1
|
Reslane I, Handke LD, Watson GF, Shinde D, Ahn JS, Endres JL, Razvi F, Gilbert EA, Bayles KW, Thomas VC, Lehman MK, Fey PD. Glutamate -dependent arginine biosynthesis requires the inactivation of spoVG, sarA, and ahrC in Staphylococcus aureus. J Bacteriol 2024; 206:e0033723. [PMID: 38299858 PMCID: PMC10883023 DOI: 10.1128/jb.00337-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Genome sequencing has demonstrated that Staphylococcus aureus encodes arginine biosynthetic genes argDCJBFGH synthesizing proteins that mediate arginine biosynthesis using glutamate as a substrate. Paradoxically, however, S. aureus does not grow in a defined, glutamate-replete medium lacking arginine and glucose (CDM-R). Studies from our laboratory have found that specific mutations are selected by S. aureus that facilitate growth in CDM-R. However, these selected mutants synthesize arginine utilizing proline as a substrate rather than glutamate. In this study, we demonstrate that the ectopic expression of the argDCJB operon supports the growth of S. aureus in CDM-R, thus documenting the functionality of this pathway. Furthermore, suppressor mutants of S. aureus JE2 putA::Tn, which is defective in synthesizing arginine from proline, were selected on CDM-R agar. Genome sequencing revealed that these mutants had compensatory mutations within both spoVG, encoding an ortholog of the Bacillus subtilis stage V sporulation protein, and sarA, encoding the staphylococcal accessory regulator. Transcriptional studies document that argD expression is significantly increased when JE2 spoVG sarA was grown in CDM-R. Lastly, we found that a mutation in ahrC was required to induce argD expression in JE2 spoVG sarA when grown in an arginine-replete medium (CDM), suggesting that AhrC also functions to repress argDCJB in an arginine-dependent manner. In conclusion, these data indicate that the argDCJB operon is functional when transcribed in vitro and that SNPs within potential putative regulatory proteins are required to alleviate the repression.IMPORTANCEAlthough Staphylococcus aureus has the capability to synthesize all 20 amino acids, it is phenotypically auxotrophic for several amino acids including arginine. This work identifies putative regulatory proteins, including SpoVG, SarA, and AhrC, that function to inhibit the arginine biosynthetic pathways using glutamate as a substrate. Understanding the ultimate mechanisms of why S. aureus is selected to repress arginine biosynthetic pathways even in the absence of arginine will add to the growing body of work assessing the interactions between metabolism and S. aureus pathogenesis.
Collapse
Affiliation(s)
- Itidal Reslane
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Luke D. Handke
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Gabrielle F. Watson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Dhananjay Shinde
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jong-Sam Ahn
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jennifer L. Endres
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Fareha Razvi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Emily A. Gilbert
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kenneth W. Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Vinai C. Thomas
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - McKenzie K. Lehman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| |
Collapse
|
2
|
Affinity, Specificity, and Cooperativity of DNA Binding by Bacterial Gene Regulatory Proteins. Int J Mol Sci 2022; 23:ijms23010562. [PMID: 35008987 PMCID: PMC8745587 DOI: 10.3390/ijms23010562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/14/2021] [Accepted: 12/22/2021] [Indexed: 12/04/2022] Open
Abstract
Nearly all of biology depends on interactions between molecules: proteins with small molecules, proteins with other proteins, nucleic acids with small molecules, and nucleic acids with proteins that regulate gene expression, our concern in this Special Issue. All those kinds of interactions, and others, constitute the vast majority of biology at the molecular level. An understanding of those interactions requires that we quantify them to learn how they interact: How strongly? With which partners? How—and how well—are different partners distinguished? This review addresses the evolution of our current understanding of the molecular origins of affinity and specificity in regulatory protein–DNA interactions, and suggests that both these properties can be modulated by cooperativity.
Collapse
|
3
|
Charlier D, Bervoets I. Separation and Characterization of Protein-DNA Complexes by EMSA and In-Gel Footprinting. Methods Mol Biol 2022; 2516:169-199. [PMID: 35922628 DOI: 10.1007/978-1-0716-2413-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In-gel footprinting enables the precise identification of protein binding sites on the DNA after separation of free and protein-bound DNA molecules by gel electrophoresis in native conditions and subsequent digestion by the nuclease activity of the 1,10-phenanthroline-copper ion [(OP)2-Cu+] within the gel matrix. Hence, the technique combines the resolving power of protein-DNA complexes in the electrophoretic mobility shift assay (EMSA) with the precision of target site identification by chemical footprinting. This approach is particularly well suited to characterize distinct molecular assemblies in a mixture of protein-DNA complexes and to identify individual binding sites within composite operators, when the concentration-dependent occupation of binding sites, with a different affinity, results in the generation of complexes with a distinct stoichiometry and migration velocity in gel electrophoresis.
