1
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Williams MT, Yee E, Larson GW, Apiche EA, Rama Damodaran A, Bhagi-Damodaran A. Metalloprotein enabled redox signal transduction in microbes. Curr Opin Chem Biol 2023; 76:102331. [PMID: 37311385 PMCID: PMC10524656 DOI: 10.1016/j.cbpa.2023.102331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 06/15/2023]
Abstract
Microbes utilize numerous metal cofactor-containing proteins to recognize and respond to constantly fluctuating redox stresses in their environment. Gaining an understanding of how these metalloproteins sense redox events, and how they communicate such information downstream to DNA to modulate microbial metabolism, is a topic of great interest to both chemists and biologists. In this article, we review recently characterized examples of metalloprotein sensors, focusing on the coordination and oxidation state of the metals involved, how these metals are able to recognize redox stimuli, and how the signal is transmitted beyond the metal center. We discuss specific examples of iron, nickel, and manganese-based microbial sensors, and identify gaps in knowledge in the field of metalloprotein-based signal transduction pathways.
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Affiliation(s)
- Murphi T Williams
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Eaindra Yee
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Grant W Larson
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Elizabeth A Apiche
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA.
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2
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Yoo BK, Kruglik SG, Lambry JC, Lamarre I, Raman CS, Nioche P, Negrerie M. The H-NOX protein structure adapts to different mechanisms in sensors interacting with nitric oxide. Chem Sci 2023; 14:8408-8420. [PMID: 37564404 PMCID: PMC10411614 DOI: 10.1039/d3sc01685d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Some classes of bacteria within phyla possess protein sensors identified as homologous to the heme domain of soluble guanylate cyclase, the mammalian NO-receptor. Named H-NOX domain (Heme-Nitric Oxide or OXygen-binding), their heme binds nitric oxide (NO) and O2 for some of them. The signaling pathways where these proteins act as NO or O2 sensors appear various and are fully established for only some species. Here, we investigated the reactivity of H-NOX from bacterial species toward NO with a mechanistic point of view using time-resolved spectroscopy. The present data show that H-NOXs modulate the dynamics of NO as a function of temperature, but in different ranges, changing its affinity by changing the probability of NO rebinding after dissociation in the picosecond time scale. This fundamental mechanism provides a means to adapt the heme structural response to the environment. In one particular H-NOX sensor the heme distortion induced by NO binding is relaxed in an ultrafast manner (∼15 ps) after NO dissociation, contrarily to other H-NOX proteins, providing another sensing mechanism through the H-NOX domain. Overall, our study links molecular dynamics with functional mechanism and adaptation.
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Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Sergei G Kruglik
- Laboratoire Jean Perrin, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS 75005 Paris France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - C S Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore Maryland 21201 USA
| | - Pierre Nioche
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, UMR S1124, Centre Universitaire des Saints-Pères, Université Paris Descartes 75006 Paris France
- Structural and Molecular Analysis Platform, BioMedTech Facilities, INSERM US36-CNRS-UMS2009, Paris Université Paris France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
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3
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Yu Z, Zhang W, Yang H, Chou SH, Galperin MY, He J. Gas and light: triggers of c-di-GMP-mediated regulation. FEMS Microbiol Rev 2023; 47:fuad034. [PMID: 37339911 PMCID: PMC10505747 DOI: 10.1093/femsre/fuad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.
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Affiliation(s)
- Zhaoqing Yu
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, Jiangsu 210014, PR China
| | - Wei Zhang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - He Yang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jin He
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
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4
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Liu R, Kang Y, Chen L. NO binds to the distal site of haem in the fully activated soluble guanylate cyclase. Nitric Oxide 2023; 134-135:17-22. [PMID: 36972843 DOI: 10.1016/j.niox.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/09/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO). The binding of NO to the haem of sGC induces a large conformational change in the enzyme and activates its cyclase activity. However, whether NO binds to the proximal site or the distal site of haem in the fully activated state remains under debate. Here, we present cryo-EM maps of sGC in the NO-activated state at high resolutions, allowing the observation of the density of NO. These cryo-EM maps show the binding of NO to the distal site of haem in the NO-activated state.
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Affiliation(s)
- Rui Liu
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, 100871, China; National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Yunlu Kang
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, 100871, China; National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Lei Chen
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, 100871, China; National Biomedical Imaging Center, Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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5
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Williams DE, Nesbitt NM, Muralidharan S, Hossain S, Boon EM. H-NOX Regulates Biofilm Formation in Agrobacterium Vitis in Response to NO. Biochemistry 2023; 62:912-922. [PMID: 36746768 DOI: 10.1021/acs.biochem.2c00639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transitions between motile and biofilm lifestyles are highly regulated and fundamental to microbial pathogenesis. H-NOX (heme-nitric oxide/oxygen-binding domain) is a key regulator of bacterial communal behaviors, such as biofilm formation. A predicted bifunctional cyclic di-GMP metabolizing enzyme, composed of diguanylate cyclase and phosphodiesterase (PDE) domains (avi_3097), is annotated downstream of an hnoX gene in Agrobacterium vitis S4. Here, we demonstrate that avH-NOX is a nitric oxide (NO)-binding hemoprotein that binds to and regulates the activity of avi_3097 (avHaCE; H-NOX-associated cyclic di-GMP processing enzyme). Kinetic analysis of avHaCE indicates a ∼four-fold increase in PDE activity in the presence of NO-bound avH-NOX. Biofilm analysis with crystal violet staining reveals that low concentrations of NO reduce biofilm growth in the wild-type A. vitis S4 strain, but the mutant ΔhnoX strain has no NO phenotype, suggesting that H-NOX is responsible for the NO biofilm phenotype in A. vitis. Together, these data indicate that avH-NOX enhances cyclic di-GMP degradation to reduce biofilm formation in response to NO in A. vitis.
