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Bosse J, Gu J, Choi J, Roddatis V, Zhuang YB, Kani NA, Hartl A, Garcia-Fernandez M, Zhou KJ, Nicolaou A, Lippert T, Cheng J, Akbashev AR. Molecular O 2 Dimers and Lattice Instability in a Perovskite Electrocatalyst. J Am Chem Soc 2024; 146:23989-23997. [PMID: 39158716 DOI: 10.1021/jacs.4c07233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Structural degradation of oxide electrodes during the electrocatalytic oxygen evolution reaction (OER) is a major challenge in water electrolysis. Although the OER is known to induce changes in the surface layer, little is known about its effect on the bulk of the electrocatalyst and its overall phase stability. Here, we show that under OER conditions, a highly active SrCoO3-x electrocatalyst develops bulk lattice instability, which results in the formation of molecular O2 dimers inside the bulk and nanoscale amorphization induced via chemo-mechanical coupling. Using high-resolution resonant inelastic X-ray scattering and first-principles calculations, we unveil the potential-dependent evolution of lattice oxygen inside the perovskite and demonstrate that O2 dimers are stable in a densely packed crystal lattice, thus challenging the assumption that O2 dimers require sufficient interatomic spacing. We also show that the energy cost of local atomic rearrangements in SrCoO3-x becomes very low under the OER conditions, leading to an unusual amorphization under intercalation-induced stress. As a result, we propose that the amorphization energy can be calculated from the first principles and can be used to assess the stability of electrocatalysts. Our study demonstrates that extreme oxidation of electrocatalysts under OER can intrinsically destabilize the lattice and result in bulk anion redox and disorder, suggesting why some oxide materials are unstable and develop a thick amorphous layer under water electrolysis conditions.
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Affiliation(s)
- Jan Bosse
- Laboratory for Multiscale Materials Experiments, PSI Center for Neutron and Muon Sciences, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Chemistry and Applied Biosciences, Laboratory of Inorganic Chemistry, ETH Zurich, 8049 Zurich, Switzerland
| | - Jian Gu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jaewon Choi
- Diamond Light Source, Harwell Campus, Didcot OX11 0DE, U.K
| | - Vladimir Roddatis
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
| | - Yong-Bin Zhuang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Nagaarjhuna A Kani
- Laboratory for Multiscale Materials Experiments, PSI Center for Neutron and Muon Sciences, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Chemistry and Applied Biosciences, Laboratory of Inorganic Chemistry, ETH Zurich, 8049 Zurich, Switzerland
| | - Anna Hartl
- Laboratory for Multiscale Materials Experiments, PSI Center for Neutron and Muon Sciences, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Chemistry and Applied Biosciences, Laboratory of Inorganic Chemistry, ETH Zurich, 8049 Zurich, Switzerland
- Center for Photon Science, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | | - Ke-Jin Zhou
- Diamond Light Source, Harwell Campus, Didcot OX11 0DE, U.K
| | - Alessandro Nicolaou
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette 91190, France
| | - Thomas Lippert
- Laboratory for Multiscale Materials Experiments, PSI Center for Neutron and Muon Sciences, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Chemistry and Applied Biosciences, Laboratory of Inorganic Chemistry, ETH Zurich, 8049 Zurich, Switzerland
| | - Jun Cheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Laboratory of AI for Electrochemistry, IKKEM, Xiamen 361005, China
| | - Andrew R Akbashev
- Laboratory for Multiscale Materials Experiments, PSI Center for Neutron and Muon Sciences, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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2
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Keppner A, Correia M, Santambrogio S, Koay TW, Maric D, Osterhof C, Winter DV, Clerc A, Stumpe M, Chalmel F, Dewilde S, Odermatt A, Kressler D, Hankeln T, Wenger RH, Hoogewijs D. Androglobin, a chimeric mammalian globin, is required for male fertility. eLife 2022; 11:72374. [PMID: 35700329 PMCID: PMC9249397 DOI: 10.7554/elife.72374] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Spermatogenesis is a highly specialized differentiation process driven by a dynamic gene expression program and ending with the production of mature spermatozoa. Whereas hundreds of genes are known to be essential for male germline proliferation and differentiation, the contribution of several genes remains uncharacterized. The predominant expression of the latest globin family member, androglobin (Adgb), in mammalian testis tissue prompted us to assess its physiological function in spermatogenesis. Adgb knockout mice display male infertility, reduced testis weight, impaired maturation of elongating spermatids, abnormal sperm shape, and ultrastructural defects in microtubule and mitochondrial organization. Epididymal sperm from Adgb knockout animals display multiple flagellar malformations including coiled, bifid or shortened flagella, and erratic acrosomal development. Following immunoprecipitation and mass spectrometry, we could identify septin 10 (Sept10) as interactor of Adgb. The Sept10-Adgb interaction was confirmed both in vivo using testis lysates and in vitro by reciprocal co-immunoprecipitation experiments. Furthermore, the absence of Adgb leads to mislocalization of Sept10 in sperm, indicating defective manchette and sperm annulus formation. Finally, in vitro data suggest that Adgb contributes to Sept10 proteolysis in a calmodulin-dependent manner. Collectively, our results provide evidence that Adgb is essential for murine spermatogenesis and further suggest that Adgb is required for sperm head shaping via the manchette and proper flagellum formation.