Collapse
Affiliation(s)
- Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| |
Collapse
|
4
|
Qu D, Hou Z, Li J, Luo L, Su S, Ye Z, Bai Y, Zhang X, Chen G, Li Z, Wang Y, Xue X, Luo X, Li M. A new coumarin compound DCH combats methicillin-resistant Staphylococcus aureus biofilm by targeting arginine repressor. SCIENCE ADVANCES 2020; 6:eaay9597. [PMID: 32832655 PMCID: PMC7439407 DOI: 10.1126/sciadv.aay9597] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 06/05/2020] [Indexed: 05/26/2023]
Abstract
Staphylococcus aureus infection is difficult to eradicate because of biofilm formation and antibiotic resistance. The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) infection necessitates the development of a new agent against bacterial biofilms. We report a new coumarin compound, termed DCH, that effectively combats MRSA in vitro and in vivo and exhibits potent antibiofilm activity without detectable resistance. Cellular proteome analysis suggests that the molecular mechanism of action of DCH involves the arginine catabolic pathway. Using molecular docking and binding affinity assays of DCH, and comparison of the properties of wild-type and ArgR-deficient MRSA strains, we demonstrate that the arginine repressor ArgR, an essential regulator of the arginine catabolic pathway, is the target of DCH. These findings indicate that DCH is a promising lead compound and validate bacterial ArgR as a potential target in the development of new drugs against MRSA biofilms.
Collapse
Affiliation(s)
- Di Qu
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Zheng Hou
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Jing Li
- Key Laboratory for Surface Engineering and Remanufacturing in Shaanxi province, School of Chemical Engineering, Xi’an University, Xi’an 710065, China
| | - Liyang Luo
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Shan Su
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Zichen Ye
- Department of Pharmacogenomics, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Yinlan Bai
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi’an 710032, China
| | - Xinlei Zhang
- Department of Medical Chemistry, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Guanghui Chen
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Zhoupeng Li
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Yikun Wang
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Xiaoyan Xue
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Xiaoxing Luo
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Mingkai Li
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
- Precision Pharmacy and Drug Development Center, The Fourth Military Medical University, Xi’an 710032, China
| |
Collapse
|
5
|
Pandey SK, Melichercik M, Řeha D, Ettrich RH, Carey J. Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors. Molecules 2020; 25:molecules25092247. [PMID: 32397647 PMCID: PMC7248756 DOI: 10.3390/molecules25092247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 11/23/2022] Open
Abstract
Hexameric arginine repressor, ArgR, is the feedback regulator of bacterial L-arginine regulons, and sensor of L-arg that controls transcription of genes for its synthesis and catabolism. Although ArgR function, as well as its secondary, tertiary, and quaternary structures, is essentially the same in E. coli and B. subtilis, the two proteins differ significantly in sequence, including residues implicated in the response to L-arg. Molecular dynamics simulations are used here to evaluate the behavior of intact B. subtilis ArgR with and without L-arg, and are compared with prior MD results for a domain fragment of E. coli ArgR. Relative to its crystal structure, B. subtilis ArgR in absence of L-arg undergoes a large-scale rotational shift of its trimeric subassemblies that is very similar to that observed in the E. coli protein, but the residues driving rotation have distinct secondary and tertiary structural locations, and a key residue that drives rotation in E. coli is missing in B. subtilis. The similarity of trimer rotation despite different driving residues suggests that a rotational shift between trimers is integral to ArgR function. This conclusion is supported by phylogenetic analysis of distant ArgR homologs reported here that indicates at least three major groups characterized by distinct sequence motifs but predicted to undergo a common rotational transition. The dynamic consequences of L-arg binding for transcriptional activation of intact ArgR are evaluated here for the first time in two-microsecond simulations of B. subtilis ArgR. L-arg binding to intact B. subtilis ArgR causes a significant further shift in the angle of rotation between trimers that causes the N-terminal DNA-binding domains lose their interactions with the C-terminal domains, and is likely the first step toward adopting DNA-binding-competent conformations. The results aid interpretation of crystal structures of ArgR and ArgR-DNA complexes.
Collapse
Affiliation(s)
- Saurabh Kumar Pandey
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, 84248 Bratislava, Slovakia
- Faculty of Sciences, University of South Bohemia, 37005 Ceske Budejovice, Czechia
| | - Milan Melichercik
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, 84248 Bratislava, Slovakia
| | - David Řeha
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Faculty of Sciences, University of South Bohemia, 37005 Ceske Budejovice, Czechia
| | - Rüdiger H. Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- College of Biomedical Sciences, Larkin University, Miami, FL 33169, USA
- Department of Cellular Biology & Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Correspondence: (R.H.E.); (J.C.); Tel.: +1-954-682-8347 (R.H.E.); +1-609-258-1631 (J.C.)
| | - Jannette Carey
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Correspondence: (R.H.E.); (J.C.); Tel.: +1-954-682-8347 (R.H.E.); +1-609-258-1631 (J.C.)
| |
Collapse
|
6
|
Bervoets I, Charlier D. Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. FEMS Microbiol Rev 2019; 43:304-339. [PMID: 30721976 PMCID: PMC6524683 DOI: 10.1093/femsre/fuz001] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Gene expression occurs in two essential steps: transcription and translation. In bacteria, the two processes are tightly coupled in time and space, and highly regulated. Tight regulation of gene expression is crucial. It limits wasteful consumption of resources and energy, prevents accumulation of potentially growth inhibiting reaction intermediates, and sustains the fitness and potential virulence of the organism in a fluctuating, competitive and frequently stressful environment. Since the onset of studies on regulation of enzyme synthesis, numerous distinct regulatory mechanisms modulating transcription and/or translation have been discovered. Mostly, various regulatory mechanisms operating at different levels in the flow of genetic information are used in combination to control and modulate the expression of a single gene or operon. Here, we provide an extensive overview of the very diverse and versatile bacterial gene regulatory mechanisms with major emphasis on their combined occurrence, intricate intertwinement and versatility. Furthermore, we discuss the potential of well-characterized basal expression and regulatory elements in synthetic biology applications, where they may ensure orthogonal, predictable and tunable expression of (heterologous) target genes and pathways, aiming at a minimal burden for the host.
