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Krol E, Werel L, Essen LO, Becker A. Structural and functional diversity of bacterial cyclic nucleotide perception by CRP proteins. MICROLIFE 2023; 4:uqad024. [PMID: 37223727 PMCID: PMC10187061 DOI: 10.1093/femsml/uqad024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
Cyclic AMP (cAMP) is a ubiquitous second messenger synthesized by most living organisms. In bacteria, it plays highly diverse roles in metabolism, host colonization, motility, and many other processes important for optimal fitness. The main route of cAMP perception is through transcription factors from the diverse and versatile CRP-FNR protein superfamily. Since the discovery of the very first CRP protein CAP in Escherichia coli more than four decades ago, its homologs have been characterized in both closely related and distant bacterial species. The cAMP-mediated gene activation for carbon catabolism by a CRP protein in the absence of glucose seems to be restricted to E. coli and its close relatives. In other phyla, the regulatory targets are more diverse. In addition to cAMP, cGMP has recently been identified as a ligand of certain CRP proteins. In a CRP dimer, each of the two cyclic nucleotide molecules makes contacts with both protein subunits and effectuates a conformational change that favors DNA binding. Here, we summarize the current knowledge on structural and physiological aspects of E. coli CAP compared with other cAMP- and cGMP-activated transcription factors, and point to emerging trends in metabolic regulation related to lysine modification and membrane association of CRP proteins.
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Affiliation(s)
- Elizaveta Krol
- Department of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Laura Werel
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Lars Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Anke Becker
- Corresponding author. Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg. E-mail:
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2
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Gárate F, Dokas S, Lanfranco MF, Canavan C, Wang I, Correia JJ, Maillard RA. cAMP is an allosteric modulator of DNA-binding specificity in the cAMP receptor protein from Mycobacterium tuberculosis. J Biol Chem 2021; 296:100480. [PMID: 33640453 PMCID: PMC8026907 DOI: 10.1016/j.jbc.2021.100480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 11/28/2022] Open
Abstract
Allosteric proteins with multiple subunits and ligand-binding sites are central in regulating biological signals. The cAMP receptor protein from Mycobacterium tuberculosis (CRPMTB) is a global regulator of transcription composed of two identical subunits, each one harboring structurally conserved cAMP- and DNA-binding sites. The mechanisms by which these four binding sites are allosterically coupled in CRPMTB remain unclear. Here, we investigate the binding mechanism between CRPMTB and cAMP, and the linkage between cAMP and DNA interactions. Using calorimetric and fluorescence-based assays, we find that cAMP binding is entropically driven and displays negative cooperativity. Fluorescence anisotropy experiments show that apo-CRPMTB forms high-order CRPMTB–DNA oligomers through interactions with nonspecific DNA sequences or preformed CRPMTB–DNA complexes. Moreover, we find that cAMP prevents and reverses the formation of CRPMTB–DNA oligomers, reduces the affinity of CRPMTB for nonspecific DNA sequences, and stabilizes a 1-to-1 CRPMTB–DNA complex, but does not increase the affinity for DNA like in the canonical CRP from Escherichia coli (CRPEcoli). DNA-binding assays as a function of cAMP concentration indicate that one cAMP molecule per homodimer dissociates high-order CRPMTB–DNA oligomers into 1-to-1 complexes. These cAMP-mediated allosteric effects are lost in the double-mutant L47P/E178K found in CRP from Mycobacterium bovis Bacille Calmette-Guérin (CRPBCG). The functional behavior, thermodynamic stability, and dimerization constant of CRPBCG are not due to additive effects of L47P and E178K, indicating long-range interactions between these two sites. Altogether, we provide a previously undescribed archetype of cAMP-mediated allosteric regulation that differs from CRPEcoli, illustrating that structural homology does not imply allosteric homology.
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Affiliation(s)
- Fernanda Gárate
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Stephen Dokas
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Maria Fe Lanfranco
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Clare Canavan
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Irina Wang
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - John J Correia
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Rodrigo A Maillard
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA.
