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Kim N, Peng D, Sandoval N. Nucleotide-level characterization and improvement of l-arabinose- and l-rhamnose-inducible systems in E. coli using a high-throughput approach. Nucleic Acids Res 2025; 53:gkaf224. [PMID: 40210244 PMCID: PMC11983282 DOI: 10.1093/nar/gkaf224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 02/24/2025] [Accepted: 03/19/2025] [Indexed: 04/12/2025] Open
Abstract
The commonly used arabinose- and rhamnose-inducible Escherichia coli promoters, PBAD and PRha, exhibit tight regulation through activation via their respective transcription factors, AraC and RhaS, alongside the cyclic AMP receptor protein. The mechanisms of these promoters have been characterized on a parts level, but nucleotide-level analysis has yet to be elucidated. Therefore, we describe here a massively parallel reporter assay that maps regulatory sites at the nucleotide level. The relative importance of nucleotides in each binding site is revealed, including loci not included in previous annotations. For PBAD, we confirm known sites and reveal novel binding sites involved in modulating gene expression. In PRha, we refine the length and sequence specificity of rhaI half-sites, updating previous annotations and providing nucleotide level insights into RhaS-mediated regulation. Mutations that lead to increased promoter strength, wider dynamic range, and altered basal expression are identified for both promoters. Engineered versions of PBAD and PRha promoters based on this data show improvements in dynamic range alongside a seven- and three-fold increase in promoter strength, respectively, with a slight increase in basal expression for the PBAD promoters and no significant increase for PRha. This work expands the genetic parts "toolkit" and increases the understanding of these important commonly used promoters.
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Affiliation(s)
- Nancy M Kim
- Interdisciplinary Bioinnovation PhD Program, Tulane University, New Orleans, LA 70118, United States
| | - Danqia Peng
- Department of Chemical & Biomolecular Engineering, Tulane University, New Orleans, LA 70118, United States
| | - Nicholas R Sandoval
- Department of Chemical & Biomolecular Engineering, Tulane University, New Orleans, LA 70118, United States
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Picard HR, Schwingen KS, Green LM, Shis DL, Egan SM, Bennett MR, Swint-Kruse L. Allosteric regulation within the highly interconnected structural scaffold of AraC/XylS homologs tolerates a wide range of amino acid changes. Proteins 2022; 90:186-199. [PMID: 34369028 PMCID: PMC8671227 DOI: 10.1002/prot.26206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 01/03/2023]
Abstract
To create bacterial transcription "circuits" for biotechnology, one approach is to recombine natural transcription factors, promoters, and operators. Additional novel functions can be engineered from existing transcription factors such as the E. coli AraC transcriptional activator, for which binding to DNA is modulated by binding L-arabinose. Here, we engineered chimeric AraC/XylS transcription activators that recognized ara DNA binding sites and responded to varied effector ligands. The first step, identifying domain boundaries in the natural homologs, was challenging because (i) no full-length, dimeric structures were available and (ii) extremely low sequence identities (≤10%) among homologs precluded traditional assemblies of sequence alignments. Thus, to identify domains, we built and aligned structural models of the natural proteins. The designed chimeric activators were assessed for function, which was then further improved by random mutagenesis. Several mutational variants were identified for an XylS•AraC chimera that responded to benzoate; two enhanced activation to near that of wild-type AraC. For an RhaR•AraC chimera, a variant with five additional substitutions enabled transcriptional activation in response to rhamnose. These five changes were dispersed across the protein structure, and combinatorial experiments testing subsets of substitutions showed significant non-additivity. Combined, the structure modeling and epistasis suggest that the common AraC/XylS structural scaffold is highly interconnected, with complex intra-protein and inter-domain communication pathways enabling allosteric regulation. At the same time, the observed epistasis and the low sequence identities of the natural homologs suggest that the structural scaffold and function of transcriptional regulation are nevertheless highly accommodating of amino acid changes.