Collapse
Affiliation(s)
- Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| |
Collapse
|
7
|
Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli. Amino Acids 2019; 51:1103-1127. [DOI: 10.1007/s00726-019-02757-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
|
8
|
Abstract
Early investigations on arginine biosynthesis brought to light basic features of metabolic regulation. The most significant advances of the last 10 to 15 years concern the arginine repressor, its structure and mode of action in both E. coli and Salmonella typhimurium, the sequence analysis of all arg structural genes in E. coli and Salmonella typhimurium, the resulting evolutionary inferences, and the dual regulation of the carAB operon. This review provides an overall picture of the pathways, their interconnections, the regulatory circuits involved, and the resulting interferences between arginine and polyamine biosynthesis. Carbamoylphosphate is a precursor common to arginine and the pyrimidines. In both Escherichia coli and Salmonella enterica serovar Typhimurium, it is produced by a single synthetase, carbamoylphosphate synthetase (CPSase), with glutamine as the physiological amino group donor. This situation contrasts with the existence of separate enzymes specific for arginine and pyrimidine biosynthesis in Bacillus subtilis and fungi. Polyamine biosynthesis has been particularly well studied in E. coli, and the cognate genes have been identified in the Salmonella genome as well, including those involved in transport functions. The review summarizes what is known about the enzymes involved in the arginine pathway of E. coli and S. enterica serovar Typhimurium; homologous genes were identified in both organisms, except argF (encoding a supplementary OTCase), which is lacking in Salmonella. Several examples of putative enzyme recruitment (homologous enzymes performing analogous functions) are also presented.
Collapse
|
9
|
Cho S, Cho YB, Kang TJ, Kim SC, Palsson B, Cho BK. The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli. Nucleic Acids Res 2015; 43:3079-88. [PMID: 25735747 PMCID: PMC4381063 DOI: 10.1093/nar/gkv150] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/13/2015] [Indexed: 01/26/2023] Open
Abstract
DNA-binding motifs that are recognized by transcription factors (TFs) have been well studied; however, challenges remain in determining the in vivo architecture of TF-DNA complexes on a genome-scale. Here, we determined the in vivo architecture of Escherichia coli arginine repressor (ArgR)-DNA complexes using high-throughput sequencing of exonuclease-treated chromatin-immunoprecipitated DNA (ChIP-exo). The ChIP-exo has a unique peak-pair pattern indicating 5′ and 3′ ends of ArgR-binding region. We identified 62 ArgR-binding loci, which were classified into three groups, comprising single, double and triple peak-pairs. Each peak-pair has a unique 93 base pair (bp)-long (±2 bp) ArgR-binding sequence containing two ARG boxes (39 bp) and residual sequences. Moreover, the three ArgR-binding modes defined by the position of the two ARG boxes indicate that DNA bends centered between the pair of ARG boxes facilitate the non-specific contacts between ArgR subunits and the residual sequences. Additionally, our approach may also reveal other fundamental structural features of TF-DNA interactions that have implications for studying genome-scale transcriptional regulatory networks.
Collapse
Affiliation(s)
- Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Yoo-Bok Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Taek Jin Kang
- Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, Seoul 100-715, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| |
Collapse
|
10
|
Pandey SK, Řeha D, Zayats V, Melichercik M, Carey J, Ettrich R. Binding-competent states for L-arginine in E. coli arginine repressor apoprotein. J Mol Model 2014; 20:2330. [PMID: 24952066 DOI: 10.1007/s00894-014-2330-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 05/28/2014] [Indexed: 11/24/2022]
Abstract
Arginine repressor of E. coli is a multifunctional hexameric protein that provides feedback regulation of arginine metabolism upon activation by the negatively cooperative binding of L-arginine. Interpretation of this complex system requires an understanding of the protein's conformational landscape. The ~50 kDa hexameric C-terminal domain was studied by 100 ns molecular dynamics simulations in the presence and absence of the six L-arg ligands that bind at the trimer-trimer interface. A rotational shift between trimers followed by rotational oscillation occurs in the production phase of the simulations only when L-arg is absent. Analysis of the system reveals that the degree of rotation is correlated with the number of hydrogen bonds across the trimer interface. The trajectory presents frames with one or more apparently open binding sites into which one L-arg could be docked successfully in three different instances, indicating that a binding-competent state of the system is occasionally sampled. Simulations of the resulting singly-liganded systems reveal for the first time that the binding of one L-arg results in a holoprotein-like conformational distribution.
Collapse
Affiliation(s)
- Saurabh Kumar Pandey
- Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic
| | | | | | | | | | | |
Collapse
|
11
|
Strawn R, Stockner T, Melichercik M, Jin L, Xue WF, Carey J, Ettrich R. Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery. Methods Enzymol 2011; 492:151-88. [PMID: 21333791 DOI: 10.1016/b978-0-12-381268-1.00017-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite decades of intensive study, allosteric effects have eluded an intellectually satisfying integrated understanding that includes a description of the reaction coordinate in terms of species distributions of structures and free energy levels in the conformational ensemble. This chapter illustrates a way to fill this gap by interpreting thermodynamic and structural results through the lens of molecular dynamics simulation analysis to link atomic-level detail with global response. In this synergistic approach molecular dynamics forms an integral part of a feedback loop of hypothesis, experimental design, and interpretation that conforms to the scientific method.