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3
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Bauer JA, Pavlović J, Bauerová-Hlinková V. Normal Mode Analysis as a Routine Part of a Structural Investigation. Molecules 2019; 24:molecules24183293. [PMID: 31510014 PMCID: PMC6767145 DOI: 10.3390/molecules24183293] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance. NMA is probably the least computationally expensive method for studying the dynamics of macromolecules, and advances in computer technology and algorithms for calculating normal modes over the last 20 years have made it nearly trivial for all but the largest systems. Despite this, it is still uncommon for NMA to be used as a component of the analysis of a structural study. In this review, we will describe NMA, outline its advantages and limitations, explain what can and cannot be learned from it, and address some criticisms and concerns that have been voiced about it. We will then review the most commonly used techniques for reducing the computational cost of this method and identify the web services making use of these methods. We will illustrate several of their possible uses with recent examples from the literature. We conclude by recommending that NMA become one of the standard tools employed in any structural study.
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Affiliation(s)
- Jacob A Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia.
| | - Jelena Pavlović
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Vladena Bauerová-Hlinková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
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4
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Ranganathan S, Cheung J, Cassidy M, Ginter C, Pata JD, McDonough KA. Novel structural features drive DNA binding properties of Cmr, a CRP family protein in TB complex mycobacteria. Nucleic Acids Res 2019; 46:403-420. [PMID: 29165665 PMCID: PMC5758884 DOI: 10.1093/nar/gkx1148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 11/13/2017] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRPMt (Rv3676). Prior studies identified distinct chromosomal binding profiles for each TF despite their recognizing overlapping DNA motifs. The present study shows that Cmr binding specificity is determined by discriminator nucleotides at motif positions 4 and 13. X-ray crystallography and targeted mutational analyses identified an arginine-rich loop that expands Cmr’s DNA interactions beyond the classical helix-turn-helix contacts common to all CRP/FNR family members and facilitates binding to imperfect DNA sequences. Cmr binding to DNA results in a pronounced asymmetric bending of the DNA and its high level of cooperativity is consistent with DNA-facilitated dimerization. A unique N-terminal extension inserts between the DNA binding and dimerization domains, partially occluding the site where the canonical cAMP binding pocket is found. However, an unstructured region of this N-terminus may help modulate Cmr activity in response to cellular signals. Cmr’s multiple levels of DNA interaction likely enhance its ability to integrate diverse gene regulatory signals, while its novel structural features establish Cmr as an atypical CRP/FNR family member.
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Affiliation(s)
- Sridevi Ranganathan
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | - Jonah Cheung
- New York Structural Biology Center, New York, NY 10027, USA
| | | | | | - Janice D Pata
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA.,Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA.,Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
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5
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Frendorf PO, Lauritsen I, Sekowska A, Danchin A, Nørholm MH. Mutations in the Global Transcription Factor CRP/CAP: Insights from Experimental Evolution and Deep Sequencing. Comput Struct Biotechnol J 2019; 17:730-736. [PMID: 31303977 PMCID: PMC6603298 DOI: 10.1016/j.csbj.2019.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/22/2019] [Accepted: 05/26/2019] [Indexed: 11/17/2022] Open
Abstract
The Escherichia coli cyclic AMP receptor protein (CRP or catabolite activator protein, CAP) provides a textbook example of bacterial transcriptional regulation and is one of the best studied transcription factors in biology. For almost five decades a large number of mutants, evolved in vivo or engineered in vitro, have shed light on the molecular structure and mechanism of CRP. Here, we review previous work, providing an overview of studies describing the isolation of CRP mutants. Furthermore, we present new data on deep sequencing of different bacterial populations that have evolved under selective pressure that strongly favors mutations in the crp locus. Our new approach identifies more than 100 new CRP mutations and paves the way for a deeper understanding of this fascinating bacterial master regulator.
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Affiliation(s)
- Pernille Ott Frendorf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, DK-2800 Kgs. Lyngby, Denmark
| | - Ida Lauritsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, DK-2800 Kgs. Lyngby, Denmark
| | - Agnieszka Sekowska
- Institut de Cardiométabolisme et Nutrition, CHU Pitié-Salpêtrière, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Antoine Danchin
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014 Paris, France
| | - Morten H.H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, DK-2800 Kgs. Lyngby, Denmark
- Corresponding author.