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Affiliation(s)
- Hunter R. Picard
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Kristen S. Schwingen
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Lisa M. Green
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - David L. Shis
- Department of Biosciences and Department of Bioengineering, Rice University, Houston, TX 77005
| | - Susan M. Egan
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045
| | - Matthew R. Bennett
- Department of Biosciences and Department of Bioengineering, Rice University, Houston, TX 77005
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160,To whom correspondence should be addressed: ; 913-588-0399
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3
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Improved Dynamic Range of a Rhamnose-Inducible Promoter for Gene Expression in Burkholderia spp. Appl Environ Microbiol 2021; 87:e0064721. [PMID: 34190606 DOI: 10.1128/aem.00647-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A diverse genetic toolkit is critical for understanding bacterial physiology and genotype-phenotype relationships. Inducible promoter systems are an integral part of this toolkit. In Burkholderia and related species, the l-rhamnose-inducible promoter is among the first choices due to its tight control and the lack of viable alternatives. To improve upon its maximum activity and dynamic range, we explored the effect of promoter system modifications in Burkholderia cenocepacia with a LacZ-based reporter. By combining the bacteriophage T7 gene 10 stem-loop and engineered rhaI transcription factor-binding sites, we obtained a rhamnose-inducible system with a 6.5-fold and 3.0-fold increases in maximum activity and dynamic range, respectively, compared to the native promoter. We then added the modified promoter system to pSCrhaB2 and pSC201, common genetic tools used for plasmid-based and chromosome-based gene expression, respectively, in Burkholderia, creating pSCrhaB2plus and pSC201plus. We demonstrated the utility of pSCrhaB2plus for gene expression in B. thailandensis, B. multivorans, and B. vietnamiensis and used pSC201plus to control highly expressed essential genes from the chromosome of B. cenocepacia. The utility of the modified system was demonstrated as we recovered viable mutants to control ftsZ, rpoBC, and rpsF, whereas the unmodified promoter was unable to control rpsF. The modified expression system allowed control of an essential gene depletion phenotype at lower levels of l-rhamnose, the inducer. pSCRhaB2plus and pSC201plus are expected to be valuable additions to the genetic toolkit for Burkholderia and related species. IMPORTANCE Species of Burkholderia are dually recognized as being of attractive biotechnological potential but also opportunistic pathogens for immunocompromised individuals. Understanding the genotype-phenotype relationship is critical for synthetic biology approaches in Burkholderia to disentangle pathogenic from beneficial traits. A diverse genetic toolkit, including inducible promoters, is the foundation for these investigations. Thus, we sought to improve on the commonly used rhamnose-inducible promoter system. Our modifications resulted in both higher levels of heterologous protein expression and broader control over highly expressed essential genes in B. cenocepacia. The significance of our work is in expanding the genetic toolkit to enable more comprehensive studies into Burkholderia and related bacteria.
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Kelly CL, Taylor GM, Hitchcock A, Torres-Méndez A, Heap JT. A Rhamnose-Inducible System for Precise and Temporal Control of Gene Expression in Cyanobacteria. ACS Synth Biol 2018; 7:1056-1066. [PMID: 29544054 DOI: 10.1021/acssynbio.7b00435] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cyanobacteria are important for fundamental studies of photosynthesis and have great biotechnological potential. In order to better study and fully exploit these organisms, the limited repertoire of genetic tools and parts must be expanded. A small number of inducible promoters have been used in cyanobacteria, allowing dynamic external control of gene expression through the addition of specific inducer molecules. However, the inducible promoters used to date suffer from various drawbacks including toxicity of inducers, leaky expression in the absence of inducer and inducer photolability, the latter being particularly relevant to cyanobacteria, which, as photoautotrophs, are grown under light. Here we introduce the rhamnose-inducible rhaBAD promoter of Escherichia coli into the model freshwater cyanobacterium Synechocystis sp. PCC 6803 and demonstrate it has superior properties to previously reported cyanobacterial inducible promoter systems, such as a non-toxic, photostable, non-metabolizable inducer, a linear response to inducer concentration and crucially no basal transcription in the absence of inducer.
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Affiliation(s)
- Ciarán L. Kelly
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - George M. Taylor
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - Andrew Hitchcock
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - Antonio Torres-Méndez
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - John T. Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
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Hoffmann J, Altenbuchner J. Functional Characterization of the Mannitol Promoter of Pseudomonas fluorescens DSM 50106 and Its Application for a Mannitol-Inducible Expression System for Pseudomonas putida KT2440. PLoS One 2015; 10:e0133248. [PMID: 26207762 PMCID: PMC4514859 DOI: 10.1371/journal.pone.0133248] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/24/2015] [Indexed: 01/29/2023] Open
Abstract
A new pBBR1MCS-2-derived vector containing the Pseudomonas fluorescens DSM10506 mannitol promoter PmtlE and mtlR encoding its AraC/XylS type transcriptional activator was constructed and optimized for low basal expression. Mannitol, arabitol, and glucitol-inducible gene expression was demonstrated with Pseudomonas putida and eGFP as reporter gene. The new vector was applied for functional characterization of PmtlE. Identification of the DNA binding site of MtlR was achieved by in vivo eGFP measurement with PmtlE wild type and mutants thereof. Moreover, purified MtlR was applied for detailed in vitro investigations using electrophoretic mobility shift assays and DNaseI footprinting experiments. The obtained data suggest that MtlR binds to PmtlE as a dimer. The proposed DNA binding site of MtlR is AGTGC-N5-AGTAT-N7-AGTGC-N5-AGGAT. The transcription activation mechanism includes two binding sites with different binding affinities, a strong upstream binding site and a weaker downstream binding site. The presence of the weak downstream binding site was shown to be necessary to sustain mannitol-inducibility of PmtlE. Two possible functions of mannitol are discussed; the effector might stabilize binding of the second monomer to the downstream half site or promote transcription activation by inducing a conformational change of the regulator that influences the contact to the RNA polymerase.