Collapse
Affiliation(s)
- Rebecca Strawn
- Chemistry Department, Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | | |
Collapse
|
12
|
Abstract
Legionella pneumophila is an intracellular pathogen that infects protozoa in aquatic environments and when inhaled by susceptible human hosts replicates in alveolar macrophages and can result in the often fatal pneumonia called Legionnaires' disease. The ability of L. pneumophila to replicate within host cells requires the establishment of a specialized compartment that evades normal phagolysosome fusion called the Legionella-containing vacuole (LCV). Elucidation of the biochemical composition of the LCV and the identification of the regulatory signals sensed during intracellular replication are inherently challenging. L-Arginine is a critical nutrient in the metabolism of both prokaryotic and eukaryotic organisms. We showed that the L. pneumophila arginine repressor homolog, ArgR, is required for maximal intracellular growth in the unicellular host Acanthamoeba castellanii. In this study, we present evidence that the concentration of L-arginine in the LCV is sensed by ArgR to produce an intracellular transcriptional response. We characterized the L. pneumophila ArgR regulon by global gene expression analysis, identified genes highly affected by ArgR, showed that ArgR repression is dependent upon the presence of L-arginine, and demonstrated that ArgR-regulated genes are derepressed during intracellular growth. Additional targets of ArgR that may account for the argR mutant's intracellular multiplication defect are discussed. These results suggest that L-arginine availability functions as a regulatory signal during Legionella intracellular growth.
Collapse
|
13
|
Briggs GS, Yu J, Mahdi AA, Lloyd RG. The RdgC protein employs a novel mechanism involving a finger domain to bind to circular DNA. Nucleic Acids Res 2010; 38:6433-46. [PMID: 20525790 PMCID: PMC2965237 DOI: 10.1093/nar/gkq509] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The DNA-binding protein RdgC has been identified as an inhibitor of RecA-mediated homologous recombination in Escherichia coli. In Neisseria species, RdgC also has a role in virulence-associated antigenic variation. We have previously solved the crystal structure of the E. coli RdgC protein and shown it to form a toroidal dimer. In this study, we have conducted a mutational analysis of residues proposed to mediate interactions at the dimer interfaces. We demonstrate that destabilizing either interface has a serious effect on in vivo function, even though a stable complex with circular DNA was still observed. We conclude that tight binding is required for inhibition of RecA activity. We also investigated the role of the RdgC finger domain, and demonstrate that it plays a crucial role in the binding of circular DNA. Together, these data allow us to propose a model for how RdgC loads onto DNA. We discuss how RdgC might inhibit RecA-mediated strand exchange, and how RdgC might be displaced by other DNA metabolism enzymes such as polymerases and helicases.
Collapse
Affiliation(s)
- Geoffrey S Briggs
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
| | | | | | | |
Collapse
|
14
|
Strawn R, Melichercik M, Green M, Stockner T, Carey J, Ettrich R. Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues. PLoS Comput Biol 2010; 6:e1000801. [PMID: 20532206 PMCID: PMC2880562 DOI: 10.1371/journal.pcbi.1000801] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 04/29/2010] [Indexed: 12/20/2022] Open
Abstract
An elegantly simple and probably ancient molecular mechanism of allostery is described for the Escherichia coli arginine repressor ArgR, the master feedback regulator of transcription in L-arginine metabolism. Molecular dynamics simulations with ArgRC, the hexameric domain that binds L-arginine with negative cooperativity, reveal that conserved arginine and aspartate residues in each ligand-binding pocket promote rotational oscillation of apoArgRC trimers by engagement and release of hydrogen-bonded salt bridges. Binding of exogenous L-arginine displaces resident arginine residues and arrests oscillation, shifting the equilibrium quaternary ensemble and promoting motions that maintain the configurational entropy of the system. A single L-arg ligand is necessary and sufficient to arrest oscillation, and enables formation of a cooperative hydrogen-bond network at the subunit interface. The results are used to construct a free-energy reaction coordinate that accounts for the negative cooperativity and distinctive thermodynamic signature of L-arginine binding detected by calorimetry. The symmetry of the hexamer is maintained as each ligand binds, despite the conceptual asymmetry of partially-liganded states. The results thus offer the first opportunity to describe in structural and thermodynamic terms the symmetric relaxed state predicted by the concerted allostery model of Monod, Wyman, and Changeux, revealing that this state is achieved by exploiting the dynamics of the assembly and the distributed nature of its cohesive free energy. The ArgR example reveals that symmetry can be maintained even when binding sites fill sequentially due to negative cooperativity, which was not anticipated by the Monod, Wyman, and Changeux model. The molecular mechanism identified here neither specifies nor requires a pathway for transmission of the allosteric signal through the protein, and it suggests the possibility that binding of free amino acids was an early innovation in the evolution of allostery.
