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Šoltysová M, Řezáčová P. Structure and function of bacterial transcription regulators of the SorC family. Transcription 2024:1-22. [PMID: 39223991 DOI: 10.1080/21541264.2024.2387895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
The SorC family is a large group of bacterial transcription regulators involved in controlling carbohydrate catabolism and quorum sensing. SorC proteins consist of a conserved C-terminal effector-binding domain and an N-terminal DNA-binding domain, whose type divides the family into two subfamilies: SorC/DeoR and SorC/CggR. Proteins of the SorC/CggR subfamily are known to regulate the key node of glycolysis-triose phosphate interconversion. On the other hand, SorC/DeoR proteins are involved in a variety of peripheral carbohydrate catabolic pathways and quorum sensing functions, including virulence. Despite the abundance and importance of this family, SorC proteins seem to be on the periphery of scientific interest, which might be caused by the fragmentary information about its representatives. This review aims to compile the existing knowledge and provide material to inspire future questions about the SorC protein family.
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Affiliation(s)
- Markéta Šoltysová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, Czechia
| | - Pavlína Řezáčová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, Czechia
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2
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Šoltysová M, Škerlová J, Pachl P, Škubník K, Fábry M, Sieglová I, Farolfi M, Grishkovskaya I, Babiak M, Nováček J, Krásný L, Řezáčová P. Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function. Nucleic Acids Res 2024; 52:7305-7320. [PMID: 38842936 PMCID: PMC11229326 DOI: 10.1093/nar/gkae434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/16/2024] [Accepted: 05/22/2024] [Indexed: 07/09/2024] Open
Abstract
The SorC family of transcriptional regulators plays a crucial role in controlling the carbohydrate metabolism and quorum sensing. We employed an integrative approach combining X-ray crystallography and cryo-electron microscopy to investigate architecture and functional mechanism of two prototypical representatives of two sub-classes of the SorC family: DeoR and CggR from Bacillus subtilis. Despite possessing distinct DNA-binding domains, both proteins form similar tetrameric assemblies when bound to their respective DNA operators. Structural analysis elucidates the process by which the CggR-regulated gapA operon is derepressed through the action of two effectors: fructose-1,6-bisphosphate and newly confirmed dihydroxyacetone phosphate. Our findings provide the first comprehensive understanding of the DNA binding mechanism of the SorC-family proteins, shedding new light on their functional characteristics.
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Affiliation(s)
- Markéta Šoltysová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia
| | - Jana Škerlová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia
| | - Petr Pachl
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia
| | - Karel Škubník
- CryoElectron Microscopy and Tomography Core Facility, Central European Institute of Technology, Brno, 601 77, Czechia
| | - Milan Fábry
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia
| | - Irena Sieglová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia
| | - Martina Farolfi
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 20, Czechia
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology, Campus-ViennaBiocenter 1, 1030 Vienna, Austria
| | - Michal Babiak
- CryoElectron Microscopy and Tomography Core Facility, Central European Institute of Technology, Brno, 601 77, Czechia
| | - Jiří Nováček
- CryoElectron Microscopy and Tomography Core Facility, Central European Institute of Technology, Brno, 601 77, Czechia
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 20, Czechia
| | - Pavlína Řezáčová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia
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3
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Alfonso C, Sobrinos-Sanguino M, Luque-Ortega JR, Zorrilla S, Monterroso B, Nuero OM, Rivas G. Studying Macromolecular Interactions of Cellular Machines by the Combined Use of Analytical Ultracentrifugation, Light Scattering, and Fluorescence Spectroscopy Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:89-107. [PMID: 38507202 DOI: 10.1007/978-3-031-52193-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Cellular machines formed by the interaction and assembly of macromolecules are essential in many processes of the living cell. These assemblies involve homo- and hetero-associations, including protein-protein, protein-DNA, protein-RNA, and protein-polysaccharide associations, most of which are reversible. This chapter describes the use of analytical ultracentrifugation, light scattering, and fluorescence-based methods, well-established biophysical techniques, to characterize interactions leading to the formation of macromolecular complexes and their modulation in response to specific or unspecific factors. We also illustrate, with several examples taken from studies on bacterial processes, the advantages of the combined use of subsets of these techniques as orthogonal analytical methods to analyze protein oligomerization and polymerization, interactions with ligands, hetero-associations involving membrane proteins, and protein-nucleic acid complexes.
