Ruminiclostridium cellobioparum subsp. termitidis CT1112
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ABSTRACT:
PROVIDER: PRJNA275928 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1811570_1.fastq.gz | Fastqsanger.gz | |||
| SRR1811570_2.fastq.gz | Fastqsanger.gz | |||
| SRR1811571_1.fastq.gz | Fastqsanger.gz | |||
| SRR1811571_2.fastq.gz | Fastqsanger.gz | |||
| SRR1811572_1.fastq.gz | Fastqsanger.gz |
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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 ?–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 ?-cellulose, xylan, cellobiose and xylose. Samples were collected from the exponential phase. 2 replicate experiments were conducted under each substrate condition
2015-05-01 | E-GEOD-66125 | biostudies-arrayexpress
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.
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Project description:Clostridium termitidis overview
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Project description:Ruminiclostridium cellobioparum subsp. termitidis CT1112 Genome sequencing and assembly
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Project description:Herbivorax saccincola A7 is an alkali-thermophilic lignocellulolytic bacterium that was known to possess a strong xylan degradation ability. They can utilize a wide range of carbon sources, however the response and regulation mechanisms to different carbon sources, in terms of genes expression, are still not identified. In this study, H. saccincola A7 was cultured with cellobiose, cellulose, xylan, cellulose-xylan mixture, and empty fruit bunch (EFB) as the sole carbon source. We carried out a comparative expression analysis, focusing on biomass degradation-related genes. The cellulosomal scaffolding proteins and cellulosomal enzymes of H. saccincola A7 were drastically induced when a cellulose-containing substrate was used as a carbon source. On the other hand, xylan induced only some non-cellulosomal enzymes that might be necessary for xylan degradation. The identification of the carbohydrate-sensing mechanism in H. saccincola A7 appeared a similar system as previously described in Clostridium thermocellum. The lignocellulose degradation ability of H. saccincola A7 may be controlled enzyme expression by cellulose-containing substrate, not by xylan. Thus, recognition in the existence of cellulosic substrates is effective in enhancing a high xylan degradation ability in H. saccincola A7.
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Project description:Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade various polysaccharide components of plant cell walls. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species C. saccharolyticus and C.bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to fourteen Caldicellulosiruptor species. The reconstruction of carbohydrate utilization regulatory network includes the predicted binding sites for 34 mostly local regulators and point to the regulatory mechanisms controlling expression of genes involved in degradation of plant biomass. The Rex and CggR regulons control the central glycolytic and primary redox reactions. The identified transcription factor binding sites and regulons were validated with transcriptomic and transcription start site data for C. bescii grown on cellulose, cellobiose, glucose, xylan, and xylose. The XylR and XynR regulons control xylan-induced transcriptional response of genes involved in degradation of xylan and xylose utilization. The reconstructed regulons informed the carbohydrate utilization reconstruction analysis and improved functional annotations of 51 transporters and 11 catabolic enzymes. Using gene deletion, we confirmed that the shared ATPase component MsmK is essential for growth on oligo- and polysaccharides but not for the utilization of monosaccharides. By elucidating the carbohydrate utilization framework in C. bescii, strategies for metabolic engineering can be pursued to optimize yields of bio-based fuels and chemicals from lignocellulose.
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