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Affiliation(s)
- Anna Keppner
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Miguel Correia
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | | | - Teng Wei Koay
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Darko Maric
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Carina Osterhof
- Institute for Organismic and Molecular Evolutionary Biology, University of Mainz, Mainz, Germany
| | - Denise V Winter
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Angèle Clerc
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Michael Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Alex Odermatt
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Dieter Kressler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Thomas Hankeln
- Institute for Organismic and Molecular Evolutionary Biology, University of Mainz, Mainz, Germany
| | - Roland H Wenger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - David Hoogewijs
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
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3
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Patterson DC, Ruiz MP, Yoon H, Walker JA, Armache JP, Yennawar NH, Weinert EE. Differential ligand-selective control of opposing enzymatic activities within a bifunctional c-di-GMP enzyme. Proc Natl Acad Sci U S A 2021; 118:e2100657118. [PMID: 34475207 PMCID: PMC8433548 DOI: 10.1073/pnas.2100657118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/02/2021] [Indexed: 01/23/2023] Open
Abstract
Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a second messenger that modulates bacterial cellular processes, including biofilm formation. While proteins containing both c-di-GMP synthesizing (GGDEF) and c-di-GMP hydrolyzing (EAL) domains are widely predicted in bacterial genomes, it is poorly understood how domains with opposing enzymatic activity are regulated within a single polypeptide. Herein, we report the characterization of a globin-coupled sensor protein (GCS) from Paenibacillus dendritiformis (DcpG) with bifunctional c-di-GMP enzymatic activity. DcpG contains a regulatory sensor globin domain linked to diguanylate cyclase (GGDEF) and phosphodiesterase (EAL) domains that are differentially regulated by gas binding to the heme; GGDEF domain activity is activated by the Fe(II)-NO state of the globin domain, while EAL domain activity is activated by the Fe(II)-O2 state. The in vitro activity of DcpG is mimicked in vivo by the biofilm formation of P. dendritiformis in response to gaseous environment, with nitric oxide conditions leading to the greatest amount of biofilm formation. The ability of DcpG to differentially control GGDEF and EAL domain activity in response to ligand binding is likely due to the unusual properties of the globin domain, including rapid ligand dissociation rates and high midpoint potentials. Using structural information from small-angle X-ray scattering and negative stain electron microscopy studies, we developed a structural model of DcpG, providing information about the regulatory mechanism. These studies provide information about full-length GCS protein architecture and insight into the mechanism by which a single regulatory domain can selectively control output domains with opposing enzymatic activities.