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Affiliation(s)
- Carlos Alfonso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Marta Sobrinos-Sanguino
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Silvia Zorrilla
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Begoña Monterroso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Oscar M Nuero
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Germán Rivas
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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4
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Šoltysová M, Sieglová I, Fábry M, Brynda J, Škerlová J, Řezáčová P. Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1411-1424. [PMID: 34726169 DOI: 10.1107/s2059798321009633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/16/2021] [Indexed: 11/11/2022]
Abstract
The SorC/DeoR family is a large family of bacterial transcription regulators that are involved in the control of carbohydrate metabolism and quorum sensing. To understand the structural basis of DNA recognition, structural studies of two functionally characterized SorC/DeoR family members from Bacillus subtilis were performed: the deoxyribonucleoside regulator bsDeoR and the central glycolytic genes regulator bsCggR. Each selected protein represents one of the subgroups that are recognized within the family. Crystal structures were determined of the N-terminal DNA-binding domains of bsDeoR and bsCggR in complex with DNA duplexes representing the minimal operator sequence at resolutions of 2.3 and 2.1 Å, respectively. While bsDeoRDBD contains a homeodomain-like HTH-type domain, bsCggRDBD contains a winged helix-turn-helix-type motif. Both proteins form C2-symmetric dimers that recognize two consecutive major grooves, and the protein-DNA interactions have been analyzed in detail. The crystal structures were used to model the interactions of the proteins with the full DNA operators, and a common mode of DNA recognition is proposed that is most likely to be shared by other members of the SorC/DeoR family.
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Affiliation(s)
- Markéta Šoltysová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Irena Sieglová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jiří Brynda
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jana Škerlová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Pavlína Řezáčová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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5
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Monteiro F, Hubmann G, Takhaveev V, Vedelaar SR, Norder J, Hekelaar J, Saldida J, Litsios A, Wijma HJ, Schmidt A, Heinemann M. Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor. Mol Syst Biol 2019; 15:e9071. [PMID: 31885198 PMCID: PMC6920703 DOI: 10.15252/msb.20199071] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022] Open
Abstract
Metabolic heterogeneity between individual cells of a population harbors significant challenges for fundamental and applied research. Identifying metabolic heterogeneity and investigating its emergence require tools to zoom into metabolism of individual cells. While methods exist to measure metabolite levels in single cells, we lack capability to measure metabolic flux, i.e., the ultimate functional output of metabolic activity, on the single-cell level. Here, combining promoter engineering, computational protein design, biochemical methods, proteomics, and metabolomics, we developed a biosensor to measure glycolytic flux in single yeast cells. Therefore, drawing on the robust cell-intrinsic correlation between glycolytic flux and levels of fructose-1,6-bisphosphate (FBP), we transplanted the B. subtilis FBP-binding transcription factor CggR into yeast. With the developed biosensor, we robustly identified cell subpopulations with different FBP levels in mixed cultures, when subjected to flow cytometry and microscopy. Employing microfluidics, we were also able to assess the temporal FBP/glycolytic flux dynamics during the cell cycle. We anticipate that our biosensor will become a valuable tool to identify and study metabolic heterogeneity in cell populations.
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Affiliation(s)
- Francisca Monteiro
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Present address:
cE3c‐Centre for Ecology, Evolution and Environmental ChangesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Georg Hubmann
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Present address:
Laboratory of Molecular Cell BiologyDepartment of BiologyInstitute of Botany and MicrobiologyKU Leuven, & Center for Microbiology, VIBHeverlee, FlandersBelgium
| | - Vakil Takhaveev
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Silke R Vedelaar
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Justin Norder
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Johan Hekelaar
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Joana Saldida
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Athanasios Litsios
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Hein J Wijma
- Biotechnology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | | | - Matthias Heinemann
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
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6
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Zorrilla S, Mónico A, Duarte S, Rivas G, Pérez-Sala D, Pajares MA. Integrated approaches to unravel the impact of protein lipoxidation on macromolecular interactions. Free Radic Biol Med 2019; 144:203-217. [PMID: 30991143 DOI: 10.1016/j.freeradbiomed.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 12/13/2022]
Abstract
Protein modification by lipid derived reactive species, or lipoxidation, is increased during oxidative stress, a common feature observed in many pathological conditions. Biochemical and functional consequences of lipoxidation include changes in the conformation and assembly of the target proteins, altered recognition of ligands and/or cofactors, changes in the interactions with DNA or in protein-protein interactions, modifications in membrane partitioning and binding and/or subcellular localization. These changes may impact, directly or indirectly, signaling pathways involved in the activation of cell defense mechanisms, but when these are overwhelmed they may lead to pathological outcomes. Mass spectrometry provides state of the art approaches for the identification and characterization of lipoxidized proteins/residues and the modifying species. Nevertheless, understanding the complexity of the functional effects of protein lipoxidation requires the use of additional methodologies. Herein, biochemical and biophysical methods used to detect and measure functional effects of protein lipoxidation at different levels of complexity, from in vitro and reconstituted cell-like systems to cells, are reviewed, focusing especially on macromolecular interactions. Knowledge generated through innovative and complementary technologies will contribute to comprehend the role of lipoxidation in pathophysiology and, ultimately, its potential as target for therapeutic intervention.