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Affiliation(s)
- Jana Hoffmann
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Josef Altenbuchner
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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Okuda K, Ito T, Goto M, Takenaka T, Hemmi H, Yoshimura T. Domain characterization of Bacillus subtilis GabR, a pyridoxal 5'-phosphate-dependent transcriptional regulator. J Biochem 2015; 158:225-34. [PMID: 25911692 DOI: 10.1093/jb/mvv040] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 03/15/2015] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis GabR is a transcriptional regulator consisting of a helix-turn-helix N-terminal DNA-binding domain, a pyridoxal 5'-phosphate (PLP)-binding C-terminal domain that has a structure homologous to aminotransferases, and a linker of 29 amino acid residues. In the presence of γ-aminobutyrate (GABA), GabR activates the transcription of gabT and gabD, which encode GABA aminotransferase and succinate semialdehyde dehydrogenase, respectively. We expressed N-terminal and C-terminal domain fragments (named N'-GabR and C'-GabR) in Escherichia coli cells, and obtained N'-GabR as a soluble monomer and C'-GabR as a soluble dimer. Spectroscopic studies suggested that C'-GabR contains PLP and binds to d-Ala, β-Ala, d-Asn and d-Gln, as well as GABA, although the intact GabR binds only to GABA. N'-GabR does not bind to the DNA fragment containing the GabR-binding sequence regardless of the presence or absence of C'-GabR. A fusion protein consisting of N'-GabR and 2-aminoadipate aminotransferase of Thermus thermophilus bound to the DNA fragment. These results suggested that each domain of GabR could be an independent folding unit. The C-terminal domain provides the N-terminal domain with DNA-binding ability via dimerization. The N-terminal domain controls the ligand specificity of the C-terminal domain. Connection by the linker is indispensable for the mutual interaction of the domains.
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Affiliation(s)
- Keita Okuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Frou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan and
| | - Tomokazu Ito
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Frou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan and
| | - Masaru Goto
- Department of Biomolecular Science, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510, Japan
| | - Takashi Takenaka
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Frou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan and
| | - Hisashi Hemmi
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Frou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan and
| | - Tohru Yoshimura
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Frou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan and
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7
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Finely tuned regulation of the aromatic amine degradation pathway in Escherichia coli. J Bacteriol 2013; 195:5141-50. [PMID: 24013633 DOI: 10.1128/jb.00837-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
FeaR is an AraC family regulator that activates transcription of the tynA and feaB genes in Escherichia coli. TynA is a periplasmic topaquinone- and copper-containing amine oxidase, and FeaB is a cytosolic NAD-linked aldehyde dehydrogenase. Phenylethylamine, tyramine, and dopamine are oxidized by TynA to the corresponding aldehydes, releasing one equivalent of H2O2 and NH3. The aldehydes can be oxidized to carboxylic acids by FeaB, and (in the case of phenylacetate) can be further degraded to enter central metabolism. Thus, phenylethylamine can be used as a carbon and nitrogen source, while tyramine and dopamine can be used only as sources of nitrogen. Using genetic, biochemical and computational approaches, we show that the FeaR binding site is a TGNCA-N8-AAA motif that occurs in 2 copies in the tynA and feaB promoters. We show that the coactivator for FeaR is the product rather than the substrate of the TynA reaction. The feaR gene is upregulated by carbon or nitrogen limitation, which we propose reflects regulation of feaR by the cyclic AMP receptor protein (CRP) and the nitrogen assimilation control protein (NAC), respectively. In carbon-limited cells grown in the presence of a TynA substrate, tynA and feaB are induced, whereas in nitrogen-limited cells, only the tynA promoter is induced. We propose that tynA and feaB expression is finely tuned to provide the FeaB activity that is required for carbon source utilization and the TynA activity required for nitrogen and carbon source utilization.
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A two-component system (XydS/R) controls the expression of genes encoding CBM6-containing proteins in response to straw in Clostridium cellulolyticum. PLoS One 2013; 8:e56063. [PMID: 23418511 PMCID: PMC3572039 DOI: 10.1371/journal.pone.0056063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 01/03/2013] [Indexed: 12/17/2022] Open
Abstract
The composition of the cellulosomes (multi enzymatic complexes involved in the degradation of plant cell wall polysaccharides) produced by Clostridium cellulolyticum differs according to the growth substrate. In particular, the expression of a cluster of 14 hemicellulase-encoding genes (called xyl-doc) seems to be induced by the presence of straw and not of cellulose. Genes encoding a putative two-component regulation system (XydS/R) were found upstream of xyl-doc. First evidence for the involvement of the response regulator, XydR, part of this two-component system, in the expression of xyl-doc genes was given by the analysis of the cellulosomes produced by a regulator overproducing strain when grown on cellulose. Nano-LC MS/MS analysis allowed the detection of the products of all xyl-doc genes and of the product of the gene at locus Ccel_1656 predicted to bear a carbohydrate binding domain targeting hemicellulose. RT-PCR experiments further demonstrated that the regulation occurs at the transcriptional level and that all xyl-doc genes are transcriptionally linked. mRNA quantification in a regulator knock-out strain and in its complemented derivative confirmed the involvement of the regulator in the expression of xyl-doc genes and of the gene at locus Ccel_1656 in response to straw. Electrophoretic mobility shift assays using the purified regulator further demonstrated that the regulator binds to DNA regions located upstream of the first gene of the xyl-doc gene cluster and upstream of the gene at locus Ccel_1656.