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Affiliation(s)
- Dominique E Williams
- Department of Chemistry and Institute of Chemical Biology and Drug Design, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Natasha M Nesbitt
- Department of Chemistry and Institute of Chemical Biology and Drug Design, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Sandhya Muralidharan
- Department of Chemistry and Institute of Chemical Biology and Drug Design, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Sajjad Hossain
- Department of Chemistry and Institute of Chemical Biology and Drug Design, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Elizabeth M Boon
- Department of Chemistry and Institute of Chemical Biology and Drug Design, Stony Brook University, Stony Brook, New York 11794-3400, United States
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6
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Lemon CM, Nissley AJ, Latorraca NR, Wittenborn EC, Marletta MA. Corrole–protein interactions in H-NOX and HasA. RSC Chem Biol 2022; 3:571-581. [PMID: 35656484 PMCID: PMC9092467 DOI: 10.1039/d2cb00004k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/20/2022] [Indexed: 02/04/2023] Open
Abstract
Mutagenesis was utilised to reveal corrole–protein interactions in H-NOX and HasA. The key interaction is a hydrogen bond between the PO unit of the corrole and a protonated histidine residue.
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Affiliation(s)
- Christopher M. Lemon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720, USA
| | - Amos J. Nissley
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Naomi R. Latorraca
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720, USA
| | - Elizabeth C. Wittenborn
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Michael A. Marletta
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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7
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H-NOX proteins in the virulence of pathogenic bacteria. Biosci Rep 2021; 42:230559. [PMID: 34939646 PMCID: PMC8738867 DOI: 10.1042/bsr20212014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 12/05/2022] Open
Abstract
Nitric oxide (NO) is a toxic gas encountered by bacteria as a product of their own metabolism or as a result of a host immune response. Non-toxic concentrations of NO have been shown to initiate changes in bacterial behaviors such as the transition between planktonic and biofilm-associated lifestyles. The heme nitric oxide/oxygen binding proteins (H-NOX) are a widespread family of bacterial heme-based NO sensors that regulate biofilm formation in response to NO. The presence of H-NOX in several human pathogens combined with the importance of planktonic–biofilm transitions to virulence suggests that H-NOX sensing may be an important virulence factor in these organisms. Here we review the recent data on H-NOX NO signaling pathways with an emphasis on H-NOX homologs from pathogens and commensal organisms. The current state of the field is somewhat ambiguous regarding the role of H-NOX in pathogenesis. However, it is clear that H-NOX regulates biofilm in response to environmental factors and may promote persistence in the environments that serve as reservoirs for these pathogens. Finally, the evidence that large subgroups of H-NOX proteins may sense environmental signals besides NO is discussed within the context of a phylogenetic analysis of this large and diverse family.
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8
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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9
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Lemon CM, Marletta MA. Designer Heme Proteins: Achieving Novel Function with Abiological Heme Analogues. Acc Chem Res 2021; 54:4565-4575. [PMID: 34890183 PMCID: PMC8754152 DOI: 10.1021/acs.accounts.1c00588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Heme proteins have proven to be a convenient platform for the development of designer proteins with novel functionalities. This is achieved by substituting the native iron porphyrin cofactor with a heme analogue that possesses the desired properties. Replacing the iron center of the porphyrin with another metal provides one inroad to novel protein function. A less explored approach is substitution of the porphyrin cofactor with an alternative tetrapyrrole macrocycle or a related ligand. In general, these ligands exhibit chemical properties and reactivity that are distinct from those of porphyrins. While these techniques have most prominently been utilized to develop artificial metalloenzymes, there are many other applications of this methodology to problems in biochemistry, health, and medicine. Incorporation of synthetic cofactors into protein environments represents a facile way to impart water solubility and biocompatibility. It circumvents the laborious synthesis of water-soluble cofactors, which often introduces substantial charge that leads to undesired bioaccumulation. To this end, the incorporation of unnatural cofactors in heme proteins has enabled the development of designer proteins as optical oxygen sensors, MRI contrast agents, spectroscopic probes, tools to interrogate protein function, antibiotics, and fluorescent proteins.Incorporation of an artificial cofactor is frequently accomplished by denaturing the holoprotein with removal of the heme; the refolded apoprotein is then reconstituted with the artificial cofactor. This process often results in substantial protein loss and does not necessarily guarantee that the refolded protein adopts the native structure. To circumvent these issues, our laboratory has pioneered the use of the RP523 strain of E. coli to incorporate artificial cofactors into heme proteins using expression-based methods. This strain lacks the ability to biosynthesize heme, and the bacterial cell wall is permeable to heme and related molecules. In this way, heme analogues supplemented in the growth medium are incorporated into heme proteins. This approach can also be leveraged for the direct expression of the apoprotein for subsequent reconstitution.These methodologies have been exploited to incorporate non-native cofactors into heme proteins that are resistant to harsh environmental conditions: the heme nitric oxide/oxygen binding protein (H-NOX) from Caldanaerobacter subterraneus (Cs) and the heme acquisition system protein A (HasA) from Pseudomonas aeruginosa (Pa). The exceptional stability of these proteins makes them ideal scaffolds for biomedical applications. Optical oxygen sensing has been accomplished using a phosphorescent ruthenium porphyrin as the artificial heme cofactor. Paramagnetic manganese and gadolinium porphyrins yield high-relaxivity, protein-based MRI contrast agents. A fluorescent phosphorus corrole serves as a heme analogue to produce fluorescent proteins. Iron complexes of nonporphyrin cofactors bound to HasA inhibit the growth of pathogenic bacteria. Moreover, HasA can deliver a gallium phthalocyanine into the bacterial cytosol to serve as a sensitizer for photochemical sterilization. Together, these examples illustrate the potential for designer heme proteins to address burgeoning problems in the areas of health and medicine. The concepts and methodologies presented in this Account can be extended to the development of next-generation biomedical sensing and imaging agents to identify and quantify clinically relevant metabolites and other key disease biomarkers.