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Affiliation(s)
- Silvia Zorrilla
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Andreia Mónico
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Sofia Duarte
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Germán Rivas
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Dolores Pérez-Sala
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - María A Pajares
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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7
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Liu Y, Orsi RH, Gaballa A, Wiedmann M, Boor KJ, Guariglia-Oropeza V. Systematic review of the Listeria monocytogenes σB regulon supports a role in stress response, virulence and metabolism. Future Microbiol 2019; 14:801-828. [DOI: 10.2217/fmb-2019-0072] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: Among the alternative sigma factors of Listeria monocytogenes, σB controls the largest regulon. The aim of this study was to perform a comprehensive review of σB-regulated genes, and the functions they confer. Materials & methods: A systematic search of PubMed and Web of Knowledge was carried out to identify members of the σB regulon based on experimental evidence of σB-dependent transcription and presence of a consensus σB-dependent promoter. Results: The literature review identified σB-dependent transcription units encompassing 304 genes encoding different functions including stress response and virulence. Conclusion: Our review supports the well-known roles of σB in virulence and stress response and provides new insight into novel roles for σB in metabolism and overall resilience of L. monocytogenes.
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Affiliation(s)
- Yichang Liu
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
| | - Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
| | - Kathryn J Boor
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
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8
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Bley Folly B, Ortega AD, Hubmann G, Bonsing-Vedelaar S, Wijma HJ, van der Meulen P, Milias-Argeitis A, Heinemann M. Assessment of the interaction between the flux-signaling metabolite fructose-1,6-bisphosphate and the bacterial transcription factors CggR and Cra. Mol Microbiol 2018; 109:278-290. [DOI: 10.1111/mmi.14008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Brenda Bley Folly
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Alvaro D. Ortega
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Department of Cell Biology, Faculty of Biology; Complutense University of Madrid; José Antonio Nováis 12 28040 Madrid Spain
| | - Georg Hubmann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Silke Bonsing-Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Hein J. Wijma
- Biotechnology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Pieter van der Meulen
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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Chubukov V, Uhr M, Le Chat L, Kleijn RJ, Jules M, Link H, Aymerich S, Stelling J, Sauer U. Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis. Mol Syst Biol 2013; 9:709. [PMID: 24281055 PMCID: PMC4039378 DOI: 10.1038/msb.2013.66] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 10/23/2013] [Indexed: 12/18/2022] Open
Abstract
Regulation of enzyme expression is one key mechanism by which cells control their metabolic programs. In this work, a quantitative analysis of metabolism in a model bacterium under different conditions shows that expression alone cannot explain the majority of the observed metabolic changes. ![]()
Most enzymes are indeed highly expressed in conditions where they are more active. Quantitatively, however, the observed changes in expression between conditions do not match the changes in activity for most enzymes. A good quantitative match is only observed for enzymes involved in the TCA cycle. Metabolomics reveals that increased substrate availability explains only a few instances of changes in activity.
One of the key ways in which microbes are thought to regulate their metabolism is by modulating the availability of enzymes through transcriptional regulation. However, the limited success of efforts to manipulate metabolic fluxes by rewiring the transcriptional network has cast doubt on the idea that transcript abundance controls metabolic fluxes. In this study, we investigate control of metabolic flux in the model bacterium Bacillus subtilis by quantifying fluxes, transcripts, and metabolites in eight metabolic states enforced by different environmental conditions. We find that most enzymes whose flux switches between on and off states, such as those involved in substrate uptake, exhibit large corresponding transcriptional changes. However, for the majority of enzymes in central metabolism, enzyme concentrations were insufficient to explain the observed fluxes—only for a number of reactions in the tricarboxylic acid cycle were enzyme changes approximately proportional to flux changes. Surprisingly, substrate changes revealed by metabolomics were also insufficient to explain observed fluxes, leaving a large role for allosteric regulation and enzyme modification in the control of metabolic fluxes.