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9
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Skredenske JM, Koppolu V, Kolin A, Deng J, Kettle B, Taylor B, Egan SM. Identification of a small-molecule inhibitor of bacterial AraC family activators. ACTA ACUST UNITED AC 2013; 18:588-98. [PMID: 23364515 DOI: 10.1177/1087057112474690] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Protein members of the AraC family of bacterial transcriptional activators have great promise as targets for the development of novel antibacterial agents. Here, we describe an in vivo high-throughput screen to identify inhibitors of the AraC family activator protein RhaS. The screen used two Escherichia coli reporter fusions: one to identify potential RhaS inhibitors and a second to eliminate nonspecific inhibitors from consideration. One compound with excellent selectivity, OSSL_051168, was chosen for further study. OSSL_051168 inhibited in vivo transcription activation by the RhaS DNA-binding domain to the same extent as the full-length protein, indicating that this domain was the target of its inhibition. Growth curves showed that OSSL_051168 did not affect bacterial cell growth at the concentrations used in this study. In vitro DNA-binding assays with purified protein suggest that OSSL_051168 inhibits DNA binding by RhaS. In addition, we found that it inhibits DNA binding by a second AraC family protein, RhaR, which shares 30% amino acid identity with RhaS. OSSL_051168 did not have a significant impact on DNA binding by the non-AraC family proteins CRP and LacI, suggesting that the inhibition is likely specific for RhaS, RhaR, and possibly additional AraC family activator proteins.
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Affiliation(s)
- Jeff M Skredenske
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
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10
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Mahon V, Fagan RP, Smith SGJ. Snap denaturation reveals dimerization by AraC-like protein Rns. Biochimie 2012; 94:2058-61. [PMID: 22627379 DOI: 10.1016/j.biochi.2012.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/14/2012] [Indexed: 11/19/2022]
Abstract
Here we show that the Rns regulator of Escherichia coli dimerises in vivo and in vitro. Furthermore, we demonstrate that Rns forms aggregates in vitro and describe a methodology to ameliorate aggregation thus permitting the analysis of Rns by cross-linking.
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Affiliation(s)
- Vivienne Mahon
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, St. James's Hospital, Dublin, Ireland
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Parra MC, Collins CM. Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression. Microbiol Res 2012; 167:433-44. [PMID: 22537874 DOI: 10.1016/j.micres.2012.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 12/22/2011] [Accepted: 03/12/2012] [Indexed: 10/28/2022]
Abstract
The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
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Affiliation(s)
- Maria C Parra
- Department of Microbiology, University of Washington, Seattle, WA 98195, United States.
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12
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Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P. In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements. Nucleic Acids Res 2011; 39:5338-55. [PMID: 21398637 PMCID: PMC3141248 DOI: 10.1093/nar/gkr129] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Specific promoter recognition by bacterial RNA polymerase is mediated by σ subunits, which assemble with RNA polymerase core enzyme (E) during transcription initiation. However, σ70 (the housekeeping σ subunit) and σS (an alternative σ subunit mostly active during slow growth) recognize almost identical promoter sequences, thus raising the question of how promoter selectivity is achieved in the bacterial cell. To identify novel sequence determinants for selective promoter recognition, we performed run-off/microarray (ROMA) experiments with RNA polymerase saturated either with σ70 (Eσ70) or with σS (EσS) using the whole Escherichia coli genome as DNA template. We found that Eσ70, in the absence of any additional transcription factor, preferentially transcribes genes associated with fast growth (e.g. ribosomal operons). In contrast, EσS efficiently transcribes genes involved in stress responses, secondary metabolism as well as RNAs from intergenic regions with yet-unknown function. Promoter sequence comparison suggests that, in addition to different conservation of the −35 sequence and of the UP element, selective promoter recognition by either form of RNA polymerase can be affected by the A/T content in the −10/+1 region. Indeed, site-directed mutagenesis experiments confirmed that an A/T bias in the −10/+1 region could improve promoter recognition by EσS.
