201
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Cyclic AMP receptor protein regulates cspD, a bacterial toxin gene, in Escherichia coli. J Bacteriol 2014; 196:1569-77. [PMID: 24509317 DOI: 10.1128/jb.01476-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
cspD, a member of cspA family of cold shock genes in Escherichia coli, is not induced during cold shock. Its expression is induced during stationary phase. CspD inhibits DNA replication, and a high level of the protein is toxic to cells. Recently, CspD was proposed to be associated with persister cell formation in E. coli. Here, we show that cyclic AMP receptor protein (CRP) upregulates cspD transcription. Sequence analysis of the cspD upstream region revealed two tandem CRP target sites, CRP site-I (the proximal site centered at -83.5 with respect to the transcription start) and CRP site-II (the distal site centered at -112.5). The results from electrophoretic mobility shift assays showed that CRP indeed binds to these two target sites in PcspD. The promoter-proximal CRP target site was found to play a major role in PcspD activation by CRP, as studied by transcriptional fusions carrying mutations in the target sites. The results from in vitro transcription assays demonstrated that CRP activates PcspD transcription in the absence of additional factors other than RNA polymerase. The requirement for activating region 1 of CRP in PcspD activation, along with the involvement of the 287, 265, and 261 determinants of the α-CTD, suggest that CRP activates by a class I-type mechanism. However, only moderate activation in vitro was observed compared to high activation in vivo, suggesting there might be additional activators of PcspD. Overall, our findings show that CRP, a global metabolic regulator in E. coli, activates a gene potentially related to persistence.
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202
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Green J, Stapleton MR, Smith LJ, Artymiuk PJ, Kahramanoglou C, Hunt DM, Buxton RS. Cyclic-AMP and bacterial cyclic-AMP receptor proteins revisited: adaptation for different ecological niches. Curr Opin Microbiol 2014; 18:1-7. [PMID: 24509484 PMCID: PMC4005916 DOI: 10.1016/j.mib.2014.01.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/08/2014] [Indexed: 11/25/2022]
Abstract
E. coli cyclic-AMP receptor protein (CRP) is a paradigm of gene regulation. Comparison of CRPs reveals differences in their affinity of cAMP. A range of dependency on cAMP for DNA-binding exists. CRPs have adapted to function in the specific niches occupied by the bacteria.
Escherichia coli cyclic-AMP receptor protein (CRP) represents one of the paradigms of bacterial gene regulation. Yet despite decades of intensive study, new information continues to emerge that prompts reassessment of this classic regulatory system. Moreover, in recent years CRPs from several other bacterial species have been characterized, allowing the general applicability of the CRP paradigm to be tested. Here the properties of the E. coli, Mycobacterium tuberculosis and Pseudomonas putida CRPs are considered in the context of the ecological niches occupied by these bacteria. It appears that the cyclic-AMP-CRP regulatory system has been adapted to respond to distinct external and internal inputs across a broad sensitivity range that is, at least in part, determined by bacterial lifestyles.
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Affiliation(s)
- Jeffrey Green
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Melanie R Stapleton
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Laura J Smith
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Peter J Artymiuk
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Christina Kahramanoglou
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Debbie M Hunt
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Roger S Buxton
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
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203
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Koike R, Ota M, Kidera A. Hierarchical Description and Extensive Classification of Protein Structural Changes by Motion Tree. J Mol Biol 2014; 426:752-62. [DOI: 10.1016/j.jmb.2013.10.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 11/25/2022]
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204
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Zhang YT, Jiang F, Tian ZX, Huo YX, Sun YC, Wang YP. CRP-cyclic AMP dependent inhibition of the xylene-responsive σ(54)-promoter Pu in Escherichia coli. PLoS One 2014; 9:e86727. [PMID: 24466213 PMCID: PMC3900584 DOI: 10.1371/journal.pone.0086727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2013] [Indexed: 11/18/2022] Open
Abstract
The expression of σ(54)-dependent Pseudomonas putida Pu promoter is activated by XylR activator when cells are exposed to a variety of aromatic inducers. In this study, the transcriptional activation of the P. putida Pu promoter was recreated in the heterologous host Escherichia coli. Here we show that the cAMP receptor protein (CRP), a well-known carbon utilization regulator, had an inhibitory effect on the expression of Pu promoter in a cAMP-dependent manner. The inhibitory effect was not activator specific. In vivo KMnO4 and DMS footprinting analysis indicated that CRP-cAMP poised the RNA polymerase at Pu promoter, inhibiting the isomerization step of the transcription initiation even in the presence of an activator. Therefore, the presence of PTS-sugar, which eliminates cAMP, could activate the poised RNA polymerase at Pu promoter to transcribe. Moreover, the activation region 1 (AR1) of CRP, which interacts directly with the αCTD (C-terminal domain of α-subunit) of RNA polymerase, was found essential for the CRP-mediated inhibition at Pu promoter. A model for the above observations is discussed.
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Affiliation(s)
- Yuan-Tao Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Feng Jiang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhe-Xian Tian
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Yi-Xin Huo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Yi-Cheng Sun
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- * E-mail:
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205
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Branchu P, Matrat S, Vareille M, Garrivier A, Durand A, Crépin S, Harel J, Jubelin G, Gobert AP. NsrR, GadE, and GadX interplay in repressing expression of the Escherichia coli O157:H7 LEE pathogenicity island in response to nitric oxide. PLoS Pathog 2014; 10:e1003874. [PMID: 24415940 PMCID: PMC3887101 DOI: 10.1371/journal.ppat.1003874] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 11/24/2013] [Indexed: 12/23/2022] Open
Abstract
Expression of genes of the locus of enterocyte effacement (LEE) is essential for adherence of enterohemorrhagic Escherichia coli (EHEC) to intestinal epithelial cells. Gut factors that may modulate LEE gene expression may therefore influence the outcome of the infection. Because nitric oxide (NO) is a critical effector of the intestinal immune response that may induce transcriptional regulation in enterobacteria, we investigated its influence on LEE expression in EHEC O157:H7. We demonstrate that NO inhibits the expression of genes belonging to LEE1, LEE4, and LEE5 operons, and that the NO sensor nitrite-sensitive repressor (NsrR) is a positive regulator of these operons by interacting directly with the RNA polymerase complex. In the presence of NO, NsrR detaches from the LEE1/4/5 promoter regions and does not activate transcription. In parallel, two regulators of the acid resistance pathway, GadE and GadX, are induced by NO through an indirect NsrR-dependent mechanism. In this context, we show that the NO-dependent LEE1 down-regulation is due to absence of NsrR-mediated activation and to the repressor effect of GadX. Moreover, the inhibition of expression of LEE4 and LEE5 by NO is due to loss of NsrR-mediated activation, to LEE1 down-regulation and to GadE up-regulation. Lastly, we establish that chemical or cellular sources of NO inhibit the adherence of EHEC to human intestinal epithelial cells. These results highlight the critical effect of NsrR in the regulation of the LEE pathogenicity island and the potential role of NO in the limitation of colonization by EHEC. Enterohemorrhagic Escherichia coli (EHEC) O157:H7 are food-borne pathogens for humans causing bloody diarrhea and, especially in children under five years old, kidney damages leading to death in 5% of cases. Antibiotics are contra-indicated because they are suspected to increase the severity of the disease. Therefore, it is crucial to develop alternative preventive or therapeutic strategies to fight EHEC infection. To reach this goal, a deeper knowledge of host-pathogen interaction is required. A critical step in EHEC infection is the adhesion of bacterial cells to intestinal epithelial cells. In response to the bacterial infection, the host triggers an immune response directed against the pathogen. The current study shows that a main effector of this immune response, nitric oxide (NO), dramatically reduces the capacity of EHEC to adhere to intestinal epithelial cells. We have investigated the molecular mechanisms involved and identified a NO-sensor regulator that controls the expression of the genes required for EHEC adhesion. This finding underlines that NO could be a potential protective factor limiting the development of EHEC-induced diseases and provides a new avenue of investigation for the development of therapeutic strategies against infections with O157:H7 bacteria.
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Affiliation(s)
- Priscilla Branchu
- INRA, UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, Saint-Genès-Champanelle, France
| | - Stéphanie Matrat
- INRA, UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, Saint-Genès-Champanelle, France
| | - Marjolaine Vareille
- INRA, UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, Saint-Genès-Champanelle, France
| | - Annie Garrivier
- INRA, UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, Saint-Genès-Champanelle, France
| | - Alexandra Durand
- INRA, UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, Saint-Genès-Champanelle, France
| | - Sébastien Crépin
- Groupe de Recherche sur les Maladies Infectieuses du Porc and Centre de Recherche en Infectiologie Porcine, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Josée Harel
- Groupe de Recherche sur les Maladies Infectieuses du Porc and Centre de Recherche en Infectiologie Porcine, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Grégory Jubelin
- INRA, UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, Saint-Genès-Champanelle, France
| | - Alain P. Gobert
- INRA, UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, Saint-Genès-Champanelle, France
- * E-mail:
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206
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Goble AM, Feng Y, Raushel FM, Cronan JE. Discovery of a cAMP deaminase that quenches cyclic AMP-dependent regulation. ACS Chem Biol 2013; 8:2622-9. [PMID: 24074367 DOI: 10.1021/cb4004628] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
An enzyme of unknown function within the amidohydrolase superfamily was discovered to catalyze the hydrolysis of the universal second messenger, cyclic-3',5'-adenosine monophosphate (cAMP). The enzyme, which we have named CadD, is encoded by the human pathogenic bacterium Leptospira interrogans. Although CadD is annotated as an adenosine deaminase, the protein specifically deaminates cAMP to cyclic-3',5'-inosine monophosphate (cIMP) with a kcat/Km of 2.7 ± 0.4 × 10(5) M(-1) s(-1) and has no activity on adenosine, adenine, or 5'-adenosine monophosphate (AMP). This is the first identification of a deaminase specific for cAMP. Expression of CadD in Escherichia coli mimics the loss of adenylate cyclase in that it blocks growth on carbon sources that require the cAMP-CRP transcriptional activator complex for expression of the cognate genes. The cIMP reaction product cannot replace cAMP as the ligand for CRP binding to DNA in vitro and cIMP is a very poor competitor of cAMP activation of CRP for DNA binding. Transcriptional analyses indicate that CadD expression represses expression of several cAMP-CRP dependent genes. CadD adds a new activity to the cAMP metabolic network and may be a useful tool in intracellular study of cAMP-dependent processes.