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6
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Abstract
All cells must adapt to changing conditions, and many use cyclic AMP (cAMP) as a second messenger to sense and respond to fluctuations in their environment. cAMP is made by adenylyl cyclases (ACs), and mycobacteria have an unusually large number of biochemically distinct ACs. cAMP is important for gene regulation in mycobacteria, and the ability to secrete cAMP into host macrophages during infection contributes to Mycobacterium tuberculosis pathogenesis. This article discusses the many roles of cAMP in mycobacteria and reviews what is known about the factors that contribute to production, destruction, and utilization of this important signal molecule. Special emphasis is placed on cAMP signaling in M. tuberculosis complex bacteria and its importance to M. tuberculosis during host infection.
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7
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Sandhu P, Akhter Y. The drug binding sites and transport mechanism of the RND pumps from Mycobacterium tuberculosis: Insights from molecular dynamics simulations. Arch Biochem Biophys 2016; 592:38-49. [PMID: 26792538 DOI: 10.1016/j.abb.2016.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/05/2016] [Accepted: 01/08/2016] [Indexed: 12/30/2022]
Abstract
RND permease superfamily drug efflux pumps are involved in multidrug transport and are attractive to study them for therapeutic purpose. In previous work we have classified 14 members of MmpL proteins belong to RND superfamily from Mycobacterium tuberculosis (Mtb) within its families [Sandhu P. and Akhter Y., 2015. Int. J. Med. Microbiol., 305:413-423]. In this study, structures of these proteins are homology modelled. The drug binding sites and channels are identified using local micro-stereochemistry and charge densities. Potential transport mechanism based on differential structural behaviour in the absence and on the binding of drug molecules is explained using the molecular dynamics simulation results. Our studies show two potential drug binding sites positioned at opposite ends of the transport tunnel leading from cytoplasmic to the periplasmic space across MmpL5 trimer. The drug binding have effects on the structural conformation of the protein leading to molecular-scale peristaltic movements. The free binding energy calculations reveal that the subsequent binding events are interdependent and may have implications on transport mechanism. Two drug binding sites and a continuous channel in the RND pump have been reported. The proposed ligand binding mechanism shows peristaltic movements in the channel leading to the drug efflux. This study would be helpful in understanding the molecular basis of drugs resistance in Mtb.
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Affiliation(s)
- Padmani Sandhu
- School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Yusuf Akhter
- School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India.
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8
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Aung HL, Dixon LL, Smith LJ, Sweeney NP, Robson JR, Berney M, Buxton RS, Green J, Cook GM. Novel regulatory roles of cAMP receptor proteins in fast-growing environmental mycobacteria. MICROBIOLOGY-SGM 2014; 161:648-61. [PMID: 25525207 DOI: 10.1099/mic.0.000015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Mycobacterium smegmatis is a fast-growing, saprophytic, mycobacterial species that contains two cAMP-receptor protein (CRP) homologues designated herein as Crp1 and Crp2. Phylogenetic analysis suggests that Crp1 (Msmeg_0539) is uniquely present in fast-growing environmental mycobacteria, whereas Crp2 (Msmeg_6189) occurs in both fast- and slow-growing species. A crp1 mutant of M. smegmatis was readily obtained, but crp2 could not be deleted, suggesting it was essential for growth. A total of 239 genes were differentially regulated in response to crp1 deletion (loss of function), including genes coding for mycobacterial energy generation, solute transport and catabolism of carbon sources. To assess the role of Crp2 in M. smegmatis, the crp2 gene was overexpressed (gain of function) and transcriptional profiling studies revealed that 58 genes were differentially regulated. Identification of the CRP promoter consensus in M. smegmatis showed that both Crp1 and Crp2 recognized the same consensus sequence (TGTGN8CACA). Comparison of the Crp1- and Crp2-regulated genes revealed distinct but overlapping regulons with 11 genes in common, including those of the succinate dehydrogenase operon (MSMEG_0417-0420, sdh1). Expression of the sdh1 operon was negatively regulated by Crp1 and positively regulated by Crp2. Electrophoretic mobility shift assays with purified Crp1 and Crp2 demonstrated that Crp1 binding to the sdh1 promoter was cAMP-independent whereas Crp2 binding was cAMP-dependent. These data suggest that Crp1 and Crp2 respond to distinct signalling pathways in M. smegmatis to coordinate gene expression in response to carbon and energy supply.