Collapse
Affiliation(s)
- Rebecca Strawn
- Chemistry Department, Princeton University, Princeton, New Jersey, United States of America
| | - Milan Melichercik
- Department of Structure and Function of Proteins, Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, and Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
| | - Michael Green
- Biology Department, The College of New Jersey, Ewing, New Jersey, United States of America
| | - Thomas Stockner
- Department of Medical Chemistry, Medical University of Vienna, Vienna, Austria
| | - Jannette Carey
- Chemistry Department, Princeton University, Princeton, New Jersey, United States of America
| | - Rüdiger Ettrich
- Department of Structure and Function of Proteins, Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, and Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
| |
Collapse
|
15
|
McLean S, Bowman LAH, Sanguinetti G, Read RC, Poole RK. Peroxynitrite toxicity in Escherichia coli K12 elicits expression of oxidative stress responses and protein nitration and nitrosylation. J Biol Chem 2010; 285:20724-31. [PMID: 20427277 DOI: 10.1074/jbc.m109.085506] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peroxynitrite is formed in macrophages by the diffusion-limited reaction of superoxide and nitric oxide. This highly reactive species is thought to contribute to bacterial killing by interaction with diverse targets and nitration of protein tyrosines. This work presents for the first time a comprehensive analysis of transcriptional responses to peroxynitrite under tightly controlled chemostat growth conditions. Up-regulation of the cysteine biosynthesis pathway and an increase in S-nitrosothiol levels suggest S-nitrosylation to be a consequence of peroxynitrite exposure. Genes involved in the assembly/repair of iron-sulfur clusters also show enhanced transcription. Unexpectedly, arginine biosynthesis gene transcription levels were also elevated after treatment with peroxynitrite. Analysis of the negative regulator for these genes, ArgR, showed that post-translational nitration of tyrosine residues within this protein is responsible for its degradation in vitro. Further up-regulation was seen in oxidative stress response genes, including katG and ahpCF. However, genes known to be up-regulated by nitric oxide and nitrosating agents (e.g. hmp and norVW) were unaffected. Probabilistic modeling of the transcriptomic data identified five altered transcription factors in response to peroxynitrite exposure, including OxyR and ArgR. Hydrogen peroxide can be present as a contaminant in commercially available peroxynitrite preparations. Transcriptomic analysis of cells treated with hydrogen peroxide alone also revealed up-regulation of oxidative stress response genes but not of many other genes that are up-regulated by peroxynitrite. Thus, the cellular responses to peroxynitrite and hydrogen peroxide are distinct.
Collapse
Affiliation(s)
- Samantha McLean
- Departments of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | | | | | | | | |
Collapse
|
16
|
Caldara M, Minh PNL, Bostoen S, Massant J, Charlier D. ArgR-dependent repression of arginine and histidine transport genes in Escherichia coli K-12. J Mol Biol 2007; 373:251-67. [PMID: 17850814 DOI: 10.1016/j.jmb.2007.08.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 07/31/2007] [Accepted: 08/02/2007] [Indexed: 10/22/2022]
Abstract
In Escherichia coli L-arginine is taken up by three periplasmic binding protein-dependent transport systems that are encoded by two genetic loci: the artPIQM-artJ and argT-hisJQMP gene clusters. The transcription of the artJ, artPIQM and hisJQMP genes and operons is repressed by liganded ArgR, whereas argT, encoding the LAO (lysine, arginine, ornithine) periplasmic binding protein, is insensitive to the repressor. Here we characterize the repressible Esigma70 P artJ, P artP and P hisJ promoters and demonstrate that the cognate operators consist of two 18 bp ARG boxes separated by 3 bp. Determination of the energy landscape of the ArgR-operator contacts by missing contact probing and mutant studies indicated that each box of a pair contributes to complex formation in vitro and to the repressibility in vivo, but to a different extent. The organization of the ARG boxes and promoter elements in the control regions of the uptake genes is distinct from that of the arginine biosynthetic genes. The hisJQMP operon is the first member of the E. coli ArgR regulon, directly repressed by liganded ArgR, where none of the core promoter elements overlaps the ARG boxes. Single round in vitro transcription assays and DNase I footprinting experiments indicate that liganded ArgR inhibits P artJ and P artP promoter activity by steric exclusion of the RNA polymerase. In contrast, ArgR-mediated repression of P hisJ by inhibition of RNA polymerase binding appears to occur through topological changes of the promoter region.
Collapse
Affiliation(s)
- Marina Caldara
- Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | | | | | | | | |
Collapse
|
17
|
Peeters E, Wartel C, Maes D, Charlier D. Analysis of the DNA-binding sequence specificity of the archaeal transcriptional regulator Ss-LrpB from Sulfolobus solfataricus by systematic mutagenesis and high resolution contact probing. Nucleic Acids Res 2006; 35:623-33. [PMID: 17178749 PMCID: PMC1802622 DOI: 10.1093/nar/gkl1095] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To determine the sequence specificity of dimeric Ss-LrpB, a high resolution contact map was constructed and a saturation mutagenesis conducted on one half of the palindromic consensus box. Premodification binding interference indicates that Ss-LrpB establishes most of its tightest contacts with a single strand of two major groove segments and interacts with the minor groove at the center of the box. The requirement for bending is reflected in the preference for an A+T rich center and confirmed with C·G and C·I substitutions. The saturation mutagenesis indicates that major groove contacts with C·G at position 5 and its symmetrical counterpart are most critical for the specificity and strength of the interaction. Conservation at the remaining positions improved the binding. Hydrogen bonding to the O6 and N7 acceptor atoms of the G5′ residue play a major role in complex formation. Unlike many other DNA-binding proteins Ss-LrpB does not establish hydrophobic interactions with the methyls of thymine residues. The binding energies determined from the saturation mutagenesis were used to construct a sequence logo, which pin-points the overwhelming importance of C·G at position 5. The knowledge of the DNA-binding specificity will constitute a precious tool for the search of new physiologically relevant binding sites for Ss-LrpB in the genome.