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Affiliation(s)
- Anna Maciag
- Department of Biomolecular Sciences and Biotechnology, Università degli Studi di Milano, Milan, Italy
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Gautam US, Chauhan S, Tyagi JS. Determinants outside the DevR C-terminal domain are essential for cooperativity and robust activation of dormancy genes in Mycobacterium tuberculosis. PLoS One 2011; 6:e16500. [PMID: 21304599 PMCID: PMC3029386 DOI: 10.1371/journal.pone.0016500] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Accepted: 01/03/2011] [Indexed: 11/23/2022] Open
Abstract
Background DevR (also called as DosR) is a two-domain response regulator of the NarL subfamily that controls dormancy adaptation of Mycobacterium tuberculosis (M. tb). In response to inducing signals such as hypoxia and ascorbic acid, the N-terminal receiver domain of DevR (DevRN) is phosphorylated at Asp54. This results in DevR binding to DNA via its C-terminal domain (DevRC) and subsequent induction of the DevR regulon. The mechanism of phosphorylation-mediated activation is not known. The present study was designed to understand the role of the N- and C-terminal domains of DevR in DevR regulon genes activation. Methodology/Principal Findings Towards deciphering the activation mechanism of DevR, we compared the DNA binding properties of DevRC and DevR and correlated the findings with their ability to activate gene expression. We show that isolated DevRC can interact with DNA, but only with the high affinity site of a representative target promoter. Therefore, one role of DevRN is to mask the intrinsic DNA binding function of DevRC. However, unlike phosphorylated DevR, isolated DevRC does not interact with the adjacent low affinity binding site suggesting that a second role of DevRN is in cooperative binding to the secondary site. Transcriptional analysis shows that consistent with unmasking of its DNA binding property, DevRC supports the aerobic induction, albeit feebly, of DevR regulon genes but is unable to sustain gene activation during hypoxia. Conclusions/Significance DevR is a unique response regulator that employs a dual activation mechanism including relief of inhibition and cooperative interaction with binding sites. Importantly, both these functions reside outside the C-terminal domain. DevRN is also essential for stabilizing DevR and sustaining autoregulation under hypoxia. Hence, both domains of DevR are required for robust transcription activation.
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Affiliation(s)
- Uma Shankar Gautam
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, Indian
| | - Santosh Chauhan
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, Indian
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, Indian
- * E-mail:
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14
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Sequential XylS-CTD binding to the Pm promoter induces DNA bending prior to activation. J Bacteriol 2010; 192:2682-90. [PMID: 20363935 DOI: 10.1128/jb.00165-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
XylS protein, a member of the AraC family of transcriptional regulators, comprises a C-terminal domain (CTD) involved in DNA binding and an N-terminal domain required for effector binding and protein dimerization. In the absence of benzoate effectors, the N-terminal domain behaves as an intramolecular repressor of the DNA binding domain. To date, the poor solubility properties of the full-length protein have restricted XylS analysis to genetic approaches in vivo. To characterize the molecular consequences of XylS binding to its operator, we used a recombinant XylS-CTD variant devoid of the N-terminal domain. The resulting protein was soluble and monomeric in solution and activated transcription from its cognate promoter in an effector-independent manner. XylS binding sites in the Pm promoter present an intrinsic curvature of 35 degrees centered at position -42 within the proximal site. Gel retardation and DNase footprint analysis showed XylS-CTD binding to Pm occurred sequentially: first a XylS-CTD monomer binds to the proximal site overlapping the RNA polymerase binding sequence to form complex I. This first event increased Pm bending to 50 degrees and was followed by the binding of the second monomer, which further increased the observed global curvature to 98 degrees. This generated a concomitant shift in the bending center to a region centered at position -51 when the two sites were occupied (complex II). We propose a model in which DNA structure and binding sequences strongly influence XylS binding events previous to transcription activation.
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Eppinger M, Worsham PL, Nikolich MP, Riley DR, Sebastian Y, Mou S, Achtman M, Lindler LE, Ravel J. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J Bacteriol 2010; 192:1685-99. [PMID: 20061468 PMCID: PMC2832528 DOI: 10.1128/jb.01518-09] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 12/25/2009] [Indexed: 11/20/2022] Open
Abstract
To gain insights into the origin and genome evolution of the plague bacterium Yersinia pestis, we have sequenced the deep-rooted strain Angola, a virulent Pestoides isolate. Its ancient nature makes this atypical isolate of particular importance in understanding the evolution of plague pathogenicity. Its chromosome features a unique genetic make-up intermediate between modern Y. pestis isolates and its evolutionary ancestor, Y. pseudotuberculosis. Our genotypic and phenotypic analyses led us to conclude that Angola belongs to one of the most ancient Y. pestis lineages thus far sequenced. The mobilome carries the first reported chimeric plasmid combining the two species-specific virulence plasmids. Genomic findings were validated in virulence assays demonstrating that its pathogenic potential is distinct from modern Y. pestis isolates. Human infection with this particular isolate would not be diagnosed by the standard clinical tests, as Angola lacks the plasmid-borne capsule, and a possible emergence of this genotype raises major public health concerns. To assess the genomic plasticity in Y. pestis, we investigated the global gene reservoir and estimated the pangenome at 4,844 unique protein-coding genes. As shown by the genomic analysis of this evolutionary key isolate, we found that the genomic plasticity within Y. pestis clearly was not as limited as previously thought, which is strengthened by the detection of the largest number of isolate-specific single-nucleotide polymorphisms (SNPs) currently reported in the species. This study identified numerous novel genetic signatures, some of which seem to be intimately associated with plague virulence. These markers are valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies.
