Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

Rodionov, Dmitry A.

doi:10.1002/chin.200746276

Cited by 34 publications

(60 citation statements)

References 60 publications

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“…To detect and characterize these key components of the transcriptional regulatory network, the annotated genome sequence of C. glutamicum ATCC 13032 was screened using various bioinformatics approaches for the presence of genes that encode putative transcription regulators (Brune et al, 2005;Brinkrolf et al, 2007). This value is in agreement with previous estimates that o 10% of the total number of predicted proteins is associated with transcriptional regulatory processes in bacterial species (Pérez-Rueda & Collado-Vides, 2000;Rodionov, 2007). This collection of candidate transcription regulators represents 5.3% of the predicted protein-coding regions of the C. glutamicum ATCC 13032 genome.…”

Section: Introductionsupporting

confidence: 78%

“…Alternative sigma factors can redirect the RNA polymerase toward a subset of promoters in front of genes that are required under specific environmental conditions, such as growth-phase transition or stress response. However, sigma factors can perform this activating regulatory role in gene expression only when they are bound to the RNA polymerase core enzyme, whereas typical DNA-binding transcription regulators affect gene expression by either blocking or allowing the RNA polymerase access to the promoter, depending on the relative location of the operator and the ligand-binding status (Madan Babu & Teichmann, 2003a;Rodionov, 2007). As a result, bacteria are able to switch between different programs of gene expression based on their repertoire of sigma factor genes (Pérez-Rueda et al, 2009).…”

Section: The Reference Database Coryneregnetmentioning

confidence: 99%

“…Three transcription regulators are apparently associated with the control of vitamin biosynthesis pathways: PdxR, NrtR and BioQ (McHardy et al, 2003;Rodionov, 2007;Rodionov et al, 2008). Three transcription regulators are apparently associated with the control of vitamin biosynthesis pathways: PdxR, NrtR and BioQ (McHardy et al, 2003;Rodionov, 2007;Rodionov et al, 2008).…”

Section: Transcriptional Regulation Of Vitamin Biosynthesismentioning

confidence: 99%

“…Evidence for a transcriptional regulatory role of the BioQ protein in biotin biosynthesis (bio) gene expression in C. glutamicum ATCC 13032 was also obtained by crossgenome comparisons (Rodionov, 2007). Biotin is an essential cofactor of numerous biotin-dependent carboxylases in a variety of bacteria.…”

Section: Transcriptional Regulation Of Vitamin Biosynthesismentioning

confidence: 99%

“…Biotin is an essential cofactor of numerous biotin-dependent carboxylases in a variety of bacteria. The BioQ protein is a member of the TetR family of transcription regulators and is considered a candidate biotin regulator because the bioQ gene is colocalized with biotin biosynthesis and transport genes in several actinobacterial genomes (Rodionov, 2007). The BioQ protein is a member of the TetR family of transcription regulators and is considered a candidate biotin regulator because the bioQ gene is colocalized with biotin biosynthesis and transport genes in several actinobacterial genomes (Rodionov, 2007).…”

Section: Transcriptional Regulation Of Vitamin Biosynthesismentioning

confidence: 99%

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Transcriptional regulation of gene expression inCorynebacterium glutamicum: the role of global, master and local regulators in the modular and hierarchical gene regulatory network

Schröder

Tauch

2010

FEMS Microbiol Rev

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The genus Corynebacterium belongs to the taxonomic class Actinobacteria representing the high G+C branch of gram-positive bacteria. Among the most prominent members of this genus is Corynebacterium glutamicum, which is used by the biotechnological industry for the fermentative production of l-amino acids. Because of its industrial importance, C. glutamicum is one of the best-studied gram-positive bacteria and an emerging model for the suborder Corynebacterineae. Over the past years, the transcriptional regulation of gene expression was intensively studied in C. glutamicum to gain insights into the regulatory gene composition and the architecture of the transcriptional regulatory network. Therefore, we have achieved considerable improvements in understanding the regulatory roles of the various transcription regulators and the topology of the gene-regulatory network. This review summarizes the current knowledge of the regulatory gene repertoire and the reconstruction of the transcriptional regulatory network. We describe the functional classification of the detected transcription regulators and their interactions in the gene-regulatory network. Moreover, we provide an overview of the molecular features of transcription regulators and their regulons to integrate these data into the gene-regulatory network and to unravel the flow of information from the environment toward the gene level.

