ArticleJournal of bacteriology2005
An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima.
Article in Journal of bacteriology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 84 citations in OpenAlex.
- Maltodextrin transport in the extremely thermophilic, lignocellulose degrading bacteriumJournal of bacteriology · 2025Article
- Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages.IMA fungus · 2023Article
- The role of solute binding proteins in signal transduction.Computational and structural biotechnology journal · 2021Review
- Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85.Scientific reports · 2019Article
- Uncoupling Fermentative Synthesis of Molecular Hydrogen from Biomass Formation in Thermotoga maritima.Applied and environmental microbiology · 2018Article
- Identification ofThe Journal of biological chemistry · 2018Article
- Impact of growth mode, phase, and rate on the metabolic state of the extremely thermophilic archaeon Pyrococcus furiosus.Biotechnology and bioengineering · 2017Article
- Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius.Journal of industrial microbiology & biotechnology · 2017Article
- Identification of the ATPase Subunit of the Primary Maltose Transporter in the Hyperthermophilic Anaerobe Thermotoga maritima.Applied and environmental microbiology · 2017Article
- Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms.Wiley interdisciplinary reviews. Systems biology and medicine · 2017Review
- Contribution of Pentose Catabolism to Molecular Hydrogen Formation by Targeted Disruption of Arabinose Isomerase (araA) in the Hyperthermophilic Bacterium Thermotoga maritima.Applied and environmental microbiology · 2017Article
- Substrate adaptabilities of Thermotogae mannan binding proteins as a function of their evolutionary histories.Extremophiles : life under extreme conditions · 2016Article
- Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.Applied and environmental microbiology · 2015Article
- Transcriptomic analysis of xylan utilization systems in Paenibacillus sp. strain JDR-2.Applied and environmental microbiology · 2015Article
- Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals.Frontiers in microbiology · 2015Review
- Duplication of genes in an ATP-binding cassette transport system increases dynamic range while maintaining ligand specificity.The Journal of biological chemistry · 2014Article
- Profile of secreted hydrolases, associated proteins, and SlpA in Thermoanaerobacterium saccharolyticum during the degradation of hemicellulose.Applied and environmental microbiology · 2014Article
- Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein.BMC structural biology · 2013Article
- Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.Nucleic acids research · 2013Article
- Global microarray analysis of carbohydrate use in alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5.PloS one · 2013Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bacterium Thermotoga maritima on 14 monosaccharide and polysaccharide substrates was undertaken with the goal of proposing carbohydrate specificities for transport systems and putative transcriptional regulators. Saccharide-induced regulons were predicted through the complementary use of comparative genomics, mixed-model analysis of genome-wide microarray expression data, and examination of upstream sequence patterns. The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. Roles in uptake of specific carbohydrates were suggested for members of the expanded Opp/Dpp family of ABC transporters. In this family, phylogenetic relationships among transport systems revealed patterns of possible duplication and divergence as a strategy for the evolution of new uptake capabilities. The presence of GC-rich hairpin sequences between substrate-binding proteins and other components of Opp/Dpp family transporters offers a possible explanation for differential regulation of transporter subunit genes. Numerous improvements to T. maritima genome annotations were proposed, including the identification of ABC transport systems originally annotated as oligopeptide transporters as candidate transporters for rhamnose, xylose, beta-xylan, and beta-glucans and identification of genes likely to encode proteins missing from current annotations of the pentose phosphate pathway. Beyond the information obtained for T. maritima, the present study illustrates how expression-based strategies can be used for improving genome annotation in other microorganisms, especially those for which genetic systems are unavailable.
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