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Affiliation(s)
- Alissa M. Goble
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77843-3012, United States
| | | | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77843-3012, United States
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207
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Huang J, Wu T, Guo Z, Lou T, Yu S, Gong W, Ji C. Crystallization and preliminary X-ray diffraction analysis of D53H mutant Escherichia coli cAMP receptor protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1436-9. [PMID: 24316848 DOI: 10.1107/s174430911303145x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 11/18/2013] [Indexed: 11/10/2022]
Abstract
The Escherichia coli cyclic AMP receptor protein (CRP) is a prokaryotic global transcription activator protein that controls the expression of many different genes. Wild-type CRP can bind to special DNA sequences in the presence of cAMP. The substitution of Asp53 by His results in the CRP* phenotype, which does not require exogenous cAMP. In the present study, the D53H CRP mutant was overexpressed, purified and crystallized. cAMP-free D53H CRP crystals were obtained and diffracted to a resolution of 2.9 Å. Based on the systematic absences of the crystals, the space group is likely to be P2(1)2(1)2(1), with unit-cell parameters a = 76.66, b = 152.14, c = 176.11 Å. The asymmetric unit was confirmed to contain four protein dimers, with a Matthews coefficient of 2.71 Å(3) Da(-1) and a solvent content of 54.68%.
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Affiliation(s)
- Jing Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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208
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Transcriptional activation of the mrkA promoter of the Klebsiella pneumoniae type 3 fimbrial operon by the c-di-GMP-dependent MrkH protein. PLoS One 2013; 8:e79038. [PMID: 24244411 PMCID: PMC3828302 DOI: 10.1371/journal.pone.0079038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 09/18/2013] [Indexed: 01/11/2023] Open
Abstract
The Gram-negative bacterial pathogen Klebsiella pneumoniae forms biofilms to facilitate colonization of biotic and abiotic surfaces. The formation of biofilms by K. pneumoniae requires the expression of type 3 fimbriae: elongate proteinaceous filaments extruded by a chaperone-usher system in the bacterial outer membrane. The expression of the mrkABCDF cluster that encodes this fimbrial system is strongly positively regulated by MrkH, a transcriptional activator that responds to the second messenger, c-di-GMP. In this study, we analyzed the mechanism by which the MrkH protein activates transcriptional initiation from the mrkA promoter. A mutational analysis supported by electrophoretic mobility shift assays demonstrated that a 12-bp palindromic sequence (the MrkH box) centered at -78.5 is the binding site of MrkH. Deletion of half a turn, but not a full turn, of DNA located between the MrkH box and the mrkA promoter destroyed the ability of MrkH to activate mrkA transcription. In addition, a 10-bp AT-rich sequence (the UP element) centered at -63.5 contributed significantly to MrkH-dependent mrkA transcription. In vivo analysis of rpoA mutants showed that the R265 and E273 determinants in the C-terminal domain of RNA polymerase α subunit are needed for MrkH-mediated activation of mrkA transcription. Furthermore, results from mutagenesis of the mrkH gene suggest that the N-terminal region of the protein is involved in transcriptional activation. Taken together, our results suggest that MrkH activates mrkA expression by interacting directly with RNA polymerase, to overcome the inefficient transcriptional initiation caused by the presence of defective core promoter elements.
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209
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Abstract
The transcription of many genes, particularly in prokaryotes, is controlled by transcription factors whose activity can be modulated by controlling their DNA binding affinity. Understanding the molecular mechanisms by which DNA binding affinity is regulated is important, but because forming definitive conclusions usually requires detailed structural information in combination with data from extensive biophysical, biochemical, and sometimes genetic experiments, little is truly understood about this topic. This review describes the biological requirements placed upon DNA binding transcription factors and their consequent properties, particularly the ways that DNA binding affinity can be modulated and methods for its study. What is known and not known about the mechanisms modulating the DNA binding affinity of a number of prokaryotic transcription factors, including CAP and lac repressor, is provided.
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Affiliation(s)
- Robert F Schleif
- Biology Department, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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210
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Rodgers TL, Townsend PD, Burnell D, Jones ML, Richards SA, McLeish TCB, Pohl E, Wilson MR, Cann MJ. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors. PLoS Biol 2013; 11:e1001651. [PMID: 24058293 PMCID: PMC3769225 DOI: 10.1371/journal.pbio.1001651] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 07/31/2013] [Indexed: 12/11/2022] Open
Abstract
Allostery in bacterial transcription factors arises from changes in global low-frequency protein dynamics. Amino acids that regulate low-frequency dynamics are identified and seen to be evolutionarily conserved. Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein “design space” that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have been selected to occupy a dynamic space that fine-tunes biological activity and thus establishes the means to engineer allosteric mechanisms driven by low-frequency dynamics. Allostery is a process by which a molecule binding to one site of a protein alters the activity of the protein at another site. Allostery is typically thought to occur through a change in protein structure, but there is now clear evidence that the dynamic properties of a protein can also regulate allostery without a change in overall conformation. Here we examine two members of a large family of bacterial transcription factors and provide a mechanism to describe the allosteric binding of their activating ligands. We demonstrate, in these systems, that allostery arises as a natural consequence of changes in global low-frequency protein fluctuations on ligand binding. We further demonstrate that the higher dimensional parameter space that describes all potential variant transcription factors can be reduced to a two-dimensional free energy landscape that determines the key molecular parameters that predominantly regulate allostery. We additionally show that the amino acids we determine as contributing sensitively to allosteric control tend to be conserved in diverse bacteria; thus we identify a link between residues that contribute to low-frequency fluctuations and evolutionary selection pressures.
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Affiliation(s)
- Thomas L. Rodgers
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Philip D. Townsend
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | - David Burnell
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Matthew L. Jones
- Department of Physics, Durham University, Durham, United Kingdom
| | - Shane A. Richards
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | - Tom C. B. McLeish
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
- Department of Physics, Durham University, Durham, United Kingdom
| | - Ehmke Pohl
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
| | - Mark R. Wilson
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Martin J. Cann
- Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
- * E-mail:
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211
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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: 1.6] [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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212
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Cyclic AMP receptor protein regulates pheromone-mediated bioluminescence at multiple levels in Vibrio fischeri ES114. J Bacteriol 2013; 195:5051-63. [PMID: 23995643 DOI: 10.1128/jb.00751-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bioluminescence in Vibrio fischeri ES114 is activated by autoinducer pheromones, and this regulation serves as a model for bacterial cell-cell signaling. As in other bacteria, pheromone concentration increases with cell density; however, pheromone synthesis and perception are also modulated in response to environmental stimuli. Previous studies suggested that expression of the pheromone-dependent bioluminescence activator LuxR is regulated in response to glucose by cyclic AMP (cAMP) receptor protein (CRP) (P. V. Dunlap and E. P. Greenberg, J. Bacteriol. 164:45-50, 1985; P. V. Dunlap and E. P. Greenberg, J. Bacteriol. 170:4040-4046, 1988; P. V. Dunlap, J. Bacteriol. 171:1199-1202, 1989; and W. F. Friedrich and E. P. Greenberg, Arch. Microbiol. 134:87-91, 1983). Consistent with this model, we found that bioluminescence in V. fischeri ES114 is modulated by glucose and stimulated by cAMP. In addition, a Δcrp mutant was ∼100-fold dimmer than ES114 and did not increase luminescence in response to added cAMP, even though cells lacking crp were still metabolically capable of producing luminescence. We further discovered that CRP regulates not only luxR but also the alternative pheromone synthase gene ainS. We found that His-tagged V. fischeri CRP could bind sequences upstream of both luxR and ainS, supporting bioinformatic predictions of direct regulation at both promoters. Luminescence increased in response to cAMP if either the ainS or luxR system was under native regulation, suggesting cAMP-CRP significantly increases luminescence through both systems. Finally, using transcriptional reporters in transgenic Escherichia coli, we elucidated two additional regulatory connections. First, LuxR-independent basal transcription of the luxI promoter was enhanced by CRP. Second, the effect of CRP on the ainS promoter depended on whether the V. fischeri regulatory gene litR was also introduced. These results suggest an integral role for CRP in pheromone signaling that goes beyond sensing cell density.
