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pH Dependence of the Stress Regulator DksA

Publication Date: March 23, 2015
Journal: PLOS ONE
Authors: Ran Furman, Eric M. Danhart, Monali Nandy Mazumdar, Chunhua Yuan, et al
Volume: 10
Issue: 3
Pages: e0120746
DOI: https://dx.plos.org/10.1371/journal.pone.0120746
Publisher URL: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0120746
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/25799498
PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370453
Europe PMC: http://europepmc.org/abstract/MED/25799498
Web of Science: 000351987300170
Scopus: 84925876489
Mendeley: http://www.mendeley.com/research/ph-dependence-stress-regulator-dksa

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Figshare 8024 Apr 19:56 UTC

Figshare

{"files"=>["https://ndownloader.figshare.com/files/1980726"], "description"=>"(A) DksA activity increases at low pH. Increasing concentrations of DksA were added to holo RNAP (30 nM), ApC dinucleotide (0.2 mM), UTP (0.2 mM), GTP (4 μM) and [α-32P]-GTP (10 μCi of 3000 Ci mmol−1) followed by incubation for 15 minutes in Transcription buffer (20 mM Tris-HCl pH 7.9, 20 mM NaCl, 10 mM MgCl2, 14 mM 2-mercaptoethanol, 0.1 mM EDTA). A linear DNA fragment containing the rrnB P1 promoter was added to initiate transcription and the formation of a 4 nucleotide RNA product was monitored on a denaturing 8% acrylamide gel. A dotted line marks the inhibition of 50% of transcription and is denoted as IC50. The IC50 values (calculated using a single-site binding equation from three independent repeats combined in a best-fit curve, in μM) were: pH 7.6 − 0.7 ± 0.28, pH 6.7 − 0.11 ± 0.016. (B) DksA affinity to core increases at lower pH. DksA binding to core RNAP was performed using the localized Fe2+ mediated cleavage assay at different pH. DksA concentrations were: 0, 25, 50, 100, 200 and 400 nM. FL—Full length protein, Cl—cleaved protein, Kd app—apparent Kd.", "links"=>[], "tags"=>["DksA activity", "ph", "histidine 39 residue", "Escherichia coli DksA", "nmr", "Stress Regulator DksA DksA controls transcription", "RNA polymerase"], "article_id"=>1349617, "categories"=>["Biological Sciences"], "users"=>["Ran Furman", "Eric M. Danhart", "Monali NandyMazumdar", "Chunhua Yuan", "Mark P. Foster", "Irina Artsimovitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0120746.g003", "stats"=>{"downloads"=>4, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DksA_is_sensitive_to_changes_in_pH_/1349617", "title"=>"DksA is sensitive to changes in pH.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:59:31"}
{"files"=>["https://ndownloader.figshare.com/files/1980729"], "description"=>"(A) CD spectra recorded at room temperature using 50 μM DksA in phosphate buffer at different pHs. (B) Normalized ellipticity at 220 nm during a 1 degree/minute increase in temperature. Data were fit to the modified Gibbs-Helmholtz equation with linear temperature dependence before and after the transition region. Melting temperatures were 55 and 65°C at pH 6 and 8, respectively.", "links"=>[], "tags"=>["DksA activity", "ph", "histidine 39 residue", "Escherichia coli DksA", "nmr", "Stress Regulator DksA DksA controls transcription", "RNA polymerase"], "article_id"=>1349620, "categories"=>["Biological Sciences"], "users"=>["Ran Furman", "Eric M. Danhart", "Monali NandyMazumdar", "Chunhua Yuan", "Mark P. Foster", "Irina Artsimovitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0120746.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_pH_on_DksA_global_structure_and_stability_/1349620", "title"=>"Effect of pH on DksA global structure and stability.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:59:31"}
{"files"=>["https://ndownloader.figshare.com/files/1980730"], "description"=>"Two-dimensional 1H-15N HSQC spectra at pH 8 (black) and 6 (red) reveal large chemical shift changes at (A) Tyr23 and (B) many other residues.", "links"=>[], "tags"=>["DksA activity", "ph", "histidine 39 residue", "Escherichia coli DksA", "nmr", "Stress Regulator DksA DksA controls transcription", "RNA polymerase"], "article_id"=>1349621, "categories"=>["Biological Sciences"], "users"=>["Ran Furman", "Eric M. Danhart", "Monali NandyMazumdar", "Chunhua Yuan", "Mark P. Foster", "Irina Artsimovitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0120746.g005", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DksA_structure_is_sensitive_to_pH_/1349621", "title"=>"DksA structure is sensitive to pH.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:59:31"}
{"files"=>["https://ndownloader.figshare.com/files/1980731"], "description"=>"(A) The effect of pH on DksA variants. DksA activity and IC50 calculations were determined as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120746#pone.0120746.g003\" target=\"_blank\">Fig. 3A</a> with the rrnB P1 promoter. Experiments were performed at least three times at each pH. (B) Thermostability of DksAH39A is low and relatively insensitive to pH. Thermostability was determined as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120746#pone.0120746.g004\" target=\"_blank\">Fig. 4</a>.", "links"=>[], "tags"=>["DksA activity", "ph", "histidine 39 residue", "Escherichia coli DksA", "nmr", "Stress Regulator DksA DksA controls transcription", "RNA polymerase"], "article_id"=>1349622, "categories"=>["Biological Sciences"], "users"=>["Ran Furman", "Eric M. Danhart", "Monali NandyMazumdar", "Chunhua Yuan", "Mark P. Foster", "Irina Artsimovitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0120746.g006", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Substitution_of_His39_alters_DksA_sensitivity_to_pH_/1349622", "title"=>"Substitution of His39 alters DksA sensitivity to pH.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:59:31"}
