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Shimizu T, Huang D, Yan F, Stranava M, Bartosova M, Fojtíková V, Martínková M. Gaseous O2, NO, and CO in signal transduction: structure and function relationships of heme-based gas sensors and heme-redox sensors. Chem Rev 2015; 115:6491-533. [PMID: 26021768 DOI: 10.1021/acs.chemrev.5b00018] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Toru Shimizu
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
- §Research Center for Compact Chemical System, National Institute of Advanced Industrial Science and Technology (AIST), Sendai 983-8551, Japan
| | - Dongyang Huang
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Fang Yan
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Martin Stranava
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Martina Bartosova
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Veronika Fojtíková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Markéta Martínková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
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52
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Erman JE, Chinchilla D, Studer J, Vitello LB. Binding of imidazole, 1-methylimidazole and 4-nitroimidazole to yeast cytochrome c peroxidase (CcP) and the distal histidine mutant, CcP(H52L). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:869-81. [PMID: 25907133 DOI: 10.1016/j.bbapap.2015.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 04/05/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
Abstract
Imidazole, 1-methylimidazole and 4-nitroimidazole bind to yeast cytochrome c peroxidase (yCcP) with apparent equilibrium dissociation constants (KD(app)) of 3.3±0.4, 0.85±0.11, and ~0.2M, respectively, at pH7. This is the weakest imidazole binding to a heme protein reported to date and it is about 120 times weaker than imidazole binding to metmyoglobin. Spectroscopic changes associated with imidazole and 1-methylimidazole binding to yCcP suggest partial ionization of bound imidazole to imidazolate. The pKa for ionization of bound imidazole is estimated to be 7.4±0.2, about 7 units lower than that of free imidazole and about 3 units lower than imidazole bound to metmyoglobin. Equilibrium binding of imidazole to CcP(H52L) is biphasic with low- and high-affinity phases having KD(app) values of 9.5±4.5 and 0.13±0.04M, respectively. CcP(H52L) binding of 1-methylimidazole is monophasic with an affinity similar to those of yCcP and rCcP. Binding of 1-methylimidazole to rCcP is associated with two kinetic phases, the initial binding complete within 10s, followed by a process that is consistent with 1-methylimidazole binding to a cavity created by movement of Trp-191 from the interior of the protein to the surface. Both the equilibrium binding and kinetics of 1-methylimidazole binding to yCcP are pH dependent. yCcP has a four-fold increase in 1-methylimidazole binding affinity on decreasing the pH from 7.5 to 4.0, an observation that is unique among the many studies on binding of imidazole and imidazole derivatives to heme proteins.
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Affiliation(s)
- James E Erman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Diana Chinchilla
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Jason Studer
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Lidia B Vitello
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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53
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Lu J, Wu R, Adkins JN, Joachimiak A, Glover JNM. Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability. Biochemistry 2014; 53:5810-9. [PMID: 25148268 PMCID: PMC4165441 DOI: 10.1021/bi500244m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
In the F family of conjugative plasmids,
TraJ is an essential transcriptional
activator of the tra operon that encodes most of
the proteins required for conjugation. Here we report for the first
time the X-ray crystal structures of the TraJ N-terminal domains from
the prototypic F plasmid (TraJF11–130) and from the Salmonella virulence
plasmid pSLT (TraJpSLT1–128). Both structures
contain similar Per-ARNT-Sim (PAS) folds, which further homodimerize
through the N-terminal helix and the structurally conserved β-sheet
of the PAS fold from each protomer. Mutational analysis reveals that
the observed dimeric interface is critical for TraJF transcriptional
activation, indicating that dimerization of TraJ is required for its in vivo function. TraJ is specific in activating its cognate tra operon promoter; however, heterologous PAS domains from
pSLT and R100 TraJ can functionally replace the TraJF PAS
domain, suggesting that the allelic specificity of TraJ is solely
mediated by the region C-terminal to the PAS domain.
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Affiliation(s)
- Jun Lu
- Department of Biochemistry, University of Alberta , Edmonton, Alberta T6G 2H7, Canada
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54
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Abstract
The haem-based sensors are chimeric multi-domain proteins responsible for the cellular adaptive responses to environmental changes. The signal transduction is mediated by the sensing capability of the haem-binding domain, which transmits a usable signal to the cognate transmitter domain, responsible for providing the adequate answer. Four major families of haem-based sensors can be recognized, depending on the nature of the haem-binding domain: (i) the haem-binding PAS domain, (ii) the CO-sensitive carbon monoxide oxidation activator, (iii) the haem NO-binding domain, and (iv) the globin-coupled sensors. The functional classification of the haem-binding sensors is based on the activity of the transmitter domain and, traditionally, comprises: (i) sensors with aerotactic function; (ii) sensors with gene-regulating function; and (iii) sensors with unknown function. We have implemented this classification with newly identified proteins, that is, the Streptomyces avermitilis and Frankia sp. that present a C-terminal-truncated globin fused to an N-terminal cofactor-free monooxygenase, the structural-related class of non-haem globins in Bacillus subtilis, Moorella thermoacetica, and Bacillus anthracis, and a haemerythrin-coupled diguanylate cyclase in Vibrio cholerae. This review summarizes the structures, the functions, and the structure-function relationships known to date on this broad protein family. We also propose unresolved questions and new possible research approaches.
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55
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Taabazuing CY, Hangasky JA, Knapp MJ. Oxygen sensing strategies in mammals and bacteria. J Inorg Biochem 2014; 133:63-72. [PMID: 24468676 PMCID: PMC4097052 DOI: 10.1016/j.jinorgbio.2013.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/23/2013] [Accepted: 12/24/2013] [Indexed: 12/21/2022]
Abstract
The ability to sense and adapt to changes in pO2 is crucial for basic metabolism in most organisms, leading to elaborate pathways for sensing hypoxia (low pO2). This review focuses on the mechanisms utilized by mammals and bacteria to sense hypoxia. While responses to acute hypoxia in mammalian tissues lead to altered vascular tension, the molecular mechanism of signal transduction is not well understood. In contrast, chronic hypoxia evokes cellular responses that lead to transcriptional changes mediated by the hypoxia inducible factor (HIF), which is directly controlled by post-translational hydroxylation of HIF by the non-heme Fe(II)/αKG-dependent enzymes FIH and PHD2. Research on PHD2 and FIH is focused on developing inhibitors and understanding the links between HIF binding and the O2 reaction in these enzymes. Sulfur speciation is a putative mechanism for acute O2-sensing, with special focus on the role of H2S. This sulfur-centered model is discussed, as are some of the directions for further refinement of this model. In contrast to mammals, bacterial O2-sensing relies on protein cofactors that either bind O2 or oxidatively decompose. The sensing modality for bacterial O2-sensors is either via altered DNA binding affinity of the sensory protein, or else due to the actions of a two-component signaling cascade. Emerging data suggests that proteins containing a hemerythrin-domain, such as FBXL5, may serve to connect iron sensing to O2-sensing in both bacteria and humans. As specific molecular machinery becomes identified, these hypoxia sensing pathways present therapeutic targets for diseases including ischemia, cancer, or bacterial infection.
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Affiliation(s)
| | - John A Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
| | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States.