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Affiliation(s)
- Htin Lin Aung
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Laura L Dixon
- The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Laura J Smith
- The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Nathan P Sweeney
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Jennifer R Robson
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Michael Berney
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Roger S Buxton
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Jeffrey Green
- The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
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9
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Townsend PD, Jungwirth B, Pojer F, Bußmann M, Money VA, Cole ST, Pühler A, Tauch A, Bott M, Cann MJ, Pohl E. The crystal structures of apo and cAMP-bound GlxR from Corynebacterium glutamicum reveal structural and dynamic changes upon cAMP binding in CRP/FNR family transcription factors. PLoS One 2014; 9:e113265. [PMID: 25469635 PMCID: PMC4254451 DOI: 10.1371/journal.pone.0113265] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/16/2014] [Indexed: 12/01/2022] Open
Abstract
The cyclic AMP-dependent transcriptional regulator GlxR from Corynebacterium glutamicum is a member of the super-family of CRP/FNR (cyclic AMP receptor protein/fumarate and nitrate reduction regulator) transcriptional regulators that play central roles in bacterial metabolic regulatory networks. In C. glutamicum, which is widely used for the industrial production of amino acids and serves as a non-pathogenic model organism for members of the Corynebacteriales including Mycobacterium tuberculosis, the GlxR homodimer controls the transcription of a large number of genes involved in carbon metabolism. GlxR therefore represents a key target for understanding the regulation and coordination of C. glutamicum metabolism. Here we investigate cylic AMP and DNA binding of GlxR from C. glutamicum and describe the crystal structures of apo GlxR determined at a resolution of 2.5 Å, and two crystal forms of holo GlxR at resolutions of 2.38 and 1.82 Å, respectively. The detailed structural analysis and comparison of GlxR with CRP reveals that the protein undergoes a distinctive conformational change upon cyclic AMP binding leading to a dimer structure more compatible to DNA-binding. As the two binding sites in the GlxR homodimer are structurally identical dynamic changes upon binding of the first ligand are responsible for the allosteric behavior. The results presented here show how dynamic and structural changes in GlxR lead to optimization of orientation and distance of its two DNA-binding helices for optimal DNA recognition.
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Affiliation(s)
- Philip D. Townsend
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Britta Jungwirth
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Florence Pojer
- Global Health Institute, Protein Crystallography Core Facility, Ecole Poytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael Bußmann
- Institute of Bio- and Geosciences, IBG-1:Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Victoria A. Money
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Stewart T. Cole
- Global Health Institute, Protein Crystallography Core Facility, Ecole Poytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Andreas Tauch
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1:Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin J. Cann
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Ehmke Pohl
- School of Biological and Biomedical Sciences & Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- * E-mail:
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10
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Sharma R, Zaveri A, Gopalakrishnapai J, Srinath T, Thiruneelakantan S, Varshney U, Visweswariah SS. Paralogous cAMP receptor proteins in Mycobacterium smegmatis show biochemical and functional divergence. Biochemistry 2014; 53:7765-76. [PMID: 25434596 DOI: 10.1021/bi500924v] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyclic AMP receptor protein (CRP) family of transcription factors consists of global regulators of bacterial gene expression. Here, we identify two paralogous CRPs in the genome of Mycobacterium smegmatis that have 78% identical sequences and characterize them biochemically and functionally. The two proteins (MSMEG_0539 and MSMEG_6189) show differences in cAMP binding affinity, trypsin sensitivity, and binding to a CRP site that we have identified upstream of the msmeg_3781 gene. MSMEG_6189 binds to the CRP site readily in the absence of cAMP, while MSMEG_0539 binds in the presence of cAMP, albeit weakly. msmeg_6189 appears to be an essential gene, while the Δmsmeg_0539 strain was readily obtained. Using promoter-reporter constructs, we show that msmeg_3781 is regulated by CRP binding, and its transcription is repressed by MSMEG_6189. Our results are the first to characterize two paralogous and functional CRPs in a single bacterial genome. This gene duplication event has subsequently led to the evolution of two proteins whose biochemical differences translate to differential gene regulation, thus catering to the specific needs of the organism.
