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Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.

Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL - Front Microbiol (2013)

Bottom Line: The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons.Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima.In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales.

View Article: PubMed Central - PubMed

Affiliation: Sanford-Burnham Medical Research Institute La Jolla, CA, USA ; A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia.

ABSTRACT
Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs) and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales.

No MeSH data available.


Maximum cell concentration for T. maritima grown on various carbon sources. Cell density was determined by optical density measured at 600 nm (OD600) after 24 h of cultivation. These values were converted to cell counts using the following equation [cells/mL] = OD600/3.58 × 10−10, which was determined from measures of OD600 taken at numerous time points in the growth curve and correlated with flow cytometric cell counts.
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Figure 5: Maximum cell concentration for T. maritima grown on various carbon sources. Cell density was determined by optical density measured at 600 nm (OD600) after 24 h of cultivation. These values were converted to cell counts using the following equation [cells/mL] = OD600/3.58 × 10−10, which was determined from measures of OD600 taken at numerous time points in the growth curve and correlated with flow cytometric cell counts.

Mentions: We further assessed the reconstructed sugar catabolic regulons by performing genome-wide transcriptional profiling of T. maritima cells grown on various mono- and disaccharides. First, the ability of T. maritima to grow on 17 different carbon sources was tested in minimal media with a 10-mM concentration of the particular carbohydrate in 500-ml bottles under anoxic conditions at 80°C. Growth phenotype testing revealed that T. maritima is able to grow on the monosaccharides rhamnose, galactose, glucose, fructose, arabinose, xylose, ribose, and mannose and the disaccharides trehalose, cellobiose, and maltose as a sole carbon and energy source (Figure 5). In contrast, N-acetylglucosamine, gluconate, glucuronate, galacturonate, mannitol, sorbitol, and inositol did not support the growth of T. maritima and thus were not used for further transcriptional analysis. The obtained phenotypes are in agreement with the previous studies that have demonstrated growth of T. maritima on simple sugars such as glucose, mannose, ribose, arabinose, xylose, and rhamnose (Conners et al., 2005), as well as on the disaccharides maltose and lactose (Nguyen et al., 2004).


Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.

Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL - Front Microbiol (2013)

Maximum cell concentration for T. maritima grown on various carbon sources. Cell density was determined by optical density measured at 600 nm (OD600) after 24 h of cultivation. These values were converted to cell counts using the following equation [cells/mL] = OD600/3.58 × 10−10, which was determined from measures of OD600 taken at numerous time points in the growth curve and correlated with flow cytometric cell counts.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750489&req=5

Figure 5: Maximum cell concentration for T. maritima grown on various carbon sources. Cell density was determined by optical density measured at 600 nm (OD600) after 24 h of cultivation. These values were converted to cell counts using the following equation [cells/mL] = OD600/3.58 × 10−10, which was determined from measures of OD600 taken at numerous time points in the growth curve and correlated with flow cytometric cell counts.
Mentions: We further assessed the reconstructed sugar catabolic regulons by performing genome-wide transcriptional profiling of T. maritima cells grown on various mono- and disaccharides. First, the ability of T. maritima to grow on 17 different carbon sources was tested in minimal media with a 10-mM concentration of the particular carbohydrate in 500-ml bottles under anoxic conditions at 80°C. Growth phenotype testing revealed that T. maritima is able to grow on the monosaccharides rhamnose, galactose, glucose, fructose, arabinose, xylose, ribose, and mannose and the disaccharides trehalose, cellobiose, and maltose as a sole carbon and energy source (Figure 5). In contrast, N-acetylglucosamine, gluconate, glucuronate, galacturonate, mannitol, sorbitol, and inositol did not support the growth of T. maritima and thus were not used for further transcriptional analysis. The obtained phenotypes are in agreement with the previous studies that have demonstrated growth of T. maritima on simple sugars such as glucose, mannose, ribose, arabinose, xylose, and rhamnose (Conners et al., 2005), as well as on the disaccharides maltose and lactose (Nguyen et al., 2004).

Bottom Line: The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons.Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima.In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales.

View Article: PubMed Central - PubMed

Affiliation: Sanford-Burnham Medical Research Institute La Jolla, CA, USA ; A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia.

ABSTRACT
Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs) and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales.

No MeSH data available.