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56
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Roy J, Sen Santara S, Bose M, Mukherjee S, Saha R, Adak S. The ferrous–dioxy complex of Leishmania major globin coupled heme containing adenylate cyclase: The role of proximal histidine on its stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:615-22. [DOI: 10.1016/j.bbapap.2014.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/06/2014] [Accepted: 01/07/2014] [Indexed: 11/16/2022]
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57
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Song SH, Madsen D, van der Steen JB, Pullman R, Freer LH, Hellingwerf KJ, Larsen DS. Primary Photochemistry of the Dark- and Light-Adapted States of the YtvA Protein from Bacillus subtilis. Biochemistry 2013; 52:7951-63. [DOI: 10.1021/bi4012258] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sang-Hun Song
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dorte Madsen
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Jeroen B. van der Steen
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences
(SILS), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Robert Pullman
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Lucy H. Freer
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Klaas J. Hellingwerf
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences
(SILS), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Delmar S. Larsen
- Department
of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
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58
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Purohit R, Weichsel A, Montfort WR. Crystal structure of the Alpha subunit PAS domain from soluble guanylyl cyclase. Protein Sci 2013; 22:1439-44. [PMID: 23934793 DOI: 10.1002/pro.2331] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 03/31/2013] [Accepted: 08/05/2013] [Indexed: 12/26/2022]
Abstract
Soluble guanylate cyclase (sGC) is a heterodimeric heme protein of ≈ 150 kDa and the primary nitric oxide receptor. Binding of NO stimulates cyclase activity, leading to regulation of cardiovascular physiology and providing attractive opportunities for drug discovery. How sGC is stimulated and where candidate drugs bind remains unknown. The α and β sGC chains are each composed of Heme-Nitric Oxide Oxygen (H-NOX), Per-ARNT-Sim (PAS), coiled-coil and cyclase domains. Here, we present the crystal structure of the α1 PAS domain to 1.8 Å resolution. The structure reveals the binding surfaces of importance to heterodimer function, particularly with respect to regulating NO binding to heme in the β1 H-NOX domain. It also reveals a small internal cavity that may serve to bind ligands or participate in signal transduction.
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Affiliation(s)
- Rahul Purohit
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721
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59
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Yano S, Ishikawa H, Mizuno M, Nakamura H, Shiro Y, Mizutani Y. Ultraviolet Resonance Raman Observations of the Structural Dynamics of Rhizobial Oxygen Sensor FixL on Ligand Recognition. J Phys Chem B 2013; 117:15786-91. [DOI: 10.1021/jp406709e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Shinji Yano
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Haruto Ishikawa
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiro Nakamura
- RIKEN SPring-8 Center, 1-1-1
Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - Yasuhisa Mizutani
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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60
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Martínková M, Kitanishi K, Shimizu T. Heme-based globin-coupled oxygen sensors: linking oxygen binding to functional regulation of diguanylate cyclase, histidine kinase, and methyl-accepting chemotaxis. J Biol Chem 2013; 288:27702-11. [PMID: 23928310 DOI: 10.1074/jbc.r113.473249] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
An emerging class of novel heme-based oxygen sensors containing a globin fold binds and senses environmental O2 via a heme iron complex. Structure-function relationships of oxygen sensors containing a heme-bound globin fold are different from those containing heme-bound PAS and GAF folds. It is thus worth reconsidering from an evolutionary perspective how heme-bound proteins with a globin fold similar to that of hemoglobin and myoglobin could act as O2 sensors. Here, we summarize the molecular mechanisms of heme-based oxygen sensors containing a globin fold in an effort to shed light on the O2-sensing properties and O2-stimulated catalytic enhancement observed for these proteins.
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Affiliation(s)
- Markéta Martínková
- From the Department of Biochemistry, Faculty of Science, Charles University in Prague, 128 43 Prague 2, Czech Republic
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61
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Abstract
Heme is a prosthetic group best known for roles in oxygen transport, oxidative catalysis, and respiratory electron transport. Recent years have seen the roles of heme extended to sensors of gases such as O2 and NO and cell redox state, and as mediators of cellular responses to changes in intracellular levels of these gases. The importance of heme is further evident from identification of proteins that bind heme reversibly, using it as a signal, e.g. to regulate gene expression in circadian rhythm pathways and control heme synthesis itself. In this minireview, we explore the current knowledge of the diverse roles of heme sensor proteins.
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Affiliation(s)
- Hazel M. Girvan
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Andrew W. Munro
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
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62
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Guo Y, Partch CL, Key J, Card PB, Pashkov V, Patel A, Bruick RK, Wurdak H, Gardner KH. Regulating the ARNT/TACC3 axis: multiple approaches to manipulating protein/protein interactions with small molecules. ACS Chem Biol 2013; 8:626-35. [PMID: 23240775 DOI: 10.1021/cb300604u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For several well-documented reasons, it has been challenging to develop artificial small molecule inhibitors of protein/protein complexes. Such reagents are of particular interest for transcription factor complexes given links between their misregulation and disease. Here we report parallel approaches to identify regulators of a hypoxia signaling transcription factor complex, involving the ARNT subunit of the HIF (Hypoxia Inducible Factor) activator and the TACC3 (Transforming Acidic Coiled Coil Containing Protein 3) coactivator. In one route, we used in vitro NMR and biochemical screening to identify small molecules that selectively bind within the ARNT PAS (Per-ARNT-Sim) domain that recruits TACC3, identifying KG-548 as an ARNT/TACC3 disruptor. A parallel, cell-based screening approach previously implicated the small molecule KHS101 as an inhibitor of TACC3 signaling. Here, we show that KHS101 works indirectly on HIF complex formation by destabilizing both TACC3 and the HIF component HIF-1α. Overall, our data identify small molecule regulators for this important complex and highlight the utility of pursuing parallel strategies to develop protein/protein inhibitors.
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Affiliation(s)
| | | | | | | | | | - Anjana Patel
- Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University
Hospital, Beckett Street, Leeds LS9 7TF, U.K
| | | | - Heiko Wurdak
- Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University
Hospital, Beckett Street, Leeds LS9 7TF, U.K
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63
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Tan E, Rao F, Pasunooti S, Pham TH, Soehano I, Turner MS, Liew CW, Lescar J, Pervushin K, Liang ZX. Solution structure of the PAS domain of a thermophilic YybT protein homolog reveals a potential ligand-binding site. J Biol Chem 2013; 288:11949-59. [PMID: 23504327 DOI: 10.1074/jbc.m112.437764] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Bacillus subtilis protein YybT (or GdpP) and its homologs were recently established as stress signaling proteins that exert their biological effect by degrading the bacterial messenger cyclic di-AMP. YybT homologs contain a small Per-ARNT-Sim (PAS) domain (~80 amino acids) that can bind b-type heme with 1:1 stoichiometry despite the small size of the domain and the lack of a conserved heme iron-coordinating residue. We determined the solution structure of the PAS domain of GtYybT from Geobacillus thermodenitrificans by NMR spectroscopy to further probe its function. The solution structure confirms that PASGtYybT adopts the characteristic PAS fold composed of a five-stranded antiparallel β sheet and a few short α-helices. One α-helix and three central β-strands of PASGtYybT are noticeably shorter than those of the typical PAS domains. Despite the small size of the protein domain, a hydrophobic pocket is formed by the side chains of nonpolar residues stemming from the β-strands and α-helices. A set of residues in the vicinity of the pocket and in the C-terminal region at the dimeric interface exhibits perturbed NMR parameters in the presence of heme or zinc protoporphyrin. Together, the results unveil a compact PAS domain with a potential ligand-binding pocket and reinforce the view that the PASYybT domains function as regulatory domains in the modulation of cellular cyclic di-AMP concentration.
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Affiliation(s)
- Edward Tan
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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64
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Airola MV, Huh D, Sukomon N, Widom J, Sircar R, Borbat PP, Freed JH, Watts KJ, Crane BR. Architecture of the soluble receptor Aer2 indicates an in-line mechanism for PAS and HAMP domain signaling. J Mol Biol 2013; 425:886-901. [PMID: 23274111 PMCID: PMC3577987 DOI: 10.1016/j.jmb.2012.12.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 01/24/2023]
Abstract
Bacterial receptors typically contain modular architectures with distinct functional domains that combine to send signals in response to stimuli. Although the properties of individual components have been investigated in many contexts, there is little information about how diverse sets of modules work together in full-length receptors. Here, we investigate the architecture of Aer2, a soluble gas-sensing receptor that has emerged as a model for PAS (Per-Arnt-Sim) and poly-HAMP (histidine kinase-adenylyl cyclase-methyl-accepting chemotaxis protein-phosphatase) domain signaling. The crystal structure of the heme-binding PAS domain in the ferric, ligand-free form, in comparison to the previously determined cyanide-bound state, identifies conformational changes induced by ligand binding that are likely essential for the signaling mechanism. Heme-pocket alternations share some similarities with the heme-based PAS sensors FixL and EcDOS but propagate to the Iβ strand in a manner predicted to alter PAS-PAS associations and the downstream HAMP junction within full-length Aer2. Small-angle X-ray scattering of PAS and poly-HAMP domain fragments of increasing complexity allow unambiguous domain assignments and reveal a linear quaternary structure. The Aer2 PAS dimeric crystal structure fits well within ab initio small-angle X-ray scattering molecular envelopes, and pulsed dipolar ESR measurements of inter-PAS distances confirm the crystallographic PAS arrangement within Aer2. Spectroscopic and pull-down assays fail to detect direct interactions between the PAS and HAMP domains. Overall, the Aer2 signaling mechanism differs from the Escherichia coli Aer paradigm, where side-on PAS-HAMP contacts are key. We propose an in-line model for Aer2 signaling, where ligand binding induces alterations in PAS domain structure and subunit association that is relayed through the poly-HAMP junction to downstream domains.