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10
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Wittenborn EC, Marletta MA. Structural Perspectives on the Mechanism of Soluble Guanylate Cyclase Activation. Int J Mol Sci 2021; 22:ijms22115439. [PMID: 34064029 PMCID: PMC8196705 DOI: 10.3390/ijms22115439] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 11/30/2022] Open
Abstract
The enzyme soluble guanylate cyclase (sGC) is the prototypical nitric oxide (NO) receptor in humans and other higher eukaryotes and is responsible for transducing the initial NO signal to the secondary messenger cyclic guanosine monophosphate (cGMP). Generation of cGMP in turn leads to diverse physiological effects in the cardiopulmonary, vascular, and neurological systems. Given these important downstream effects, sGC has been biochemically characterized in great detail in the four decades since its discovery. Structures of full-length sGC, however, have proven elusive until very recently. In 2019, advances in single particle cryo–electron microscopy (cryo-EM) enabled visualization of full-length sGC for the first time. This review will summarize insights revealed by the structures of sGC in the unactivated and activated states and discuss their implications in the mechanism of sGC activation.
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11
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Ultrafast dynamics of heme distortion in the O 2-sensor of a thermophilic anaerobe bacterium. Commun Chem 2021; 4:31. [PMID: 36697566 PMCID: PMC9814294 DOI: 10.1038/s42004-021-00471-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/05/2021] [Indexed: 01/28/2023] Open
Abstract
Heme-Nitric oxide and Oxygen binding protein domains (H-NOX) are found in signaling pathways of both prokaryotes and eukaryotes and share sequence homology with soluble guanylate cyclase, the mammalian NO receptor. In bacteria, H-NOX is associated with kinase or methyl accepting chemotaxis domains. In the O2-sensor of the strict anaerobe Caldanaerobacter tengcongensis (Ct H-NOX) the heme appears highly distorted after O2 binding, but the role of heme distortion in allosteric transitions was not yet evidenced. Here, we measure the dynamics of the heme distortion triggered by the dissociation of diatomics from Ct H-NOX using transient electronic absorption spectroscopy in the picosecond to millisecond time range. We obtained a spectroscopic signature of the heme flattening upon O2 dissociation. The heme distortion is immediately (<1 ps) released after O2 dissociation to produce a relaxed state. This heme conformational change occurs with different proportions depending on diatomics as follows: CO < NO < O2. Our time-resolved data demonstrate that the primary structural event of allostery is the heme distortion in the Ct H-NOX sensor, contrastingly with hemoglobin and the human NO receptor, in which the primary structural events are respectively the motion of the proximal histidine and the rupture of the iron-histidine bond.
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12
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Chen CY, Lee W, Renhowe PA, Jung J, Montfort WR. Solution structures of the Shewanella woodyi H-NOX protein in the presence and absence of soluble guanylyl cyclase stimulator IWP-051. Protein Sci 2020; 30:448-463. [PMID: 33236796 DOI: 10.1002/pro.4005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/05/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022]
Abstract
Heme-nitric oxide/oxygen binding (H-NOX) domains bind gaseous ligands for signal transduction in organisms spanning prokaryotic and eukaryotic kingdoms. In the bioluminescent marine bacterium Shewanella woodyi (Sw), H-NOX proteins regulate quorum sensing and biofilm formation. In higher animals, soluble guanylyl cyclase (sGC) binds nitric oxide with an H-NOX domain to induce cyclase activity and regulate vascular tone, wound healing and memory formation. sGC also binds stimulator compounds targeting cardiovascular disease. The molecular details of stimulator binding to sGC remain obscure but involve a binding pocket near an interface between H-NOX and coiled-coil domains. Here, we report the full NMR structure for CO-ligated Sw H-NOX in the presence and absence of stimulator compound IWP-051, and its backbone dynamics. Nonplanar heme geometry was retained using a semi-empirical quantum potential energy approach. Although IWP-051 binding is weak, a single binding conformation was found at the interface of the two H-NOX subdomains, near but not overlapping with sites identified in sGC. Binding leads to rotation of the subdomains and closure of the binding pocket. Backbone dynamics are similar across both domains except for two helix-connecting loops, which display increased dynamics that are further enhanced by compound binding. Structure-based sequence analyses indicate high sequence diversity in the binding pocket, but the pocket itself appears conserved among H-NOX proteins. The largest dynamical loop lies at the interface between Sw H-NOX and its binding partner as well as in the interface with the coiled coil in sGC, suggesting a critical role for the loop in signal transduction.
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Affiliation(s)
- Cheng-Yu Chen
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Woonghee Lee
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Chemistry, University of Colorado Denver, Denver, Colorado, USA
| | | | - Joon Jung
- Cyclerion Therapeutics, Cambridge, Massachusetts, USA
| | - William R Montfort
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
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13
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Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
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Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
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14
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Mukhopadhyay R, Chacón KN, Jarvis JM, Talipov MR, Yukl ET. Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae. Biochem J 2020; 477:1123-1136. [PMID: 32141496 PMCID: PMC7108781 DOI: 10.1042/bcj20200124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 02/07/2023]
Abstract
Bacterial heme nitric oxide/oxygen (H-NOX) domains are nitric oxide (NO) or oxygen sensors. This activity is mediated through binding of the ligand to a heme cofactor. However, H-NOX from Vibrio cholerae (Vc H-NOX) can be easily purified in a heme-free state that is capable of reversibly responding to oxidation, suggesting a heme-independent function as a redox sensor. This occurs by oxidation of Cys residues at a zinc-binding site conserved in a subset of H-NOX homologs. Remarkably, zinc is not lost from the protein upon oxidation, although its ligation environment is significantly altered. Using a combination of computational and experimental approaches, we have characterized localized structural changes that accompany the formation of specific disulfide bonds between Cys residues upon oxidation. Furthermore, the larger-scale structural changes accompanying oxidation appear to mimic those changes observed upon NO binding to the heme-bound form. Thus, Vc H-NOX and its homologs may act as both redox and NO sensors by completely separate mechanisms.
