Identification of activating region (AR) of <i>Escherichia coli</i> LysR‐type transcription factor CysB and CysB contact site on RNA polymerase alpha subunit at the <i>cysP</i> promoter

Łochowska, Anna; Iwanicka-Nowicka, Roksana; Zaim, Jolanta; Witkowska-Zimny, Małgorzata; Bolewska, Krystyna; Hryniewicz, Monika M.

doi:10.1111/j.1365-2958.2004.04161.x

Cited by 46 publications

(40 citation statements)

References 72 publications

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“…There are several studies that show LTTR interactions with RNA polymerase or sigma factors (50)(51)(52)(53)(54)(55), but there are few examples of interactions of LTTR proteins (not including CbbRs) with other transcriptional regulators (56,57). By and large, this is a testament to the ability of LTTRs to independently and adequately regulate their operons in the prokaryotic kingdom.…”

Section: Interactions With Cbbr: the Case Of Dueling Transcription Famentioning

confidence: 99%

CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation

Dangel

Tabita

2015

J Bacteriol

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Biological carbon dioxide fixation is an essential and crucial process catalyzed by both prokaryotic and eukaryotic organisms to allow ubiquitous atmospheric CO 2 to be reduced to usable forms of organic carbon. This process, especially the CalvinBassham-Benson (CBB) pathway of CO 2 fixation, provides the bulk of organic carbon found on earth. The enzyme ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) performs the key and rate-limiting step whereby CO 2 is reduced and incorporated into a precursor organic metabolite. This is a highly regulated process in diverse organisms, with the expression of genes that comprise the CBB pathway (the cbb genes), including RubisCO, specifically controlled by the master transcriptional regulator protein CbbR. Many organisms have two or more cbb operons that either are regulated by a single CbbR or employ a specific CbbR for each cbb operon. CbbR family members are versatile and accommodate and bind many different effector metabolites that influence CbbR's ability to control cbb transcription. Moreover, two members of the CbbR family are further posttranslationally modified via interactions with other transcriptional regulator proteins from two-component regulatory systems, thus augmenting CbbR-dependent control and optimizing expression of specific cbb operons. In addition to interactions with small effector metabolites and other regulator proteins, CbbR proteins may be selected that are constitutively active and, in some instances, elevate the level of cbb expression relative to wild-type CbbR. Optimizing CbbR-dependent control is an important consideration for potentially using microbes to convert CO 2 to useful bioproducts.

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Section: Interactions With Cbbr: the Case Of Dueling Transcription Famentioning

confidence: 99%

CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation

Dangel

Tabita

2015

J Bacteriol

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“…At the hut and put operons, NAC activates transcription by a mechanism that requires NAC binding to a site centered at Ϫ64 relative to the start of transcription (15). Data from other LysR-type regulators suggest by analogy that NAC may interact with the ␣-subunit of RNA polymerase in such cases (22,38). At the dad, ure, and cod operons, NAC activates transcription by a mechanism that requires binding to a site centered at Ϫ44, Ϫ49, and Ϫ59, respectively (20, 29; unpublished data).…”

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confidence: 99%

Importance of Tetramer Formation by the Nitrogen Assimilation Control Protein for Strong Repression of Glutamate Dehydrogenase Formation in Klebsiella pneumoniae

Rosario

Bender

2005

J Bacteriol

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The nitrogen assimilation control protein (NAC) from Klebsiella pneumoniae is a very versatile regulatory protein. NAC activates transcription of operons such as hut (histidine utilization) and ure (urea utilization), whose products generate ammonia. NAC also represses the transcription of genes such as gdhA, whose products use ammonia. NAC exerts a weak repression at gdhA by competing with the binding of a lysinesensitive activator. NAC also strongly represses transcription of gdhA (about 20-fold) by binding to two separated sites, suggesting a model involving DNA looping. We have identified negative control mutants that are unable to exert this strong repression of gdhA expression but still activate hut and ure expression normally. Some of these negative control mutants (e.g., NAC 86ter and NAC 132ter ) delete the C-terminal domain, thought to be required for tetramerization. Other negative control mutants (e.g., NAC L111K and NAC L125R ) alter single amino acids involved in tetramerization. In this work we used gel filtration to show that NAC 86ter and NAC L111K are dimers in solution, even at high concentration (NAC WT is a tetramer). Moreover, using a combination of DNase I footprints and gel mobility shifts assays, we showed that when NAC WT binds to two adjacent sites on a DNA fragment, NAC WT binds as a tetramer that bends the DNA fragment significantly. NAC L111K binds to such a fragment as two independent dimers without inducing the strong bend. Thus, NAC L111K is a dimer in solution or when bound to DNA. NAC L111K (typical of the negative control mutants) is wild type for every other property tested: (i) it activates transcription at hut and ure; (ii) it competes with the lysine-sensitive activator for binding at gdhA; (iii) it binds to the same sites at the hut, ure, nac, and gdhA promoters as NAC WT ; (iv) the relative affinity of NAC L111K for these sites follows the same order as NAC WT (ure > gdhA > nac > hut); (v) it induces the same slight bend as dimers of NAC WT ; and (vi) its DNase I footprints at these sites are indistinguishable from those of NAC WT (except for features ascribed to tetramer formation). The only two phenotypes we know for negative control mutants of NAC are their inability to tetramerize and their inability to cause the strong repression of gdhA. Thus, we propose that in order for NAC WT to exert the strong repression, it must form a tetramer that bridges the two sites at gdhA (similar to other DNA looping models) and that the negative control mutants of NAC, which fail to tetramerize, cannot form this loop and thus fail to exert the strong repression at gdhA.