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Affiliation(s)
- Michael V. Airola
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Doowon Huh
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nattakan Sukomon
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Joanne Widom
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ria Sircar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Peter P. Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Advanced ESR Studies, Cornell University, Ithaca, NY 14853, USA
| | - Jack H. Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Advanced ESR Studies, Cornell University, Ithaca, NY 14853, USA
| | - Kylie J. Watts
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA 92350, USA
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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65
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Wang C, Sang J, Wang J, Su M, Downey JS, Wu Q, Wang S, Cai Y, Xu X, Wu J, Senadheera DB, Cvitkovitch DG, Chen L, Goodman SD, Han A. Mechanistic insights revealed by the crystal structure of a histidine kinase with signal transducer and sensor domains. PLoS Biol 2013; 11:e1001493. [PMID: 23468592 PMCID: PMC3582566 DOI: 10.1371/journal.pbio.1001493] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 01/14/2013] [Indexed: 02/02/2023] Open
Abstract
A crystal structure reveals an elegant mechanistic switch whereby helical bending and catalytic domain rotation allow self-activation of a histidine kinase during a bacterial stress response. Two-component systems (TCSs) are important for the adaptation and survival of bacteria and fungi under stress conditions. A TCS is often composed of a membrane-bound sensor histidine kinase (SK) and a response regulator (RR), which are relayed through sequential phosphorylation steps. However, the mechanism for how an SK is switched on in response to environmental stimuli remains obscure. Here, we report the crystal structure of a complete cytoplasmic portion of an SK, VicK from Streptococcus mutans. The overall structure of VicK is a long-rod dimer that anchors four connected domains: HAMP, Per-ARNT-SIM (PAS), DHp, and catalytic and ATP binding domain (CA). The HAMP, a signal transducer, and the PAS domain, major sensor, adopt canonical folds with dyad symmetry. In contrast, the dimer of the DHp and CA domains is asymmetric because of different helical bends in the DHp domain and spatial positions of the CA domains. Moreover, a conserved proline, which is adjacent to the phosphoryl acceptor histidine, contributes to helical bending, which is essential for the autokinase and phosphatase activities. Together, the elegant architecture of VicK with a signal transducer and sensor domain suggests a model where DHp helical bending and a CA swing movement are likely coordinated for autokinase activation. Two-component signal transduction systems (TCSs) are promising targets for new antimicrobial research because they help bacteria and fungi adapt and survive. One of the main components of TCSs is a sensor histidine kinase (SK), which relays extracellular signals to intracellular pathways. Despite intensive research, a full-length structure of an SK has yet to be solved. In this study, we report the first crystal structure of the complete cytoplasmic region of VicK, an important SK in the tooth decay pathogen S. mutans. VicK is composed of several domains (HAMP, PAS, DHp, and catalytic and ATP binding domain [CA]) in addition to a short transmembrane domain. We find that the dimeric VicK protein has an elegant rod-shaped structure with the domains linearly connected like beads on a string. The structure suggests that VicK kinase activates itself by helical bending of the DHp domain and coordinated swinging around of the catalytic CA domain to engage with the target histidine. Structure-based mutagenesis experiments also helped us to identify key residues that are required for VicK's opposing phosphatase activity. Our studies of the multi-modular VicK protein suggest a sequential kinase activation model that may involve helical bending of the DHp domain and repositioning of the CA domains.
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Affiliation(s)
- Chen Wang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Jiayan Sang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Jiawei Wang
- Department of Biology and Technology, Tsinghua University, Beijing, China
| | - Mingyan Su
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Jennifer S. Downey
- Division of Biomedical Science, Herman Ostrow School of Dentistry of University of Southern California, Los Angeles, California, United States of America
| | - Qinggan Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Shida Wang
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Xiaozheng Xu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Jun Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Dilani B. Senadheera
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Dennis G. Cvitkovitch
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Lin Chen
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Steven D. Goodman
- Division of Biomedical Science, Herman Ostrow School of Dentistry of University of Southern California, Los Angeles, California, United States of America
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
- * E-mail:
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66
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Aono S. The Dos family of globin-related sensors using PAS domains to accommodate haem acting as the active site for sensing external signals. Adv Microb Physiol 2013; 63:273-327. [PMID: 24054799 DOI: 10.1016/b978-0-12-407693-8.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sensor proteins play crucial roles in maintaining homeostasis of cells by sensing changes in extra- and intracellular chemical and physical conditions to trigger biological responses. It has recently become clear that gas molecules function as signalling molecules in these biological regulatory systems responsible for transcription, chemotaxis, synthesis/hydrolysis of nucleotide second messengers, and other complex physiological processes. Haem-containing sensor proteins are widely used to sense gas molecules because haem can bind gas molecules reversibly. Ligand binding to the haem in the sensor proteins triggers conformational changes around the haem, which results in their functional regulation. Spectroscopic and crystallographic studies are essential to understand how these sensor proteins function in these biological regulatory systems. In this chapter, I discuss structural and functional relationships of haem-containing PAS and PAS-related families of the sensor proteins.
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67
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Zamorano-Sánchez D, Reyes-González A, Gómez-Hernández N, Rivera P, Georgellis D, Girard L. FxkR provides the missing link in the fixL-fixK signal transduction cascade in Rhizobium etli CFN42. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1506-1517. [PMID: 22809273 DOI: 10.1094/mpmi-05-12-0136-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Transcriptional control of the fixK gene in Rhizobium etli and R. leguminosarum bv. viciae is governed by a two-component signal transduction system that diverts from the conventional FixL-FixJ cascade that occurs in model rhizobia. Although a fixL gene, encoding a hybrid histidine kinase (hFixL), is present in R. etli, no fixJ, the cognate response regulator, has been identified. In this work, we present evidence that the pRet42f-located open reading frame RHE_PF00530 (fxkR) encodes a novel response regulator indispensable for fixKf activation under microaerobic growth. Moreover, results from complementation assays demonstrate that the activation of fixKf expression requires the presence of both hFixL and FxkR, and that the fxkR ortholog from R. leguminosarum bv. viciae is able to substitute for FxkR transcriptional control in R. etli. In addition, in these two organisms, hFixL- and FxkR-related proteins were identified in other bacteria, located in close proximity to a fixK-related gene. Using reporter fusions, site-directed mutagenesis, and electrophoretic mobility shift assays, we identified the FxkR binding site upstream from the transcriptional start site of fixKf. Similar to our previous observations for fixL and fixKf mutants, a null mutation in fxkR does not affect the symbiotic effectiveness of the strain. Thus, our findings reveal that FxkR is the long-standing missing key regulator that allows the transduction of the microaerobic signal for the activation of the FixKf regulon.