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Affiliation(s)
- Victor Chubukov
- Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland
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10
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Ha JH, Eo Y, Grishaev A, Guo M, Smith JAI, Sintim HO, Kim EH, Cheong HK, Bentley WE, Ryu KS. Crystal structures of the LsrR proteins complexed with phospho-AI-2 and two signal-interrupting analogues reveal distinct mechanisms for ligand recognition. J Am Chem Soc 2013; 135:15526-35. [PMID: 24047255 DOI: 10.1021/ja407068v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quorum sensing (QS) is a cell-to-cell communication system responsible for a variety of bacterial phenotypes including virulence and biofilm formation. QS is mediated by small molecules, autoinducers (AIs), including AI-2 that is secreted by both Gram-positive and -negative microbes. LsrR is a key transcriptional regulator that governs the varied downstream processes by perceiving AI-2 signal, but its activation via autoinducer-binding remains poorly understood. Here, we provide detailed regulatory mechanism of LsrR from the crystal structures in complexes with the native signal (phospho-AI-2, D5P) and two quorum quenching antagonists (ribose-5-phosphate, R5P; phospho-isobutyl-AI-2, D8P). Interestingly, the bound D5P and D8P molecules are not the diketone forms but rather hydrated, and the hydrated moiety forms important H-bonds with the carboxylate of D243. The D5P-binding flipped out F124 of the binding pocket, and resulted in the disruption of the dimeric interface-1 by unfolding the α7 segment. However, the same movement of F124 by the D8P'-binding did not cause the unfolding of the α7 segment. Although the LsrR-binding affinity of R5P (Kd, ∼1 mM) is much lower than that of D5P and D8P (∼2.0 and ∼0.5 μM), the α-anomeric R5P molecule fits into the binding pocket without any structural perturbation, and thus stabilizes the LsrR tetramer. The binding of D5P, not D8P and R5P, disrupted the tetrameric structure and thus is able to activate LsrR. The detailed structural and mechanistic insights from this study could be useful for facilitating design of new antivirulence and antibiofilm agents based on LsrR.
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Affiliation(s)
- Jung-Hye Ha
- Division of Magnetic Resonance Research, Korea Basic Science Institute , Yangcheong-Ri 804-1, Ochang-Eup, Cheongwon-Gun, Chungcheongbuk-Do 363-883, Republic of Korea
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11
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Wu M, Tao Y, Liu X, Zang J. Structural basis for phosphorylated autoinducer-2 modulation of the oligomerization state of the global transcription regulator LsrR from Escherichia coli. J Biol Chem 2013; 288:15878-87. [PMID: 23589368 DOI: 10.1074/jbc.m112.417634] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Quorum-sensing systems are widely used by bacteria to control behavior in response to fluctuations in cell density. Several small diffusible molecules called autoinducers act as signaling molecules in quorum-sensing processes through interplay with sensors. Autoinducers modulate vital physiological functions such as nutrient acquisition, gene transcription, and virulence factor production. In Escherichia coli, LsrR serves as a global transcription regulator that responds to autoinducer-2 to regulate the expression of a variety of genes, including the lsr operon and the lsrR gene. Here, we report the crystal structure of full-length LsrR from E. coli, which has an N-terminal DNA-binding domain and a C-terminal ligand-binding domain connected by a β-strand. Although only two molecules are found in one asymmetric unit, two neighboring dimers pack to form a tetramer that is consistent with the oligomerization state of LsrR in solution. Mutagenesis experiments and gel shift assays indicated that Gln-33 and Tyr-26 might be involved in interactions between LsrR and DNA. The LsrR-binding site for phosphorylated autoinducer-2 was predicted by structural comparisons of LsrR with CggR and SorC. Cross-linking, size exclusion chromatography, and gel shift assays determined that phosphorylated autoinducer-2 triggered the disassembly of the LsrR tetramer into dimers and reduced the DNA binding ability of LsrR. Our findings reveal a mechanism for the change in the oligomerization state of LsrR in the presence of phosphorylated autoinducer-2. Based on these observations, we propose that phosphorylated autoinducer-2 triggers the disassembly of the LsrR tetramer to activate the transcription of its target genes.
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Affiliation(s)
- Minhao Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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12
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Wenzel M, Altenbuchner J. The Bacillus subtilis mannose regulator, ManR, a DNA-binding protein regulated by HPr and its cognate PTS transporter ManP. Mol Microbiol 2013; 88:562-76. [PMID: 23551403 DOI: 10.1111/mmi.12209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2013] [Indexed: 11/28/2022]
Abstract
The transcriptional activator ManR of the Bacillus subtilis mannose utilization operon is composed of an N-terminal DNA-binding domain, two phosphotransferase system (PTS) regulation domains (PRDs), an EIIB(Bgl) - and an EIIA(Fru) -like domain. Site-specific mutagenesis of ManR revealed the role of conserved amino acids representing potential phosphorylation sites. This was investigated by β-galactosidase activity tests and by mobility shift assays after incubation with the PTS components HPr and EI. In analogy to other PRD-containing regulators we propose stimulation of ManR activity by phosphorylation. Mutations in PRD1 lowered ManR activity, whereas mutations in PRD2 abolished ManR activity completely. The Cys415Ala (EIIB(Bgl)) and the His570Ala mutations (EIIA(Fru)) provoked constitutive activities to different degrees, whereas the latter had the greater influence. Addition of EIIBA(Man) reduced the binding capability significantly in a wild-type and a Cys415Ala background, but had no effect on a His570Ala mutant. The different expression levels originating from the two promoters PmanR and PmanP could be ascribed to different 5'-untranslated mRNA regions. Sequences of 44 bp were identified and confirmed as the ManR binding sites by DNase I footprinting. The binding properties of ManR, in particular the equilibrium dissociation constant KD and the dissociation rate kdiss, were determined for both promoter regions.