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Section: Introductionsupporting

confidence: 78%

Section: The Reference Database Coryneregnetmentioning

confidence: 99%

Section: Transcriptional Regulation Of Vitamin Biosynthesismentioning

confidence: 99%

Section: Transcriptional Regulation Of Vitamin Biosynthesismentioning

confidence: 99%

Section: Transcriptional Regulation Of Vitamin Biosynthesismentioning

confidence: 99%

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Transcriptional regulation of gene expression inCorynebacterium glutamicum: the role of global, master and local regulators in the modular and hierarchical gene regulatory network

Schröder

Tauch

2010

FEMS Microbiol Rev

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Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections

Zhang

Ravcheev

et al. 2015

MicrobiologyOpen

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Bacterial pathogens can exploit metabolic pathways to facilitate their successful infection cycles, but little is known about roles of d‐galactosamine (GalN)/N‐acetyl‐d‐galactosamine (GalNAc) catabolism pathway in bacterial pathogenesis. Here, we report the genomic reconstruction of GalN/GalNAc utilization pathway in Streptococci and the diversified aga regulons. We delineated two new paralogous AgaR regulators for the GalN/GalNAc catabolism pathway. The electrophoretic mobility shift assays experiment demonstrated that AgaR2 (AgaR1) binds the predicted palindromes, and the combined in vivo data from reverse transcription quantitative polymerase chain reaction and RNA‐seq suggested that AgaR2 (not AgaR1) can effectively repress the transcription of the target genes. Removal of agaR2 (not agaR1) from Streptococcus suis 05ZYH33 augments significantly the abilities of both adherence to Hep‐2 cells and anti‐phagocytosis against RAW264.7 macrophage. As anticipated, the dysfunction in AgaR2‐mediated regulation of S. suis impairs its pathogenicity in experimental models of both mice and piglets. Our finding discovered two novel regulators specific for GalN/GalNAc catabolism and assigned them distinct roles into bacterial infections. To the best of our knowledge, it might represent a first paradigm that links the GalN/GalNAc catabolism pathway to bacterial pathogenesis.

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Structure and function of a TetR family transcriptional regulator, SbtR, from thermus thermophilus HB8

et al. 2013

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SbtR is one of the four TetR family transcriptional regulators present in the extremely thermophilic bacterium, Thermus thermophilus HB8. We identified 10 genes controlled by four promoters with negative regulation by SbtR in vitro. The SbtR-regulated gene products include probable transporters, probable enzymes for sugar or amino acid metabolism, and nucleic acid-related enzymes. SbtR binds pseudopalindromic sequences, with the consensus sequence of 5'-TGACCCNNKGGTCA-3' surrounding the promoters, and has a proposed 1:1 dimer binding stoichiometry. The X-ray crystal structure analysis revealed that SbtR comprises either nine or 10 α-helices and forms a dimer, as in the typical TetR family proteins. Similar to many characterized TetR family regulators, SbtR has a predicted ligand-binding pocket at the center of each monomer. Interestingly, the SbtR dimer contains an intermolecular disulfide bridge, formed between the Cys164 residues at the entrance of the pocket. The Cys164Ser and Cys164Ala mutant SbtR proteins formed homodimers similar to that of the wild type, but their thermal stabilities were lower by about 8°C, indicating that the disulfide bridge contributes to the thermal stability of the protein. However, altered repression activity of the mutants was not observed in vitro. From these results, we propose that ligand-binding is essential for SbtR to disengage from DNA, in a similar manner to the other characterized TetR family regulators. The formation and reduction of the disulfide bond might function in controlling the ligand-binding affinity of this transcriptional regulator.

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Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

Abstract: ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Cited by 34 publications

References 60 publications

Transcriptional regulation of gene expression inCorynebacterium glutamicum: the role of global, master and local regulators in the modular and hierarchical gene regulatory network

Transcriptional regulation of gene expression inCorynebacterium glutamicum: the role of global, master and local regulators in the modular and hierarchical gene regulatory network

Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections

Structure and function of a TetR family transcriptional regulator, SbtR, from thermus thermophilus HB8

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