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213
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Li J, Fan C, Pei H, Shi J, Huang Q. Smart drug delivery nanocarriers with self-assembled DNA nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:4386-96. [PMID: 23765613 DOI: 10.1002/adma.201300875] [Citation(s) in RCA: 308] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/15/2013] [Indexed: 05/23/2023]
Abstract
Self-assembled DNA nanostructures have emerged as a type of nano-biomaterials with precise structures, versatile functions and numerous applications. One particularly promising application of these DNA nanostructures is to develop universal nanocarriers for smart and targeted drug delivery. DNA is the genetic material in nature, and inherently biocompatible. Nevertheless, cell membranes are barely permeable to naked DNA molecules, either single- or double- stranded; transport across the cell membrane is only possible with the assistance of transfection agents. Interestingly, recent studies revealed that many DNA nanostructures could readily go into cells with high cell uptake efficiency. In this Progress Report, we will review recent advances on using various DNA nanostructures, e.g., DNA nanotubes, DNA tetrahedra, and DNA origami nanorobot, as drug delivery nanocarriers, and demonstrate several examples aiming at therapeutic applications with CpG-based immunostimulatory and siRNA-based gene silencing oligonucleotides.
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Affiliation(s)
- Jiang Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
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214
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Aykaç Fas B, Tutar Y, Haliloğlu T. Dynamic fluctuations provide the basis of a conformational switch mechanism in apo cyclic AMP receptor protein. PLoS Comput Biol 2013; 9:e1003141. [PMID: 23874183 PMCID: PMC3715548 DOI: 10.1371/journal.pcbi.1003141] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 05/31/2013] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli cyclic AMP Receptor Protein (CRP) undergoes conformational changes with cAMP binding and allosterically promotes CRP to bind specifically to the DNA. In that, the structural and dynamic properties of apo CRP prior to cAMP binding are of interest for the comprehension of the activation mechanism. Here, the dynamics of apo CRP monomer/dimer and holo CRP dimer were studied by Molecular Dynamics (MD) simulations and Gaussian Network Model (GNM). The interplay of the inter-domain hinge with the cAMP and DNA binding domains are pre-disposed in the apo state as a conformational switch in the CRP's allosteric communication mechanism. The hinge at L134-D138 displaying intra- and inter-subunit coupled fluctuations with the cAMP and DNA binding domains leads to the emergence of stronger coupled fluctuations between the two domains and describes an on state. The flexible regions at K52-E58, P154/D155 and I175 maintain the dynamic coupling of the two domains. With a shift in the inter-domain hinge position towards the N terminus, nevertheless, the latter correlations between the domains loosen and become disordered; L134-D138 dynamically interacts only with the cAMP and DNA binding domains of its own subunit, and an off state is assumed. We present a mechanistic view on how the structural dynamic units are hierarchically built for the allosteric functional mechanism; from apo CRP monomer to apo-to-holo CRP dimers.
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Affiliation(s)
- Burcu Aykaç Fas
- Department of Chemical Engineering and Polymer Research Center, Boğaziçi University, Bebek, İstanbul, Turkey
| | - Yusuf Tutar
- Department of Chemistry, Department of Biochemistry and CUTFAM Research Center, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Türkan Haliloğlu
- Department of Chemical Engineering and Polymer Research Center, Boğaziçi University, Bebek, İstanbul, Turkey
- * E-mail:
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215
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Sun Y, Bernardy EE, Hammer BK, Miyashiro T. Competence and natural transformation in vibrios. Mol Microbiol 2013; 89:583-95. [PMID: 23803158 DOI: 10.1111/mmi.12307] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2013] [Indexed: 01/01/2023]
Abstract
Natural transformation is a major mechanism of horizontal gene transfer in bacteria. By incorporating exogenous DNA elements into chromosomes, bacteria are able to acquire new traits that can enhance their fitness in different environments. Within the past decade, numerous studies have revealed that natural transformation is prevalent among members of the Vibrionaceae, including the pathogen Vibrio cholerae. Four environmental factors: (i) nutrient limitation, (ii) availability of extracellular nucleosides, (iii) high cell density and (iv) the presence of chitin, promote genetic competence and natural transformation in Vibrio cholerae by co-ordinating expression of the regulators CRP, CytR, HapR and TfoX respectively. Studies of other Vibrionaceae members highlight the general importance of natural transformation within this bacterial family.
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Affiliation(s)
- Yan Sun
- Department of Biochemistry and Molecular Biology Eberly College of Science The Pennsylvania State University 219 Wartik Lab University Park, PA 16802, USA
| | - Eryn E Bernardy
- School of Biology Georgia Institute of Technology 310 Ferst Drive, Atlanta, GA 30332-0230
| | - Brian K Hammer
- School of Biology Georgia Institute of Technology 310 Ferst Drive, Atlanta, GA 30332-0230
| | - Tim Miyashiro
- Department of Biochemistry and Molecular Biology Eberly College of Science The Pennsylvania State University 219 Wartik Lab University Park, PA 16802, USA
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216
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Analysis of activator and repressor functions reveals the requirements for transcriptional control by LuxR, the master regulator of quorum sensing in Vibrio harveyi. mBio 2013; 4:mBio.00378-13. [PMID: 23839217 PMCID: PMC3705450 DOI: 10.1128/mbio.00378-13] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
LuxR-type transcription factors are the master regulators of quorum sensing in vibrios. LuxR proteins are unique members of the TetR superfamily of transcription factors because they activate and repress large regulons of genes. Here, we used chromatin immunoprecipitation and nucleotide sequencing (ChIP-seq) to identify LuxR binding sites in the Vibrio harveyi genome. Bioinformatics analyses showed that the LuxR consensus binding site at repressed promoters is a symmetric palindrome, whereas at activated promoters it is asymmetric and contains only half of the palindrome. Using a genetic screen, we isolated LuxR mutants that separated activation and repression functions at representative promoters. These LuxR mutants exhibit sequence-specific DNA binding defects that restrict activation or repression activity to subsets of target promoters. Altering the LuxR DNA binding site sequence to one more closely resembling the ideal LuxR consensus motif can restore in vivo function to a LuxR mutant. This study provides a mechanistic understanding of how a single protein can recognize a variety of binding sites to differentially regulate gene expression. Bacteria use the cell-cell communication process called quorum sensing to regulate collective behaviors. In vibrios, LuxR-type transcription factors control the quorum-sensing gene expression cascade. LuxR-type proteins are structural homologs of TetR-type transcription factors. LuxR proteins were assumed to function analogously to TetR proteins, which typically bind to a single conserved binding site to repress transcription of one or two genes. We find here that unlike TetR proteins, LuxR acts a global regulator, directly binding upstream of and controlling more than 100 genes. Again unlike TetR, LuxR functions as both an activator and a repressor, and these two activities can be separated by mutagenesis. Finally, the consensus binding motifs driving LuxR-activated and -repressed genes are distinct. This work shows that LuxR, although structurally similar to TetR, has evolved unique features enabling it to differentially control a large regulon of genes in response to quorum-sensing cues.
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217
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Expression of the Rhizobium leguminosarum bv. trifolii pssA gene, involved in exopolysaccharide synthesis, is regulated by RosR, phosphate, and the carbon source. J Bacteriol 2013; 195:3412-23. [PMID: 23708137 DOI: 10.1128/jb.02213-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobium leguminosarum bv. trifolii pssA encodes a glucosyl-isoprenylphosphate (IP)-transferase involved in the first step of exopolysaccharide (EPS) synthesis. It was found that the pssA gene is an important target for regulation of this biosynthetic pathway. The data of this study indicate that pssA transcription is a very complex and mainly positively regulated process. A detailed analysis of a 767-bp-long pssA upstream region revealed the presence of several sequence motifs recognized by regulatory proteins that are associated with phosphate-, carbon-, and iron-dependent regulation. In addition, numerous inverted repeats of different lengths have been identified in this region. pssA transcription is directed from two distal P1 and proximal P3 promoters whose sequences demonstrate a significant identity to promoters recognized by RNA polymerase sigma factor σ(70). Among rhizobial proteins, RosR seems to be a primary regulator that positively affects pssA expression. This protein binds to RosR box 1 located downstream of the P1 promoter. In addition, phosphate and the carbon source strongly affect pssA transcription. A significantly lower level of pssA expression was observed in both the wild-type strain growing under phosphate-rich conditions and the phoB mutant. In this regulation, the PhoB protein and Pho box 2 located upstream of the P3 promoter were engaged. pssA transcription is also significantly affected by glucose. Transcriptional analysis of a set of pssA-lacZ fusions expressed in Escherichia coli wild-type and cyaA and crp mutants confirmed that cyclic AMP (cAMP) receptor protein (CRP) and two cAMP-CRP boxes located upstream of the P1 are required for this upregulation. Moreover, the production of EPS was totally abolished in R. leguminosarum bv. trifolii mutant strains 4440 and 1012 containing a Tn5 insertion downstream of the P3 promoter and downstream of the P3 -35 hexamer, respectively.
