Structural and Biochemical Study of Effector Molecule Recognition by the E.coli Glyoxylate and Allantoin Utilization Regulatory Protein AllR

Walker, John R.; Altamentova, Svetlana M.; Ezersky, A.; Lorca, Graciela L.; Skarina, T.; Kudritska, M.; Ball, Linda; Bochkarev, A.; Savchenko, Alexei

doi:10.1016/j.jmb.2006.02.034

Cited by 26 publications

(34 citation statements)

References 73 publications

(58 reference statements)

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“…1c, d), confirming the notion that glyoxylate is an inducer for derepression of AllR action (Rintoul et al, 2002). Altering the residues Cys217, Ser234 and Ser236 is known to change AllR to a glyoxylate-independent repressive form (Walker et al, 2006). Structurally related compounds such as glyconate or D-lactate did not affect the DNA-binding activity of AllR (data not shown).…”

Section: Confirmation Of Allr Binding To Selex Fragments and Search Fsupporting

confidence: 72%

“…The E. coli K-12 genome contains eight members of the IclR family, while a total of about 450 member genes have been identified in bacteria and archaea (Walker et al, 2006). The crystal structures of the C-terminal effector-binding domain of the AllR regulator and its complex with glyoxylate have been determined at the resolution of 1.7 and 1.8 Å (0.17 and 0.18 nm), respectively (cited in Walker et al, 2006). The active protomer of AllR is a dimer of dimers.…”

Section: Resultsmentioning

confidence: 99%

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The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines

et al. 2008

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Purines are degraded via uric acid to yield allantoin. Under anaerobic conditions, allantoin is further degraded via carbamoylphosphate to NH z 4 to provide a nitrogen source and, under aerobic conditions, to 3-phosphoglycerate via glyoxylate for energy production. In this study, we found that a DNA-binding transcription factor AllR, together with AllS, plays a key role in switching control of two pathways, nitrogen assimilation and energy production. The repressor function of AllR is activated in the presence of allantoin, the common substrate for both pathways, leading to repression of the genes for energy production. On the other hand, when glyoxylate is accumulated, AllR is inactivated for derepression of the pathway for energy production. RutR, the master regulator for pyrimidines and arginine, is also involved in this pathway-switching control.

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Section: Confirmation Of Allr Binding To Selex Fragments and Search Fsupporting

confidence: 72%

Section: Resultsmentioning

confidence: 99%

The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines

et al. 2008

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“…Based on structural and mutagenesis data, a hydrophobic pocket on the surface of the b sheet is proposed to be the effectorbinding site (Fig. 1B, white ball and stick; Guazzaroni et al 2005;Walker et al 2006). Importantly, there are very few interactions between the CTD and the DBD within the same monomer (Fig.…”

Section: Crystal Structure Of the Apo Ttgv Tetramermentioning

confidence: 99%

Crystal structure of TtgV in complex with its DNA operator reveals a general model for cooperative DNA binding of tetrameric gene regulators

Lü¹,

Fillet²,

Meng³

et al. 2010

Genes Dev.

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The majority of bacterial gene regulators bind as symmetric dimers to palindromic DNA operators of 12-20 base pairs (bp). Multimeric forms of proteins, including tetramers, are able to recognize longer operator sequences in a cooperative manner, although how this is achieved is not well understood due to the lack of complete structural information. Models, instead of structures, of complete tetrameric assembly on DNA exist in literature. Here we present the crystal structures of the multidrug-binding protein TtgV, a gene repressor that controls efflux pumps, alone and in complex with a 42-bp DNA operator containing two TtgV recognition sites at 2.9 Å and 3.4 Å resolution. These structures represent the first full-length functional tetrameric protein in complex with its intact DNA operator containing two continuous recognition sites. TtgV binds to its DNA operator as a highly asymmetric tetramer and induces considerable distortions in the DNA, resulting in a 60°bend. Upon binding to its operator, TtgV undergoes large conformational changes at the monomeric, dimeric, and tetrameric levels. The structures here reveal a general model for cooperative DNA binding of tetrameric gene regulators and provide a structural basis for a large body of biochemical data and a reinterpretation of previous models for tetrameric gene regulators derived from partial structural data.

