Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria

Rodionov, Dmitry A.; Mironov, Andrey A.; Gelfand, Mikhail S.

doi:10.1111/j.1574-6968.2001.tb10965.x

Cited by 83 publications

(84 citation statements)

References 40 publications

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“…This motif shows strong similarity to the LacI family protein CcpA consensus CRE site within the Bacillus/Clostridium group of bacteria (36). Thus, the LacI family regulator TM1218, located downstream of the TM1219 -TM1223 gene string, might be involved in local regulation of these ABC transporters and other members of the CMC degradation pathway proposed below.…”

Section: Regulation Of T Maritima Glycoside Hydrolasesmentioning

confidence: 99%

Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima

Chhabra¹,

Shockley²,

Conners³

et al. 2003

Journal of Biological Chemistry

121

126

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The hyperthermophilic bacterium Thermotoga maritima MSB8 was grown on a variety of carbohydrates to determine the influence of carbon and energy source on differential gene expression. Despite the fact that T. maritima has been phylogenetically characterized as a primitive microorganism from an evolutionary perspective, results here suggest that it has versatile and discriminating mechanisms for regulating and effecting complex carbohydrate utilization. Growth of T. maritima on monosaccharides was found to be slower than growth on polysaccharides, although growth to cell densities of 10 8 to 10 9 cells/ml was observed on all carbohydrates tested. Differential expression of genes encoding carbohydrate-active proteins encoded in the T. maritima genome was followed using a targeted cDNA microarray in conjunction with mixed model statistical analysis. Coordinated regulation of genes responding to specific carbohydrates was noted. Although glucose generally repressed expression of all glycoside hydrolase genes, other sugars induced or repressed these genes to varying extents. Expression profiles of most endo-acting glycoside hydrolase genes correlated well with their reported biochemical properties, although exo-acting glycoside hydrolase genes displayed less specific expression patterns. Genes encoding selected putative ABC sugar transporters were found to respond to specific carbohydrates, and in some cases putative oligopeptide transporter genes were also found to respond to specific sugar substrates. Several genes encoding putative transcriptional regulators were expressed during growth on specific sugars, thus suggesting functional assignments. The transcriptional response of T. maritima to specific carbohydrate growth substrates indicated that sugar backbone-and linkage-specific regulatory networks are operational in this organism during the uptake and utilization of carbohydrate substrates. Furthermore, the wide ranging collection of such networks in T. maritima suggests that this organism is capable of adapting to a variety of growth environments containing carbohydrate growth substrates.

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Section: Regulation Of T Maritima Glycoside Hydrolasesmentioning

confidence: 99%

Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima

Chhabra¹,

Shockley²,

Conners³

et al. 2003

Journal of Biological Chemistry

121

126

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“…Many of the gene clusters involved in sugar metabolism contain LacI-type regulators, which suggest that the transcription of such gene clusters are subject to substratedependent repression [63,83,107,108,124,126]. However, in just a few cases the precise action of the LacI-type regulator has been investigated in bifidobacteria [97,132].…”

Section: Control Of Carbohydrate Metabolism In Bifidobacteriamentioning

confidence: 99%

Carbohydrate metabolism in Bifidobacteria

2011

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Members of the genus Bifidobacterium can be found as components of the gastrointestinal microbiota, and are believed to play an important role in maintaining and promoting human health by eliciting a number of beneficial properties. Bifidobacteria can utilize a diverse range of dietary carbohydrates that escape degradation in the upper parts of the intestine, many of which are plantderived oligo-and polysaccharides. The gene content of a bifidobacterial genome reflects this apparent metabolic adaptation to a complex carbohydrate-rich gastrointestinal tract environment as it encodes a large number of predicted carbohydrate-modifying enzymes. Different bifidobacterial strains may possess different carbohydrate utilizing abilities, as established by a number of studies reviewed here. Carbohydrate-degrading activities described for bifidobacteria and their relevance to the deliberate enhancement of number and/or activity of bifidobacteria in the gut are also discussed in this review.

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“…As a direct result of the increasing pool of genome sequences, such sets are increasing constituted by orthologous genes under the assumption that orthologs across species of moderate evolutionary distance remain subject to the control of the same cis-RE. The latter method, called phylogenetic footprinting, has proven effective in studies of transcriptional regulation in Escherichia coli and related ␥-proteo-bacteria Laikova et al 2001;McCue et al 2001;Panina et al 2001Panina et al , 2003Rajewsky et al 2002;Panina et al 2003), bacteria from the Bacillus/Clostridium cluster (Rodionov et al 2001;Terai et al 2001) and Archea (Gelfand et al 2000a).…”

mentioning

confidence: 99%

Regulog Analysis: Detection of Conserved Regulatory Networks Across Bacteria: Application to Staphylococcus aureus

Alkema¹,

Lenhard²,

Wasserman³

2004

Genome Res.

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A transcriptional regulatory network encompasses sets of genes (regulons) whose expression states are directly altered in response to an activating signal, mediated by trans-acting regulatory proteins and cis-acting regulatory sequences. Enumeration of these network components is an essential step toward the creation of a framework for systems-based analysis of biological processes. Profile-based methods for the detection of cis-regulatory elements are often applied to predict regulon members, but they suffer from poor specificity. In this report we describe Regulogger, a novel computational method that uses comparative genomics to eliminate spurious members of predicted gene regulons. Regulogger produces regulogs, sets of coregulated genes for which the regulatory sequence has been conserved across multiple organisms. The quantitative method assigns a confidence score to each predicted regulog member on the basis of the degree of conservation of protein sequence and regulatory mechanisms. When applied to a reference collection of regulons from Escherichia coli, Regulogger increased the specificity of predictions up to 25-fold over methods that use cis-element detection in isolation. The enhanced specificity was observed across a wide range of biologically meaningful parameter combinations, indicating a robust and broad utility for the method. The power of computational pattern discovery methods coupled with Regulogger to unravel transcriptional networks was demonstrated in an analysis of the genome of Staphylococcus aureus. A total of 125 regulogs were found in this organism, including both well-defined functional groups and a subset with unknown functions.

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Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria

Cited by 83 publications

References 40 publications

Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima

Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima

Carbohydrate metabolism in Bifidobacteria

Regulog Analysis: Detection of Conserved Regulatory Networks Across Bacteria: Application to Staphylococcus aureus

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