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Affiliation(s)
- Ritu Sharma
- Department of Molecular Reproduction, Development and Genetics and ‡Department of Microbiology and Cell Biology, Indian Institute of Science , Bangalore 560012, India
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11
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Lee HN, Lee NO, Han SJ, Ko IJ, Oh JI. Regulation of the ahpC gene encoding alkyl hydroperoxide reductase in Mycobacterium smegmatis. PLoS One 2014; 9:e111680. [PMID: 25365321 PMCID: PMC4218801 DOI: 10.1371/journal.pone.0111680] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 09/29/2014] [Indexed: 12/04/2022] Open
Abstract
The ahpC (MSMEG_4891) gene encodes alkyl hydroperoxide reductase C in Mycobacterium smegmatis mc2155 and its expression is induced under oxidative stress conditions. Two well-defined inverted repeat sequences (IR1 and IR2) were identified in the upstream region of ahpC. Using a crp (cAMP receptor protein: MSMEG_6189) mutant and in vitro DNA-binding assay, it was demonstrated that the IR1 sequence serves as a Crp-binding site and that Crp functions as an activator in the regulation of ahpC expression. The expression level of ahpC was shown to be proportional to intracellular cAMP levels. Intracellular levels of cAMP were increased in M. smegmatis, when it was treated with oxidative stress inducers. The IR2 sequence is very similar to the known consensus sequence of FurA-binding sites and involved in the negative regulation of ahpC expression. Taken together, these results suggest that the induction of ahpC expression under oxidative stress conditions probably results from a combinatory effect of both inactivation of FurA by oxidative stress and activation of Crp in response to increased levels of cAMP.
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Affiliation(s)
- Ha-Na Lee
- Department of Microbiology, Pusan National University, Busan, Korea
| | - Na-On Lee
- Department of Microbiology, Pusan National University, Busan, Korea
| | - Seung J. Han
- Department of Microbiology and Institute for Immunology and Immunological Diseases, Yonsei University, Seoul, Korea
| | - In-Jeong Ko
- Korea Science Academy of KAIST, Busan, Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan, Korea
- * E-mail:
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12
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Seok SH, Im H, Won HS, Seo MD, Lee YS, Yoon HJ, Cha MJ, Park JY, Lee BJ. Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers. ACTA ACUST UNITED AC 2014; 70:1726-42. [PMID: 24914983 DOI: 10.1107/s139900471400724x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/01/2014] [Indexed: 11/10/2022]
Abstract
The prokaryotic global transcription factor CRP has been considered to be an ideal model for in-depth study of both the allostery of the protein and the differential utilization of the homologous cyclic nucleotide second messengers cAMP and cGMP. Here, atomic details from the crystal structures of two inactive CRP species, an apo form and a cGMP-bound form, in comparison with a known active conformation, the cAMP-CRP complex, provide macroscopic and microscopic insights into CRP allostery, which is coupled to specific discrimination between the two effectors. The cAMP-induced conformational transition, including dynamic fluctuations, can be driven by the fundamental folding forces that cause water-soluble globular proteins to construct an optimized hydrophobic core, including secondary-structure formation. The observed conformational asymmetries underlie a negative cooperativity in the sequential binding of cyclic nucleotides and a stepwise manner of binding with discrimination between the effector molecules. Additionally, the finding that cGMP, which is specifically recognized in a syn conformation, induces an inhibitory conformational change, rather than a null effect, on CRP supports the intriguing possibility that cGMP signalling could be widely utilized in prokaryotes, including in aggressive inhibition of CRP-like proteins.
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Affiliation(s)
- Seung-Hyeon Seok
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hookang Im
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyung-Sik Won
- Department of Biotechnology, RIBHS and RIID, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, Republic of Korea
| | - Min-Duk Seo
- College of Pharmacy, Ajou University, Suwon, Kyeonggi 443-749, Republic of Korea
| | - Yoo-Sup Lee
- Department of Biotechnology, RIBHS and RIID, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Min-Jeong Cha
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jin-Young Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
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13
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Green J, Stapleton MR, Smith LJ, Artymiuk PJ, Kahramanoglou C, Hunt DM, Buxton RS. Cyclic-AMP and bacterial cyclic-AMP receptor proteins revisited: adaptation for different ecological niches. Curr Opin Microbiol 2014; 18:1-7. [PMID: 24509484 PMCID: PMC4005916 DOI: 10.1016/j.mib.2014.01.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/08/2014] [Indexed: 11/25/2022]
Abstract
E. coli cyclic-AMP receptor protein (CRP) is a paradigm of gene regulation. Comparison of CRPs reveals differences in their affinity of cAMP. A range of dependency on cAMP for DNA-binding exists. CRPs have adapted to function in the specific niches occupied by the bacteria.