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68
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Mao D, Tao J, Li C, Luo C, Zheng L, He C. Identification of novel oxygen sensors using a combined approach in Xanthomonas campestris pv. campestris. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-011-0334-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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69
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Farmahin R, Manning GE, Crump D, Wu D, Mundy LJ, Jones SP, Hahn ME, Karchner SI, Giesy JP, Bursian SJ, Zwiernik MJ, Fredricks TB, Kennedy SW. Amino acid sequence of the ligand-binding domain of the aryl hydrocarbon receptor 1 predicts sensitivity of wild birds to effects of dioxin-like compounds. Toxicol Sci 2012; 131:139-52. [PMID: 22923492 DOI: 10.1093/toxsci/kfs259] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The sensitivity of avian species to the toxic effects of dioxin-like compounds (DLCs) varies up to 1000-fold among species, and this variability has been associated with interspecies differences in aryl hydrocarbon receptor 1 ligand-binding domain (AHR1 LBD) sequence. We previously showed that LD(50) values, based on in ovo exposures to DLCs, were significantly correlated with in vitro EC(50) values obtained with a luciferase reporter gene (LRG) assay that measures AHR1-mediated induction of cytochrome P4501A in COS-7 cells transfected with avian AHR1 constructs. Those findings suggest that the AHR1 LBD sequence and the LRG assay can be used to predict avian species sensitivity to DLCs. In the present study, the AHR1 LBD sequences of 86 avian species were studied, and differences at amino acid sites 256, 257, 297, 324, 337, and 380 were identified. Site-directed mutagenesis, the LRG assay, and homology modeling highlighted the importance of each amino acid site in AHR1 sensitivity to 2,3,7,8-tetrachlorodibenzo-p-dioxin and other DLCs. The results of the study revealed that (1) only amino acids at sites 324 and 380 affect the sensitivity of AHR1 expression constructs of the 86 avian species to DLCs and (2) in vitro luciferase activity of AHR1 constructs containing only the LBD of the species of interest is significantly correlated (r (2) = 0.93, p < 0.0001) with in ovo toxicity data for those species. These results indicate promise for the use of AHR1 LBD amino acid sequences independently, or combined with the LRG assay, to predict avian species sensitivity to DLCs.
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Affiliation(s)
- Reza Farmahin
- Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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70
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Dai Z, Farquhar ER, Arora DP, Boon EM. Is histidine dissociation a critical component of the NO/H-NOX signaling mechanism? Insights from X-ray absorption spectroscopy. Dalton Trans 2012; 41:7984-93. [PMID: 22430114 PMCID: PMC3671924 DOI: 10.1039/c2dt30147d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The H-NOX (Heme-Nitric oxide/OXygen binding) family of diatomic gas sensing hemoproteins has attracted great interest. Soluble guanylate cyclase (sGC), the well-characterized eukaryotic nitric oxide (NO) sensor is an H-NOX family member. When NO binds sGC at the ferrous histidine-ligated protoporphyrin-IX, the proximal histidine ligand dissociates, resulting in a 5-coordinate (5c) complex; formation of this 5c complex is viewed as necessary for activation of sGC. Characterization of other H-NOX family members has revealed that while most also bind NO in a 5c complex, some bind NO in a 6-coordinate (6c) complex or as a 5c/6c mixture. To gain insight into the heme pocket structural differences between 5c and 6c Fe(ii)-NO H-NOX complexes, we investigated the extended X-ray absorption fine structure (EXAFS) of the Fe(II)-unligated and Fe(II)-NO complexes of H-NOX domains from three species, Thermoanaerobacter tengcongensis, Shewanella woodyi, and Pseudoalteromonas atlantica. Although the Fe(II)-NO complex of TtH-NOX is formally 6c, we found the Fe-N(His) bond is substantially lengthened. Furthermore, although NO binds to SwH-NOX and PaH-NOX as a 5c complex, consistent with histidine dissociation, the EXAFS data do not exclude a very weakly associated histidine. Regardless of coordination number, upon NO-binding, the Fe-N(porphyrin) bond lengths in all three H-NOXs contract by ~0.07 Å. This study reveals that the overall heme structure of 5c and 6c Fe(II)-NO H-NOX complexes are substantially similar, suggesting that formal histidine dissociation may not be required to trigger NO/H-NOX signal transduction. The study has refined our understanding of the molecular mechanisms underlying NO/H-NOX signaling.
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Affiliation(s)
- Zhou Dai
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Erik R. Farquhar
- Case Western Reserve University Center for Synchrotron Biosciences and Center for Proteomics and Bioinformatics, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Dhruv P. Arora
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Elizabeth M. Boon
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
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71
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Cyclic Di-GMP phosphodiesterases RmdA and RmdB are involved in regulating colony morphology and development in Streptomyces coelicolor. J Bacteriol 2012; 194:4642-51. [PMID: 22753061 DOI: 10.1128/jb.00157-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyclic dimeric GMP (c-di-GMP) regulates numerous processes in Gram-negative bacteria, yet little is known about its role in Gram-positive bacteria. Here we characterize two c-di-GMP phosphodiesterases from the filamentous high-GC Gram-positive actinobacterium Streptomyces coelicolor, involved in controlling colony morphology and development. A transposon mutation in one of the two phosphodiesterase genes, SCO0928, hereby designated rmdA (regulator of morphology and development A), resulted in decreased levels of spore-specific gray pigment and a delay in spore formation. The RmdA protein contains GGDEF-EAL domains arranged in tandem and possesses c-di-GMP phosphodiesterase activity, as is evident from in vitro enzymatic assays using the purified protein. RmdA contains a PAS9 domain and is a hemoprotein. Inactivation of another GGDEF-EAL-encoding gene, SCO5495, designated rmdB, resulted in a phenotype identical to that of the rmdA mutant. Purified soluble fragment of RmdB devoid of transmembrane domains also possesses c-di-GMP phosphodiesterase activity. The rmdA rmdB double mutant has a bald phenotype and is impaired in aerial mycelium formation. This suggests that RmdA and RmdB functions are additive and at least partially overlapping. The rmdA and rmdB mutations likely result in increased local pools of intracellular c-di-GMP, because intracellular c-di-GMP levels in the single mutants did not differ significantly from those of the wild type, whereas in the double rmdA rmdB mutant, c-di-GMP levels were 3-fold higher than those in the wild type. This study highlights the importance of c-di-GMP-dependent signaling in actinomycete colony morphology and development and identifies two c-di-GMP phosphodiesterases controlling these processes.
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72
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Carrica MDC, Fernandez I, Martí MA, Paris G, Goldbaum FA. The NtrY/X two-component system of Brucella spp. acts as a redox sensor and regulates the expression of nitrogen respiration enzymes. Mol Microbiol 2012; 85:39-50. [DOI: 10.1111/j.1365-2958.2012.08095.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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73
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Zhou Z, Shen M, Cao C, Liu Q, Yan Z. Opposing Influences of Ruffling and Doming Deformation on the 4-N Cavity Size of Porphyrin Macrocycles: The Role of Heme Deformations Revealed. Chemistry 2012; 18:7675-9. [DOI: 10.1002/chem.201200722] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Indexed: 01/09/2023]
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74
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Song C, Essen LO, Gärtner W, Hughes J, Matysik J. Solid-state NMR spectroscopic study of chromophore-protein interactions in the Pr ground state of plant phytochrome A. MOLECULAR PLANT 2012; 5:698-715. [PMID: 22419823 DOI: 10.1093/mp/sss017] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Despite extensive study, the molecular structure of the chromophore-binding pocket of phytochrome A (phyA), the principal photoreceptor controlling photomorphogenesis in plants, has not yet been successfully resolved. Here, we report a series of two-dimensional (2-D) magic-angle spinning solid-state NMR experiments on the recombinant N-terminal, 65-kDa PAS-GAF-PHY light-sensing module of phytochrome A3 from oat (Avena sativa), assembled with uniformly 13C- and 15N-labeled phycocyanobilin (u-[13C,15N]-PCB-As.phyA3). The Pr state of this protein was studied regarding the electronic structure of the chromophore and its interactions with the proximal amino acids. Using 2-D 13C-13C and 1H-15N experiments, a complete set of 13C and 15N assignments for the chromophore were obtained. Also, a large number of 1H-13C distance restraints between the chromophore and its binding pocket were revealed by interfacial heteronuclear correlation spectroscopy. 13C doublings of the chromophore A-ring region and the C-ring carboxylate moiety, together with the observation of two Pr isoforms, Pr-I and Pr-II, demonstrate the local mobility of the chromophore and the plasticity of its protein environment. It appears that the interactions and dynamics in the binding pocket of phyA in the Pr state are remarkably similar to those of cyanobacterial phytochrome (Cph1). The N-terminus of the region modeled (residues 56-66 of phyA) is highly mobile. Differences in the regulatory processes involved in plant and Cph1 phytochromes are discussed.