{"files"=>["https://ndownloader.figshare.com/files/1980746", "https://ndownloader.figshare.com/files/1980747", "https://ndownloader.figshare.com/files/1980748", "https://ndownloader.figshare.com/files/1980749", "https://ndownloader.figshare.com/files/1980750", "https://ndownloader.figshare.com/files/1980751", "https://ndownloader.figshare.com/files/1980752", "https://ndownloader.figshare.com/files/1980753"], "description"=>"<div>DksA controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. DksA binds within the secondary channel of RNA polymerase, extending its long coiled-coil domain towards the active site. The cellular expression of DksA remains constant due to a negative feedback autoregulation, raising the question of whether DksA activity is directly modulated during stress. Here, we show that Escherichia coli DksA is essential for survival in acidic conditions and that, while its cellular levels do not change significantly, DksA activity and binding to RNA polymerase are increased at lower pH, with a concomitant decrease in its stability. NMR data reveal pH-dependent structural changes centered at the interface of the N and C-terminal regions of DksA. Consistently, we show that a partial deletion of the N-terminal region and substitutions of a histidine 39 residue at the domain interface abolish pH sensitivity in vitro. Together, these data suggest that DksA responds to changes in pH by shifting between alternate conformations, in which competing interactions between the N- and C-terminal regions modify the protein activity.</div>", "links"=>[], "tags"=>["DksA activity", "ph", "histidine 39 residue", "Escherichia coli DksA", "nmr", "Stress Regulator DksA DksA controls transcription", "RNA polymerase"], "article_id"=>1349624, "categories"=>["Biological Sciences"], "users"=>["Ran Furman", "Eric M. Danhart", "Monali NandyMazumdar", "Chunhua Yuan", "Mark P. Foster", "Irina Artsimovitch"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0120746.s001", "https://dx.doi.org/10.1371/journal.pone.0120746.s002", "https://dx.doi.org/10.1371/journal.pone.0120746.s003", "https://dx.doi.org/10.1371/journal.pone.0120746.s004", "https://dx.doi.org/10.1371/journal.pone.0120746.s005", "https://dx.doi.org/10.1371/journal.pone.0120746.s006", "https://dx.doi.org/10.1371/journal.pone.0120746.s007", "https://dx.doi.org/10.1371/journal.pone.0120746.s008"], "stats"=>{"downloads"=>25, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_pH_Dependence_of_the_Stress_Regulator_DksA_/1349624", "title"=>"pH Dependence of the Stress Regulator DksA", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-03-23 02:59:31"}
{"files"=>["https://ndownloader.figshare.com/files/1980722"], "description"=>"(A) WT and ΔdksA E. coli strains were grown overnight in rich medium at pH 7.8. Cultures were diluted 1:50 into LB medium at pH 2.5. At selected time points aliquots were taken and the percentage of survival of bacteria was determined using viable count. (B) WT and ΔdksA E. coli strains were grown at pH 7.8, followed by 2.5 hour adaptation at pH 6.5–4.5, and then diluted into LB medium at pH 3.5. Survival was determined using viable counts; the result after 2 hour incubation at pH 3.5 is shown. (C) DksA concentration remains relatively constant at low pH. Samples taken at different time points after a change in pH were analyzed using Western blotting with anti-DksA antibodies. Extract from the ΔdksA strain and purified DksA were loaded as controls.", "links"=>[], "tags"=>["DksA activity", "ph", "histidine 39 residue", "Escherichia coli DksA", "nmr", "Stress Regulator DksA DksA controls transcription", "RNA polymerase"], "article_id"=>1349613, "categories"=>["Biological Sciences"], "users"=>["Ran Furman", "Eric M. Danhart", "Monali NandyMazumdar", "Chunhua Yuan", "Mark P. Foster", "Irina Artsimovitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0120746.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_dksA_mutants_are_sensitive_to_acidic_conditions_/1349613", "title"=>"ΔdksA mutants are sensitive to acidic conditions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:59:31"}
{"files"=>["https://ndownloader.figshare.com/files/1980724"], "description"=>"(A) Hybrid model of DksA (PDB id: 1TJL_a) docked in the secondary channel of the E. coli RNAP core (PDB id: 3LU0). Clash between N-terminus and rim helix (RH) implies required conformational change and remodeling of domain interface (circle). (B) DksA structure reveals a large interface between the globular domain of the protein and parts of the CC domain. Residues that can contribute to the interdomain interactions are indicated. The CC domain is shown in orange, the N-terminal region in blue, and the C-terminal region in green.", "links"=>[], "tags"=>["DksA activity", "ph", "histidine 39 residue", "Escherichia coli DksA", "nmr", "Stress Regulator DksA DksA controls transcription", "RNA polymerase"], "article_id"=>1349615, "categories"=>["Biological Sciences"], "users"=>["Ran Furman", "Eric M. Danhart", "Monali NandyMazumdar", "Chunhua Yuan", "Mark P. Foster", "Irina Artsimovitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0120746.g002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conformational_changes_may_be_required_to_accommodate_DksA_in_the_secondary_channel_/1349615", "title"=>"Conformational changes may be required to accommodate DksA in the secondary channel.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:59:31"}

PMC Usage Stats 61717 Jan 21:39 UTC

PMC Usage Stats | Further Information

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Relative Metric10 May 17:59 UTC

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}

F1000Prime20 Jan 13:34 UTC

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