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Affiliation(s)
- Mark Eppinger
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Patricia L. Worsham
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Mikeljon P. Nikolich
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - David R. Riley
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Yinong Sebastian
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Sherry Mou
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Mark Achtman
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Luther E. Lindler
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
| | - Jacques Ravel
- Institute for Genome Sciences (IGS) and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Bacteriology Division, Fort Detrick, Maryland 21702, Walter Reed Army Institute of Research (WRAIR), Division of Bacterial & Rickettsial Diseases, Silver Spring, Maryland 20910, J. Craig Venter Institute, Rockville, Maryland 20850, Environmental Research Institute (ERI), University College Cork, Lee Road, Cork, Ireland, Department of Defense, Global Emerging Infections Surveillance and Response System, 503 Robert Grant Ave., Silver Spring, Maryland 20910
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The AraC/XylS family activator RhaS negatively autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation. J Bacteriol 2010; 192:225-32. [PMID: 19854903 DOI: 10.1128/jb.00829-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli RhaR protein activates expression of the rhaSR operon in the presence of its effector, L-rhamnose. The resulting RhaS protein (plus L-rhamnose) activates expression of the L-rhamnose catabolic and transport operons, rhaBAD and rhaT, respectively. Here, we further investigated our previous finding that rhaS deletion resulted in a threefold increase in rhaSR promoter activity, suggesting RhaS negative autoregulation of rhaSR. We found that RhaS autoregulation required the cyclic AMP receptor protein (CRP) binding site at rhaSR and that RhaS was able to bind to the RhaR binding site at rhaSR. In contrast to the expected repression, we found that in the absence of both RhaR and the CRP binding site at the rhaSR promoter, RhaS activated expression to a level comparable with RhaR activation of the same promoter. However, when the promoter included the RhaR and CRP binding sites, the level of activation by RhaS and CRP was much lower than that by RhaR and CRP, suggesting that CRP could not fully coactivate with RhaS. Taken together, our results indicate that RhaS negative autoregulation involves RhaS competition with RhaR for binding to the RhaR binding site at rhaSR. Although RhaS and RhaR activate rhaSR transcription to similar levels, CRP cannot effectively coactivate with RhaS. Therefore, once RhaS reaches a relatively high protein concentration, presumably sufficient to saturate the RhaS-activated promoters, there will be a decrease in rhaSR transcription. We propose a model in which differential DNA bending by RhaS and RhaR may be the basis for the difference in CRP coactivation.
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Abstract
ExsA is a transcriptional activator of the Pseudomonas aeruginosa type III secretion system (T3SS). The T3SS consists of >40 genes organized within 10 transcriptional units, each of which is controlled by the transcriptional activator ExsA. ExsA-dependent promoters contain two adjacent ExsA binding sites that when occupied protect the -30 to -70 region from DNase I cleavage. The promoters also possess regions bearing strong resemblance to the consensus -10 and -35 regions of sigma(70)-dependent promoters. The spacing distance between the putative -10 and -35 regions of ExsA-dependent promoters, however, is increased by 4 to 5 bp compared to that in typical sigma(70)-dependent promoters. In the present study, we demonstrate that ExsA-dependent transcriptional activation requires a 21- or 22-bp spacer length between the -10 and -35 regions. Despite the atypical spacing in this region, in vitro transcription assays using sigma(70)-saturated RNA polymerase holoenzyme (RNAP-sigma(70)) confirm that ExsA-dependent promoters are indeed sigma(70) dependent. Potassium permanganate footprinting experiments indicate that ExsA facilitates an early step in transcriptional initiation. Although RNAP-sigma(70) binds to the promoters with low affinity in the absence of ExsA, the activator stimulates transcription by enhancing recruitment of RNAP-sigma(70) to the P(exsC) and P(exsD) promoters. Abortive initiation assays confirm that ExsA enhances the equilibrium binding constant for RNAP while having only a modest effect on the isomerization rate constant.