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Affiliation(s)
- Chen Song
- Leids Instituut voor Chemisch Onderzoek, Universiteit Leiden, PO Box 9502, 2300 RA Leiden, The Netherlands
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75
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Abstract
The recent discovery that heme proteins can serve as molecular biosensors has opened up a new direction in heme biochemistry directed towards elucidating their structure-function relationships. Examples of such sensory heme proteins include the FixL proteins of Rhizobia involved in oxygen sensing, the CooA protein of Rhodospirillum rubrum that senses CO, and the mammalian soluble guanylate cyclase—the only proven nitric oxide receptor. This overview summarizes the current state of knowledge regarding the roles and mechanisms of these novel proteins and discusses the evidence for other putative heme protein sensors. These topics will be presented in the Heme Protein Biosensors Symposium at the First International Conference of Porphyrins and Phthalocyanines in Dijon, France.
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Affiliation(s)
- MICHAEL K. CHAN
- Departments of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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76
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Muralidharan S, Boon EM. Heme flattening is sufficient for signal transduction in the H-NOX family. J Am Chem Soc 2012; 134:2044-6. [PMID: 22257139 DOI: 10.1021/ja211576b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The H-NOX family of nitric oxide (NO) sensing proteins has received considerable attention because its members include the mammalian NO sensor, soluble guanylate cyclase. Despite this attention, the mechanism of signal transduction has not been elucidated. Structural studies of bacterial members of the family have revealed that the H-NOX heme cofactor is extremely distorted from planarity. Furthermore, it has been determined that heme distortion is maintained primarily by a conserved proline residue located in the proximal heme pocket. It has been suggested that changes in heme planarity may contribute to signal transduction. Here we demonstrate that heme flattening is, indeed, sufficient for signal transduction in the H-NOX family. Using our previously described H-NOX/diguanylate cyclase functional partners from Shewanella woodyi, we demonstrate that mutation of the conserved proline (P117 in SwH-NOX) to alanine, which results in heme flattening, has the same affect on phosphodiesterase activity as NO binding to wildtype SwH-NOX. This study demonstrates, for the first time, that heme flattening mimics the activated, NO-bound state of H-NOX and suggests that NO binding induces heme flattening as part of the signal transduction mechanism in the H-NOX family.
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Affiliation(s)
- Sandhya Muralidharan
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, USA
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77
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Sun F, Ji Q, Jones MB, Deng X, Liang H, Frank B, Telser J, Peterson SN, Bae T, He C. AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus. J Am Chem Soc 2011; 134:305-14. [PMID: 22122613 DOI: 10.1021/ja2071835] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Oxygen sensing and redox signaling significantly affect bacterial physiology and host-pathogen interaction. Here we show that a Staphylococcus aureus two-component system, AirSR (anaerobic iron-sulfur cluster-containing redox sensor regulator, formerly YhcSR), responds to oxidation signals (O(2), H(2)O(2), NO, etc) by using a redox-active [2Fe-2S] cluster in the sensor kinase AirS. Mutagenesis studies demonstrate that the [2Fe-2S] cluster is essential for the kinase activity of AirS. We have also discovered that a homologue of IscS (SA1450) in S. aureus is active as a cysteine desulfurase, which enables the in vitro reconstitution of the [2Fe-2S] cluster in AirS. Phosphorylation assays show that the oxidized AirS with a [2Fe-2S](2+) cluster is the fully active form of the kinase but not the apo-AirS nor the reduced AirS possessing a [2Fe-2S](+) cluster. Overoxidation by prolonged exposure to O(2) or contact with H(2)O(2) or NO led to inactivation of AirS. Transcriptome analysis revealed that mutation of airR impacts the expression of ~355 genes under anaerobic conditions. Moreover, the mutant strain displayed increased resistance toward H(2)O(2), vancomycin, norfloxacin, and ciprofloxacin under anaerobic conditions. Together, our results show that S. aureus AirSR is a redox-dependent global regulatory system that plays important roles in gene regulation using a redox active Fe-S cluster under O(2)-limited conditions.
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Affiliation(s)
- Fei Sun
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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78
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Preu J, Panjikar S, Morth P, Jaiswal R, Karunakar P, Tucker PA. The sensor region of the ubiquitous cytosolic sensor kinase, PdtaS, contains PAS and GAF domain sensing modules. J Struct Biol 2011; 177:498-505. [PMID: 22115998 DOI: 10.1016/j.jsb.2011.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 11/03/2011] [Accepted: 11/07/2011] [Indexed: 11/18/2022]
Abstract
Two-component systems, a sensor histidine kinase (HK) and a response regulator (RR), are ubiquitous signaling systems that allow prokaryotes to respond to external challenges. HKs normally have sensing modules and highly conserved cytosolic histidine kinase and ATPase domains. The interaction between the activated phosphohistidine and the cognate RR allows an external signal to be passed from the exterior of gram-positive bacteria (GPB) to the cytoplasm. Orthologs of the PdtaS/PdtaR regulatory system, found in most GPB phyla, are unusual in two respects. The HK is not membrane anchored, and the RR acts at the level of transcriptional antitermination. The structure of the complete sensor region of the cytosolic HK, PdtaS, from Mycobacterium tuberculosis consists of closely linked GAF and PAS domains. The structure and sequence analysis suggest that the PdtaS/PdtaR regulatory system is structurally equivalent to the EutW/EutV system regulating ethanolamine catabolism in some phyla but that the effector for the PAS domain is not ethanolamine in the Actinobacteria.
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Affiliation(s)
- Julia Preu
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D22603 Hamburg, Germany
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79
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Abstract
Many bacteria use 'quorum sensing' (QS) as a mechanism to regulate gene induction in a population-dependent manner. In its simplest sense this involves the accumulation of a signaling metabolite during growth; the binding of this metabolite to a regulator or multiple regulators activates induction or repression of gene expression. However QS regulation is seldom this simple, because other inputs are usually involved. In this review we have focussed on how those other inputs influence QS regulation and as implied by the title, this often occurs by environmental or physiological effects regulating the expression or activity of the QS regulators. The rationale of this review is to briefly introduce the main QS signals used in Gram-negative bacteria and then introduce one of the earliest understood mechanisms of regulation of the regulator, namely the plant-mediated control of expression of the TraR QS regulator in Agrobacterium tumefaciens. We then describe how in several species, multiple QS regulatory systems can act as integrated hierarchical regulatory networks and usually this involves the regulation of QS regulators. Such networks can be influenced by many different physiological and environmental inputs and we describe diverse examples of these. In the final section, we describe different examples of how eukaryotes can influence QS regulation in Gram-negative bacteria.
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Affiliation(s)
- Marijke Frederix
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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80
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Quintas PO, Catarino T, Todorovic S, Turner DL. Highly selective ligand binding by Methylophilus methylotrophus cytochrome c''. Biochemistry 2011; 50:5624-32. [PMID: 21599015 DOI: 10.1021/bi200480a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c'' (cyt c'') from Methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. Despite cyt c'' having an axial site available for binding small ligands, we show here that only NO binds readily to the ferrous cyt c''. Binding of CO, as well as CN(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. Standard free energies for the binding of NO and CO reveal high selectivity of the ferrous cyt c'' for NO, indicating its putative physiological role. In this work, we characterize in detail the kinetics of NO binding and the structural features of the Fe(2+)-NO adduct by stopped-flow and resonance Raman spectroscopy, respectively.
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Affiliation(s)
- Pedro O Quintas
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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81
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Goblirsch B, Kurker RC, Streit BR, Wilmot CM, DuBois JL. Chlorite dismutases, DyPs, and EfeB: 3 microbial heme enzyme families comprise the CDE structural superfamily. J Mol Biol 2011; 408:379-98. [PMID: 21354424 PMCID: PMC3075325 DOI: 10.1016/j.jmb.2011.02.047] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 02/15/2011] [Accepted: 02/16/2011] [Indexed: 11/28/2022]
Abstract
Heme proteins are extremely diverse, widespread, and versatile biocatalysts, sensors, and molecular transporters. The chlorite dismutase family of hemoproteins received its name due to the ability of the first-isolated members to detoxify anthropogenic ClO(2)(-), a function believed to have evolved only in the last few decades. Family members have since been found in 15 bacterial and archaeal genera, suggesting ancient roots. A structure- and sequence-based examination of the family is presented, in which key sequence and structural motifs are identified, and possible functions for family proteins are proposed. Newly identified structural homologies moreover demonstrate clear connections to two other large, ancient, and functionally mysterious protein families. We propose calling them collectively the CDE superfamily of heme proteins.