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Affiliation(s)
- Dayna C Patterson
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Myrrh Perez Ruiz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Hyerin Yoon
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | | | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Emily E Weinert
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802;
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
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4
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Increased c-di-GMP Levels Lead to the Production of Alginates of High Molecular Mass in Azotobacter vinelandii. J Bacteriol 2020; 202:JB.00134-20. [PMID: 32989088 DOI: 10.1128/jb.00134-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
Azotobacter vinelandii produces the linear exopolysaccharide alginate, a compound of significant biotechnological importance. The biosynthesis of alginate in A. vinelandii and Pseudomonas aeruginosa has several similarities but is regulated somewhat differently in the two microbes. Here, we show that the second messenger cyclic dimeric GMP (c-di-GMP) regulates the production and the molecular mass of alginate in A. vinelandii The hybrid protein MucG, containing conserved GGDEF and EAL domains and N-terminal HAMP and PAS domains, behaved as a c-di-GMP phosphodiesterase (PDE). This activity was found to negatively affect the amount and molecular mass of the polysaccharide formed. On the other hand, among the diguanylate cyclases (DGCs) present in A. vinelandii, AvGReg, a globin-coupled sensor (GCS) DGC that directly binds to oxygen, was identified as the main c-di-GMP-synthesizing contributor to alginate production. Overproduction of AvGReg in the parental strain phenocopied a ΔmucG strain with regard to alginate production and the molecular mass of the polymer. MucG was previously shown to prevent the synthesis of high-molecular-mass alginates in response to reduced oxygen transfer rates (OTRs). In this work, we show that cultures exposed to reduced OTRs accumulated higher levels of c-di-GMP; this finding strongly suggests that at least one of the molecular mechanisms involved in modulation of alginate production and molecular mass by oxygen depends on a c-di-GMP signaling module that includes the PAS domain-containing PDE MucG and the GCS DGC AvGReg.IMPORTANCE c-di-GMP has been widely recognized for its essential role in the production of exopolysaccharides in bacteria, such as alginate produced by Pseudomonas and Azotobacter spp. This study reveals that the levels of c-di-GMP also affect the physical properties of alginate, favoring the production of high-molecular-mass alginates in response to lower OTRs. This finding opens up new alternatives for the design of tailor-made alginates for biotechnological applications.
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5
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Lessons from the post-genomic era: Globin diversity beyond oxygen binding and transport. Redox Biol 2020; 37:101687. [PMID: 32863222 PMCID: PMC7475203 DOI: 10.1016/j.redox.2020.101687] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Vertebrate hemoglobin (Hb) and myoglobin (Mb) were among the first proteins whose structures and sequences were determined over 50 years ago. In the subsequent pregenomic period, numerous related proteins came to light in plants, invertebrates and bacteria, that shared the myoglobin fold, a signature sequence motif characteristic of a 3-on-3 α-helical sandwich. Concomitantly, eukaryote and bacterial globins with a truncated 2-on-2 α-helical fold were discovered. Genomic information over the last 20 years has dramatically expanded the list of known globins, demonstrating their existence in a limited number of archaeal genomes, a majority of bacterial genomes and an overwhelming majority of eukaryote genomes. In vertebrates, 6 additional globin types were identified, namely neuroglobin (Ngb), cytoglobin (Cygb), globin E (GbE), globin X (GbX), globin Y (GbY) and androglobin (Adgb). Furthermore, functions beyond the familiar oxygen transport and storage have been discovered within the vertebrate globin family, including NO metabolism, peroxidase activity, scavenging of free radicals, and signaling functions. The extension of the knowledge on globin functions suggests that the original roles of bacterial globins must have been enzymatic, involved in defense against NO toxicity, and perhaps also as sensors of O2, regulating taxis away or towards high O2 concentrations. In this review, we aimed to discuss the evolution and remarkable functional diversity of vertebrate globins with particular focus on the variety of non-canonical expression sites of mammalian globins and their according impressive variability of atypical functions.