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218
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Chen B, Liang W, Wu R, Liang P, Kan B. Phenotype microarray screening of carbon sources used by Vibrio cholerae identifies genes regulated by the cAMP receptor protein. Can J Microbiol 2013; 59:472-8. [PMID: 23826956 DOI: 10.1139/cjm-2013-0084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The cyclic AMP receptor protein (CRP) regulates genes involved in carbon source metabolism, iron uptake, and virulence in bacteria. Identifying the carbon sources utilized by bacteria that are regulated by CRP will help elucidate the CRP regulation cascade and associated responses to environmental stimuli. CRP-dependent regulation of carbon source metabolism in Vibrio cholerae is not thoroughly understood. To identify the candidate carbon sources utilized by V. cholerae that are affected by CRP, we used high-throughput screening to compare the metabolic differences between wild-type and CRP mutant strains of V. cholerae O1 El Tor. Phenotype microarray was used for primary screening of the wild-type and mutant strains, followed by minimal media growth assays and quantitative RT-PCR to validate the candidate carbon sources. In total, 24 carbon sources were subject to CRP regulation, 11 of which have not been previously reported in bacteria. The genes known to be involved in the metabolism of 4 of the carbon sources identified were verified by quantitative RT-PCR. In addition, gel shift experiments showed that CRP bound directly to VCA0053 and VC0391 promoters. Overall, this comprehensive analysis of CRP-mediated catabolite control in V. cholerae has identified new candidate carbon sources for in-depth experimental studies.
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Affiliation(s)
- Baoli Chen
- National Institute for Communicable Disease Control and Prevention and State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, P.O. Box 5, Changping, Beijing 102206, People's Republic of China
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219
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Huang J, Liu J, Tao W, Yang Z, Qiu R, Yu S, Ji C. Crystallization and preliminary X-ray analysis of the CRP-cAMP-DNA (full length) complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:562-5. [PMID: 23695578 DOI: 10.1107/s1744309113009925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 04/10/2013] [Indexed: 11/10/2022]
Abstract
The Escherichia coli cyclic AMP receptor protein (CRP) is a well known transcription activator protein. In this study, CRP was overexpressed, purified and cocrystallized with cAMP and a 38 bp full-length double-stranded DNA fragment. The full-length segment differed from the half-site fragments used in previous crystallization experiments and is more similar to the environment in vivo. CRP-cAMP-DNA crystals were obtained and diffracted to 2.9 Å resolution. The crystals belonged to space group P3121, with unit-cell parameters a = b = 76.03, c = 144.00 Å. The asymmetric unit was found to contain one protein molecule and half a 38 bp full-length double-stranded DNA fragment, with a Matthews coefficient of 2.62 Å(3) Da(-1) and a solvent content of 53.14%.
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Affiliation(s)
- Jing Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, PR China
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220
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Bonnet M, Kurz M, Mesa S, Briand C, Hennecke H, Grütter MG. The structure of Bradyrhizobium japonicum transcription factor FixK2 unveils sites of DNA binding and oxidation. J Biol Chem 2013; 288:14238-14246. [PMID: 23546876 DOI: 10.1074/jbc.m113.465484] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FixK2 is a regulatory protein that activates a large number of genes for the anoxic and microoxic, endosymbiotic, and nitrogen-fixing life styles of the α-proteobacterium Bradyrhizobium japonicum. FixK2 belongs to the cAMP receptor protein (CRP) superfamily. Although most CRP family members are coregulated by effector molecules, the activity of FixK2 is negatively controlled by oxidation of its single cysteine (Cys-183) located next to the DNA-binding domain and possibly also by proteolysis. Here, we report the three-dimensional x-ray structure of FixK2, a representative of the FixK subgroup of the CRP superfamily. Crystallization succeeded only when (i) an oxidation- and protease-insensitive protein variant (FixK2(C183S)-His6) was used in which Cys-183 was replaced with serine and the C terminus was fused with a hexahistidine tag and (ii) this protein was allowed to form a complex with a 30-mer double-stranded target DNA. The structure of the FixK2-DNA complex was solved at a resolution of 1.77 Å, at which the protein formed a homodimer. The precise protein-DNA contacts were identified, which led to an affirmation of the canonical target sequence, the so-called FixK2 box. The C terminus is surface-exposed, which might explain its sensitivity to specific cleavage and degradation. The oxidation-sensitive Cys-183 is also surface-exposed and in close proximity to DNA. Therefore, we propose a mechanism whereby the oxo acids generated after oxidation of the cysteine thiol cause an electrostatic repulsion, thus preventing specific DNA binding.
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Affiliation(s)
- Mariette Bonnet
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland
| | - Mareike Kurz
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Socorro Mesa
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland
| | - Christophe Briand
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Hauke Hennecke
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland
| | - Markus G Grütter
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland.
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221
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Lin CT, Chen YC, Jinn TR, Wu CC, Hong YM, Wu WH. Role of the cAMP-dependent carbon catabolite repression in capsular polysaccharide biosynthesis in Klebsiella pneumoniae. PLoS One 2013; 8:e54430. [PMID: 23408939 PMCID: PMC3569464 DOI: 10.1371/journal.pone.0054430] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/11/2012] [Indexed: 12/11/2022] Open
Abstract
K. pneumoniae is the predominant pathogen isolated from liver abscesses of diabetic patients in Asian countries. Although elevated blood glucose levels cause various immune problems, its effects on K. pneumoniae virulence are unknown. This study investigated the regulation of capsular polysaccharide (CPS) biosynthesis, a major determinant for K. pneumoniae virulence, in response to exogenous glucose. We found that K. pneumoniae produce more CPS in glucose-rich medium via reduction in cyclic AMP (cAMP) levels. Individual deletion of cyaA or crp, which respectively encode adenylate cyclase and cAMP receptor protein in K. pneumoniae, markedly increased CPS production, while deletion of cpdA, which encodes cAMP phosphodiesterase, decreased CPS production. These results indicate that K. pneumoniae CPS biosynthesis is controlled by the cAMP-dependent carbon catabolite repression (CCR). To investigate the underlying mechanism, quantitative real-time PCR and promoter-reporter assays were used to verify that the transcription of CPS biosynthesis genes, which are organized into 3 transcription units (orf1-2, orf3-15, and orf16-17), were activated by the deletion of crp. Sequence analysis revealed putative CRP binding sites located on Porf3-15 and Porf16-17, suggesting direct CRP-cAMP regulation on the promoters. These results were then confirmed by electrophoretic mobility shift assay. In addition, we found putative CRP binding sites located in the promoter region of rcsA, which encodes a cps transcriptional activator, demonstrating a direct repression of CRP-cAMP and PrcsA. The deletion of rcsA in mutation of crp partially reduced CPS biosynthesis and the transcription of orf1-2 but not of orf3-15 or orf16-17. These results suggest that RcsA participates in the CRP-cAMP regulation of orf1-2 transcription and influences CPS biosynthesis. Finally, the effect of glucose and CCR proteins on CPS biosynthesis also reflects bacterial resistance to serum killing. We here provide evidence that K. pneumoniae increases CPS biosynthesis for successful infection in response to exogenous glucose via cAMP-dependent CCR.
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Affiliation(s)
- Ching-Ting Lin
- School of Chinese Medicine, China Medical University, Taichung, Taiwan. Republic of China.
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222
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GenR, an IclR-type regulator, activates and represses the transcription of gen genes involved in 3-hydroxybenzoate and gentisate catabolism in Corynebacterium glutamicum. J Bacteriol 2013; 195:1598-609. [PMID: 23354754 DOI: 10.1128/jb.02216-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genes required for 3-hydroxybenzoate and gentisate catabolism in Corynebacterium glutamicum are closely clustered in three operons. GenR, an IclR-type regulator, can activate the transcription of genKH and genDFM operons in response to 3-hydroxybenzoate and gentisate, and it can repress its own expression. Footprinting analyses demonstrated that GenR bound to four sites with different affinities. Two GenR-binding sites (DFMn01 and DFMn02) were found to be located between positions --41 and --84 upstream of the --35 and --10 regions of the genDFM promoter, which was involved in positive regulation of genDFM transcription. The GenR binding site R-KHn01 (located between positions --47 and --16) overlapped the --35 region of the genKH promoter sequence and is involved in positive regulation of its transcription. The binding site R-KHn02, at which GenR binds to its own promoter, was found within a footprint extending from position --44 to --67. It appeared to be involved in negative regulation of the activity of the genR promoter. A consensus motif with a 5-bp imperfect palindromic sequence [ATTCC-N(7(5))-GGAAT] was identified among all four GenR binding sites and found to be necessary to GenR regulation through site-directed mutagenesis. The results reveal a new regulatory function of the IclR family in the catabolism of aromatic compounds.