Escherichia coli cyclic-AMP receptor protein (CRP) represents one of the paradigms of bacterial gene regulation. Yet despite decades of intensive study, new information continues to emerge that prompts reassessment of this classic regulatory system. Moreover, in recent years CRPs from several other bacterial species have been characterized, allowing the general applicability of the CRP paradigm to be tested. Here the properties of the E. coli, Mycobacterium tuberculosis and Pseudomonas putida CRPs are considered in the context of the ecological niches occupied by these bacteria. It appears that the cyclic-AMP-CRP regulatory system has been adapted to respond to distinct external and internal inputs across a broad sensitivity range that is, at least in part, determined by bacterial lifestyles.
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Affiliation(s)
- Jeffrey Green
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Melanie R Stapleton
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Laura J Smith
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Peter J Artymiuk
- The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Christina Kahramanoglou
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Debbie M Hunt
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Roger S Buxton
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
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Basak S, Geng H, Jiang R. Rewiring global regulator cAMP receptor protein (CRP) to improve E. coli tolerance towards low pH. J Biotechnol 2014; 173:68-75. [PMID: 24452100 DOI: 10.1016/j.jbiotec.2014.01.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/07/2014] [Accepted: 01/11/2014] [Indexed: 11/19/2022]
Abstract
Bioprocesses such as production of organic acids or acid hydrolysis of bioresources during biofuel production often suffer limitations due to microbial sensitivity under acidic conditions. Approaches for improving the acid tolerance of these microbes have mainly focused on using metabolic engineering tools. Here, we tried to improve strain acidic tolerance from its transcription level, i.e. we adopted error-prone PCR method to engineer global regulator cAMP receptor protein (CRP) of Escherichia coli to improve its performance at low pH. The best mutant AcM1 was identified from random mutagenesis libraries based on its growth performance. AcM1 almost doubled (0.113h(-1)) the growth rate of the control (0.062h(-1)) at pH 4.24. It also demonstrated better thermotolerance than the control at 48°C, whose growth was completely inhibited at this temperature. Quantitative real time reverse transcription PCR results revealed a stress response overlap among low pH stress-, oxidative stress- and osmotic stress-related genes. The chief enzyme responsible for cell acid tolerance, glutamate decarboxylase, demonstrated over twofold activity in AcM1 compared to the control. Differential binding properties of AcM1 mutant CRP with Class-I, II, and III CRP-dependent promoters suggested that modifications to native CRP may lead to transcription profile changes. Hence, we believe that transcriptional engineering of global regulator CRP can provide a new strain engineering alternative for E. coli.
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Affiliation(s)
- Souvik Basak
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Hefang Geng
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Rongrong Jiang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore.
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15
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Huang J, Wu T, Guo Z, Lou T, Yu S, Gong W, Ji C. Crystallization and preliminary X-ray diffraction analysis of D53H mutant Escherichia coli cAMP receptor protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1436-9. [PMID: 24316848 DOI: 10.1107/s174430911303145x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 11/18/2013] [Indexed: 11/10/2022]
Abstract
The Escherichia coli cyclic AMP receptor protein (CRP) is a prokaryotic global transcription activator protein that controls the expression of many different genes. Wild-type CRP can bind to special DNA sequences in the presence of cAMP. The substitution of Asp53 by His results in the CRP* phenotype, which does not require exogenous cAMP. In the present study, the D53H CRP mutant was overexpressed, purified and crystallized. cAMP-free D53H CRP crystals were obtained and diffracted to a resolution of 2.9 Å. Based on the systematic absences of the crystals, the space group is likely to be P2(1)2(1)2(1), with unit-cell parameters a = 76.66, b = 152.14, c = 176.11 Å. The asymmetric unit was confirmed to contain four protein dimers, with a Matthews coefficient of 2.71 Å(3) Da(-1) and a solvent content of 54.68%.