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Affiliation(s)
- Brandon Goblirsch
- Department of Biochemistry, Molecular Biology and Biophysics, 6-155 Jackson Hall, 321 Church St. SE, University of Minnesota, Minnesota 55455, USA
| | - Richard C. Kurker
- Department of Chemistry and Biochemistry, 251 Nieuwland Hall, University of Notre Dame, Notre Dame, Indiana 46556 USA
| | - Bennett R. Streit
- Department of Chemistry and Biochemistry, 251 Nieuwland Hall, University of Notre Dame, Notre Dame, Indiana 46556 USA
| | - Carrie M. Wilmot
- Department of Biochemistry, Molecular Biology and Biophysics, 6-155 Jackson Hall, 321 Church St. SE, University of Minnesota, Minnesota 55455, USA
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, 251 Nieuwland Hall, University of Notre Dame, Notre Dame, Indiana 46556 USA
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82
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King-Scott J, Konarev PV, Panjikar S, Jordanova R, Svergun DI, Tucker PA. Structural characterization of the multidomain regulatory protein Rv1364c from Mycobacterium tuberculosis. Structure 2011; 19:56-69. [PMID: 21220116 DOI: 10.1016/j.str.2010.11.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 11/15/2010] [Accepted: 11/16/2010] [Indexed: 01/29/2023]
Abstract
The open reading frame rv1364c of Mycobacterium tuberculosis, which regulates the stress-dependent σ factor, σ(F), has been analyzed structurally and functionally. Rv1364c contains domains with sequence similarity to the RsbP/RsbW/RsbV regulatory system of the stress-response σ factor of Bacillus subtilis. Rv1364c contains, sequentially, a PAS domain (which shows sequence similarity to the PAS domain of the B. subtilis RsbP protein), an active phosphatase domain, a kinase (anti-σ(F) like) domain and a C-terminal anti-σ(F) antagonist like domain. The crystal structures of two PAS domain constructs (at 2.3 and 1.6 Å) and a phosphatase/kinase dual domain construct (at 2.6 Å) are described. The PAS domain is shown to bind palmitic acid but to have 100 times greater affinity for palmitoleic acid. The full-length protein can exist in solution as both monomer and dimer. We speculate that a switch between monomer and dimer, possibly resulting from fatty acid binding, affects the accessibility of the serine of the C-terminal, anti-σ(F) antagonist domain for dephosphorylation by the phosphatase domain thus indirectly altering the availability of σ(F).
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Affiliation(s)
- Jack King-Scott
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D22603, Hamburg, Germany
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83
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Sugawara M, Shah GR, Sadowsky MJ, Paliy O, Speck J, Vail AW, Gyaneshwar P. Expression and functional roles of Bradyrhizobium japonicum genes involved in the utilization of inorganic and organic sulfur compounds in free-living and symbiotic conditions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:451-7. [PMID: 21190435 DOI: 10.1094/mpmi-08-10-0184] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Strains of Bradyrhizobium spp. form nitrogen-fixing symbioses with many legumes, including soybean. Although inorganic sulfur is preferred by bacteria in laboratory conditions, sulfur in agricultural soil is mainly present as sulfonates and sulfur esters. Here, we show that Bradyrhizobium japonicum and B. elkanii strains were able to utilize sulfate, cysteine, sulfonates, and sulfur-ester compounds as sole sulfur sources for growth. Expression and functional analysis revealed that two sets of gene clusters (bll6449 to bll6455 or bll7007 to bll7011) are important for utilization of sulfonates sulfur source. The bll6451 or bll7010 genes are also expressed in the symbiotic nodules. However, B. japonicum mutants defective in either of the sulfonate utilization operons were not affected for symbiosis with soybean, indicating the functional redundancy or availability of other sulfur sources in planta. In accordance, B. japonicum bacteroids possessed significant sulfatase activity. These results indicate that strains of Bradyrhizobium spp. likely use organosulfur compounds for growth and survival in soils, as well as for legume nodulation and nitrogen fixation.
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Affiliation(s)
- Masayuki Sugawara
- Department of Soil Water and Climate, University of Minnesota, St. Paul, USA
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84
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Origins of aging mass loss in recombinant N-terminus and C-terminus deletion mutants of the heme-PAS biosensor domain BjFixLH(140-270). J Inorg Biochem 2011; 105:609-15. [PMID: 21443850 DOI: 10.1016/j.jinorgbio.2011.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 01/20/2011] [Accepted: 01/21/2011] [Indexed: 11/22/2022]
Abstract
Nine recombinant FixL heme domains from Bradyrhizobium japonicum previously were shown to exhibit mass instability independent of many environmental factors (J.D. Satterlee, C. Suquet, A. Bidwai, J. Erman, L. Schwall, R. Jimenez, Biochemistry 47 (2008) 1540-1553). Two of those recombinant proteins were produced in remote laboratories. Mass losses begin appearing at completion of isolation and comprise a substantial proportion of samples within 1-3 days of storage and handling. Thus, degradation occurs during the time frame of experiments and crystallization. Detailed understanding of this instability is desired in order to formulate stable heme-PAS sensor domains for experimentation and for a mechanistic interpretation. However, mass spectra of the full length heme-PAS domain, BjFixLH(140-270), are complex by 1-3 days following isolation due to broad features and a high density of overlapping peaks, so that individual peak assignments are at present ambiguous. This stymies direct, quantitative interpretation of the source of the observed mass losses. To solve this dilemma amino-terminal primary sequencing and MALDI-TOF (Matrix Assisted Laser Desorption Ionization-Time of Flight) mass spectrometry monitoring of three terminal variants of BjFixLH(140-270) have been achieved. The working hypothesis, that the experimentally observed mass losses originate in the PAS protein sequence termini, has been substantiated. This establishes a basis for interpreting the more complex results from aging full length BjFixLH(140-270).
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85
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Drepper T, Krauss U, Meyer zu Berstenhorst S, Pietruszka J, Jaeger KE. Lights on and action! Controlling microbial gene expression by light. Appl Microbiol Biotechnol 2011; 90:23-40. [PMID: 21336931 DOI: 10.1007/s00253-011-3141-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/05/2011] [Accepted: 01/05/2011] [Indexed: 01/10/2023]
Abstract
Light-mediated control of gene expression and thus of any protein function and metabolic process in living microbes is a rapidly developing field of research in the areas of functional genomics, systems biology, and biotechnology. The unique physical properties of the environmental factor light allow for an independent photocontrol of various microbial processes in a noninvasive and spatiotemporal fashion. This mini review describes recently developed strategies to generate photo-sensitive expression systems in bacteria and yeast. Naturally occurring and artificial photoswitches consisting of light-sensitive input domains derived from different photoreceptors and regulatory output domains are presented and individual properties of light-controlled expression systems are discussed.
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Affiliation(s)
- Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.
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86
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Abstract
YybT family proteins (COG3887) are functionally unknown proteins that are widely distributed among the firmicutes, including the human pathogens Staphylococcus aureus and Listeria monocytogenes. Recent studies suggested that YybT family proteins are crucial for the in vivo survival of bacterial pathogens during host infection. YybT family proteins contain an N-terminal domain that shares minimum sequence homology with Per-ARNT-Sim (PAS) domains. Despite the lack of an apparent residue for heme coordination, the putative PAS domains of BsYybT and GtYybT, two representative members of the YybT family proteins from Bacillus subtilis and Geobacillus thermodenitrificans, respectively, are found to bind b-type heme with 1:1 stoichiometry. Heme binding suppresses the catalytic activity of the DHH/DHHA1 phosphodiesterase domain and the degenerate GGDEF domain. Absorption spectroscopic studies indicate that YybT proteins do not form stable oxyferrous complexes due to the rapid oxidation of the ferrous iron upon O(2) binding. The ferrous heme, however, forms a hexacoordinated complex with carbon monoxide (CO) and a pentacoordinated complex with nitric oxide (NO). The coordination of NO, but not CO, to the heme stimulates the phosphodiesterase activity. These results suggest that YybT family proteins function as stress-signaling proteins for monitoring cellular heme or the NO level by using a heme-binding PAS domain that features an unconventional heme coordination environment.
