Repressor for the sn-glycerol 3-phosphate regulon of Escherichia coli K-12: primary structure and identification of the DNA-binding domain

SummaryThe adjacent, divergently transcribed glpACB and glpTQ operons of Escherichia coli encode the anaerobic glycerol 3-phosphate dehydrogenase and glycerol 3-phosphate transporter/phosphodiesterase, respectively. These operons are negatively controlled by glp repressor binding to operators that overlap the glpA promoter elements. Using DNase I footprinting, three additional operators (O T 1-3) were identified at positions þ307 to þ359 within the glpT coding region. To assess a potential regulatory role for these remote operators in vivo, a glpT-lacZ transcriptional fusion containing all of the glpA and glpT operators was constructed. The response of this fusion to the glp repressor was compared to fusion constructs in which O T 1 and O T 3 were inactivated, either by deletion or by sitedirected mutagenesis. It was found that repression of glpT conferred by binding of glp repressor to glpA operators was increased about three-to fourfold upon introduction of the remote glpT operators. In addition, two integration host factor (IHF) binding sites were identified downstream of the glpT transcriptional start site at positions þ15 to þ51 and þ193 to þ227. A regulatory role for IHF was demonstrated by showing that repression of glpT mediated by GlpR was decreased about twofold in strains deficient in IHF and that mutations in IHF1 and/or IHF2 decreased repression about two-to threefold. The effect of IHF was apparent only when the remote operators were present. All of the results are consistent with a model of repression involving GlpR binding simultaneously to the glpA and remote glpT operators, with intervening DNA forming a loop.

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“…Specific negative regulation of the glp regulon is exerted by the glp repressor (GlpR). The inducer for GlpR is glycerol-P Zeng et al, 1996).…”

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confidence: 99%

Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K‐12

Yang

Gerhardt

Larson

1997

Molecular Microbiology

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“…As a result, the HTH DNA-binding region of a repressor for the sn-glycerol 3-phosphate regulon of Escherichia coli K-12 (GlpR) was found to have a distinctive homology, particularly in the second helix (the so-called recognition helix), to the amino-terminal region of HrcA (Fig. 1A) (34). GlpR, belonging to the repressor family of carbohydrate catabolic systems, possesses the DNA-binding motif near the amino terminus (residues 22 to 41) (34).…”

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“…In addition, the difference in the changes in K d s reflected that the recognition helix is conserved more highly than the preceding helix; therefore, the recognition helix is more critical than the preceding helix in the binding of the HrcA molecule to the CIRCE element. In a previous study, Arg38 of E. coli GlpR, which is equivalent to Asn44 of B. thermoglucosidasius HrcA, was determined to be significant in recognizing the DNA (34).…”

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confidence: 99%

“…1A) (34). GlpR, belonging to the repressor family of carbohydrate catabolic systems, possesses the DNA-binding motif near the amino terminus (residues 22 to 41) (34). In addition, other members of the family, the repressors GutR (glucitol operon, E. coli) (31), FucR (fucose operon, E. coli) (13), and IolR (inositol utilization operon, B. subtilis) (32), showed similar homologies in the recognition helix (Fig.…”

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Identification of a Helix-Turn-Helix Motif of Bacillus thermoglucosidasius HrcA Essential for Binding to the CIRCE Element and Thermostability of the HrcA-CIRCE Complex, Indicating a Role as a Thermosensor