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“…Moreover, the regulatory mechanism of these proteins and the structure of the effector binding domain in the free and the effector-bound states have been poorly characterized so far, with the sole exceptions of the regulator AllR and the model system IclR (12,47).…”

Section: Discussionmentioning

confidence: 99%

“…However, TtgV is a tetramer in solution both in the presence and absence of effectors and also in its DNA-bound state (57). The addition of ligand drastically increased AllR tetramerization, whereas three species (monomer, dimer, and tetramer) were detected in solution in the absence of effectors (47). Nevertheless, very few data have been reported so far about the interactions of these regulators with aromatic effectors or synergistic regulatory mechanisms.…”

Section: Discussionmentioning

confidence: 99%

3-Hydroxyphenylpropionate and Phenylpropionate Are Synergistic Activators of the MhpR Transcriptional Regulator from Escherichia coli

Manso¹,

Torres²,

Andreu

et al. 2009

Journal of Biological Chemistry

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The degradation of the aromatic compound phenylpropionate (PP) in Escherichia coli K-12 requires the activation of two different catabolic pathways coded by the hca and the mhp gene clusters involved in the mineralization of PP and 3-hydroxyphenylpropionate (3HPP), respectively. The compound 3-(2,3-dihydroxyphenyl)propionate (DHPP) is a common intermediate of both pathways which must be cleaved by the MhpB dioxygenase before entering into the primary cell metabolism. Therefore, the degradation of PP has to be controlled by both its specific regulator (HcaR) but also by the MhpR regulator of the mhp cluster. We have demonstrated that 3HPP and DHPP are the true and best activators of MhpR, whereas PP only induces no response. However, in vivo and in vitro transcription experiments have demonstrated that PP activates the MhpR regulator synergistically with the true inducers, representing the first case of such a peculiar synergistic effect described for a bacterial regulator. The three compounds enhanced the interaction of MhpR with its DNA operator in electrophoretic mobility shift assays. Inducer binding to MhpR is detected by circular dichroism and fluorescence spectroscopies. Fluorescence quenching measurements have revealed that the true inducers (3HPP and DHPP) and PP bind with similar affinities and independently to MhpR. This type of dual-metabolite synergy provides great potential for a rapid modulation of gene expression and represents an important feature of transcriptional control. The mhp regulatory system is an example of the high complexity achievable in prokaryotes.Phenylpropanoic and phenylpropenoic acids and their hydroxylated derivatives are widely distributed in the environment, arising from digestion of aromatic amino acids or as breakdown products of lignin and other plant-derived phenylpropanoids and flavonoids. The bacterial catabolism of these aromatic compounds plays a key role in recycling of such carbon sources in the ecosystem (1, 2). Most Escherichia coli strains are able to degrade these compounds via a meta-fission pathway (3). A scheme of the biochemical pathway for the catabolism of 3-hydroxyphenylpropionate (3HPP) 2 and 3-hydoxycinnamate (3HCI) in E. coli K-12 is shown in Fig. 1B. The first step is catalyzed by the MhpA hydroxylase, which inserts one atom of molecular oxygen at the position 2 of the phenyl ring of 3HPP to give 3-(2,3-dihydroxyphenyl)propionic acid (DHPP). This intermediate is then converted to succinate, pyruvate, and acetyl-CoA through the action of a meta-cleavage hydrolytic route whose enzymes are encoded by the mhp cluster located at minute 8.0 of the genome (Fig. 1A), being the first hydroxyphenylpropionate degradation pathway described both at the biochemical and genetic levels (3-6). The mhp cluster is arranged as follows: (i) six catabolic genes encoding the initial monooxygenase (mhpA), the extradiol dioxygenase (mhpB), and the hydrolytic meta-cleavage enzymes (mhpC-DFE); (ii) a gene (mhpT) that encodes a potential transporter; (iii) a regulatory gene (mh...

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Structural and Biochemical Study of Effector Molecule Recognition by the E.coli Glyoxylate and Allantoin Utilization Regulatory Protein AllR

Cited by 26 publications

References 73 publications

The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines

The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines

Crystal structure of TtgV in complex with its DNA operator reveals a general model for cooperative DNA binding of tetrameric gene regulators

3-Hydroxyphenylpropionate and Phenylpropionate Are Synergistic Activators of the MhpR Transcriptional Regulator from Escherichia coli

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