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Affiliation(s)
- Roma Mukhopadhyay
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, U.S.A
| | - Kelly N. Chacón
- Department of Chemistry, Reed College, Portland, OR 97202, U.S.A
| | - Jacqueline M. Jarvis
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, U.S.A
| | - Marat R. Talipov
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, U.S.A
| | - Erik T. Yukl
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, U.S.A
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15
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Sanyal R, Bhagi-Damodaran A. An enzymatic method for precise oxygen affinity measurements over nanomolar-to-millimolar concentration regime. J Biol Inorg Chem 2020; 25:181-186. [PMID: 31897725 DOI: 10.1007/s00775-019-01750-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
Oxygen affinity is an important property of metalloproteins that helps elucidate their reactivity profile and mechanism. Heretofore, oxygen affinity values were determined either using flash photolysis and polarography techniques that require expensive instrumentation, or using oxygen titration methods which are erroneous at low nanomolar and at high millimolar oxygen concentrations. Here, we describe an inexpensive, easy-to-setup, and a one-pot method for oxygen affinity measurements that uses the enzyme chlorite dismutase (Cld) as a precise in situ oxygen source. Using this method, we measure thermodynamic and kinetic oxygen affinities (Kd and KM) of different classes of heme and non-heme metalloproteins involved in oxygen transport, sensing, and catalysis. The method enables oxygen affinity measurements over a wide concentration range from 10 nM to 5 mM which is unattainable by simply diluting oxygen-saturated buffers. In turn, we were able to precisely measure oxygen affinities of a model set of eight different metalloproteins with affinities ranging from 48 ± 3 nM to 1.18 ± 0.03 mM. Overall, the Cld method is easy and inexpensive to set up, requires significantly lower quantities of protein, enables precise oxygen affinity measurements, and is applicable for proteins exhibiting nanomolar-to-millimolar affinity values.
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Affiliation(s)
- Ria Sanyal
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, 55455, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, 55455, USA.
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16
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Makrynitsa GI, Zompra AA, Argyriou AI, Spyroulias GA, Topouzis S. Therapeutic Targeting of the Soluble Guanylate Cyclase. Curr Med Chem 2019; 26:2730-2747. [PMID: 30621555 DOI: 10.2174/0929867326666190108095851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/13/2018] [Accepted: 04/03/2018] [Indexed: 11/22/2022]
Abstract
The soluble guanylate cyclase (sGC) is the physiological sensor for nitric oxide and alterations of its function are actively implicated in a wide variety of pathophysiological conditions. Intense research efforts over the past 20 years have provided significant information on its regulation, culminating in the rational development of approved drugs or investigational lead molecules, which target and interact with sGC through novel mechanisms. However, there are numerous questions that remain unanswered. Ongoing investigations, with the critical aid of structural chemistry studies, try to further elucidate the enzyme's structural characteristics that define the association of "stimulators" or "activators" of sGC in the presence or absence of the heme moiety, respectively, as well as the precise conformational attributes that will allow the design of more innovative and effective drugs. This review relates the progress achieved, particularly in the past 10 years, in understanding the function of this enzyme, and focusses on a) the rationale and results of its therapeutic targeting in disease situations, depending on the state of enzyme (oxidized or not, heme-carrying or not) and b) the most recent structural studies, which should permit improved design of future therapeutic molecules that aim to directly upregulate the activity of sGC.
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Affiliation(s)
| | - Aikaterini A Zompra
- Department of Pharmacy, School of Health Sciences, University of Patras, Rio, 26505, Greece
| | - Aikaterini I Argyriou
- Department of Pharmacy, School of Health Sciences, University of Patras, Rio, 26505, Greece
| | - Georgios A Spyroulias
- Department of Pharmacy, School of Health Sciences, University of Patras, Rio, 26505, Greece
| | - Stavros Topouzis
- Department of Pharmacy, School of Health Sciences, University of Patras, Rio, 26505, Greece
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17
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Horst BG, Stewart EM, Nazarian AA, Marletta MA. Characterization of a Carbon Monoxide-Activated Soluble Guanylate Cyclase from Chlamydomonas reinhardtii. Biochemistry 2019; 58:2250-2259. [DOI: 10.1021/acs.biochem.9b00190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin G. Horst
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Edna M. Stewart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Aren A. Nazarian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Michael A. Marletta
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
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18
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Abstract
SIGNIFICANCE The molecule nitric oxide (NO) has been shown to regulate behaviors in bacteria, including biofilm formation. NO detection and signaling in bacteria is typically mediated by hemoproteins such as the bis-(3',5')-cyclic dimeric adenosine monophosphate-specific phosphodiesterase YybT, the transcriptional regulator dissimilative nitrate respiration regulator, or heme-NO/oxygen binding (H-NOX) domains. H-NOX domains are well-characterized primary NO sensors that are capable of detecting nanomolar NO and influencing downstream signal transduction in many bacterial species. However, many bacteria, including the human pathogen Pseudomonas aeruginosa, respond to nanomolar concentrations of NO but do not contain an annotated H-NOX domain, indicating the existence of an additional nanomolar NO-sensing protein (NosP). Recent Advances: A newly discovered bacterial hemoprotein called NosP may also act as a primary NO sensor in bacteria, in addition to, or in place of, H-NOX. NosP was first described as a regulator of a histidine kinase signal transduction pathway that is involved in biofilm formation in P. aeruginosa. CRITICAL ISSUES The molecular details of NO signaling in bacteria are still poorly understood. There are still many bacteria that are NO responsive but do encode either H-NOX or NosP domains in their genomes. Even among bacteria that encode H-NOX or NosP, many questions remain. FUTURE DIRECTIONS The molecular mechanisms of NO regulation in many bacteria remain to be established. Future studies are required to gain knowledge about the mechanism of NosP signaling. Advancements on structural and molecular understanding of heme-based sensors in bacteria could lead to strategies to alleviate or control bacterial biofilm formation or persistent biofilm-related infections.