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223
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Crawford R, Erben CM, Periz J, Hall LM, Brown T, Turberfield AJ, Kapanidis AN. Non-covalent Single Transcription Factor Encapsulation Inside a DNA Cage. Angew Chem Int Ed Engl 2013; 52:2284-8. [DOI: 10.1002/anie.201207914] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/27/2012] [Indexed: 12/20/2022]
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224
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Crawford R, Erben CM, Periz J, Hall LM, Brown T, Turberfield AJ, Kapanidis AN. Non-covalent Single Transcription Factor Encapsulation Inside a DNA Cage. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207914] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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225
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Heroven AK, Sest M, Pisano F, Scheb-Wetzel M, Steinmann R, Böhme K, Klein J, Münch R, Schomburg D, Dersch P. Crp induces switching of the CsrB and CsrC RNAs in Yersinia pseudotuberculosis and links nutritional status to virulence. Front Cell Infect Microbiol 2012; 2:158. [PMID: 23251905 PMCID: PMC3523269 DOI: 10.3389/fcimb.2012.00158] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/27/2012] [Indexed: 12/18/2022] Open
Abstract
Colonization of the intestinal tract and dissemination into deeper tissues by the enteric pathogen Yersinia pseudotuberculosis demands expression of a special set of virulence factors important for the initiation and the persistence of the infection. In this study we demonstrate that many virulence-associated functions are coregulated with the carbohydrate metabolism. This link is mediated by the carbon storage regulator (Csr) system, including the regulatory RNAs CsrB and CsrC, and the cAMP receptor protein (Crp), which both control virulence gene expression in response to the nutrient composition of the medium. Here, we show that Crp regulates the synthesis of both Csr RNAs in an opposite manner. A loss of the crp gene resulted in a strong upregulation of CsrB synthesis, whereas CsrC levels were strongly reduced leading to downregulation of the virulence regulator RovA. Switching of the Csr RNA involves Crp-mediated repression of the response regulator UvrY which activates csrB transcription. To elucidate the regulatory links between virulence and carbon metabolism, we performed comparative metabolome, transcriptome, and phenotypic microarray analyses and found that Crp promotes oxidative catabolism of many different carbon sources, whereas fermentative patterns of metabolism are favored when crp is deleted. Mouse infection experiments further demonstrated that Crp is pivotal for a successful Y. pseudotuberculosis infection. In summary, placement of the Csr system and important virulence factors under control of Crp enables this pathogen to link its nutritional status to virulence in order to optimize biological fitness and infection efficiency through the infectious life cycle.
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Affiliation(s)
- Ann Kathrin Heroven
- Abteilung Molekulare Infektionsbiologie, Helmholtz-Zentrum für Infektionsforschung Braunschweig, Germany
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226
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Error-prone PCR of global transcription factor cyclic AMP receptor protein for enhanced organic solvent (toluene) tolerance. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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227
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Antonova ES, Bernardy EE, Hammer BK. Natural competence in Vibrio cholerae is controlled by a nucleoside scavenging response that requires CytR-dependent anti-activation. Mol Microbiol 2012; 86:1215-31. [PMID: 23016895 DOI: 10.1111/mmi.12054] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2012] [Indexed: 01/10/2023]
Abstract
Competence for genetic transformation in Vibrio cholerae is triggered by chitin-induced transcription factor TfoX and quorum sensing (QS) regulator HapR. Transformation requires expression of ComEA, described as a DNA receptor in other competent bacteria. A screen for mutants that poorly expressed a comEA-luciferase fusion identified cytR, encoding the nucleoside scavenging cytidine repressor, previously shown in V. cholerae to be a biofilm repressor and positively regulated by TfoX, but not linked to transformation. A ΔcytR mutant was non-transformable and defective in expression of comEA and additional TfoX-induced genes, including pilA (transformation pseudopilus) and chiA-1 (chitinase). In Escherichia coli, 'anti-activation' of nucleoside metabolism genes, via protein-protein interactions between critical residues in CytR and CRP (cAMP receptor protein), is disrupted by exogenous cytidine. Amino acid substitutions of the corresponding V. cholerae CytR residues impaired expression of comEA, pilA and chiA-1, and halted DNA uptake; while exogenous cytidine hampered comEA expression levels and prevented transformation. Our results support a speculative model that when V. cholerae reaches high density on chitin, CytR-CRP interactions 'anti-activate' multiple genes, including a possible factor that negatively controls DNA uptake. Thus, a nucleoside scavenging mechanism couples nutrient stress and cell-cell signalling to natural transformation in V. cholerae as described in other bacterial pathogens.
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Affiliation(s)
- Elena S Antonova
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
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228
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Kalia D, Merey G, Nakayama S, Zheng Y, Zhou J, Luo Y, Guo M, Roembke BT, Sintim HO. Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis. Chem Soc Rev 2012; 42:305-41. [PMID: 23023210 DOI: 10.1039/c2cs35206k] [Citation(s) in RCA: 261] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
For an organism to survive, it must be able to sense its environment and regulate physiological processes accordingly. Understanding how bacteria integrate signals from various environmental factors and quorum sensing autoinducers to regulate the metabolism of various nucleotide second messengers c-di-GMP, c-di-AMP, cGMP, cAMP and ppGpp, which control several key processes required for adaptation is key for efforts to develop agents to curb bacterial infections. In this review, we provide an update of nucleotide signaling in bacteria and show how these signals intersect or integrate to regulate the bacterial phenotype. The intracellular concentrations of nucleotide second messengers in bacteria are regulated by synthases and phosphodiesterases and a significant number of these metabolism enzymes had been biochemically characterized but it is only in the last few years that the effector proteins and RNA riboswitches, which regulate bacterial physiology upon binding to nucleotides, have been identified and characterized by biochemical and structural methods. C-di-GMP, in particular, has attracted immense interest because it is found in many bacteria and regulate both biofilm formation and virulence factors production. In this review, we discuss how the activities of various c-di-GMP effector proteins and riboswitches are modulated upon c-di-GMP binding. Using V. cholerae, E. coli and B. subtilis as models, we discuss how both environmental factors and quorum sensing autoinducers regulate the metabolism and/or processing of nucleotide second messengers. The chemical syntheses of the various nucleotide second messengers and the use of analogs thereof as antibiofilm or immune modulators are also discussed.
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Affiliation(s)
- Dimpy Kalia
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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229
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Sernova NV, Gelfand MS. Comparative genomics of CytR, an unusual member of the LacI family of transcription factors. PLoS One 2012; 7:e44194. [PMID: 23028500 PMCID: PMC3454398 DOI: 10.1371/journal.pone.0044194] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 07/30/2012] [Indexed: 11/19/2022] Open
Abstract
CytR is a transcription regulator from the LacI family, present in some gamma-proteobacteria including Escherichia coli and known not only for its cellular role, control of transport and utilization of nucleosides, but for a number of unusual structural properties. The present study addressed three related problems: structure of CytR-binding sites and motifs, their evolutionary conservation, and identification of new members of the CytR regulon. While the majority of CytR-binding sites are imperfect inverted repeats situated between binding sites for another transcription factor, CRP, other architectures were observed, in particular, direct repeats. While the similarity between sites for different genes in one genome is rather low, and hence the consensus motif is weak, there is high conservation of orthologous sites in different genomes (mainly in the Enterobacteriales) arguing for the presence of specific CytR-DNA contacts. On larger evolutionary distances candidate CytR sites may migrate but the approximate distance between flanking CRP sites tends to be conserved, which demonstrates that the overall structure of the CRP-CytR-DNA complex is gene-specific. The analysis yielded candidate CytR-binding sites for orthologs of known regulon members in less studied genomes of the Enterobacteriales and Vibrionales and identified a new candidate member of the CytR regulon, encoding a transporter named NupT (YcdZ).
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Affiliation(s)
- Natalia V. Sernova
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (IITP RAS), Moscow, Russia
| | - Mikhail S. Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (IITP RAS), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V.Lomonosov Moscow State University, Moscow, Russia
- * E-mail:
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230
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Shin M, Lagda AC, Lee JW, Bhat A, Rhee JH, Kim JS, Takeyasu K, Choy HE. Gene silencing by H-NS from distal DNA site. Mol Microbiol 2012; 86:707-19. [PMID: 22924981 DOI: 10.1111/mmi.12012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2012] [Indexed: 11/29/2022]
Abstract
In the modern concept of gene regulation, 'DNA looping' is the most common underlying mechanism in the interaction between RNA polymerase (RNAP) and transcription factors acting at a distance. This study demonstrates an additional mechanism by which DNA-bound proteins communicate with each other, by analysing the bacterial histone-like nucleoid-structuring protein (H-NS), a general transcriptional silencer. The LEE5 promoter (LEE5p) of enteropathogenic Escherichia coli was used as a model system to investigate the mechanism of H-NS-mediated transcription repression. We found that H-NS represses LEE5p by binding to a cluster of A tracks upstream of -114, followed by spreading to a site at the promoter through the oligomerization of H-NS molecules. At the promoter, the H-NS makes a specific contact with the carboxy terminal domain of the α subunit of RNAP, which prevents the processing of RNAP-promoter complexes into initiation-competent open promoter complexes, thereby regulating LEE5p from distance.
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Affiliation(s)
- Minsang Shin
- Center for Host Defense against Enteropathogenic Bacteria Infection, Kwangju, 501-746, South Korea
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231
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Lee DJ, Busby SJW. Repression by cyclic AMP receptor protein at a distance. mBio 2012; 3:e00289-12. [PMID: 22967981 PMCID: PMC3445967 DOI: 10.1128/mbio.00289-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 08/16/2012] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED In a previous study of promoters dependent on the Escherichia coli cyclic AMP receptor protein (CRP), carrying tandem DNA sites for CRP, we found that the upstream-bound CRP could either enhance or repress transcription, depending on its location. Here, we have analyzed the interactions between CRP and the C-terminal domains of the RNA polymerase α subunits at some of these promoters. We report that the upstream-bound CRP interacts with these domains irrespective of whether it up- or downregulates promoter activity. Hence, disruption of this interaction can lead to either down- or upregulation, depending on its location. IMPORTANCE Many bacterial promoters carry multiple DNA sites for transcription factors. While most factors that downregulate promoter activity bind to targets that overlap or are downstream of the transcription start and -10 element, very few cases of repression from upstream locations have been reported. Since more Escherichia coli promoters are regulated by cyclic AMP receptor protein (CRP) than by any other transcription factor, and since multiple DNA sites for CRP are commonplace at promoters, our results suggest that promoter downregulation by transcription factors may be more prevalent than hitherto thought, and this will have implications for the annotation of promoters from new bacterial genome sequences.