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Germani F, Nardini M, De Schutter A, Cuypers B, Berghmans H, Van Hauwaert ML, Bruno S, Mozzarelli A, Moens L, Van Doorslaer S, Bolognesi M, Pesce A, Dewilde S. Structural and Functional Characterization of the Globin-Coupled Sensors of Azotobacter vinelandii and Bordetella pertussis. Antioxid Redox Signal 2020; 32:378-395. [PMID: 31559835 DOI: 10.1089/ars.2018.7690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aims: Structural and functional characterization of the globin-coupled sensors (GCSs) from Azotobacter vinelandii (AvGReg) and Bordetella pertussis (BpeGReg). Results: Ultraviolet/visible and resonance Raman spectroscopies confirm the presence in AvGReg and BpeGReg of a globin domain capable of reversible gaseous ligand binding. In AvGReg, an influence of the transmitter domain on the heme proximal region of the globin domain can be seen, and k'CO is higher than for other GCSs. The O2 binding kinetics suggests the presence of an open and a closed conformation. As for BpeGReg, the fully oxygenated AvGReg show a very high diguanylate cyclase activity. The carbon monoxide rebinding to BpeGReg indicates that intra- and intermolecular interactions influence the ligand binding. The globin domains of both proteins (AvGReg globin domain and BpeGRegGb with cysteines (Cys16, 45, 114, 154) mutated to serines [BpeGReg-Gb*]) share the same GCS fold, a similar proximal but a different distal side structure. They homodimerize through a G-H helical bundle as in other GCSs. However, BpeGReg-Gb* shows also a second dimerization mode. Innovation: This article extends our knowledge on the GCS proteins and contributes to a better understanding of the GCSs role in the formation of bacterial biofilms. Conclusions:AvGReg and BpeGReg conform to the GCS family, share a similar overall structure, but they have different properties in terms of the ligand binding. In particular, AvGReg shows an open and a closed conformation that in the latter form will very tightly bind oxygen. BpeGReg has only one closed conformation. In both proteins, it is the fully oxygenated GCS form that catalyzes the production of the second messenger.
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Affiliation(s)
- Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | - Amy De Schutter
- Department of Physics, University of Antwerp, Wilrijk, Belgium
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Wilrijk, Belgium
| | - Herald Berghmans
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | | | - Stefano Bruno
- Department of Food and Drugs, University of Parma, Parma, Italy
| | | | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | | | | | | | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
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7
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Lengalova A, Fojtikova-Proskova V, Vavra J, Martínek V, Stranava M, Shimizu T, Martinkova M. Kinetic analysis of a globin-coupled diguanylate cyclase, YddV: Effects of heme iron redox state, axial ligands, and heme distal mutations on catalysis. J Inorg Biochem 2019; 201:110833. [PMID: 31520879 DOI: 10.1016/j.jinorgbio.2019.110833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/03/2019] [Accepted: 09/05/2019] [Indexed: 12/19/2022]
Abstract
Heme-based oxygen sensors allow bacteria to regulate their activity based on local oxygen levels. YddV, a globin-coupled oxygen sensor with diguanylate cyclase activity from Escherichia coli, regulates cyclic-di-GMP synthesis based on oxygen availability. Stable and active samples of the full-length YddV protein were prepared by attaching it to maltose binding protein (MBP). To better understand the full-length protein's structure, the interactions between its domains were examined by performing a kinetic analysis. The diguanylate cyclase reaction catalyzed by YddV-MBP exhibited Michaelis-Menten kinetics. Its pH optimum was 8.5-9.0, and catalysis required either Mg2+ or Mn2+; other divalent metal ions gave no activity. The most active form of YddV-MBP had a 5-coordinate Fe(III) heme complex; its kinetic parameters were KmGTP 84 ± 21 μM and kcat 1.2 min-1. YddV-MBP with heme Fe(II), heme Fe(II)-O2, and heme Fe(II)-CO complexes had kcat values of 0.3 min-1, 0.95 min-1, and 0.3 min-1, respectively, suggesting that catalysis is regulated by the heme iron's redox state and axial ligand binding. The kcat values for heme Fe(III) complexes of L65G, L65Q, and Y43A YddV-MBP mutants bearing heme distal amino acid replacements were 0.15 min-1, 0.26 min-1 and 0.54 min-1, respectively, implying that heme distal residues play key regulatory roles by mediating signal transduction between the sensing and functional domains. Ultracentrifugation and size exclusion chromatography experiments showed that YddV-MBP is primarily dimeric in solution, with a sedimentation coefficient around 8. The inactive heme-free H93A mutant is primarily octameric, suggesting that catalytically active dimer formation requires heme binding.
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Affiliation(s)
- Alzbeta Lengalova
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Veronika Fojtikova-Proskova
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Jakub Vavra
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Václav Martínek
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Martin Stranava
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Marketa Martinkova
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic.
