Ss‐LrpB, a novel Lrp‐like regulator of <i>Sulfolobus solfataricus</i> P2, binds cooperatively to three conserved targets in its own control region

Peeters, Eveline; Thia-Toong, Thia-Lin; Gigot, Daniel; Maes, Dominique; Charlier, Daniël

doi:10.1111/j.1365-2958.2004.04274.x

Cited by 58 publications

(108 citation statements)

References 47 publications

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“…The first step to reveal the mechanism of ald regulation was to identify cis-regulatory elements in the upstream region of ald. According to previously reported footprinting results, a long stretch of DNA was generally protected by Lrp/AsnC family regulators (48)(49)(50)(51)(52)(53)(54)(55)(56)(57)(58)(59)(60)(61), which indicates the presence of multiple binding sites on DNA. Likewise, four AldR-binding sites (O2, O1, O4, and O3) with a consensus sequence of GA/T-N 2 -WWN/NWW-N 2 -T/AC were identified upstream of the ald gene by sequence analysis in conjunction with DNase I footprinting analysis and EMSAs.…”

Section: Discussionmentioning

confidence: 99%

Regulation Mechanism of the ald Gene Encoding Alanine Dehydrogenase in Mycobacterium smegmatis and Mycobacterium tuberculosis by the Lrp/AsnC Family Regulator AldR

Jeong

Hyun

2015

J Bacteriol

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In the presence of alanine, AldR, which belongs to the Lrp/AsnC family of transcriptional regulators and regulates ald encoding alanine dehydrogenase in Mycobacterium smegmatis, changes its quaternary structure from a homodimer to an octamer with an open-ring conformation. Four AldR-binding sites (O2, O1, O4, and O3) with a consensus sequence of GA/T-N 2 -NWW/WWN-N 2 -A/TC were identified upstream of the M. smegmatis ald gene by means of DNase I footprinting analysis. O2, O1, and O4 are required for the induction of ald expression by alanine, while O3 is directly involved in the repression of ald expression. In addition to O3, both O1 and O4 are also necessary for full repression of ald expression in the absence of alanine, due to cooperative binding of AldR dimers to O1, O4, and O3. Binding of a molecule of the AldR octamer to the ald control region was demonstrated to require two AldR-binding sites separated by three helical turns between their centers and one additional binding site that is in phase with the two AldR-binding sites. The cooperative binding of AldR dimers to DNA requires three AldR-binding sites that are aligned with a periodicity of three helical turns. The aldR gene is negatively autoregulated independently of alanine. Comparative analysis of ald expression of M. smegmatis and Mycobacterium tuberculosis in conjunction with sequence analysis of both ald control regions led us to suggest that the expression of the ald genes in both mycobacterial species is regulated by the same mechanism. IMPORTANCEIn mycobacteria, alanine dehydrogenase (Ald) is the enzyme required both to utilize alanine as a nitrogen source and to grow under hypoxic conditions by maintaining the redox state of the NADH/NAD ؉ pool. Expression of the ald gene was reported to be regulated by the AldR regulator that belongs to the Lrp/AsnC (feast/famine) family, but the underlying mechanism was unknown. This study revealed the regulation mechanism of ald in Mycobacterium smegmatis and Mycobacterium tuberculosis. Furthermore, a generalized arrangement pattern of cis-acting regulatory sites for Lrp/AsnC (feast/famine) family regulators is suggested in this study. N AD(H)-dependent alanine dehydrogenase (Ald; EC 1.4.1.1) catalyzes the oxidative deamination of L-alanine to pyruvate and reversibly catalyzes the reductive amination of pyruvate to L-alanine. Ald is required for mycobacteria to utilize alanine as a nitrogen source via the oxidative deamination reaction (1-3). It was also proposed that Ald helps mycobacteria maintain the redox state of the NADH/NAD ϩ pool under respiration-inhibiting conditions, such as hypoxic conditions, by regenerating NAD ϩ from NADH via its reductive amination reaction (2, 4, 5). The enzyme forms a hexamer of identical subunits with the N-terminal catalytic domain and the C-terminal NAD(H)-binding domain (6, 7). Ald was shown to be one of the major antigens found in culture filtrates of Mycobacterium tuberculosis (8,9).Expression of the ald gene as well as the synthesis and activity of Ald we...

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Section: Discussionmentioning

confidence: 99%

Regulation Mechanism of the ald Gene Encoding Alanine Dehydrogenase in Mycobacterium smegmatis and Mycobacterium tuberculosis by the Lrp/AsnC Family Regulator AldR

Jeong

Hyun

2015

J Bacteriol

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“…K D values were estimated based on these EMSAs, as the protein concentration at which about 50 % of the DNA was bound (expressed in dimer equivalents). In-gel OP-Cu footprinting was performed as described previously (Peeters et al, 2004). Reference ladders were generated by chemical sequencing methods (Maxam & Gilbert, 1980).…”

Section: Methodsmentioning

confidence: 99%

LmrR-mediated gene regulation of multidrug resistance in Lactococcus lactis

et al. 2011

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Multidrug resistance (MDR) in Lactococcus lactis is due to the expression of the membrane ATP-binding cassette (ABC) transporter LmrCD. In the absence of drugs, the transcriptional regulator LmrR prevents expression of the lmrCD operon by binding to its operator site. Through an autoregulatory mechanism LmrR also suppresses its own expression. Although the lmrR and lmrCD genes have their own promoters, primer extension analysis showed the presence of a long transcript spanning the entire lmrR-lmrCD cluster, in addition to various shorter transcripts harbouring the lmrCD genes only. 'In-gel' Cu-phenanthroline footprinting analysis indicated an extensive interaction between LmrR and the lmrR promoter/operator region. Atomic force microscopy imaging of the binding of LmrR to the control region of lmrR DNA showed severe deformations indicative of DNA wrapping and looping, while LmrR binding to a fragment containing the lmrCD control region induced DNA bending. The results further suggest a drugdependent regulation mechanism in which the lmrCD genes are co-transcribed with lmrR as a polycistronic messenger. This leads to an LmrR-mediated regulation of lmrCD expression that is exerted from two different locations and by distinct regulatory mechanisms.

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“…For SsoLrpB, a function in the regulation of genes involved in central carbohydrate metabolism was demonstrated. First, autoregulation of LrpB by binding to the control region of its own gene (508) and, later on, binding to promoter regions of adjacent genes encoding two putative permeases (SSO2126/SSO2127) as well as the first gene (porD) of the porDAB operon, encoding pyruvate-ferredoxin oxidoreductase, were demonstrated (509). A mutant strain (PBL2025 [510]) lacking LrpB was generated but showed no effect during growth with tryptone or glucose (509).…”

Section: Sulfolobus Solfataricusmentioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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Ss‐LrpB, a novel Lrp‐like regulator of Sulfolobus solfataricus P2, binds cooperatively to three conserved targets in its own control region

Cited by 58 publications

References 47 publications

Regulation Mechanism of the ald Gene Encoding Alanine Dehydrogenase in Mycobacterium smegmatis and Mycobacterium tuberculosis by the Lrp/AsnC Family Regulator AldR

Regulation Mechanism of the ald Gene Encoding Alanine Dehydrogenase in Mycobacterium smegmatis and Mycobacterium tuberculosis by the Lrp/AsnC Family Regulator AldR

LmrR-mediated gene regulation of multidrug resistance in Lactococcus lactis

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

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