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Affiliation(s)
- Marian Wenzel
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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García de la Torre J, Harding SE. Hydrodynamic modelling of protein conformation in solution: ELLIPS and HYDRO. Biophys Rev 2013; 5:195-206. [PMID: 23646070 PMCID: PMC3641304 DOI: 10.1007/s12551-013-0102-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 01/22/2013] [Indexed: 11/21/2022] Open
Abstract
The last three decades has seen some important advances in our ability to represent the conformation of proteins in solution on the basis of hydrodynamic measurements. Advances in theoretical modeling capabilities have been matched by commensurate advances in the precision of hydrodynamic measurements. We consider the advances in whole-body (simple ellipsoid-based) modeling—still useful for providing an overall idea of molecular shape, particularly for those systems where only a limited amount of data is available—and outline the ELLIPS suite of algorithms which facilitates the use of this approach. We then focus on bead modeling strategies, particularly the surface or shell–bead approaches and the HYDRO suite of algorithms. We demonstrate how these are providing great insights into complex issues such as the conformation of immunoglobulins and other multi-domain complexes.
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Affiliation(s)
- José García de la Torre
- Departamento de Quimica Fisica, Universidad de Murcia, Regional Campus Mare Nostrum, 30071 Murcia, Spain
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14
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Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states. Proc Natl Acad Sci U S A 2011; 109:155-60. [PMID: 22190493 DOI: 10.1073/pnas.1110541108] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Assessing gene expression noise in order to obtain mechanistic insights requires accurate quantification of gene expression on many individual cells over a large dynamic range. We used a unique method based on 2-photon fluorescence fluctuation microscopy to measure directly, at the single cell level and with single-molecule sensitivity, the absolute concentration of fluorescent proteins produced from the two Bacillus subtilis promoters that control the switch between glycolysis and gluconeogenesis. We quantified cell-to-cell variations in GFP concentrations in reporter strains grown on glucose or malate, including very weakly transcribed genes under strong catabolite repression. Results revealed strong transcriptional bursting, particularly for the glycolytic promoter. Noise pattern parameters of the two antagonistic promoters controlling the nutrient switch were differentially affected on glycolytic and gluconeogenic carbon sources, discriminating between the different mechanisms that control their activity. Our stochastic model for the transcription events reproduced the observed noise patterns and identified the critical parameters responsible for the differences in expression profiles of the promoters. The model also resolved apparent contradictions between in vitro operator affinity and in vivo repressor activity at these promoters. Finally, our results demonstrate that negative feedback is not noise-reducing in the case of strong transcriptional bursting.
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15
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Comparison of the regulation, metabolic functions, and roles in virulence of the glyceraldehyde-3-phosphate dehydrogenase homologues gapA and gapB in Staphylococcus aureus. Infect Immun 2010; 78:5223-32. [PMID: 20876289 DOI: 10.1128/iai.00762-10] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-positive bacterium Staphylococcus aureus contains two glyceraldehyde-3-phosphate dehydrogenase (GAPDH) homologues known as GapA and GapB. GapA has been characterized as a functional GAPDH protein, but currently there is no biological evidence for the role of GapB in metabolism in S. aureus. In this study we show through a number of complementary methods that S. aureus GapA is essential for glycolysis while GapB is essential in gluconeogenesis. These proteins are reciprocally regulated in response to glucose concentrations, and both are influenced by the glycolysis regulator protein GapR, which is the first demonstration of the role of this regulator in S. aureus and the first indication that GapR homologues control genes other than those within the glycolytic operon. Furthermore, we show that both GapA and GapB are important in the pathogenesis of S. aureus in a Galleria mellonella model of infection, showing for the first time in any bacteria that both glycolysis and gluconeogenesis have important roles in virulence.