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Affiliation(s)
| | - Lisa-Marie Nisbett
- 2 Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York
| | - Bezalel Bacon
- 2 Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York
| | - Elizabeth Boon
- 1 Department of Chemistry, Stony Brook University , Stony Brook, New York.,2 Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York.,3 Institute of Chemical Biology and Drug Design, Stony Brook University , Stony Brook, New York
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19
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Guo Y, Cooper MM, Bromberg R, Marletta MA. A Dual-H-NOX Signaling System in Saccharophagus degradans. Biochemistry 2018; 57:6570-6580. [PMID: 30398342 DOI: 10.1021/acs.biochem.8b01058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitric oxide (NO) is a critical signaling molecule involved in the regulation of a wide variety of physiological processes across every domain of life. In most aerobic and facultative anaerobic bacteria, heme-nitric oxide/oxygen binding (H-NOX) proteins selectively sense NO and inhibit the activity of a histidine kinase (HK) located on the same operon. This NO-dependent inhibition of the cognate HK alters the phosphorylation of the downstream response regulators. In the marine bacterium Saccharophagus degradans ( Sde), in addition to a typical H-NOX ( Sde 3804)/HK ( Sde 3803) pair, an orphan H-NOX ( Sde 3557) with no associated signaling protein has been identified distant from the H-NOX/HK pair in the genome. The characterization reported here elucidates the function of both H-NOX proteins. Sde 3557 exhibits a weaker binding affinity with the kinase, yet both Sde 3804 and Sde 3557 are functional H-NOXs with proper gas binding properties and kinase inhibition activity. Additionally, Sde 3557 has an NO dissociation rate that is significantly slower than that of Sde 3804, which may confer prolonged kinase inhibition in vivo. While it is still unclear whether Sde 3557 has another signaling partner or shares the histidine kinase with Sde 3804, Sde 3557 is the only orphan H-NOX characterized to date. S. degradans is likely using a dual-H-NOX system to fine-tune the downstream response of NO signaling.
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Affiliation(s)
- Yirui Guo
- California Institute for Quantitative Biosciences , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Matthew M Cooper
- Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Raquel Bromberg
- Department of Biophysics , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Michael A Marletta
- California Institute for Quantitative Biosciences , University of California, Berkeley , Berkeley , California 94720 , United States.,Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , California 94720 , United States.,Department of Chemistry , University of California, Berkeley , Berkeley , California 94720 , United States
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20
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Guo Y, Marletta MA. Structural Insight into H‐NOX Gas Sensing and Cognate Signaling Protein Regulation. Chembiochem 2018; 20:7-19. [DOI: 10.1002/cbic.201800478] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Yirui Guo
- California Institute for Quantitative BiosciencesUniversity of California, Berkeley Berkeley, CA 94720 USA
| | - Michael A. Marletta
- California Institute for Quantitative BiosciencesUniversity of California, Berkeley Berkeley, CA 94720 USA
- Department of Molecular and Cell BiologyUniversity of California, Berkeley Berkeley, CA 94720 USA
- Department of ChemistryUniversity of California, Berkeley Berkeley, CA 94720 USA
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21
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A novel thermophilic hemoprotein scaffold for rational design of biocatalysts. J Biol Inorg Chem 2018; 23:1295-1307. [PMID: 30209579 DOI: 10.1007/s00775-018-1615-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
Hemoproteins are commonly found in nature, and involved in many important cellular processes such as oxygen transport, electron transfer, and catalysis. Rational design of hemoproteins can not only inspire novel biocatalysts but will also lead to a better understanding of structure-function relationships in native hemoproteins. Here, the heme nitric oxide/oxygen-binding protein from Caldanaerobacter subterraneus subsp. tengcongensis (TtH-NOX) is used as a novel scaffold for oxidation biocatalyst design. We show that signaling protein TtH-NOX can be reengineered to catalyze H2O2 decomposition and oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) by H2O2. In addition, the role of the distal tyrosine (Tyr140) in catalysis is investigated. The mutation of Tyr140 to alanine hinders the catalysis of the oxidation reactions. On the other hand, the mutation of Tyr140 to histidine, which is commonly observed in peroxidases, leads to a significant increase of the catalytic activity. Taken together, these results show that, while the distal histidine plays an important role in hemoprotein reactions with H2O2, it is not always essential for oxidation activity. We show that TtH-NOX protein can be used as an alternative scaffold for the design of novel biocatalysts with desired reactivity or functionality. H-NOX proteins are homologous to the nitric oxide sensor soluble guanylate cyclase. Here, we show that the gas sensor protein TtH-NOX shows limited capacity for catalysis of redox reactions and it can be used as a novel scaffold in biocatalysis design.
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22
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Horst BG, Marletta MA. Physiological activation and deactivation of soluble guanylate cyclase. Nitric Oxide 2018; 77:65-74. [PMID: 29704567 PMCID: PMC6919197 DOI: 10.1016/j.niox.2018.04.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 01/24/2023]
Abstract
Soluble guanylate cyclase (sGC) is responsible for transducing the gaseous signaling molecule nitric oxide (NO) into the ubiquitous secondary signaling messenger cyclic guanosine monophosphate in eukaryotic organisms. sGC is exquisitely tuned to respond to low levels of NO, allowing cells to respond to non-toxic levels of NO. In this review, the structure of sGC is discussed in the context of sGC activation and deactivation. The sequence of events in the activation pathway are described into a comprehensive model of in vivo sGC activation as elucidated both from studies with purified enzyme and those done in cells. This model is then used to discuss the deactivation of sGC, as well as the molecular mechanisms of pathophysiological deactivation.
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Affiliation(s)
- Benjamin G Horst
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Michael A Marletta
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
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23
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Hespen CW, Bruegger JJ, Guo Y, Marletta MA. Native Alanine Substitution in the Glycine Hinge Modulates Conformational Flexibility of Heme Nitric Oxide/Oxygen (H-NOX) Sensing Proteins. ACS Chem Biol 2018; 13:1631-1639. [PMID: 29757599 DOI: 10.1021/acschembio.8b00248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heme nitric oxide/oxygen sensing (H-NOX) domains are direct NO sensors that regulate a variety of biological functions in both bacteria and eukaryotes. Previous work on H-NOX proteins has shown that upon NO binding, a conformational change occurs along two glycine residues on adjacent helices (termed the glycine hinge). Despite the apparent importance of the glycine hinge, it is not fully conserved in all H-NOX domains. Several H-NOX sensors from the family Flavobacteriaceae contain a native alanine substitution in one of the hinge residues. In this work, the effect of the increased steric bulk within the Ala-Gly hinge on H-NOX function was investigated. The hinge in Kordia algicida OT-1 ( Ka H-NOX) is composed of A71 and G145. Ligand-binding properties and signaling function for this H-NOX were characterized. The variant A71G was designed to convert the hinge region of Ka H-NOX to the typical Gly-Gly motif. In activity assays with its cognate histidine kinase (HnoK), the wild type displayed increased signal specificity compared to A71G. Increasing titrations of unliganded A71G gradually inhibits HnoK autophosphorylation, while increasing titrations of unliganded wild type H-NOX does not inhibit HnoK. Crystal structures of both wild type and A71G Ka H-NOX were solved to 1.9 and 1.6 Å, respectively. Regions of H-NOX domains previously identified as involved in protein-protein interactions with HnoK display significantly higher b-factors in A71G compared to wild-type H-NOX. Both biochemical and structural data indicate that the hinge region controls overall conformational flexibility of the H-NOX, affecting NO complex formation and regulation of its HnoK.