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Gebhard S, Gaballa A, Helmann JD, Cook GM. Direct stimulus perception and transcription activation by a membrane-bound DNA binding protein. Mol Microbiol 2009; 73:482-91. [PMID: 19602149 PMCID: PMC2752741 DOI: 10.1111/j.1365-2958.2009.06787.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Few membrane proteins with a role in transcriptional regulation have been studied, and none are able to perceive their respective stimuli and activate transcription of their regulons without the aid of auxiliary proteins. The bacitracin resistance regulator, BcrR, of Enterococcus faecalis is a membrane-bound DNA binding protein and is required for bacitracin-dependent expression of the bacitracin resistance genes, bcrABD. Here, we show that BcrR interacts directly with Zn2+ bacitracin (Kd = 2-5 micropM), but not metal-free bacitracin. A solution-based DNA binding assay demonstrated that the affinity of BcrR for its target DNA is much higher (Kd = 40 nM) than previously found for transmembrane regulators and is comparable to that of soluble DNA binding proteins. A construct of BcrR that lacked the transmembrane domain was unable to bind to DNA, indicating that membrane localization was important for DNA binding. Bacitracin did not cause a change in the DNaseI footprint of BcrR on the bcrA promoter, but in vitro transcription assays with BcrR proteoliposomes showed bacitracin-dependent activation of transcription. These findings demonstrate that BcrR is a bona fide one-component transmembrane signal transduction system, which perceives an extracellular stimulus (presence of bacitracin) and relays it to an intracellular transcriptional response independent of any auxiliary proteins.
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Affiliation(s)
- Susanne Gebhard
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Ahmed Gaballa
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin, New Zealand
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Functional domains of ExsA, the transcriptional activator of the Pseudomonas aeruginosa type III secretion system. J Bacteriol 2009; 191:3811-21. [PMID: 19376850 DOI: 10.1128/jb.00002-09] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa utilizes a type III secretion system (T3SS) to evade phagocytosis and damage eukaryotic cells. Transcription of the T3SS regulon is controlled by ExsA, a member of the AraC/XylS family of transcriptional regulators. These family members generally consist of an approximately 100-amino acid carboxy-terminal domain (CTD) with two helix-turn-helix DNA binding motifs and an approximately 200-amino acid amino-terminal domain (NTD) with known functions including oligomerization and ligand binding. In the present study, we show that the CTD of ExsA binds to ExsA-dependent promoters in vitro and activates transcription from ExsA-dependent promoters both in vitro and in vivo. Despite possessing these activities, the CTD lacks the cooperative binding properties observed for full-length ExsA at the P(exsC) promoter. In addition, the CTD is unaffected by the negative regulatory activity of ExsD, an inhibitor of ExsA activity. Binding studies confirm that ExsD interacts directly with the NTD of ExsA. Our data are consistent with a model in which a single ExsA molecule first binds to a high-affinity site on the P(exsC) promoter. Protein-protein interactions mediated by the NTD then recruit an additional ExsA molecule to a second site on the promoter to form a complex capable of stimulating wild-type levels of transcription. These findings provide important insight into the mechanisms of transcriptional activation by ExsA and inhibition of ExsA activity by ExsD.
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Kolin A, Balasubramaniam V, Skredenske J, Wickstrum J, Egan SM. Differences in the mechanism of the allosteric l-rhamnose responses of the AraC/XylS family transcription activators RhaS and RhaR. Mol Microbiol 2008; 68:448-61. [PMID: 18366439 PMCID: PMC2377013 DOI: 10.1111/j.1365-2958.2008.06164.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins in the largest subset of AraC/XylS family transcription activators, including RhaS and RhaR, have C-terminal domains (CTDs) that mediate DNA-binding and transcription activation, and N-terminal domains (NTDs) that mediate dimerization and effector binding. The mechanism of the allosteric effector response in this family has been identified only for AraC. Here, we investigated the mechanism by which RhaS and RhaR respond to their effector, l-rhamnose. Unlike AraC, N-terminal truncations suggested that RhaS and RhaR do not use an N-terminal arm to inhibit activity in the absence of effector. We used random mutagenesis to isolate RhaS and RhaR variants with enhanced activation in the absence of l-rhamnose. NTD substitutions largely clustered around the predicted l-rhamnose-binding pockets, suggesting that they mimic the structural outcome of effector binding to the wild-type proteins. RhaS-CTD substitutions clustered in the first HTH motif, and suggested that l-rhamnose induces improved DNA binding. In contrast, RhaR-CTD substitutions clustered at a single residue in the second HTH motif, at a position consistent with improved RNAP contacts. We propose separate allosteric mechanisms for the two proteins: Without l-rhamnose, RhaS does not effectively bind DNA while RhaR does not effectively contact RNAP. Upon l-rhamnose binding, both proteins undergo structural changes that enable transcription activation.