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Affiliation(s)
- Jing Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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Crawford R, Erben CM, Periz J, Hall LM, Brown T, Turberfield AJ, Kapanidis AN. Non-covalent Single Transcription Factor Encapsulation Inside a DNA Cage. Angew Chem Int Ed Engl 2013; 52:2284-8. [DOI: 10.1002/anie.201207914] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/27/2012] [Indexed: 12/20/2022]
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17
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Crawford R, Erben CM, Periz J, Hall LM, Brown T, Turberfield AJ, Kapanidis AN. Non-covalent Single Transcription Factor Encapsulation Inside a DNA Cage. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207914] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Basak S, Jiang R. Enhancing E. coli tolerance towards oxidative stress via engineering its global regulator cAMP receptor protein (CRP). PLoS One 2012; 7:e51179. [PMID: 23251448 PMCID: PMC3522674 DOI: 10.1371/journal.pone.0051179] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/30/2012] [Indexed: 12/11/2022] Open
Abstract
Oxidative damage to microbial hosts often occurs under stressful conditions during bioprocessing. Classical strain engineering approaches are usually both time-consuming and labor intensive. Here, we aim to improve E. coli performance under oxidative stress via engineering its global regulator cAMP receptor protein (CRP), which can directly or indirectly regulate redox-sensing regulators SoxR and OxyR, and other ~400 genes in E. coli. Error-prone PCR technique was employed to introduce modifications to CRP, and three mutants (OM1~OM3) were identified with improved tolerance via H(2)O(2) enrichment selection. The best mutant OM3 could grow in 12 mM H(2)O(2) with the growth rate of 0.6 h(-1), whereas the growth of wild type was completely inhibited at this H(2)O(2) concentration. OM3 also elicited enhanced thermotolerance at 48°C as well as resistance against cumene hydroperoxide. The investigation about intracellular reactive oxygen species (ROS), which determines cell viability, indicated that the accumulation of ROS in OM3 was always lower than in WT with or without H(2)O(2) treatment. Genome-wide DNA microarray analysis has shown not only CRP-regulated genes have demonstrated great transcriptional level changes (up to 8.9-fold), but also RpoS- and OxyR-regulated genes (up to 7.7-fold). qRT-PCR data and enzyme activity assay suggested that catalase (katE) could be a major antioxidant enzyme in OM3 instead of alkyl hydroperoxide reductase or superoxide dismutase. To our knowledge, this is the first work on improving E. coli oxidative stress resistance by reframing its transcription machinery through its native global regulator. The positive outcome of this approach may suggest that engineering CRP can be successfully implemented as an efficient strain engineering alternative for E. coli.
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Affiliation(s)
- Souvik Basak
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rongrong Jiang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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19
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Hegde SR, Rajasingh H, Das C, Mande SS, Mande SC. Understanding communication signals during mycobacterial latency through predicted genome-wide protein interactions and boolean modeling. PLoS One 2012; 7:e33893. [PMID: 22448278 PMCID: PMC3309013 DOI: 10.1371/journal.pone.0033893] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 02/18/2012] [Indexed: 12/18/2022] Open
Abstract
About 90% of the people infected with Mycobacterium tuberculosis carry latent bacteria that are believed to get activated upon immune suppression. One of the fundamental challenges in the control of tuberculosis is therefore to understand molecular mechanisms involved in the onset of latency and/or reactivation. We have attempted to address this problem at the systems level by a combination of predicted functional protein:protein interactions, integration of functional interactions with large scale gene expression studies, predicted transcription regulatory network and finally simulations with a boolean model of the network. Initially a prediction for genome-wide protein functional linkages was obtained based on genome-context methods using a Support Vector Machine. This set of protein functional linkages along with gene expression data of the available models of latency was employed to identify proteins involved in mediating switch signals during dormancy. We show that genes that are up and down regulated during dormancy are not only coordinately regulated under dormancy-like conditions but also under a variety of other experimental conditions. Their synchronized regulation indicates that they form a tightly regulated gene cluster and might form a latency-regulon. Conservation of these genes across bacterial species suggests a unique evolutionary history that might be associated with M. tuberculosis dormancy. Finally, simulations with a boolean model based on the regulatory network with logical relationships derived from gene expression data reveals a bistable switch suggesting alternating latent and actively growing states. Our analysis based on the interaction network therefore reveals a potential model of M. tuberculosis latency.