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Affiliation(s)
- David J Lee
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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232
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Lima BP, Thanh Huyen TT, Bäsell K, Becher D, Antelmann H, Wolfe AJ. Inhibition of acetyl phosphate-dependent transcription by an acetylatable lysine on RNA polymerase. J Biol Chem 2012; 287:32147-60. [PMID: 22829598 DOI: 10.1074/jbc.m112.365502] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ability of bacteria to adapt to environmental changes has allowed these organisms to thrive in all parts of the globe. By monitoring their extracellular and intracellular environments, bacteria assure their most appropriate response for each environment. Post-translational modification of proteins is one mechanism by which cells respond to their changing environments. Here, we report that two post-translational modifications regulate transcription of the extracytoplasmic stress-responsive promoter cpxP: (i) acetyl phosphate-dependent phosphorylation of the response regulator CpxR and (ii) acetyl coenzyme A-dependent acetylation of the α subunit of RNA polymerase. Together, these two post-translational modifications fine-tune cpxP transcription in response to changes in the intracellular environment.
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Affiliation(s)
- Bruno P Lima
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois 60153, USA
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233
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Garcia HG, Sanchez A, Boedicker JQ, Osborne M, Gelles J, Kondev J, Phillips R. Operator sequence alters gene expression independently of transcription factor occupancy in bacteria. Cell Rep 2012; 2:150-61. [PMID: 22840405 DOI: 10.1016/j.celrep.2012.06.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 05/14/2012] [Accepted: 06/06/2012] [Indexed: 11/17/2022] Open
Abstract
A canonical quantitative view of transcriptional regulation holds that the only role of operator sequence is to set the probability of transcription factor binding, with operator occupancy determining the level of gene expression. In this work, we test this idea by characterizing repression in vivo and the binding of RNA polymerase in vitro in experiments where operators of various sequences were placed either upstream or downstream from the promoter in Escherichia coli. Surprisingly, we find that operators with a weaker binding affinity can yield higher repression levels than stronger operators. Repressor bound to upstream operators modulates promoter escape, and the magnitude of this modulation is not correlated with the repressor-operator binding affinity. This suggests that operator sequences may modulate transcription by altering the nature of the interaction of the bound transcription factor with the transcriptional machinery, implying a new layer of sequence dependence that must be confronted in the quantitative understanding of gene expression.
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Affiliation(s)
- Hernan G Garcia
- Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
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234
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Abstract
Bacteria use a variety of mechanisms to direct RNA polymerase to specific promoters in order to activate transcription in response to growth signals or environmental cues. Activation can be due to factors that interact at specific promoters, thereby increasing transcription directed by these promoters. We examine the range of architectures found at activator-dependent promoters and outline the mechanisms by which input from different factors is integrated. Alternatively, activation can be due to factors that interact with RNA polymerase and change its preferences for target promoters. We summarize the different mechanistic options for activation that are focused directly on RNA polymerase.
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Affiliation(s)
- David J Lee
- School of Biosciences, University of Birmingham, United Kingdom.
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235
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Leuze MR, Karpinets TV, Syed MH, Beliaev AS, Uberbacher EC. Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA. GENE REGULATION AND SYSTEMS BIOLOGY 2012; 6:93-107. [PMID: 22701314 PMCID: PMC3370831 DOI: 10.4137/grsb.s9357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Bacterial gene regulation involves transcription factors (TF) that bind to DNA recognition sequences in operon promoters. These recognition sequences, many of which are palindromic, are known as regulatory elements or transcription factor binding sites (TFBS). Some TFs are global regulators that can modulate the expression of hundreds of genes. In this study we examine global regulator half-sites, where a half-site, which we shall call a binding motif (BM), is one half of a palindromic TFBS. We explore the hypothesis that the number of BMs plays an important role in transcriptional regulation, examining empirical data from transcriptional profiling of the CRP and ArcA regulons. We compare the power of BM counts and of full TFBS characteristics to predict induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full TFBS quality or location.
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Affiliation(s)
- Michael R. Leuze
- Computer Science and Mathematics Division, Oak Ridge National
Laboratory, Oak Ridge, TN, USA
| | - Tatiana V. Karpinets
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN,
USA
- Department of Plant Sciences, University of Tennessee, Knoxville,
TN, USA
| | - Mustafa H. Syed
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN,
USA
| | - Alexander S. Beliaev
- Biological Sciences Division, Pacific Northwest National Laboratory,
Richland, WA, USA
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236
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Carrión VJ, Arrebola E, Cazorla FM, Murillo J, de Vicente A. The mbo operon is specific and essential for biosynthesis of mangotoxin in Pseudomonas syringae. PLoS One 2012; 7:e36709. [PMID: 22615797 PMCID: PMC3355146 DOI: 10.1371/journal.pone.0036709] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 04/05/2012] [Indexed: 12/31/2022] Open
Abstract
Mangotoxin is an antimetabolite toxin produced by certain Pseudomonas syringae pv. syringae strains. This toxin is an oligopeptide that inhibits ornithine N-acetyl transferase, a key enzyme in the biosynthesis of ornithine and arginine. Previous studies have reported the involvement of the putative nonribosomal peptide synthetase MgoA in virulence and mangotoxin production. In this study, we analyse a new chromosomal region of P. syringae pv. syringae UMAF0158, which contains six coding sequences arranged as an operon (mbo operon). The mbo operon was detected in only mangotoxin-producing strains, and it was shown to be essential for the biosynthesis of this toxin. Mutants in each of the six ORFs of the mbo operon were partially or completely impaired in the production of the toxin. In addition, Pseudomonas spp. mangotoxin non-producer strains transformed with the mbo operon gained the ability to produce mangotoxin, indicating that this operon contains all the genetic information necessary for mangotoxin biosynthesis. The generation of a single transcript for the mbo operon was confirmed and supported by the allocation of a unique promoter and Rho-independent terminator. The phylogenetic analysis of the P. syringae strains harbouring the mbo operon revealed that these strains clustered together.
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Affiliation(s)
- Víctor J. Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Estación Experimental La Mayora, Málaga, Spain
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Jesús Murillo
- Laboratorio de Patología Vegetal, ETS de Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
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237
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Transcription activation by NtcA in the absence of consensus NtcA-binding sites in an anabaena heterocyst differentiation gene promoter. J Bacteriol 2012; 194:2939-48. [PMID: 22467790 DOI: 10.1128/jb.05994-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heterocyst differentiation is orchestrated by the N control transcriptional regulator NtcA and the differentiation-specific factor HetR. In Anabaena sp. strain PCC 7120, the devBCA operon is expressed from two different promoters activated upon N stepdown. The distal devB promoter (transcription start point [TSP] located at position -704) represents a canonical class II NtcA-activated promoter, including a consensus NtcA-binding site centered 39.5 nucleotides upstream from the TSP. Transcription activation from a second TSP (-454) requires NtcA and is impaired in hetR mutants. In a wild-type background, three different DNA fragments, including both or each individual promoter, directed gfp expression localized mainly to proheterocysts and heterocysts. Expression was undetectable in an ntcA background and, for the fragment including the proximal promoter alone, also in a hetR background. In spite of the absence of consensus NtcA-binding sequences between the two TSPs, NtcA was shown to interact with this DNA region, and NtcA and its effector, 2-oxoglutarate, were necessary and sufficient for in vitro transcription from the -454 TSP. No HetR binding to the DNA or in vitro transcription from the proximal devB TSP promoted by HetR alone were detected. However, a moderate positive effect of HetR on NtcA binding to the DNA between the two devB TSPs was observed. The proximal devB promoter appears to represent a suboptimal NtcA-activated promoter for which HetR may act as a coactivator, with the physiological effect of restricting gene activation to conditions of prevalence of high NtcA and HetR levels, such as those taking place during heterocyst differentiation.
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238
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Taliaferro LP, Keen EF, Sanchez-Alberola N, Wolf RE. Transcription activation by Escherichia coli Rob at class II promoters: protein-protein interactions between Rob's N-terminal domain and the σ(70) subunit of RNA polymerase. J Mol Biol 2012; 419:139-57. [PMID: 22465792 DOI: 10.1016/j.jmb.2012.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 03/18/2012] [Accepted: 03/20/2012] [Indexed: 11/16/2022]
Abstract
Bacterial transcription activators regulate transcription by making essential protein-protein interactions with RNA polymerase, for example, with region 4 of the σ(70) subunit (σ(70) R4). Rob, SoxS, and MarA comprise a closely related subset of members of the AraC/XylS family of transcription factors that activate transcription of both class I and class II promoters. Recently, we showed that interactions between SoxS and σ(70) R4 occlude the binding of σ(70) R4 to the -35 promoter element of class II promoters. Although Rob shares many similarities with SoxS, it contains a C-terminal domain (CTD) that the other paralogs do not. Thus, a goal of this study was to determine whether Rob makes protein-protein interactions with σ(70) R4 at class II promoters and, if so, whether the interactions occlude the binding of σ(70) R4 to the -35 hexamer despite the presence of the CTD. We found that although Rob makes fewer interactions with σ(70) R4 than SoxS, the two proteins make the same, unusual, position-dependent interactions. Importantly, we found that Rob occludes σ(70) R4 from binding the -35 hexamer, just as does SoxS. Thus, the CTD does not substantially alter the way Rob interacts with σ(70) R4 at class II promoters. Moreover, in contrast to inferences drawn from the co-crystal structure of Rob bound to robbox DNA, which showed that only one of Rob's dual helix-turn-helix (HTH) DNA binding motifs binds a recognition element of the promoter's robbox, we determined that the two HTH motifs each bind a recognition element in vivo.