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87
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Abstract
Per-Arnt-Sim (PAS) domains occur in proteins from all kingdoms of life. In the bacterial kingdom, PAS domains are commonly positioned at the amino terminus of signaling proteins such as sensor histidine kinases, cyclic-di-GMP synthases/hydrolases, and methyl-accepting chemotaxis proteins. Although these domains are highly divergent at the primary sequence level, the structures of dozens of PAS domains across a broad section of sequence space have been solved, revealing a conserved three-dimensional architecture. An all-versus-all alignment of 63 PAS structures demonstrates that the PAS domain family forms structural clades on the basis of two principal variables: (a) topological location inside or outside the plasma membrane and (b) the class of small molecule that they bind. The binding of a chemically diverse range of small-molecule metabolites is a hallmark of the PAS domain family. PAS ligand binding either functions as a primary cue to initiate a cellular signaling response or provides the domain with the capacity to respond to secondary physical or chemical signals such as gas molecules, redox potential, or photons. This review synthesizes the current state of knowledge of the structural foundations and evolution of ligand recognition and binding by PAS domains.
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Affiliation(s)
- Jonathan T. Henry
- The Committee on Microbiology, The University of Chicago, Chicago, IL 60637
| | - Sean Crosson
- The Committee on Microbiology, The University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
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88
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Watts KJ, Taylor BL, Johnson MS. PAS/poly-HAMP signalling in Aer-2, a soluble haem-based sensor. Mol Microbiol 2010; 79:686-99. [PMID: 21255112 DOI: 10.1111/j.1365-2958.2010.07477.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Poly-HAMP domains are widespread in bacterial chemoreceptors, but previous studies have focused on receptors with single HAMP domains. The Pseudomonas aeruginosa chemoreceptor, Aer-2, has an unusual domain architecture consisting of a PAS-sensing domain sandwiched between three N-terminal and two C-terminal HAMP domains, followed by a conserved kinase control module. The structure of the N-terminal HAMP domains was recently solved, making Aer-2 the first protein with resolved poly-HAMP structure. The role of Aer-2 in P. aeruginosa is unclear, but here we show that Aer-2 can interact with the chemotaxis system of Escherichia coli to mediate repellent responses to oxygen, carbon monoxide and nitric oxide. Using this model system to investigate signalling and poly-HAMP function, we determined that the Aer-2 PAS domain binds penta-co-ordinated b-type haem and that reversible signalling requires four of the five HAMP domains. Deleting HAMP 2 and/or 3 resulted in a kinase-off phenotype, whereas deleting HAMP 4 and/or 5 resulted in a kinase-on phenotype. Overall, these data support a model in which ligand-bound Aer-2 PAS and HAMP 2 and 3 act together to relieve inhibition of the kinase control module by HAMP 4 and 5, resulting in the kinase-on state of the Aer-2 receptor.
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Affiliation(s)
- Kylie J Watts
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA 92350, USA.
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89
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Modulation of Pseudomonas aeruginosa biofilm dispersal by a cyclic-Di-GMP phosphodiesterase with a putative hypoxia-sensing domain. Appl Environ Microbiol 2010; 76:8160-73. [PMID: 20971871 DOI: 10.1128/aem.01233-10] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas aeruginosa encodes many enzymes that are potentially associated with the synthesis or degradation of the widely conserved second messenger cyclic-di-GMP (c-di-GMP). In this study, we show that mutation of rbdA, which encodes a fusion protein consisting of PAS-PAC-GGDEF-EAL multidomains, results in decreased biofilm dispersal. RbdA contains a highly conserved GGDEF domain and EAL domain, which are involved in the synthesis and degradation of c-di-GMP, respectively. However, in vivo and in vitro analyses show that the full-length RbdA protein only displays phosphodiesterase activity, causing c-di-GMP degradation. Further analysis reveals that the GGDEF domain of RbdA plays a role in activating the phosphodiesterase activity of the EAL domain in the presence of GTP. Moreover, we show that deletion of the PAS domain or substitution of the key residues implicated in sensing low-oxygen stress abrogates the functionality of RbdA. Subsequent study showed that RbdA is involved in positive regulation of bacterial motility and production of rhamnolipids, which are associated with biofilm dispersal, and in negative regulation of production of exopolysaccharides, which are required for biofilm formation. These data indicate that the c-di-GMP-degrading regulatory protein RbdA promotes biofilm dispersal through its two-pronged effects on biofilm development, i.e., downregulating biofilm formation and upregulating production of the factors associated with biofilm dispersal.
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90
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Purcell EB, McDonald CA, Palfey BA, Crosson S. An analysis of the solution structure and signaling mechanism of LovK, a sensor histidine kinase integrating light and redox signals. Biochemistry 2010; 49:6761-70. [PMID: 20593779 DOI: 10.1021/bi1006404] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Flavin-binding LOV domains are broadly conserved in plants, fungi, archaea, and bacteria. These approximately 100-residue photosensory modules are generally encoded within larger, multidomain proteins that control a range of blue light-dependent physiologies. The bacterium Caulobacter crescentus encodes a soluble LOV-histidine kinase, LovK, that regulates the adhesive properties of the cell. Full-length LovK is dimeric as are a series of systematically truncated LovK constructs containing only the N-terminal LOV sensory domain. Nonconserved sequence flanking the LOV domain functions to tune the signaling lifetime of the protein. Size exclusion chromatography and small-angle X-ray scattering (SAXS) demonstrate that the LOV sensor domain does not undergo a large conformational change in response to photon absorption. However, limited proteolysis identifies a sequence flanking the C-terminus of the LOV domain as a site of light-induced change in protein conformation and dynamics. On the basis of SAXS envelope reconstruction and bioinformatic prediction, we propose this dynamic region of structure is an extended C-terminal coiled coil that links the LOV domain to the histidine kinase domain. To test the hypothesis that LOV domain signaling is affected by cellular redox state in addition to light, we measured the reduction potential of the LovK FMN cofactor. The measured potential of -258 mV is congruent with the redox potential of Gram-negative cytoplasm during logarithmic growth (-260 to -280 mV). Thus, a fraction of LovK in the cytosol may be in the reduced state under typical growth conditions. Chemical reduction of the FMN cofactor of LovK attenuates the light-dependent ATPase activity of the protein in vitro, demonstrating that LovK can function as a conditional photosensor that is regulated by the oxidative state of the cellular environment.
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Affiliation(s)
- Erin B Purcell
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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91
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Functional analysis of the fixL/fixJ and fixK genes in Azospirillum brasilense Sp7. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0065-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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92
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Affiliation(s)
- Taku YAMASHITA
- Laboratory of Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University
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93
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Jaiswal RK, Manjeera G, Gopal B. Role of a PAS sensor domain in the Mycobacterium tuberculosis transcription regulator Rv1364c. Biochem Biophys Res Commun 2010; 398:342-9. [PMID: 20541534 DOI: 10.1016/j.bbrc.2010.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 06/06/2010] [Indexed: 02/01/2023]
Abstract
The Mycobacterium tuberculosis transcriptional regulator Rv1364c regulates the activity of the stress response sigma factor sigma(F). This multi-domain protein has several components: a signaling PAS domain and an effector segment comprising of a phosphatase, a kinase and an anti-anti-sigma factor domain. Based on Small Angle X-ray Scattering (SAXS) data, Rv1364c was recently shown to be a homo-dimer and adopt an elongated conformation in solution. The PAS domain could not be modeled into the structural envelope due to poor sequence similarity with known PAS proteins. The crystal structure of the PAS domain described here provides a structural basis for the dimerization of Rv1364c. It thus appears likely that the PAS domain regulates the anti-sigma activity of Rv1364c by oligomerization. A structural comparison with other characterized PAS domains reveal several sequence and conformational features that could facilitate ligand binding - a feature which suggests that the function of Rv1364c could potentially be governed by specific cellular signals or metabolic cues.
