Mutant forms of the enhancer-binding protein NtrC can activate transcription from solution

North, Anne K.; Kustu, Sydney

doi:10.1006/jmbi.1996.0838

Cited by 54 publications

(49 citation statements)

References 62 publications

(88 reference statements)

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“…DNase I footprinting of DctD (⌬1-142) at the dctA UAS revealed changes in the footprint in response to ADP ⅐ AlF x , consistent with the idea that the DNA-binding domain can communicate with the AAAϩ domain, at least in the transition state during ATP hydrolysis (45). Alternatively, intermolecular interactions between the DNA-binding domains of DctD monomers may interfere with assembly of a functional oligomeric complex, which may be supported by the observation that introduction of three alanine substitutions in the enhancer recognition helix of S. enterica serovar Typhimurium NtrC eliminates DNAbinding activity and stabilizes the dimeric state of the protein (26).…”

Section: Discussionsupporting

confidence: 72%

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ⁵⁴-Dependent Transcriptional Activator

Nixon

et al. 2004

J Bacteriol

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Section: Discussionsupporting

confidence: 72%

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ⁵⁴-Dependent Transcriptional Activator

Nixon

et al. 2004

J Bacteriol

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“…This activation was similar by using templates with or without an enhancer. Thus, the roles of the enhancer can be bypassed if the protein is present at high concentrations in solution (201).…”

Section: Nitrogen Regulator Imentioning

confidence: 99%

“…Two NRI-P dimers strongly bind the enhancer in a cooperative way (470,471). The function of the enhancer is to increase the local concentration of NRI-P (201,457,458,471,473,480,481). This facilitates oligomerization (472).…”

Section: Gene Expression Regulationmentioning

confidence: 99%

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

Heeswijk¹,

Westerhoff

Boogerd³

2013

Microbiol Mol Biol Rev

228

246

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SUMMARY We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli . The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.

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“…It seems that contact with enhancer DNA adds efficiency to formation of the NtrC oligomer (Porter et al 1995), but is not essential for the remodeling of 54 . At high concentrations many of the 54 -dependent ATPase domains (including NtrC's) can act in the absence of DNAbinding activity and in an enhancer-independent fashion (North and Kustu 1997). However, substitutions in the GAFTGA loop of NtrC caused binding to the enhancer or even nonspecific DNA to act as a negative allosteric regulator of the interaction with RNA polymerase , and prior studies of DctD, activated by deleting its N-terminal receiver domain, showed that ADP-AlF x , but not ADP or ADP-BeF x , caused hypersensitivity to DNase I to appear between the tandem binding sites in the dctA UAS (Wang et al 2003).…”

Section: Dna-binding Nucleotide Cycle and Interaction With 54 : Thementioning

confidence: 99%

The structural basis for regulated assembly and function of the transcriptional activator NtrC

Carlo¹,

Chen²,

Hoover³

et al. 2006

Genes Dev.

111

180

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In two-component signal transduction, an input triggers phosphorylation of receiver domains that regulate the status of output modules. One such module is the AAA+ ATPase domain in bacterial enhancer-binding proteins that remodel the 54 form of RNA polymerase. We report X-ray solution scattering and electron microscopy structures of the activated, full-length nitrogen-regulatory protein C (NtrC) showing a novel mechanism for regulation of AAA+ ATPase assembly via the juxtaposition of the receiver domains and ATPase ring. Accompanying the hydrolysis cycle that is required for transcriptional activation, we observed major order-disorder changes in the GAFTGA loops involved in 54 binding, as well as in the DNA-binding domains. The 54 holoenzyme form of RNA polymerase forms closed DNA complexes that open only with the help of enhancer-binding proteins (EBPs). For the nitrogen-regulatory protein C of enteric bacteria (NtrC), such activity starts a cascade of events that may ultimately lead to the activation of transcription for as much as 2% of the genome (Zimmer et al. 2000). Sequence analysis of >160054 -dependent transcriptional activators shows that in addition to their oligomerization/AAA+ ATPase domain, they also have a DNA-binding domain and a regulatory domain, which in 50% of cases is a twocomponent receiver domain (Bateman et al. 2004). The helix-turn-helix DNA-binding domain recognizes enhancer-like sequences between 100 and 150 bp upstream of the promoter. In their inactive states these proteins are usually dimers that bind to pairs of tandem sites in the enhancer elements. Upon activation via the regulatory domains, they oligomerize into ATPase-active rings that use the energy from ATP hydrolysis to physically remodel closed complexes of 54 holoenzyme and promoter DNA (Rombel et al. 1998;Neuwald et al. 1999;Chaney et al. 2001;Lee et al. 2003).Crystal or NMR structures are available for several isolated domains and truncation constructs of EBPs including NtrC, DctD, PspF, ZraR, and NtrC1 (Volkman et al. 1995;Kern et al. 1999;Pelton et al. 1999;Meyer et al. 2001;Park et al. 2002;Hastings et al. 2003;Lee et al. 2003;Doucleff et al. 2005;Rappas et al. 2005;Sallai and Tucker 2005). Existing structural information on DctD and NtrC1 has been used to provide a model of how two-component signal transduction can regulate assembly of their AAA+ ATPase domains ), but this model fails to explain regulation in the closely related protein NtrC (40% sequence identity, 60% sequence similarity) Hastings et al. 2003). Here we report both SAXS/WAXS (small-and wide-angle X-ray scattering) and EM (electron microscopy) structures of the full-length, activated form of NtrC from Salmonella typhimurium. Docking of atomic models for the individual domains into the structures reveals their organization within the activated ring and uncovers a novel mechanism for the use of two-compo-

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Mutant forms of the enhancer-binding protein NtrC can activate transcription from solution

Cited by 54 publications

References 62 publications

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ⁵⁴-Dependent Transcriptional Activator

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ⁵⁴-Dependent Transcriptional Activator

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

The structural basis for regulated assembly and function of the transcriptional activator NtrC

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Mutant forms of the enhancer-binding protein NtrC can activate transcription from solution

Cited by 54 publications

References 62 publications

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ54-Dependent Transcriptional Activator

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ54-Dependent Transcriptional Activator

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

The structural basis for regulated assembly and function of the transcriptional activator NtrC

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Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ⁵⁴-Dependent Transcriptional Activator

Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ⁵⁴-Dependent Transcriptional Activator