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Affiliation(s)
| | | | - Jeff Skredenske
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | | | - Susan M. Egan
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
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Basturea GN, Bodero MD, Moreno ME, Munson GP. Residues near the amino terminus of Rns are essential for positive autoregulation and DNA binding. J Bacteriol 2008; 190:2279-85. [PMID: 18223083 PMCID: PMC2293220 DOI: 10.1128/jb.01705-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 01/13/2008] [Indexed: 11/20/2022] Open
Abstract
Most members of the AraC/XylS family contain a conserved carboxy-terminal DNA binding domain and a less conserved amino-terminal domain involved in binding small-molecule effectors and dimerization. However, there is no evidence that Rns, a regulator of enterotoxigenic Escherichia coli virulence genes, responds to an effector ligand, and in this study we found that the amino-terminal domain of Rns does not form homodimers in vivo. Exposure of Rns to the chemical cross-linker glutaraldehyde revealed that the full-length protein is also a monomer in vitro. Nevertheless, deletion analysis of Rns demonstrated that the first 60 amino acids of the protein are essential for the activation and repression of Rns-regulated promoters in vivo. Amino-terminal truncation of Rns abolished DNA binding in vitro, and two randomly generated mutations, I14T and N16D, that independently abolished Rns autoregulation were isolated. Further analysis of these mutations revealed that they have disparate effects at other Rns-regulated promoters and suggest that they may be involved in an interaction with the carboxy-terminal domain of Rns. Thus, evolution may have preserved the amino terminus of Rns because it is essential for the regulator's activity even though it apparently lacks the two functions, dimerization and ligand binding, usually associated with the amino-terminal domains of AraC/XylS family members.
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Affiliation(s)
- Georgeta N Basturea
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, P.O. Box 016960 (R-138), Miami, FL 33101, USA
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Roles of effectors in XylS-dependent transcription activation: intramolecular domain derepression and DNA binding. J Bacteriol 2008; 190:3118-28. [PMID: 18296514 DOI: 10.1128/jb.01784-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
XylS, an AraC family protein, activates transcription from the benzoate degradation pathway Pm promoter in the presence of a substrate effector such as 3-methylbenzoate (3MB). We developed a procedure to obtain XylS-enriched preparations which proved suitable to analyze its activation mechanism. XylS showed specific 3MB-independent binding to its target operator, which became strictly 3MB dependent in a dimerization-defective mutant. We demonstrated that the N-terminal domain of the protein can make linker-independent interactions with the C-terminal domain and inhibit its capacity to bind DNA. Interactions are hampered in the presence of 3MB effector. We propose two independent roles for 3MB in XylS activation: in addition to its known influence favoring protein dimerization, the effector is able to modify XylS conformation to trigger N-terminal domain intramolecular derepression. We also show that activation by XylS involves RNA polymerase recruitment to the Pm promoter as demonstrated by chromatin immunoprecipitation assays. RNA polymerase switching in Pm transcription was reproduced in in vitro transcription assays. All sigma(32)-, sigma(38)-, and sigma(70)-dependent RNA polymerases were able to carry out Pm transcription in a rigorous XylS-dependent manner, as demonstrated by the formation of open complexes only in the presence of the regulator.
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Domínguez-Cuevas P, Marín P, Marqués S, Ramos JL. XylS-Pm promoter interactions through two helix-turn-helix motifs: identifying XylS residues important for DNA binding and activation. J Mol Biol 2007; 375:59-69. [PMID: 18005985 DOI: 10.1016/j.jmb.2007.10.047] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Revised: 10/15/2007] [Accepted: 10/16/2007] [Indexed: 11/25/2022]
Abstract
The XylS protein is the positive transcription regulator of the TOL plasmid meta-cleavage pathway operon Pm. XylS belongs to the AraC family of transcriptional regulators and exhibits an N-terminal domain involved in effector recognition, and a C-terminal domain, made up of seven alpha-helices conforming two helix-turn-helix DNA-binding domains. alpha-Helix 3 and alpha-helix 6 are the recognition helices. In consonance with XylS structural organization, Pm exhibits a bipartite DNA-binding motif consisting of two boxes, called A and B, whose sequences are TGCA and GGNTA, respectively. This bipartite motif is repeated at the Pm promoter so that one of the XylS monomers binds to each of the repeats. An extensive series of genetic epistasis assays combining mutant Pm promoters and XylS single substitution mutant proteins revealed that alpha-helix 3 contacts A box nucleotides, whereas alpha-helix 6 residues contact B box nucleotides. In alpha-helix 3, Asn246 and Arg242 are involved in specific contacts with the TG dinucleotide at box A, whereas Arg296 and Glu299 contact the second G and T nucleotides at box B. On the basis of our results and of the three-dimensional model of the XylS C-terminal domain, we propose that Ser243, Glu249 and Lys250 in alpha-helix 3, and Asn299 and Arg302 in alpha-helix 6 contact the phosphate backbones. Alanine substitutions at the predicted phosphate backbone-contacting residues yielded mutants with low levels of activity, suggesting that XylS-Pm binding specificity not only involves specific amino acid-base interactions, but also relies on secondary DNA structure, which, although at another level, also comes into play. We propose a model in which a XylS dimer binds to the direct repeats in Pm in a head-to-tail conformation that allows the direct interaction of the XylS proximal subunit with the RNA polymerase sigma factor.
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Affiliation(s)
- Patricia Domínguez-Cuevas
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Protection, E-18008 Granada, Spain
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