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16
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Chaix D, Ferguson ML, Atmanene C, Van Dorsselaer A, Sanglier-Cianférani S, Royer CA, Declerck N. Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex. Nucleic Acids Res 2010; 38:5944-57. [PMID: 20462860 PMCID: PMC2943609 DOI: 10.1093/nar/gkq334] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 04/14/2010] [Accepted: 04/18/2010] [Indexed: 11/12/2022] Open
Abstract
The Central glycolytic genes Repressor (CggR) from Bacillus subtilis belongs to the SorC family of transcription factors that control major carbohydrate metabolic pathways. Recent studies have shown that CggR binds as a tetramer to its tandem operator DNA sequences and that the inducer metabolite, fructose 1,6-bisphosphate (FBP), reduces the binding cooperativity of the CggR/DNA complex. Here, we have determined the effect of FBP on the size, shape and stoichiometry of CggR complexes with full-length and half-site operator sequence by small-angle X-ray scattering, size-exclusion chromatography, fluorescence cross-correlation spectroscopy and noncovalent mass spectrometry (MS). Our results show that CggR forms a compact tetrameric assembly upon binding to either the full-length operator or two half-site DNAs and that FBP triggers a tetramer-dimer transition that leaves a single dimer on the half-site or two physically independent dimers on the full-length target. Although the binding of other phospho-sugars was evidenced by MS, only FBP was found to completely disrupt dimer-dimer contacts. We conclude that inducer-dependent dimer-dimer bridging interactions constitute the physical basis for CggR cooperative binding to DNA and the underlying repression mechanism. This work provides experimental evidences for a cooperativity-based regulation model that should apply to other SorC family members.
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Affiliation(s)
- Denis Chaix
- Centre de Biochimie Structurale, INSERM U554, Université de Montpellier, CNRS UMR 5048, 29 rue de Navacelles, F-34090 Montpellier, Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel and CNRS UMR7178, 67087 Strasbourg, France
| | - Matthew L. Ferguson
- Centre de Biochimie Structurale, INSERM U554, Université de Montpellier, CNRS UMR 5048, 29 rue de Navacelles, F-34090 Montpellier, Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel and CNRS UMR7178, 67087 Strasbourg, France
| | - Cedric Atmanene
- Centre de Biochimie Structurale, INSERM U554, Université de Montpellier, CNRS UMR 5048, 29 rue de Navacelles, F-34090 Montpellier, Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel and CNRS UMR7178, 67087 Strasbourg, France
| | - Alain Van Dorsselaer
- Centre de Biochimie Structurale, INSERM U554, Université de Montpellier, CNRS UMR 5048, 29 rue de Navacelles, F-34090 Montpellier, Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel and CNRS UMR7178, 67087 Strasbourg, France
| | - Sarah Sanglier-Cianférani
- Centre de Biochimie Structurale, INSERM U554, Université de Montpellier, CNRS UMR 5048, 29 rue de Navacelles, F-34090 Montpellier, Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel and CNRS UMR7178, 67087 Strasbourg, France
| | - Catherine A. Royer
- Centre de Biochimie Structurale, INSERM U554, Université de Montpellier, CNRS UMR 5048, 29 rue de Navacelles, F-34090 Montpellier, Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel and CNRS UMR7178, 67087 Strasbourg, France
| | - Nathalie Declerck
- Centre de Biochimie Structurale, INSERM U554, Université de Montpellier, CNRS UMR 5048, 29 rue de Navacelles, F-34090 Montpellier, Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel and CNRS UMR7178, 67087 Strasbourg, France
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17
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Bagh S, Mandal M, McMillen DR. Minimal genetic device with multiple tunable functions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:021911. [PMID: 20866841 DOI: 10.1103/physreve.82.021911] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 07/21/2010] [Indexed: 05/29/2023]
Abstract
The ability to design artificial genetic devices with predictable functions is critical to the development of synthetic biology. Given the highly variable requirements of biological designs, the ability to tune the behavior of a genetic device is also of key importance; such tuning will allow devices to be matched with other components into larger systems, and to be shifted into the correct parameter regimes to elicit desired behaviors. Here, we have developed a minimal synthetic genetic system that acts as a multifunction, tunable biodevice in the bacterium Escherichia coli. First, it acts as a biochemical AND gate, sensing the extracellular small molecules isopropyl β-D -1-thiogalactopyranoside and anhydrotetracycline as two input signals and expressing enhanced green fluorescent protein as an output signal. Next, the output signal of the AND gate can be amplified by the application of another extracellular chemical, arabinose. Further, the system can generate a wide range of chemically tunable single input-output response curves, without any genetic alteration of the circuit, by varying the concentrations of a set of extracellular small molecules. We have developed and parameterized a simple transfer function model for the system, and shown that the model successfully explains and predicts the quantitative relationships between input and output signals in the system.