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Affiliation(s)
- Ravi Kumar Jaiswal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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94
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The role of PAS kinase in PASsing the glucose signal. SENSORS 2010; 10:5668-82. [PMID: 22219681 PMCID: PMC3247726 DOI: 10.3390/s100605668] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/20/2010] [Accepted: 05/12/2010] [Indexed: 01/07/2023]
Abstract
PAS kinase is an evolutionarily conserved nutrient responsive protein kinase that regulates glucose homeostasis. Mammalian PAS kinase is activated by glucose in pancreatic beta cells, and knockout mice are protected from obesity, liver triglyceride accumulation, and insulin resistance when fed a high-fat diet. Yeast PAS kinase is regulated by both carbon source and cell integrity stress and stimulates the partitioning of glucose toward structural carbohydrate biosynthesis. In our current model for PAS kinase regulation, a small molecule metabolite binds the sensory PAS domain and activates the enzyme. Although bona fide PAS kinase substrates are scarce, in vitro substrate searches provide putative targets for exploration.
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95
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Campbell AJ, Watts KJ, Johnson MS, Taylor BL. Gain-of-function mutations cluster in distinct regions associated with the signalling pathway in the PAS domain of the aerotaxis receptor, Aer. Mol Microbiol 2010; 77:575-86. [PMID: 20545849 DOI: 10.1111/j.1365-2958.2010.07231.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The Aer receptor monitors internal energy (redox) levels in Escherichia coli with an FAD-containing PAS domain. Here, we randomly mutagenized the region encoding residues 14-119 of the PAS domain and found 72 aerotaxis-defective mutants, 24 of which were gain-of-function, signal-on mutants. The mutations were mapped onto an Aer homology model based on the structure of the PAS-FAD domain in NifL from Azotobacter vinlandii. Signal-on lesions clustered in the FAD binding pocket, the beta-scaffolding and in the N-cap loop. We suggest that the signal-on lesions mimic the 'signal-on' state of the PAS domain, and therefore may be markers for the signal-in and signal-out regions of this domain. We propose that the reduction of FAD rearranges the FAD binding pocket in a way that repositions the beta-scaffolding and the N-cap loop. The resulting conformational changes are likely to be conveyed directly to the HAMP domain, and on to the kinase control module. In support of this hypothesis, we demonstrated disulphide band formation between cysteines substituted at residues N98C or I114C in the PAS beta-scaffold and residue Q248C in the HAMP AS-2 helix.
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Affiliation(s)
- Asharie J Campbell
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA 92350, USA
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96
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Cheung J, Hendrickson WA. Sensor domains of two-component regulatory systems. Curr Opin Microbiol 2010; 13:116-23. [PMID: 20223701 DOI: 10.1016/j.mib.2010.01.016] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/22/2010] [Accepted: 01/27/2010] [Indexed: 11/26/2022]
Abstract
Two-component systems regulate crucial cellular processes in microorganisms, and each comprises a homodimeric histidine kinase receptor and a cytoplasmic response regulator. Histidine kinases, often membrane associated, detect environmental input at sensor domains and propagate resulting signals to catalytic cytoplasmic transmitter domains. Recent studies on the great diversity of sensor domains reveal patterns of domain organization and biochemical properties that provide insight into mechanisms of signaling. Despite the enormous sequence variability found within sensor input domains, they fall into a relatively small number of discrete structural classes. Subtle rearrangements along a structurally labile dimer interface, in the form of possible sliding or rotational motions, are propagated from the sensor domain to the transmitter domain to modulate activity of the receptor.
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Affiliation(s)
- Jonah Cheung
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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97
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Torres-Quesada O, Oruezabal RI, Peregrina A, Jofré E, Lloret J, Rivilla R, Toro N, Jiménez-Zurdo JI. The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa. BMC Microbiol 2010; 10:71. [PMID: 20205931 PMCID: PMC2848018 DOI: 10.1186/1471-2180-10-71] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 03/06/2010] [Indexed: 01/12/2023] Open
Abstract
Background The bacterial Hfq protein is able to interact with diverse RNA molecules, including regulatory small non-coding RNAs (sRNAs), and thus it is recognized as a global post-transcriptional regulator of gene expression. Loss of Hfq has an extensive impact in bacterial physiology which in several animal pathogens influences virulence. Sinorhizobium meliloti is a model soil bacterium known for its ability to establish a beneficial nitrogen-fixing intracellular symbiosis with alfalfa. Despite the predicted general involvement of Hfq in the establishment of successful bacteria-eukaryote interactions, its function in S. meliloti has remained unexplored. Results Two independent S. meliloti mutants, 2011-3.4 and 1021Δhfq, were obtained by disruption and deletion of the hfq gene in the wild-type strains 2011 and 1021, respectively, both exhibiting similar growth defects as free-living bacteria. Transcriptomic profiling of 1021Δhfq revealed a general down-regulation of genes of sugar transporters and some enzymes of the central carbon metabolism, whereas transcripts specifying the uptake and metabolism of nitrogen sources (mainly amino acids) were more abundant than in the wild-type strain. Proteomic analysis of the 2011-3.4 mutant independently confirmed these observations. Symbiotic tests showed that lack of Hfq led to a delayed nodulation, severely compromised bacterial competitiveness on alfalfa roots and impaired normal plant growth. Furthermore, a large proportion of nodules (55%-64%) elicited by the 1021Δhfq mutant were non-fixing, with scarce content in bacteroids and signs of premature senescence of endosymbiotic bacteria. RT-PCR experiments on RNA from bacteria grown under aerobic and microoxic conditions revealed that Hfq contributes to regulation of nifA and fixK1/K2, the genes controlling nitrogen fixation, although the Hfq-mediated regulation of fixK is only aerobiosis dependent. Finally, we found that some of the recently identified S. meliloti sRNAs co-inmunoprecipitate with a FLAG-epitope tagged Hfq protein. Conclusions Our results support that the S. meliloti RNA chaperone Hfq contributes to the control of central metabolic pathways in free-living bacteria and influences rhizospheric competence, survival of the microsymbiont within the nodule cells and nitrogen fixation during the symbiotic interaction with its legume host alfalfa. The identified S. meliloti Hfq-binding sRNAs are predicted to participate in the Hfq regulatory network.
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Affiliation(s)
- Omar Torres-Quesada
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, CSIC, Profesor Albareda, 1, 18008 Granada, Spain
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98
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Tuckerman JR, Gonzalez G, Sousa EHS, Wan X, Saito JA, Alam M, Gilles-Gonzalez MA. An oxygen-sensing diguanylate cyclase and phosphodiesterase couple for c-di-GMP control. Biochemistry 2009; 48:9764-74. [PMID: 19764732 DOI: 10.1021/bi901409g] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A commonly observed coupling of sensory domains to GGDEF-class diguanylate cyclases and EAL-class phosphodiesterases has long suggested that c-di-GMP synthesizing and degrading enzymes sense environmental signals. Nevertheless, relatively few signal ligands have been identified for these sensors, and even fewer instances of in vitro switching by ligand have been demonstrated. Here we describe an Escherichia coli two-gene operon, dosCP, for control of c-di-GMP by oxygen. In this operon, the gene encoding the oxygen-sensing c-di-GMP phosphodiesterase Ec Dos (here renamed Ec DosP) follows and is translationally coupled to a gene encoding a diguanylate cyclase, here designated DosC. We present the first characterizations of DosC and a detailed study of the ligand-dose response of DosP. Our results show that DosC is a globin-coupled sensor with an apolar but accessible heme pocket that binds oxygen with a K(d) of 20 microM. The response of DosP activation to increasing oxygen concentration is a complex function of its ligand saturation such that over 80% of the activation occurs in solutions that exceed 30% of air saturation (oxygen >75 microM). Finally, we find that DosP and DosC associate into a functional complex. We conclude that the dosCP operon encodes two oxygen sensors that cooperate in the controlled production and removal of c-di-GMP.
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Affiliation(s)
- Jason R Tuckerman
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA
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99
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Plakunov VK, Shelemekh OV. Mechanisms of oxygen regulation in microorganisms. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709050026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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100
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Structure of PAS-Linked Histidine Kinase and the Response Regulator Complex. Structure 2009; 17:1333-44. [DOI: 10.1016/j.str.2009.07.016] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 07/22/2009] [Accepted: 07/29/2009] [Indexed: 11/24/2022]
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