Collapse
Affiliation(s)
| | | | - Dominique Maes
- Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel and Vlaams interuniversitair Instituut voor Biotechnologie (VIB)Pleinlaan 2, B-1050 Brussel, Belgium
| | - Daniel Charlier
- To whom correspondence should be addressed. Tel: +32 2 629 13 42; Fax: +32 2 629 13 45;
| |
Collapse
|
18
|
Hiromoto T, Matsue H, Yoshida M, Tanaka T, Higashibata H, Hosokawa K, Yamaguchi H, Fujiwara S. Characterization of MobR, the 3-hydroxybenzoate-responsive transcriptional regulator for the 3-hydroxybenzoate hydroxylase gene of Comamonas testosteroni KH122-3s. J Mol Biol 2006; 364:863-77. [PMID: 17046018 DOI: 10.1016/j.jmb.2006.08.098] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 08/12/2006] [Accepted: 08/31/2006] [Indexed: 11/24/2022]
Abstract
Comamonas testosteroni KH122-3s is an aerobic soil bacterium that utilizes 3-hydroxybenzoate as a sole carbon and energy source. In this strain, 3-hydroxybenzoate hydroxylase (MobA) acts on the initial step of the degradation to produce 3,4-dihydroxybenzoate, which is subsequently subjected to the meta-cleavage pathway leading to tricarboxylic acid cycle intermediates. Gene walking analysis of the upstream region of mobA revealed an open reading frame (mobR) that encodes a transcriptional regulator of the MarR family. Here, we report that MobR negatively regulates the expression of mobA, and that the repression is relieved by binding of 3-hydroxybenzoate, the substrate for MobA. A primer extension experiment was performed to determine the transcription start site for mobA and identified it at 83 bp upstream of the mobA start codon, accompanied by a typical sigma70-type promoter. The mobR gene was expressed in Escherichia coli cells and the recombinant product was purified to homogeneity. Gel mobility-shift assays and DNase I footprinting analyses indicated that MobR binds as a homodimer to an imperfect inverted repeat within the mobA-mobR intergenic region, with an apparent dissociation constant of 11.5(+/- 0.5) nM. The operator site is located between the start codon and the promoter region for mobA, suggesting that MobR functions as a transcriptional repressor for mobA expression. The results of effector-binding assays indicated that MobR, but not its isomers 4-hydroxybenzoate and salicylate, is released from the operator site by the addition of 3-hydroxybenzoate. This dissociation process is highly cooperative, with a Hill coefficient of approximately 2. In addition, CD spectroscopic studies demonstrated that MobR adopts two conformational states corresponding to the effector-bound and unbound forms. These results suggest that the MobR dimer possesses at least two effector-binding sites, and that the effector binding to MobR induces an allosteric conformational change required for dissociation of the protein-DNA complex.
Collapse
Affiliation(s)
- Takeshi Hiromoto
- Department of Chemistry, Nanobiothechnology Research Center, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Schaumburg CS, Tan M. Arginine-dependent gene regulation via the ArgR repressor is species specific in chlamydia. J Bacteriol 2006; 188:919-27. [PMID: 16428395 PMCID: PMC1347356 DOI: 10.1128/jb.188.3.919-927.2006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Accepted: 11/02/2005] [Indexed: 11/20/2022] Open
Abstract
Some, but not all, Chlamydia spp. are predicted to encode a homolog of ArgR, a master regulatory molecule that modulates arginine biosynthesis and catabolism in bacteria in response to intracellular arginine levels. While genes for arginine biosynthesis are apparently missing in Chlamydia, a putative arginine transport system encoded by glnP, glnQ, and artJ is present. We found that recombinant Chlamydia pneumoniae ArgR functions as an arginine-dependent aporepressor that bound specifically to operator sequences upstream of the glnPQ operon. ArgR was able to repress transcription in a promoter-specific manner that was dependent on the concentration of the corepressor l-arginine. We were able to locate ArgR operators upstream of glnPQ in C. pneumoniae and Chlamydophila caviae but not Chlamydia trachomatis, which corresponded to the predicted presence or absence of ArgR in these chlamydial species. Our findings indicate that only some members of the family Chlamydiaceae have an arginine-responsive mechanism of gene regulation that is predicted to control arginine uptake from the host cell. This is the first study to directly demonstrate a species-specific mechanism of transcriptional regulation in Chlamydia.
Collapse
Affiliation(s)
- Chris S Schaumburg
- Department of Microbiology and Molecular Genetics, B240 Med Sci I, University of California, Irvine, CA 92697-4025, USA
| | | |
Collapse
|
20
|
Samalíková M, Carey J, Grandori R. Assembly of the hexameric Escherichia coli arginine repressor investigated by nano-electrospray ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:2549-52. [PMID: 16106344 DOI: 10.1002/rcm.2094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The arginine repressor (ArgR) from Escherichia coli regulates genes for L-arginine metabolism and is a required recombination factor for colE1 plasmid replication. Both functions require binding of L-arginine to the protein. In this work, nano-electrospray ionization time-of-flight mass spectrometry (nano-ESI-TOFMS) is used to study conformational and oligomeric states of intact ArgR and its isolated structural domains. In agreement with X-ray diffraction studies, it is shown that ArgR oligomerizes to form hexamers in both the presence and absence of L-arginine, and the basic unit of oligomerization appears to be the trimer. Higher-order assembly into dodecamers is also detected. The isolated C-terminal domain is found to associate into trimers and hexamers whereas the N-terminal domain is detected in its monomeric form. The observed species distributions suggest a role for the N-terminal domain in hexamer stabilization.