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Affiliation(s)
- Shubhada R. Hegde
- Structural Biology Laboratory, Centre for DNA Fingerprinting and Diagnostics, Gruhakalpa, Nampally, Hyderabad, India
| | - Hannah Rajasingh
- Bio-Sciences R & D Division, TCS Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Chandrani Das
- Structural Biology Laboratory, Centre for DNA Fingerprinting and Diagnostics, Gruhakalpa, Nampally, Hyderabad, India
- Bio-Sciences R & D Division, TCS Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Sharmila S. Mande
- Bio-Sciences R & D Division, TCS Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Shekhar C. Mande
- Structural Biology Laboratory, Centre for DNA Fingerprinting and Diagnostics, Gruhakalpa, Nampally, Hyderabad, India
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Bai G, Schaak DD, Smith EA, McDonough KA. Dysregulation of serine biosynthesis contributes to the growth defect of a Mycobacterium tuberculosis crp mutant. Mol Microbiol 2011; 82:180-98. [PMID: 21902733 DOI: 10.1111/j.1365-2958.2011.07806.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis CRP(Mt), encoded by Rv3676 (crp), is a CRP-like transcription factor that binds with the serC-Rv0885 intergenic region. In the present study, we evaluated CRP(Mt) 's regulation of serC and Rv0885 in M. tuberculosis and M. bovis BCG, using site-specific mutagenesis, promoter fusions and reverse-transcriptase PCR (RT-PCR). The CRP(Mt) binding site was required for full expression of serC and Rv0885, and expression of both genes was reduced in M. tuberculosis and M. bovis BCG crp mutants. These data show that CRP(Mt) binding directly activates both serC and Rv0885 expression. M. tuberculosis serC restored the ability of an Escherichia coli serC mutant to grow in serine-dropout medium, demonstrating that M. tuberculosis serC encodes a phosphoserine aminotransferase. Serine supplementation, or overexpression of serC, accelerated the growth of M. tuberculosis and M. bovis BCG crp mutants in mycomedium, but not within macrophages. These results establish a role for CRP(Mt) in the regulation of amino acid biosynthesis, and show that reduced serine production contributes to the slow-growth phenotype of M. tuberculosis and M. bovis BCG crp mutants in vitro. Restoration of serine biosynthesis by serC expression will facilitate identification of additional CRP(Mt)-regulated factors required by M. tuberculosis during macrophage and host infection.
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Affiliation(s)
- Guangchun Bai
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
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Arora A, Chandra NR, Das A, Gopal B, Mande SC, Prakash B, Ramachandran R, Sankaranarayanan R, Sekar K, Suguna K, Tyagi AK, Vijayan M. Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts. Tuberculosis (Edinb) 2011; 91:456-68. [DOI: 10.1016/j.tube.2011.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 03/15/2011] [Accepted: 03/16/2011] [Indexed: 01/23/2023]
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22
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Bai G, Knapp GS, McDonough KA. Cyclic AMP signalling in mycobacteria: redirecting the conversation with a common currency. Cell Microbiol 2010; 13:349-58. [PMID: 21199259 DOI: 10.1111/j.1462-5822.2010.01562.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
cAMP is an ancient second messenger, and is used by many organisms to regulate a wide range of cellular functions. Mycobacterium tuberculosis complex bacteria are exceptional in that they have genes for at least 15 biochemically distinct adenylyl cyclases, the enzymes that generate cAMP. cAMP-associated gene regulation within tubercle bacilli is required for their virulence, and secretion of cAMP produced by M. tuberculosis bacteria into host macrophages disrupts the host's immune response to infection. In this review, we discuss recent advances in our understanding of the means by which cAMP levels are controlled within mycobacteria, the importance of cAMP to M. tuberculosis during host infection, and the role of cAMP in mycobacterial gene regulation. Understanding the myriad aspects of cAMP signalling in tubercle bacilli will establish new paradigms for cAMP signalling, and may contribute to new approaches for prevention and/or treatment of tuberculosis disease.
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Affiliation(s)
- Guangchun Bai
- Wadsworth Center, New York State Department of Health, Albany, NY 12201-2002, USA
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23
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Jensen F, Palmer DS. Harmonic Vibrational Analysis in Delocalized Internal Coordinates. J Chem Theory Comput 2010; 7:223-30. [DOI: 10.1021/ct100463a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frank Jensen
- Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark
| | - David S. Palmer
- Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark
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