor of neighboring genes with repressor activity relieved in the presence of laminaribiose (a β-1,3 disaccharide). The current work is aimed at understanding if a homolog of this LacI transcriptional regulator in C. thermocellum DSM1313 and two others putatively characterized as LacI regulators are in fact global regulatory proteins with extensive regulons or, if like the majority of LacI transcription factors, the regulation is limited to local genomic regions. Each of the three LacI regulators was deleted in C. thermocellum DSM1313. Genome re-sequencing was used to confirm the deletion and ensure nonspecific recombination events were avoided during the gene deletion strategy. Growth of each strain on cellobiose was unaffected by any of the gene deletions under pH controlled fermentations. Global gene expression patterns taken at mid-log phase for each strain identified glycoside hydrolase genes encoding hemicellulases, including cellulosomal enzymes, that were highly up-regulated (up to 9 fold) in the absence of each LacI regulator. Thus suggesting these were repressed under wild type conditions. Electrophoretic mobility shift assays have confirmed LacI transcription factor binding to specific regions of gene promoters with putative motifs ranging from 16-18 bp. Work is ongoing to confirm the specific binding motif recognized by the two previously un-characterized transcription factors and assess the occurrence of this motif in the C. thermocellum DSM1313 genome. The identification of LacI repressor activity on hemicellulose gene expression is a key result of this work and will add to the small body of existing literature on the area of gene regulation in C. thermocellum. Four strains of C. thermocellum DSM1313 including a parental strain (Δhpt) and three others with deletion in lacI transcription factors were characterised by RNA-seq. The strains were grown in 1L bioreactors, cells (from 50 ml samples) were harvested at mid exponential, late exponential and 30 min after acid production halted during the transition to stationary phase. The growth studies were performed in triplicate and thirty six samples were analyzed by RNA-sequencing.
Project description:Roberts2010 - Genome-scale metabolic network
of Clostridium thermocellum (iSR432)
This model is described in the article:
analysis of Clostridium thermocellum for bioethanol
Roberts SB, Gowen CM, Brooks JP,
BMC Syst Biol 2010; 4: 31
BACKGROUND: Microorganisms possess diverse metabolic
capabilities that can potentially be leveraged for efficient
production of biofuels. Clostridium thermocellum (ATCC 27405)
is a thermophilic anaerobe that is both cellulolytic and
ethanologenic, meaning that it can directly use the plant
sugar, cellulose, and biochemically convert it to ethanol. A
major challenge in using microorganisms for chemical production
is the need to modify the organism to increase production
efficiency. The process of properly engineering an organism is
typically arduous. RESULTS: Here we present a genome-scale
model of C. thermocellum metabolism, iSR432, for the purpose of
establishing a computational tool to study the metabolic
network of C. thermocellum and facilitate efforts to engineer
C. thermocellum for biofuel production. The model consists of
577 reactions involving 525 intracellular metabolites, 432
genes, and a proteomic-based representation of a cellulosome.
The process of constructing this metabolic model led to
suggested annotation refinements for 27 genes and
identification of areas of metabolism requiring further study.
The accuracy of the iSR432 model was tested using experimental
growth and by-product secretion data for growth on cellobiose
and fructose. Analysis using this model captures the
relationship between the reduction-oxidation state of the cell
and ethanol secretion and allowed for prediction of gene
deletions and environmental conditions that would increase
ethanol production. CONCLUSIONS: By incorporating genomic
sequence data, network topology, and experimental measurements
of enzyme activities and metabolite fluxes, we have generated a
model that is reasonably accurate at predicting the cellular
phenotype of C. thermocellum and establish a strong foundation
for rational strain design. In addition, we are able to draw
some important conclusions regarding the underlying metabolic
mechanisms for observed behaviors of C. thermocellum and
highlight remaining gaps in the existing genome
This model is hosted on
and identified by:
To cite BioModels Database, please use:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
Public Domain Dedication for more information.
Project description:Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium that ferments cellulose into ethanol. It is a candidate industrial consolidated bioprocess (CBP) biocatalyst for lignocellulosic bioethanol production. However, C. thermocellum is relatively sensitive to ethanol compared to yeast. Previous studies have investigated the membrane and protein composition of wild-type and ethanol tolerant strains, but relatively little is known about the genome changes associated with the ethanol tolerant C. thermocellum strain. In this study, C. thermocellum cultures were grown to mid-exponential phase and then either shocked with the supplementation of ethanol to a final concentration of 3.95 g/L (equal to 0.5% [v/v]) or were untreated. Samples were taken pre-shock and 2, 12, 30, 60, 120, 240 min post-shock for multiple systems biology analyses. The addition of ethanol dramatically reduced the C. thermocellum growth and the final cell density was approximately half of the control fermentations, with concomitant reductions in substrate consumption in the treated cultures. The response of C. thermocellum to ethanol was dynamic and involved more than six hundred genes that were significantly and differentially expressed between the different conditions over time and every functional category was represented. Cellobiose was accumulated within the ethanol-shocked C. thermocellum cells, as well as the sugar phosphates such as fructose-6-P and cellobiose-6-P. The comparison and correlation among intracellular metabolites, proteomic and transcriptomics profiles as well as the ethanol effects on cellulosome, hydrogenase glycolysis and nitrogen metabolism are discussed, which led us to propose that C. thermocellum may utilize the nitrogen metabolism to bypass the arrested carbon metabolism in responding to ethanol stress shock, and the nitrogen metabolic pathway and redox balance may be the key target for improving ethanol tolerance and production in C. thermocellum. Overall design: A thirty array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different time points of 0, 12, 30, 60, 120, and 240 min post-inoculation with 3.95 g/L [0.5% (v/v)] treatment compred to that of control without ethanol supplementation. Two biological replicates for treatment and control condition.