Collapse
Affiliation(s)
- Mária Samalíková
- Institute of Organic Chemistry, Johannes Kepler University, Altenbergerstrasse 69, 4040 Linz, Austria
| | | | | |
Collapse
|
21
|
Jin L, Xue WF, Fukayama JW, Yetter J, Pickering M, Carey J. Asymmetric allosteric activation of the symmetric ArgR hexamer. J Mol Biol 2004; 346:43-56. [PMID: 15663926 DOI: 10.1016/j.jmb.2004.11.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Revised: 11/10/2004] [Accepted: 11/11/2004] [Indexed: 11/25/2022]
Abstract
Hexameric arginine repressor, ArgR, bound to L-arginine serves both as the master transcriptional repressor/activator at diverse regulons in a wide range of bacteria and as a required cofactor for resolution of ColE1 plasmid multimers. Multifunctional ArgR is thus unusual in possessing features of specific gene regulators, global regulators, and non-specific gene organizers; its closest functional analog is probably CAP, the cyclic AMP receptor/activator protein. Isothermal titration calorimetry, surface plasmon resonance, and proteolysis indicate that binding of a single L-argine [corrected] per ArgR hexamer triggers a global conformation [corrected] change and resets the affinities of the remaining five sites, making them 100-fold weaker. The analysis suggests a novel thermodynamic signature for this mechanism of activation.
Collapse
Affiliation(s)
- Lihua Jin
- Chemistry Department, DePaul University, Chicago, IL 60614, USA.
| | | | | | | | | | | |
Collapse
|
22
|
Suiter AM, Bänziger O, Dean AM. Fitness consequences of a regulatory polymorphism in a seasonal environment. Proc Natl Acad Sci U S A 2003; 100:12782-6. [PMID: 14555766 PMCID: PMC240695 DOI: 10.1073/pnas.2134994100] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2003] [Indexed: 12/27/2022] Open
Abstract
Gene regulation is commonly assumed to have evolved in response to environmental variability. Although tightly regulated in Escherichia coli strain K12, transcriptional control of arginine biosynthesis is deregulated in strain B. Caused by a single amino acid replacement in the arginine repressor, these contrasting regulatory strategies result in a fitness tradeoff. The K12 repressor is selectively favored in the presence of arginine and disfavored in its absence. In environments that cycle between high and low arginine, short seasons favor the K12 allele, whereas long seasons favor the B allele. Unexpectedly then, deregulated expression is adaptive in some seasonal habitats.
Collapse
Affiliation(s)
- Amy M. Suiter
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108; Department of Biotechnology, University of Applied Sciences, P.O. Box 335, Waedenswil CH8820, Switzerland; and Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108
| | - Otmar Bänziger
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108; Department of Biotechnology, University of Applied Sciences, P.O. Box 335, Waedenswil CH8820, Switzerland; and Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108
| | - Antony M. Dean
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108; Department of Biotechnology, University of Applied Sciences, P.O. Box 335, Waedenswil CH8820, Switzerland; and Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108
| |
Collapse
|
23
|
Morin A, Huysveld N, Braun F, Dimova D, Sakanyan V, Charlier D. Hyperthermophilic Thermotoga arginine repressor binding to full-length cognate and heterologous arginine operators and to half-site targets. J Mol Biol 2003; 332:537-53. [PMID: 12963366 DOI: 10.1016/s0022-2836(03)00951-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The degree of sequence conservation of arginine repressor proteins (ArgR) and of the cognate operators (tandem pairs of 18 bp imperfect palindromes, ARG boxes) in evolutionarily distant bacteria is unusually high, and the global mechanism of ArgR-mediated regulation appears to be similar. However, here we demonstrate that the arginine repressor from the hyperthermophilic bacterium Thermotoga neapolitana (ArgR(Tn)) exhibits characteristics that clearly distinguish this regulator from the well-studied homologues from Escherichia coli, Bacillus subtilis and B.stearothermophilus. A high-resolution contact map of ArgR(Tn) binding to the operator of the biosynthetic argGHCJBD operon of Thermotoga maritima indicates that ArgR(Tn) establishes all of its strong contacts with a single ARG box-like sequence of the operator only. Protein array and electrophoretic mobility-shift data demonstrate that ArgR(Tn) has a remarkable capacity to bind to arginine operators from Gram-negative and Gram-positive bacteria, and to single ARG box-bearing targets. Moreover, the overall effect of L-arginine on the apparent K(d) of ArgR(Tn) binding to various cognate and heterologous operator fragments was minor with respect to that observed with diverse bacterial arginine repressors. We demonstrate that this unusual behaviour for an ArgR protein can, to a large extent, be ascribed to the presence of a serine residue at position 107 of ArgR(Tn), instead of the highly conserved glutamine that is involved in arginine binding in the E.coli repressor. Consistent with these results, ArR(Tn) was found to behave as a superrepressor in E.coli, inhibiting growth in minimal medium, even supplemented with arginine, whereas similar constructs bearing the S107Q mutant allele did not inhibit growth. We assume that ArgR(Tn), owing to its broad target specificity and its ability to bind single ARG box sequences, might play a more general regulatory role in Thermotoga
Collapse
Affiliation(s)
- Amélie Morin
- Laboratoire de Biotechnologie, FRE CNRS 2230 Unité Biocatalyse, Faculté des Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière, 44322, Nantes, France
| | | | | | | | | | | |
Collapse
|
24
|
Snapyan M, Lecocq M, Guével L, Arnaud MC, Ghochikyan A, Sakanyan V. Dissecting DNA-protein and protein-protein interactions involved in bacterial transcriptional regulation by a sensitive protein array method combining a near-infrared fluorescence detection. Proteomics 2003; 3:647-57. [PMID: 12748944 DOI: 10.1002/pmic.200300390] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The protein array methodology is used to study DNA-protein and protein-protein interactions governing gene expression from the Bacillus stearothermophilus PargCo promoter-operator region. Using probes labelled with near-infrared fluorescence dyes with exitation characteristics close to 700 or 800 nm, it is possible to detect signals from proteins (purified or non-purified in Escherichia coli cell extracts) immobilised on a nitrocellulose membrane with a high sensitivity (almost 12 amol of a spotted protein for protein-DNA interactions). Protein array data are confirmed by other methods indicating that molecular interactions of the order 10(-7) M can be monitored with the proposed protein array approach. We show that the PargCo region is a target for binding at least three types of regulatory proteins, ArgR repressors from thermophilic bacteria, the E. coli RNA polymerase alpha subunit and cyclic AMP binding protein CRP. We also demonstrate that the high strength of the PargC promoter is related to an upstream element that binds to the E. coli RNA polymerase alpha subunit.