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Affiliation(s)
- Charles W. Hespen
- QB3 Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
| | - Joel J. Bruegger
- QB3 Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
| | - Yirui Guo
- QB3 Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
| | - Michael A. Marletta
- QB3 Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
- Department of Chemistry, Department of Molecular and Cell Biology, QB3 Institute, University of California—Berkeley, 374B Stanley Hall, Berkeley, California 94720-3220, United States
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24
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Kearney C, Olenginski LT, Hirn TD, Fowler GD, Tariq D, Brewer SH, Phillips-Piro CM. Exploring local solvation environments of a heme protein using the spectroscopic reporter 4-cyano-l-phenylalanine. RSC Adv 2018; 8:13503-13512. [PMID: 29780583 PMCID: PMC5944249 DOI: 10.1039/c8ra02000k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/20/2018] [Indexed: 11/21/2022] Open
Abstract
The vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNF) was genetically incorporated individually at three sites (5, 36, and 78) in the heme protein Caldanaerobacter subterraneus H-NOX to probe local hydration environments. The UAA pCNF was incorporated site-specifically using an engineered, orthogonal tRNA synthetase in E. coli. The ability of all of the pCNF-containing H-NOX proteins to form the ferrous CO, NO, or O2 ligated and unligated states was confirmed with UV-Vis spectroscopy. The solvation state at each site of the three sites of pCNF incorporation was assessed using temperature-dependent infrared spectroscopy. Specifically, the frequency-temperature line slope (FTLS) method was utilized to show that the nitrile group at site 36 was fully solvated and the nitrile group at site 78 was de-solvated (buried) in the heme pocket. The nitrile group at site 5 was found to be partially solvated suggesting that the nitrile group was involved in moderate strength hydrogen bonds. These results were confirmed by the determination of the X-ray crystal structure of the H-NOX protein construct containing pCNF at site 5.
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Affiliation(s)
- Caroline Kearney
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Lukasz T Olenginski
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Trexler D Hirn
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Gwendolyn D Fowler
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Daniyal Tariq
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
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25
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Shah RC, Sanker S, Wood KC, Durgin BG, Straub AC. Redox regulation of soluble guanylyl cyclase. Nitric Oxide 2018; 76:97-104. [PMID: 29578056 DOI: 10.1016/j.niox.2018.03.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/28/2018] [Accepted: 03/19/2018] [Indexed: 11/15/2022]
Abstract
The nitric oxide/soluble guanylyl cyclase (NO-sGC) signaling pathway regulates the cardiovascular, neuronal, and gastrointestinal systems. Impaired sGC signaling can result in disease and system-wide organ failure. This review seeks to examine the redox control of sGC through heme and cysteine regulation while discussing therapeutic drugs that target various conditions. Heme regulation involves mechanisms of insertion of the heme moiety into the sGC protein, the molecules and proteins that control switching between the oxidized (Fe3+) and reduced states (Fe2+), and the activity of heme degradation. Modifications to cysteine residues by S-nitrosation on the α1 and β1 subunits of sGC have been shown to be important in sGC signaling. Moreover, redox balance and localization of sGC is thought to control downstream effects. In response to altered sGC activity due to changes in the redox state, many therapeutic drugs have been developed to target decreased NO-sGC signaling. The importance and relevance of sGC continues to grow as sGC dysregulation leads to numerous disease conditions.
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Affiliation(s)
- Rohan C Shah
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Subramaniam Sanker
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Katherine C Wood
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brittany G Durgin
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adam C Straub
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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26
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Guo Y, Iavarone AT, Cooper MM, Marletta MA. Mapping the H-NOX/HK Binding Interface in Vibrio cholerae by Hydrogen/Deuterium Exchange Mass Spectrometry. Biochemistry 2018; 57:1779-1789. [PMID: 29457883 DOI: 10.1021/acs.biochem.8b00027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme-nitric oxide/oxygen binding (H-NOX) proteins are a group of hemoproteins that bind diatomic gas ligands such as nitric oxide (NO) and oxygen (O2). H-NOX proteins typically regulate histidine kinases (HK) located within the same operon. It has been reported that NO-bound H-NOXs inhibit cognate histidine kinase autophosphorylation in bacterial H-NOX/HK complexes; however, a detailed mechanism of NO-mediated regulation of the H-NOX/HK activity remains unknown. In this study, the binding interface of Vibrio cholerae ( Vc) H-NOX/HK complex was characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) and further validated by mutagenesis, leading to a new model for NO-dependent kinase inhibition. A conformational change in Vc H-NOX introduced by NO generates a new kinase-binding interface, thus locking the kinase in an inhibitory conformation.