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Affiliation(s)
- Sangram Bagh
- Department of Chemical and Physical Sciences, Institute for Optical Sciences, University of Toronto Mississauga, Ontario, Canada
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18
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Atmanene C, Chaix D, Bessin Y, Declerck N, Van Dorsselaer A, Sanglier-Cianferani S. Combination of Noncovalent Mass Spectrometry and Traveling Wave Ion Mobility Spectrometry Reveals Sugar-Induced Conformational Changes of Central Glycolytic Genes Repressor/DNA Complex. Anal Chem 2010; 82:3597-605. [DOI: 10.1021/ac902784n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Cédric Atmanene
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Denix Chaix
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Yannick Bessin
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Nathalie Declerck
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
| | - Sarah Sanglier-Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 STRASBOURG, France, CNRS UMR7178, 67087 Strasbourg, France and INSERM U554, Centre de Biochimie Structurale, CNRS UMR5048 and Université Montpellier 1, 29 rue de Navacelles, F-34090 Montpellier, France
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19
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Crystal Structure of the Full-Length Sorbitol Operon Regulator SorC from Klebsiella pneumoniae: Structural Evidence for a Novel Transcriptional Regulation Mechanism. J Mol Biol 2009; 387:759-70. [DOI: 10.1016/j.jmb.2009.02.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/06/2009] [Accepted: 02/10/2009] [Indexed: 11/23/2022]
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20
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Doan T, Martin L, Zorrilla S, Chaix D, Aymerich S, Labesse G, Declerck N. A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor. Proteins 2008; 71:2038-50. [PMID: 18186488 DOI: 10.1002/prot.21883] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
CggR belongs to the SorC family of bacterial transcriptional regulators which control the expression of genes and operons involved in carbohydrate catabolism. CggR was first identified in Bacillus subtilis where it represses the gapA operon encoding the five enzymes that catalyze the central part of glycolysis. Here we present a structure/function study demonstrating that the C-terminal region of CggR regulates the DNA binding activity of this repressor in response to binding of a phosphorylated sugar. Molecular modeling of CggR revealed a winged-helix DNA-binding motif followed by a C-terminal domain presenting weak but significant homology with glucosamine-6-phosphate deaminases from the NagB family. In silico ligand screening suggested that the CggR C-terminal domain would bind preferentially bi-phosphorylated compounds, in agreement with previous studies that proposed fructuose-1,6-biphosphate (FBP) as the inducer metabolite. In vitro, FBP was the only sugar compound capable of interfering with CggR cooperative binding to DNA. FBP was also found to protect CggR against trypsin degradation at two arginine residues predicted to reside in a mobile loop forming the active site lid of the NagB enzymes. Replacement of residues predicted to interact with FBP led to mutant CggR with altered repressor activity in vivo but retaining their structural integrity and DNA binding activity in vitro. Interestingly, some of the mutant repressors responded with different specificity towards mono- and di-phospho-fructosides. Based on these results, we propose that the activity of the CggR-like repressors is controlled by a phospho-sugar binding (PSB) domain presenting structural and functional homology with NagB enzymes.
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Affiliation(s)
- Thierry Doan
- Microbiologie et Génétique Moléculaire, INRA (UMR1238)-CNRS (UMR2585)-AgroParisTech, F-78850 Thiverval-Grignon, France
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21
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Characterization of the control catabolite protein of gluconeogenic genes repressor by fluorescence cross-correlation spectroscopy and other biophysical approaches. Biophys J 2008; 95:4403-15. [PMID: 18658229 DOI: 10.1529/biophysj.108.135863] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Determination of the physical parameters underlying protein-DNA interactions is crucial for understanding the regulation of gene expression. In particular, knowledge of the stoichiometry of the complexes is a prerequisite to determining their energetics and functional molecular mechanisms. However, the experimental determination of protein-DNA complex stoichiometries remains challenging. We used fluorescence cross-correlation spectroscopy (FCCS) to investigate the interactions of the control catabolite protein of gluconeogenic genes, a key metabolic regulator in Gram-positive bacteria, with two oligonucleotides derived from its target operator sequences, gapB and pckA. According to our FCCS experiments, the stoichiometry of binding is twofold larger for the pckA target than for gapB. Correcting the FCCS data for protein self-association indicated that control catabolite protein of gluconeogenic genes forms dimeric complexes on the gapB target and tetrameric complexes on the pckA target. Analytical ultracentrifugation coupled with fluorescence anisotropy and hydrodynamic modeling allowed unambiguous confirmation of this result. The use of multiple complementary techniques to characterize these complexes should be employed wherever possible. However, there are cases in which analytical ultracentrifugation is precluded, due to protein stability, solubility, or availability, or, more obviously, when the studies are carried out in live cells. If information concerning the self-association of the protein is available, FCCS can be used for the direct and simultaneous determination of the affinity, cooperativity, and stoichiometry of protein-DNA complexes in a concentration range and conditions relevant to the regulation of these interactions.