Collapse
Affiliation(s)
- Marina Snapyan
- Laboratoire de Biotechnologie, FRE-CNRS 2230 Biocatalyse, Université de Nantes, Nantes, France
| | | | | | | | | | | |
Collapse
|
25
|
Bonanomi A, Dohm C, Rickenbach Z, Altwegg M, Fischer J, Gygi D, Nadal D. Monitoring intracellular replication of Chlamydophila (Chlamydia) pneumoniae in cell cultures and comparing clinical samples by real-time PCR. Diagn Microbiol Infect Dis 2003; 46:39-47. [PMID: 12742318 DOI: 10.1016/s0732-8893(02)00572-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Strains of Chlamydophila pneumoniae may be associated with respiratory disease or atherosclerosis. Two real-time quantitative PCR assays targeting the species-specific genes Cpn0278 and ArgR were developed to compare the in vitro growth of respiratory strains AR39 and K6 with that of atherosclerotic strain A03 and to quantify C. pneumoniae in clinical samples. A third real-time PCR assay was designed to assess contamination with Mycoplasma spp. The assays targeting C. pneumoniae detected DNA concentrations corresponding to 10(4) to 10(-4) inclusion-forming units (IFU)/reaction and were highly specific. AR39 exhibited the longest lag phase and period of exponential growth; K6 augmented growth rates at higher inocula; and A03 grew at highest rates. Contamination with Mycoplasma spp. of AR39 and A03 unlikely accounted for growth differences between them. Numbers of IFU in C. pneumoniae-positive respiratory secretions varied within 4 to 5 orders of magnitude. The assays described may prove valuable for pathogenicity studies.
Collapse
Affiliation(s)
- Athos Bonanomi
- Division of Infectious Diseases, University Children's Hospital of Zurich, CH-8032 Zurich, Switzerland
| | | | | | | | | | | | | |
Collapse
|
26
|
Ghochikyan A, Karaivanova IM, Lecocq M, Vusio P, Arnaud MC, Snapyan M, Weigel P, Guével L, Buckle M, Sakanyan V. Arginine operator binding by heterologous and chimeric ArgR repressors from Escherichia coli and Bacillus stearothermophilus. J Bacteriol 2002; 184:6602-14. [PMID: 12426349 PMCID: PMC135427 DOI: 10.1128/jb.184.23.6602-6614.2002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2002] [Accepted: 08/27/2002] [Indexed: 11/20/2022] Open
Abstract
Bacillus stearothermophilus ArgR binds efficiently to the Escherichia coli carAB operator, whereas the E. coli repressor binds very poorly to the argCo operator of B. stearothermophilus. In order to elucidate this contradictory behavior between ArgRs, we constructed chimeric proteins by swapping N-terminal DNA-binding and C-terminal oligomerization domains or by exchanging the linker peptide. Chimeras carrying the E. coli DNA-binding domain and the B. stearothermophilus oligomerization domain showed sequence-nonspecific rather than sequence-specific interactions with arg operators. Chimeras carrying the B. stearothermophilus DNA-binding domain and E. coli oligomerization domain exhibited a high DNA-binding affinity for the B. stearothermophilus argCo and E. coli carAB operators and repressed the reporter-gene transcription from the B. stearothermophilus PargCo control region in vitro; arginine had no effect on, and indeed even decreased, their DNA-binding affinity. With the protein array method, we showed that the wild-type B. stearothermophilus ArgR and derivatives of it containing only the exchanged linker from E. coli ArgR or carrying the B. stearothermophilus DNA-binding domain along with the linker and the alpha4 regions were able to bind argCo containing the single Arg box. This binding was weaker than binding to the two-box operator but was no longer arginine dependent. Several lines of observations indicate that the alpha4 helix in the oligomerization domain and the linker peptide can contribute to the recognition of single or double Arg boxes and therefore to the operator DNA-binding specificity in similar but not identical ArgR repressors from two distant bacteria.
Collapse
Affiliation(s)
- Anahit Ghochikyan
- Laboratoire de Biotechnologie, FRE CNRS 2230, Unité Biocatalyse, Faculté des Sciences et des Techniques, Université de Nantes, 44322 Nantes. IFR 26, INSERM, 44035 Nantes, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|