et al. 2003

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In the heat shock response of bacillary cells, HrcA repressor proteins negatively control the expression of the major heat shock genes, the groE and dnaK operons, by binding the CIRCE (controlling inverted repeat of chaperone expression) element. Studies on two critical but yet unresolved issues related to the structure and function of HrcA were performed using mainly the HrcA from the obligate thermophile Bacillus thermoglucosidasius KP1006. These two critical issues are (i) identifying the region at which HrcA binds to the CIRCE element and (ii) determining whether HrcA can play the role of a thermosensor. We identified the position of a helix-turn-helix (HTH) motif in B. thermoglucosidasius HrcA, which is typical of DNA-binding proteins, and indicated that two residues in the HTH motif are crucial for the binding of HrcA to the CIRCE element. Furthermore, we compared the thermostabilities of the HrcA-CIRCE complexes derived from Bacillus subtilis and B. thermoglucosidasius, which grow at vastly different ranges of temperature. The thermostability profiles of their HrcA-CIRCE complexes were quite consistent with the difference in the growth temperatures of B. thermoglucosidasius and B. subtilis and, thus, suggested that HrcA can function as a thermosensor to detect temperature changes in cells.In the heat shock response of Bacillus subtilis, HrcA repressor proteins negatively control the expression of the major heat shock genes, the groE and dnaK operons, by binding the CIRCE (controlling inverted repeat of chaperone expression) element (9, 17). Studies of HrcA and hrcA, its gene in various microorganisms, have clarified that HrcA molecules have similar features, e.g., the primary sequences of HrcA are strikingly conserved among organisms; based on phylogenetic analysis, this characteristic has evolutionary implications (1,22,33). On the other hand, common and unfavorable characteristics are that HrcA is hardly soluble and easily forms aggregates. This disadvantage has prevented the clarification of the real nature of HrcA. To circumvent this disadvantage, it was demonstrated in a previous report that HrcA from the obligate thermophile Bacillus thermoglucosidasius KP1006 was most efficiently renatured by the addition of DNA, including the CIRCE element, and that the HrcA-CIRCE complex was stable in the soluble form in the absence of GroEL (29).Two critical issues related to the structure and function of HrcA are outstanding. One is the identification of the region at which HrcA binds to the CIRCE element. Although three conserved regions have been previously pointed out (22,33), no extended analysis of the DNA-binding region of HrcA has been conducted. The other issue is whether HrcA can play the role of a thermosensor. When bacillary cells are exposed to heat stress, the expression of genes controlled by the HrcA-CIRCE complex is turned on. This implies that the HrcA-CIRCE complex must be decomposed by heat stress to release the regulation system. However, no direct evidence that the HrcA-CIRCE complex is dec...

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“…78) According to its primary structure, YcnK is classified into the DeoR family of bacterial transcriptional factors. 79) To date, many members of the DeoR family from various Gram-positive and Gram-negative bacteria have been characterized and were found to share several common features. They contain a highly conserved region near the N terminus that includes an HTH DNA-binding motif.…”

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Transcriptional response machineries of Bacillus subtilis conducive to plant growth promotion

Hirooka

2014

Bioscience, Biotechnology, and Biochemistry

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Bacillus subtilis collectively inhabits the rhizosphere, where it contributes to the promotion of plant growth, although it does not have a direct symbiotic relationship to plants as observed in the case of rhizobia between leguminous plants. As rhizobia sense the flavonoids released from their host roots through the NodD transcriptional factor, which triggers transcription of the nod genes involved in the symbiotic processes, we supposed that B. subtilis utilizes certain flavonoids as signaling molecules to perceive and adapt to the rhizospheric environment that it is in. Our approaches to identify the flavonoid-responsive transcriptional regulatory system from B. subtilis resulted in the findings that three transcriptional factors (LmrA/QdoR, YetL, and Fur) are responsive to flavonoids, with the modes of action being different from each other. We also revealed a unique regulatory system by two transcriptional factors, YcnK and CsoR, for copper homeostasis in B. subtilis. In this review, we summarize the molecular mechanisms of these regulatory systems with the relevant information and discuss their physiological significances in the mutually beneficial interaction between B. subtilis and plants, considering the possibility of their application for plant cultivation.

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Repressor for the sn-glycerol 3-phosphate regulon of Escherichia coli K-12: primary structure and identification of the DNA-binding domain

Cited by 62 publications

References 57 publications

Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K‐12

Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K‐12

Identification of a Helix-Turn-Helix Motif of Bacillus thermoglucosidasius HrcA Essential for Binding to the CIRCE Element and Thermostability of the HrcA-CIRCE Complex, Indicating a Role as a Thermosensor

Transcriptional response machineries of Bacillus subtilis conducive to plant growth promotion

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