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27
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Wales JA, Chen CY, Breci L, Weichsel A, Bernier SG, Sheppeck JE, Solinga R, Nakai T, Renhowe PA, Jung J, Montfort WR. Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase. J Biol Chem 2017; 293:1850-1864. [PMID: 29222330 DOI: 10.1074/jbc.ra117.000457] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/18/2017] [Indexed: 11/06/2022] Open
Abstract
Soluble guanylyl cyclase (sGC) is the receptor for nitric oxide and a highly sought-after therapeutic target for the management of cardiovascular diseases. New compounds that stimulate sGC show clinical promise, but where these stimulator compounds bind and how they function remains unknown. Here, using a photolyzable diazirine derivative of a novel stimulator compound, IWP-051, and MS analysis, we localized drug binding to the β1 heme domain of sGC proteins from the hawkmoth Manduca sexta and from human. Covalent attachments to the stimulator were also identified in bacterial homologs of the sGC heme domain, referred to as H-NOX domains, including those from Nostoc sp. PCC 7120, Shewanella oneidensis, Shewanella woodyi, and Clostridium botulinum, indicating that the binding site is highly conserved. The identification of photoaffinity-labeled peptides was aided by a signature MS fragmentation pattern of general applicability for unequivocal identification of covalently attached compounds. Using NMR, we also examined stimulator binding to sGC from M. sexta and bacterial H-NOX homologs. These data indicated that stimulators bind to a conserved cleft between two subdomains in the sGC heme domain. L12W/T48W substitutions within the binding pocket resulted in a 9-fold decrease in drug response, suggesting that the bulkier tryptophan residues directly block stimulator binding. The localization of stimulator binding to the sGC heme domain reported here resolves the longstanding question of where stimulators bind and provides a path forward for drug discovery.
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Affiliation(s)
- Jessica A Wales
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
| | - Cheng-Yu Chen
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
| | - Linda Breci
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
| | - Andrzej Weichsel
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
| | | | | | - Robert Solinga
- Ironwood Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Takashi Nakai
- Ironwood Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Paul A Renhowe
- Ironwood Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Joon Jung
- Ironwood Pharmaceuticals, Cambridge, Massachusetts 02142
| | - William R Montfort
- From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 and
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28
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Regulation of nitric oxide signaling by formation of a distal receptor-ligand complex. Nat Chem Biol 2017; 13:1216-1221. [PMID: 28967923 PMCID: PMC5698159 DOI: 10.1038/nchembio.2488] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/28/2017] [Indexed: 12/23/2022]
Abstract
The binding of nitric oxide (NO) to the heme cofactor of heme-nitric oxide/oxygen binding (H-NOX) proteins can lead to the dissociation of the heme-ligating histidine residue and yield a five-coordinate nitrosyl complex, which is an important step for NO-dependent signaling. In the five-coordinate nitrosyl complex, NO can reside either on the distal or proximal side of the heme, which could have a profound influence over the lifetime of the in vivo signal. To investigate this central molecular question, the Shewanella oneidensis H-NOX (So H-NOX)–NO complex was biophysically characterized under limiting and excess NO. The results show that So H-NOX preferably forms a distal NO species under both limiting and excess NO. Therefore, signal strength and complex lifetime in vivo will be dictated by the dissociation rate of NO from the distal complex and the return of the histidine ligand to the heme.
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Hossain S, Nisbett LM, Boon EM. Discovery of Two Bacterial Nitric Oxide-Responsive Proteins and Their Roles in Bacterial Biofilm Regulation. Acc Chem Res 2017; 50:1633-1639. [PMID: 28605194 PMCID: PMC5654536 DOI: 10.1021/acs.accounts.7b00095] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacterial biofilms form when bacteria adhere to a surface and produce an exopolysaccharide matrix ( Costerton Science 1999 , 284 , 1318 ; Davies Science 1998 , 280 , 295 ; Flemming Nat. Rev. Microbiol. 2010 , 8 , 623 ). Because biofilms are resistant to antibiotics, they are problematic in many aspects of human health and welfare, causing, for instance, persistent fouling of medical implants such as catheters and artificial joints ( Brunetto Chimia 2008 , 62 , 249 ). They are responsible for chronic infections in the lungs of cystic fibrosis patients and in open wounds, such as those associated with burns and diabetes. They are also a major contributor to hospital-acquired infections ( Sievert Infec. Control Hosp. Epidemiol. 2013 , 34 , 1 ; Tatterson Front. Biosci. 2001 , 6 , D890 ). It has been hypothesized that effective methods of biofilm control will have widespread application ( Landini Appl. Microbiol. Biotechnol. 2010 , 86 , 813 ). A promising strategy is to target the mechanisms that drive biofilm dispersal, because dispersal results in biofilm removal and in the restoration of antibiotic sensitivity. First documented in Nitrosomonas europaea ( Schmidt J. Bacteriol. 2004 , 186 , 2781 ) and the cystic fibrosis-associated pathogen Pseudomonas aeruginosa ( Barraud J. Bacteriol. 2006 , 188 , 7344 ; J. Bacteriol. 2009 , 191 , 7333 ), regulation of biofilm formation by nanomolar levels of the diatomic gas nitric oxide (NO) has now been documented in numerous bacteria ( Barraud Microb. Biotechnol. 2009 , 2 , 370 ; McDougald Nat. Rev. Microbiol. 2012 , 10 , 39 ; Arora Biochemistry 2015 , 54 , 3717 ; Barraud Curr. Pharm. Des. 2015 , 21 , 31 ). NO-mediated pathways are, therefore, promising candidates for biofilm regulation. Characterization of the NO sensors and NO-regulated signaling pathways should allow for rational manipulation of these pathways for therapeutic applications. Several laboratories, including our own, have shown that a class of NO sensors called H-NOX (heme-nitric oxide or oxygen binding domain) affects biofilm formation by regulating intracellular cyclic di-GMP concentrations and quorum sensing ( Arora Biochemistry 2015 , 54 , 3717 ; Plate Trends Biochem. Sci. 2013 , 38 , 566 ; Nisbett Biochemistry 2016 , 55 , 4873 ). Many bacteria that respond to NO do not encode an hnoX gene, however. My laboratory has now discovered an additional family of bacterial NO sensors, called NosP (nitric oxide sensing protein). Importantly, NosP domains are widely conserved in bacteria, especially Gram-negative bacteria, where they are encoded as fusions with or in close chromosomal proximity to histidine kinases or cyclic di-GMP synthesis or phosphodiesterase enzyme, consistent with signaling. In this Account, we briefly review NO and H-NOX signaling in bacterial biofilms, describe our discovery of the NosP family, and provide support for its role in biofilm regulation in Pseudomonas aeruginosa, Vibrio cholerae, Legionella pneumophila, and Shewanella oneidensis.