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22
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Rezácová P, Kozísek M, Moy SF, Sieglová I, Joachimiak A, Machius M, Otwinowski Z. Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates. Mol Microbiol 2008; 69:895-910. [PMID: 18554327 DOI: 10.1111/j.1365-2958.2008.06318.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Expression of genes in the gapA operon encoding five enzymes for triose phosphate interconversion in Bacillus subtilis is negatively regulated by the Central glycolytic genes Regulator (CggR). CggR belongs to the large SorC/DeoR family of prokaryotic transcriptional regulators, characterized by an N-terminal DNA-binding domain and a large C-terminal effector-binding domain. When no glucose is present in growth media, CggR binds to its target DNA sequence and blocks the transcription of genes in the gapA operon. In the presence of glucose, binding of the known effector molecule fructose-1,6-bisphosphate abolishes this interaction. We have identified dihydroxyacetone phosphate, glucose-6-phosphate and fructose-6-phosphate as additional CggR ligands that can bind to the effector-binding site. Crystal structures of C-CggR, the C-terminal effector-binding domain of CggR, both unliganded as well as in complex with the four ligands at resolutions between 1.65 and 1.80 A reveal unique ligand-specific structural changes in the binding site that affect the dimer interface. Binding affinities of these ligands were determined by isothermal titration calorimetry. Chemical cross-linking shows that CggR oligomerization is mediated through its effector-binding domain, and that binding of the different ligands differentially affects the distribution of oligomers. Electrophoretic mobility shift assays (EMSAs) confirmed a destabilizing effect of fructose-1,6-bisphosphate on the CggR/DNA complex, and also showed similar effects for dihydroxyacetone phosphate. Our results suggest that CggR stability and function may be modulated by various effectors in a complex fashion.
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Affiliation(s)
- Pavlína Rezácová
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA.
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23
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Zorrilla S, Lillo MP, Chaix D, Margeat E, Royer CA, Declerck N. Investigating Transcriptional Regulation by Fluorescence Spectroscopy, from Traditional Methods to State-of-the-Art Single-Molecule Approaches. Ann N Y Acad Sci 2008; 1130:44-51. [DOI: 10.1196/annals.1430.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Zorrilla S, Chaix D, Ortega A, Alfonso C, Doan T, Margeat E, Rivas G, Aymerich S, Declerck N, Royer CA. Fructose-1,6-bisphosphate Acts Both as an Inducer and as a Structural Cofactor of the Central Glycolytic Genes Repressor (CggR). Biochemistry 2007; 46:14996-5008. [DOI: 10.1021/bi701805e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Silvia Zorrilla
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Denis Chaix
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Alvaro Ortega
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Carlos Alfonso
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Thierry Doan
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Emmanuel Margeat
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Germán Rivas
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Stephan Aymerich
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Nathalie Declerck
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Catherine A. Royer
- INSERM (U554), Montpellier, France, and Centre de Biochimie Structurale, CNRS (UMR5048), Université Montpellier 1, 29, rue de Navacelles, F-34090 Montpellier, France, Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon, F-78850 Thiverval-Grignon, France, and Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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25
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Transcriptomic and phenotypic analyses suggest a network between the transcriptional regulators HrcA and sigmaB in Listeria monocytogenes. Appl Environ Microbiol 2007; 73:7981-91. [PMID: 17965207 DOI: 10.1128/aem.01281-07] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Listeria monocytogenes HrcA and CtsR negatively regulate class I and III stress response genes, respectively, while sigma(B) positively regulates the transcription of class II stress response genes. To define the HrcA regulon and identify interactions between HrcA, CtsR, and sigma(B), we characterized newly generated L. monocytogenes DeltahrcA, DeltactsR DeltahrcA, and DeltahrcA DeltasigB strains, along with previously described DeltasigB, DeltactsR, and DeltactsR DeltasigB strains, using phenotypic assays (i.e., heat resistance, acid resistance, and invasion of human intestinal epithelial cells) and performed whole-genome transcriptome analysis of the DeltahrcA strain. The hrcA and sigB deletions had significant effects on heat resistance. While the hrcA deletion had no significant effect on acid resistance or invasion efficiency in Caco-2 cells, a linear regression model revealed a significant (P = 0.0493) effect of interactions between the hrcA deletion and the ctsR deletion on invasiveness. Microarray-based transcriptome analyses and promoter searches identified (i) 25 HrcA-repressed genes, including two operons (the groESL and dnaK operons, both confirmed as HrcA regulated by quantitative real-time PCR) and one gene directly repressed by HrcA, and (ii) 36 genes that showed lower transcript levels in the DeltahrcA strain and thus appear to be indirectly upregulated by HrcA. A number of genes were found to be coregulated by either HrcA and CtsR (2 genes), HrcA and sigma(B) (31 genes), or all three regulators (5 genes, e.g., gadCB). Combined with previous evidence that sigma(B) appears to directly regulate hrcA transcription, our data suggest that HrcA and sigma(B), as well as CtsR, form a regulatory network that contributes to the transcription of a number of L. monocytogenes genes.
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