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“…The global regulator, responsive to select cellular stimuli, binds to specific sites in the control regions of these operons. Examples of such pleiotropic transcription factors in E. coli include Crp, a primary sensor of carbon availability (8,15,23,65), NtrBC, a sensor of nitrogen availability (32, 63, 77), CysB, the sensor of sulfur availability (38,39,41,42), and Fur, a dominant sensor of iron availability (30,31,50,71). Crp when complexed with cyclic AMP (cAMP) binds to a consensus sequence in the DNA and activates transcription of many genes while repressing transcription of a few others.…”

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Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli

et al. 2005

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In Escherichia coli, the ferric uptake regulator (Fur) controls expression of the iron regulon in response to iron availability while the cyclic AMP receptor protein (Crp) regulates expression of the carbon regulon in response to carbon availability. We here identify genes subject to significant changes in expression level in response to the loss of both Fur and Crp. Many iron transport genes and several carbon metabolic genes are subject to dual control, being repressed by the loss of Crp and activated by the loss of Fur. However, the sodB gene, encoding superoxide dismutase, and the aceBAK operon, encoding the glyoxalate shunt enzymes, show the opposite responses, being activated by the loss of Crp and repressed by the loss of Fur. Several other genes including the sdhA-D, sucA-D, and fumA genes, encoding key constituents of the Krebs cycle, proved to be repressed by the loss of both transcription factors. Finally, the loss of both Crp and Fur activated a heterogeneous group of genes under S control encoding, for example, the cyclopropane fatty acid synthase, Cfa, the glycogen synthesis protein, GlgS, the 30S ribosomal protein, S22, and the mechanosensitive channel protein, YggB. Many genes appeared to be regulated by the two transcription factors in an apparently additive fashion, but apparent positive or negative cooperativity characterized several putative Crp/Fur interactions. Relevant published data were evaluated, putative Crp and Fur binding sites were identified, and representative results were confirmed by real-time PCR. Molecular explanations for some, but not all, of these effects are provided.Processes that alter the rates of transcriptional initiation, elongation and termination, mRNA degradation, and mRNA translation control gene expression in all living organisms. Of these, regulation of transcriptional initiation is of greatest physiological importance in bacteria (34). About one-fourth of all Escherichia coli proteins interact functionally with nucleic acids, and about one-fourth of these are pleiotropic transcriptional regulators that control expression of multioperon regulons, primarily by influencing the transcriptional initiation step (57, 72). In fact, each regulon is defined by the activity of a transcription factor that coordinately controls expression of the operons included within that regulon (28). The global regulator, responsive to select cellular stimuli, binds to specific sites in the control regions of these operons. Examples of such pleiotropic transcription factors in E. coli include Crp, a primary sensor of carbon availability (8,15,23,65), NtrBC, a sensor of nitrogen availability (32, 63, 77), CysB, the sensor of sulfur availability (38,39,41,42), and Fur, a dominant sensor of iron availability (30,31,50,71). Crp when complexed with cyclic AMP (cAMP) binds to a consensus sequence in the DNA and activates transcription of many genes while repressing transcription of a few others. Some genes are subject to both positive and negative regulation by the cAMP-Crp complex due to th...

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Identification of activating region (AR) of Escherichia coli LysR‐type transcription factor CysB and CysB contact site on RNA polymerase alpha subunit at the cysP promoter

Cited by 46 publications

References 72 publications

CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation

CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation

Importance of Tetramer Formation by the Nitrogen Assimilation Control Protein for Strong Repression of Glutamate Dehydrogenase Formation in Klebsiella pneumoniae

Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli

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