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Affiliation(s)
- Sajjad Hossain
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Lisa-Marie Nisbett
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | - Elizabeth M. Boon
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
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Gaseous ligand selectivity of the H-NOX sensor protein from Shewanella oneidensis and comparison to those of other bacterial H-NOXs and soluble guanylyl cyclase. Biochimie 2017; 140:82-92. [PMID: 28655588 DOI: 10.1016/j.biochi.2017.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/23/2017] [Indexed: 01/11/2023]
Abstract
To delineate the commonalities and differences in gaseous ligand discrimination among the heme-based sensors with Heme Nitric oxide/OXygen binding protein (H-NOX) scaffold, the binding kinetic parameters for gaseous ligands NO, CO, and O2, including KD, kon, and koff, of Shewanella oneidensis H-NOX (So H-NOX) were characterized in detail in this study and compared to those of previously characterized H-NOXs from Clostridium botulinum (Cb H-NOX), Nostoc sp. (Ns H-NOX), Thermoanaerobacter tengcongensis (Tt H-NOX), Vibrio cholera (Vc H-NOX), and human soluble guanylyl cyclase (sGC), an H-NOX analogue. The KD(NO) and KD(CO) of each bacterial H-NOX or sGC follow the "sliding scale rule"; the affinities of the bacterial H-NOXs for NO and CO vary in a small range but stronger than those of sGC by at least two orders of magnitude. On the other hand, each bacterial H-NOX exhibits different characters in the stability of its 6c NO complex, reactivity with secondary NO, stability of oxyferrous heme and autoxidation to ferric heme. A facile access channel for gaseous ligands is also identified, implying that ligand access has only minimal effect on gaseous ligand selectivity of H-NOXs or sGC. This comparative study of the binding parameters of the bacterial H-NOXs and sGC provides a basis to guide future new structural and functional studies of each specific heme sensor with the H-NOX protein fold.
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Abstract
Low concentrations of nitric oxide (NO) modulate varied behaviours in bacteria including biofilm dispersal and quorum sensing-dependent light production. H-NOX (haem-nitric oxide/oxygen binding) is a haem-bound protein domain that has been shown to be involved in mediating these bacterial responses to NO in several organisms. However, many bacteria that respond to nanomolar concentrations of NO do not contain an annotated H-NOX domain. Nitric oxide sensing protein (NosP), a newly discovered bacterial NO-sensing haemoprotein, may fill this role. The focus of this review is to discuss structure, ligand binding, and activation of H-NOX proteins, as well as to discuss the early evidence for NO sensing and regulation by NosP domains. Further, these findings are connected to the regulation of bacterial biofilm phenotypes and symbiotic relationships.
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Affiliation(s)
- Bezalel Bacon
- Stony Brook University, Stony Brook, NY, United States
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Rao M, Herzik MA, Iavarone AT, Marletta MA. Nitric Oxide-Induced Conformational Changes Govern H-NOX and Histidine Kinase Interaction and Regulation in Shewanella oneidensis. Biochemistry 2017; 56:1274-1284. [PMID: 28170222 DOI: 10.1021/acs.biochem.6b01133] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nitric oxide (NO) is implicated in biofilm regulation in several bacterial families via heme-nitric oxide/oxygen binding (H-NOX) protein signaling. Shewanella oneidensis H-NOX (So H-NOX) is associated with a histidine kinase (So HnoK) encoded on the same operon, and together they form a multicomponent signaling network whereby the NO-bound state of So H-NOX inhibits So HnoK autophosphorylation activity, affecting the phosphorylation state of three response regulators. Although the conformational changes of So H-NOX upon NO binding have been structurally characterized, the mechanism of HnoK inhibition by NO-bound So H-NOX remains unclear. In the present study, the molecular details of So H-NOX and So HnoK interaction and regulation are characterized. The N-terminal domain in So HnoK was determined to be the site of H-NOX interaction, and the binding interface on So H-NOX was identified using a combination of hydrogen-deuterium exchange mass spectrometry and surface-scanning mutagenesis. Binding kinetics measurements and analytical gel filtration revealed that NO-bound So H-NOX has a tighter affinity for So HnoK compared that of H-NOX in the unliganded state, correlating binding affinity with kinase inhibition. Kinase activity assays with binding-deficient H-NOX mutants further indicate that while formation of the H-NOX-HnoK complex is required for HnoK to be catalytically active, H-NOX conformational changes upon NO-binding are necessary for HnoK inhibition.
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Affiliation(s)
- Minxi Rao
- Department of Chemistry, ‡Department of Molecular and Cell Biology, §QB3 Institute, University of California , Berkeley, California 94720, United States
| | - Mark A Herzik
- Department of Chemistry, ‡Department of Molecular and Cell Biology, §QB3 Institute, University of California , Berkeley, California 94720, United States
| | - Anthony T Iavarone
- Department of Chemistry, ‡Department of Molecular and Cell Biology, §QB3 Institute, University of California , Berkeley, California 94720, United States
| | - Michael A Marletta
- Department of Chemistry, ‡Department of Molecular and Cell Biology, §QB3 Institute, University of California , Berkeley, California 94720, United States
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Abstract
Nitric oxide (NO) is a freely diffusible, radical gas that has now been established as an integral signaling molecule in eukaryotes and bacteria. It has been demonstrated that NO signaling is initiated upon ligation to the heme iron of an H-NOX domain in mammals and in some bacteria. Bacterial H-NOX proteins have been found to interact with enzymes that participate in signaling pathways and regulate bacterial processes such as quorum sensing, biofilm formation, and symbiosis. Here, we review the biochemical characterization of these signaling pathways and, where available, describe how ligation of NO to H-NOX specifically regulates the activity of these pathways and their associated bacterial phenotypes.
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Affiliation(s)
- Lisa-Marie Nisbett
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY, 11794-3400
| | - Elizabeth M. Boon
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY, 11794-3400
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY, 11794-3400
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