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Affiliation(s)
- Lanyn P Taliaferro
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
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239
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Zwir I, Latifi T, Perez JC, Huang H, Groisman EA. The promoter architectural landscape of the Salmonella PhoP regulon. Mol Microbiol 2012; 84:463-85. [PMID: 22435712 PMCID: PMC3335776 DOI: 10.1111/j.1365-2958.2012.08036.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The DNA-binding protein PhoP controls virulence and Mg2+ homeostasis in the Gram-negative pathogen Salmonella enterica serovar Typhimurium. PhoP regulates expression of a large number of genes that differ both in their ancestry and in the biochemical functions and physiological roles of the encoded products. This suggests that PhoP-regulated genes are differentially expressed. To understand how a bacterial activator might generate varied gene expression behaviour, we investigated the cis-acting promoter features (i.e. the number of PhoP binding sites, as well as their orientation and location with respect to the sites bound by RNA polymerase and the sequences that constitute the PhoP binding sites) in 23 PhoP-activated promoters. Our results show that natural PhoP-activated promoters utilize only a limited number of combinations of cis-acting features – or promoter architectures. We determine that PhoP activates transcription by different mechanisms, and that ancestral and horizontally acquired PhoP-activated genes have distinct promoter architectures.
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Affiliation(s)
- Igor Zwir
- Section of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, 354D, New Haven, CT 06536, USA
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240
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Evidence that a single monomer of Spx can productively interact with RNA polymerase in Bacillus subtilis. J Bacteriol 2012; 194:1697-707. [PMID: 22307755 DOI: 10.1128/jb.06660-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Spx activates transcription initiation in Bacillus subtilis by directly interacting with the C-terminal domain of the RNA polymerase (RNAP) holoenzyme α subunit, which generates a complex that recognizes the promoter regions of genes within the Spx regulon. Many Gram-positive species possess multiple paralogs of Spx, suggesting that two paralogous forms of Spx could simultaneously contact RNAP. The composition of Spx/RNAP was examined in vitro using an Spx variant (SpxΔCHA) bearing a 12-amino-acid deletion of the C terminus (SpxΔC) and a hemagglutinin (HA) epitope tag and Spxc-Myc, a full-length Spx with a C-terminal myelocytomatosis oncoprotein (c-Myc) epitope tag. All Spx/RNAP complexes bearing deletion or C-terminal-tagged variants were transcriptionally active in vivo and in vitro. Reaction mixtures containing SpxΔCHA and Spxc-Myc combined with RNAP were applied to either anti-HA or anti-c-Myc affinity columns. Eluted fractions contained RNAP with only one of the epitope-tagged Spx derivatives. The resin-bound RNAP complex bearing a single epitope-tagged Spx derivative was transcriptionally active. In vivo production of SpxΔC and SpxΔCHA followed by anti-HA affinity column chromatography of a cleared lysate resulted in retrieval of Spx/RNAP with only the SpxΔCHA derivative. Binding reactions that combined active Spxc-Myc, inactive Spx(R60E)ΔCHA, and RNAP, when applied to the anti-HA affinity column, yielded only inactive Spx(R60E)ΔCHA/RNAP complexes. The results strongly argue for a model in which a single Spx monomer engages RNAP to generate an active transcriptional complex.
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241
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The TonB3 system in the human pathogen Vibrio vulnificus is under the control of the global regulators Lrp and cyclic AMP receptor protein. J Bacteriol 2012; 194:1897-911. [PMID: 22307757 DOI: 10.1128/jb.06614-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
TonB systems transduce the proton motive force of the cytoplasmic membrane to energize substrate transport through a specific TonB-dependent transporter across the outer membrane. Vibrio vulnificus, an opportunistic marine pathogen that can cause a fatal septicemic disease in humans and eels, possesses three TonB systems. While the TonB1 and TonB2 systems are iron regulated, the TonB3 system is induced when the bacterium grows in human serum. In this work we have determined the essential roles of the leucine-responsive protein (Lrp) and cyclic AMP (cAMP) receptor protein (CRP) in the transcriptional activation of this system. Whereas Lrp shows at least four very distinctive DNA binding regions spread out from position -59 to -509, cAMP-CRP binds exclusively in a region centered at position -122.5 from the start point of the transcription. Our results suggest that both proteins bind simultaneously to the region closer to the RNA polymerase binding site. Importantly, we report that the TonB3 system is induced not only by serum but also during growth in minimal medium with glycerol as the sole carbon source and low concentrations of Casamino Acids. In addition to catabolite repression by glucose, l-leucine acts by inhibiting the binding of Lrp to the promoter region, hence preventing transcription of the TonB3 operon. Thus, this TonB system is under the direct control of two global regulators that can integrate different environmental signals (i.e., glucose starvation and the transition between "feast" and "famine"). These results shed light on new mechanisms of regulation for a TonB system that could be widespread in other organisms.
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242
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Jeong JH, Kim HJ, Kim KH, Shin M, Hong Y, Rhee JH, Schneider TD, Choy HE. An unusual feature associated with LEE1 P1 promoters in enteropathogenic Escherichia coli (EPEC). Mol Microbiol 2012; 83:612-22. [PMID: 22229878 PMCID: PMC3480209 DOI: 10.1111/j.1365-2958.2011.07956.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Transcription start points in bacteria are influenced by the nature of the RNA polymerase·promoter interaction. For Escherichia coli RNA polymerase holoenzyme containing σ70, it is presumed that specific sequence in one or more of the -10, extended -10 and -35 elements of the promoter guides the RNAP to select the cognate start point. Here, we investigated the promoter driving expression of the LEE1 operon in enteropathogenic E. coli and found two promoters separated by 10 bp, LEE1 P1A (+1) and LEE1 P1B (+10) using various in vitro biochemical tools. A unique feature of P1B was the presence of multiple transcription starts from five neighbouring As at the initial transcribed region. The multiple products did not arise from stuttering synthesis. Analytical software based on information theory was employed to determine promoter elements. The concentration of the NTP pool altered the preferred transcription start points, albeit the underlying mechanism is elusive. Under in vivo conditions, dominant P1B, but not P1A, was subject to regulation by IHF.
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Affiliation(s)
- Jae-Ho Jeong
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Hyun-Ju Kim
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Kun-Hee Kim
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Minsang Shin
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Yeongjin Hong
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Joon Haeng Rhee
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Thomas D. Schneider
- National Cancer Institute, National Institutes of Health, Gene Regulation and Chromosome Biology Laboratory, Building 539, Room 129A, NCI-Frederick, Maryland, United States
| | - Hyon E. Choy
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
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243
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Su G, Zhang X, Liu H, Giesy JP, Lam MHW, Lam PKS, Siddiqui MA, Musarrat J, Al-Khedhairy A, Yu H. Toxicogenomic mechanisms of 6-HO-BDE-47, 6-MeO-BDE-47, and BDE-47 in E. coli. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:1185-1191. [PMID: 22111525 DOI: 10.1021/es203212w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cytotoxicity of 6-HO-BDE-47 and its two analogues, BDE-47 and 6-MeO-BDE-47, and the associated molecular mechanisms were assessed by use of a live cell reporter assay system which contains a library of 1820 modified green fluorescent protein (GFP) expressing promoter reporter vectors constructed from E. coli K12 strains. 6-HO-BDE-47 inhibited growth of E. coli with a 4 h median effect concentration (EC50) of 22.52 ± 2.20 mg/L, but neither BDE-47 nor 6-MeO-BDE-47 were cytotoxic. Thus, 6-HO-BDE-47 might serve as an antibiotic in some living organisms. Exposure to 6-HO-BDE-47 resulted in 65 (fold change >2) or 129 (fold change >1.5) genes being differentially expressed. The no observed transcriptional effect concentration (NOTEC) and median transcriptional effect concentration (TEC50) based on transcriptional end points, of 6-HO-BDE-47 were 0.0438 and 0.580 mg/L, respectively. The transcriptional responses were 514- and 39-fold more sensitive than the acute EC50 to inhibit cell growth. Most of the genes that were differentially expressed in response to 6-HO-BDE-47 were not modulated by BDE-47 or 6-MeO-BDE-47. These results suggest that cytotoxicity of 6-HO-BDE-47 to E. coli was via a mechanism that was different from that of either BDE-47 or 6-MeO-BDE-47. Gene expression associated with metabolic pathways was more responsive to 6-HO-BDE-47, which suggests that this pathway might be the primary target of this compound.
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Affiliation(s)
- Guanyong Su
- State Key Laboratory of Pollution Control and Resource Reuse & School of the Environment, Nanjing University, Nanjing, People's Republic of China
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244
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López-Igual R, Picossi S, López-Garrido J, Flores E, Herrero A. N and C control of ABC-type bicarbonate transporter Cmp and its LysR-type transcriptional regulator CmpR in a heterocyst-forming cyanobacterium, Anabaena sp. Environ Microbiol 2012; 14:1035-48. [PMID: 22221957 DOI: 10.1111/j.1462-2920.2011.02683.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the model, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120, gene cluster alr2877-alr2880, which encodes an ABC-type transport system, was induced under conditions of carbon limitation and its inactivation impaired the uptake of bicarbonate. Thus, this gene cluster encodes a Cmp bicarbonate transporter. ORF all0862, encoding a LysR-type transcriptional regulator, was expressed under carbon limitation and at higher levels in the absence than in the presence of combined nitrogen, with a positive effect of the N-control transcription factor NtcA. all0862 was expressed from two putative transcription start sites located 164 and 64 bp upstream from the gene respectively. The latter was induced under carbon limitation and was dependent on positive autoregulation by All0862. All0862 was required for the induction of the Cmp bicarbonate transporter, thus representing a CmpR regulator of Anabaena sp. These results show a novel mode of co-regulation by C and N availability through the concerted action of N- and C-responsive transcription factors.
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Affiliation(s)
- Rocío López-Igual
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville, Spain
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245
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Mellata M, Maddux JT, Nam T, Thomson N, Hauser H, Stevens MP, Mukhopadhyay S, Sarker S, Crabbé A, Nickerson CA, Santander J, Curtiss R. New insights into the bacterial fitness-associated mechanisms revealed by the characterization of large plasmids of an avian pathogenic E. coli. PLoS One 2012; 7:e29481. [PMID: 22238616 PMCID: PMC3251573 DOI: 10.1371/journal.pone.0029481] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 11/29/2011] [Indexed: 11/18/2022] Open
Abstract
Extra-intestinal pathogenic E. coli (ExPEC), including avian pathogenic E. coli (APEC), pose a considerable threat to both human and animal health, with illness causing substantial economic loss. APEC strain χ7122 (O78∶K80∶H9), containing three large plasmids [pChi7122-1 (IncFIB/FIIA-FIC), pChi7122-2 (IncFII), and pChi7122-3 (IncI(2))]; and a small plasmid pChi7122-4 (ColE2-like), has been used for many years as a model strain to study the molecular mechanisms of ExPEC pathogenicity and zoonotic potential. We previously sequenced and characterized the plasmid pChi7122-1 and determined its importance in systemic APEC infection; however the roles of the other pChi7122 plasmids were still ambiguous. Herein we present the sequence of the remaining pChi7122 plasmids, confirming that pChi7122-2 and pChi7122-3 encode an ABC iron transport system (eitABCD) and a putative type IV fimbriae respectively, whereas pChi7122-4 is a cryptic plasmid. New features were also identified, including a gene cluster on pChi7122-2 that is not present in other E. coli strains but is found in Salmonella serovars and is predicted to encode the sugars catabolic pathways. In vitro evaluation of the APEC χ7122 derivative strains with the three large plasmids, either individually or in combinations, provided new insights into the role of plasmids in biofilm formation, bile and acid tolerance, and the interaction of E. coli strains with 3-D cultures of intestinal epithelial cells. In this study, we show that the nature and combinations of plasmids, as well as the background of the host strains, have an effect on these phenomena. Our data reveal new insights into the role of extra-chromosomal sequences in fitness and diversity of ExPEC in their phenotypes.
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Affiliation(s)
- Melha Mellata
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.
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Burnside K, Rajagopal L. Regulation of prokaryotic gene expression by eukaryotic-like enzymes. Curr Opin Microbiol 2012; 15:125-31. [PMID: 22221896 DOI: 10.1016/j.mib.2011.12.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 12/01/2011] [Accepted: 12/14/2011] [Indexed: 12/30/2022]
Abstract
A growing body of evidence indicates that serine/threonine kinases (STKs) and phosphatases (STPs) regulate gene expression in prokaryotic organisms. As prokaryotic STKs and STPs are not DNA binding proteins, regulation of gene expression is accomplished through post-translational modification of their targets. These include two-component response regulators, DNA binding proteins and proteins that mediate transcription and translation. This review summarizes our current understanding of how STKs and STPs mediate gene expression in prokaryotes. Further studies to identify environmental signals that trigger the signaling cascade and elucidation of mechanisms that regulate crosstalk between eukaryotic-like signaling enzymes, two-component systems, and components of the transcriptional and translational machinery will facilitate a greater understanding of prokaryotic gene regulation.
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Affiliation(s)
- Kellie Burnside
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Hospital Research Institute, Seattle, WA 98101-1304, United States
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Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 2011; 78:1168-77. [PMID: 22156435 DOI: 10.1128/aem.05666-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ΔDVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ΔDVU2547 mutant (JW9011) under nitrite stress conditions and a ΔDVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.
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Santander J, Mitra A, Curtiss R. Phenotype, virulence and immunogenicity of Edwardsiella ictaluri cyclic adenosine 3',5'-monophosphate receptor protein (Crp) mutants in catfish host. FISH & SHELLFISH IMMUNOLOGY 2011; 31:1142-1153. [PMID: 22015784 DOI: 10.1016/j.fsi.2011.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/11/2011] [Accepted: 10/04/2011] [Indexed: 05/31/2023]
Abstract
Edwardsiella ictaluri is an Enterobacteriaceae that causes lethal enteric septicemia in catfish. Being a mucosal facultative intracellular pathogen, this bacterium is an excellent candidate to develop immersion-oral live attenuated vaccines for the catfish aquaculture industry. Deletion of the cyclic 3',5'-adenosine monophosphate (cAMP) receptor protein (crp) gene in several Enterobacteriaceae has been utilized in live attenuated vaccines for mammals and birds. Here we characterize the crp gene and report the effect of a crp deletion in E. ictaluri. The E. ictaluri crp gene and encoded protein are similar to other Enterobacteriaceae family members, complementing Salmonella enterica Δcrp mutants in a cAMP-dependent fashion. The E. ictaluri Δcrp-10 in-frame deletion mutant demonstrated growth defects, loss of maltose utilization, and lack of flagella synthesis. We found that the E. ictaluri Δcrp-10 mutant was attenuated, colonized lymphoid tissues, and conferred immune protection against E. ictaluri infection to zebrafish (Danio rerio) and catfish (Ictalurus punctatus). Evaluation of the IgM titers indicated that bath immunization with the E. ictaluri Δcrp-10 mutant triggered systemic and skin immune responses in catfish. We propose that deletion of the crp gene in E. ictaluri is an effective strategy to develop immersion live attenuated antibiotic-sensitive vaccines for the catfish aquaculture industry.
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Affiliation(s)
- Javier Santander
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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MATSUTANI SACHIKO. THE INTERNAL SEQUENCE OF IS1STIMULATES RNA SYNTHESIS FROM THE IS1OWN AND EXOGENOUS PROMOTERS. J BIOL SYST 2011. [DOI: 10.1142/s0218339005001513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The bacterial IS1 contains the genes insA and B′-insB encoding transposition related-proteins. The expression of these genes is driven by a promoter within the left end of IS1. Using IS1-lacZ constructs in which lacZs were fused in-frame at various sites of IS1 genes, it was found that the presence of the internal region of insA results in about a 100-fold increase in lacZ expression. The lacZ expression of the fusion constructs in which the IS1 own promoter was displaced by an exogenous promoter, was also stimulated by the presence of the IS1 internal region. Similarly, when lacZ was transcriptionally fused to the internal region of IS1, the lacZ expression from an exogenous promoter was stimulated. This result shows that the IS1 internal region acts as a cis-element to stimulate RNA synthesis from the upstream promoter. This was confirmed by Northern blot analyses. Furthermore, the gene which encodes the factor working with the IS1 internal sequence to stimulate transcription, was cloned. The gene was artA in the transfer region of the Escherichia coli F factor. Interestingly, the cis-element for transcription stimulation is found downstream, whereas many such elements are located upstream, of the promoter.
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Affiliation(s)
- SACHIKO MATSUTANI
- Division of Microbiology, National Institute of Health Sciences, Tokyo 158-8501, Japan
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Burnside K, Rajagopal L. Aspects of eukaryotic-like signaling in Gram-positive cocci: a focus on virulence. Future Microbiol 2011; 6:747-61. [PMID: 21797690 DOI: 10.2217/fmb.11.62] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Living organisms adapt to the dynamic external environment for their survival. Environmental adaptation in prokaryotes is thought to be primarily accomplished by signaling events mediated by two-component systems, consisting of histidine kinases and response regulators. However, eukaryotic-like serine/threonine kinases (STKs) have recently been described to regulate growth, antibiotic resistance and virulence of pathogenic bacteria. This article summarizes the role of STKs and their cognate phosphatases (STPs) in Gram-positive cocci that cause invasive infections in humans. Given that a large number of inhibitors to eukaryotic STKs are approved for use in humans, understanding how serine/threonine phosphorylation regulates virulence and antibiotic resistance will be beneficial for the development of novel therapeutic strategies against bacterial infections.
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Affiliation(s)
- Kellie Burnside
- Department of Pediatric Infectious Diseases, University of Washington & Seattle Children's Hospital Research Institute, 1900 Ninth Avenue, Seattle, WA 98101-1304, USA
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