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8
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Wan X, Saito JA, Newhouse JS, Hou S, Alam M. The importance of conserved amino acids in heme-based globin-coupled diguanylate cyclases. PLoS One 2017; 12:e0182782. [PMID: 28792538 PMCID: PMC5549716 DOI: 10.1371/journal.pone.0182782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 02/05/2023] Open
Abstract
Globin-coupled diguanylate cyclases contain globin, middle, and diguanylate cyclase domains that sense O2 to synthesize c-di-GMP and regulate bacterial motility, biofilm formation, and virulence. However, relatively few studies have extensively examined the roles of individual residues and domains of globin-coupled diguanylate cyclases, which can shed light on their signaling mechanisms and provide drug targets. Here, we report the critical residues of two globin-coupled diguanylate cyclases, EcGReg from Escherichia coli and BpeGReg from Bordetella pertussis, and show that their diguanylate cyclase activity requires an intact globin domain. In the distal heme pocket of the globin domain, residues Phe42, Tyr43, Ala68 (EcGReg)/Ser68 (BpeGReg), and Met69 are required to maintain full diguanylate cyclase activity. The highly conserved amino acids His223/His225 and Lys224/Lys226 in the middle domain of EcGReg/BpeGReg are essential to diguanylate cyclase activity. We also identified sixteen important residues (Leu300, Arg306, Asp333, Phe337, Lys338, Asn341, Asp342, Asp350, Leu353, Asp368, Arg372, Gly374, Gly375, Asp376, Glu377, and Phe378) in the active site and inhibitory site of the diguanylate cyclase domain of EcGReg. Moreover, BpeGReg266 (residues 1–266) and BpeGReg296 (residues 1–296), which only contain the globin and middle domains, can inhibit bacterial motility. Our findings suggest that the distal residues of the globin domain affect diguanylate cyclase activity and that BpeGReg may interact with other c-di-GMP-metabolizing proteins to form mixed signaling teams.
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Affiliation(s)
- Xuehua Wan
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
- * E-mail:
| | - Jennifer A. Saito
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - James S. Newhouse
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Maqsudul Alam
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
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9
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Abstract
The discovery of the globin-coupled sensor (GCS) family of haem proteins has provided new insights into signalling proteins and pathways by which organisms sense and respond to changing oxygen levels. GCS proteins consist of a sensor globin domain linked to a variety of output domains, suggesting roles in controlling numerous cellular pathways, and behaviours in response to changing oxygen concentration. Members of this family of proteins have been identified in the genomes of numerous organisms and characterization of GCS with output domains, including methyl accepting chemotaxis proteins, kinases, and diguanylate cyclases, have yielded an understanding of the mechanism by which oxygen controls activity of GCS protein output domains, as well as downstream proteins and pathways regulated by GCS signalling. Future studies will expand our understanding of these proteins both in vitro and in vivo, likely demonstrating broad roles for GCS in controlling oxygen-dependent microbial physiology and phenotypes.
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10
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Tarnawski M, Barends TRM, Schlichting I. Structural analysis of an oxygen-regulated diguanylate cyclase. ACTA ACUST UNITED AC 2015; 71:2158-77. [PMID: 26527135 DOI: 10.1107/s139900471501545x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/18/2015] [Indexed: 11/10/2022]
Abstract
Cyclic di-GMP is a bacterial second messenger that is involved in switching between motile and sessile lifestyles. Given the medical importance of biofilm formation, there has been increasing interest in understanding the synthesis and degradation of cyclic di-GMPs and their regulation in various bacterial pathogens. Environmental cues are detected by sensing domains coupled to GGDEF and EAL or HD-GYP domains that have diguanylate cyclase and phosphodiesterase activities, respectively, producing and degrading cyclic di-GMP. The Escherichia coli protein DosC (also known as YddV) consists of an oxygen-sensing domain belonging to the class of globin sensors that is coupled to a C-terminal GGDEF domain via a previously uncharacterized middle domain. DosC is one of the most strongly expressed GGDEF proteins in E. coli, but to date structural information on this and related proteins is scarce. Here, the high-resolution structural characterization of the oxygen-sensing globin domain, the middle domain and the catalytic GGDEF domain in apo and substrate-bound forms is described. The structural changes between the iron(III) and iron(II) forms of the sensor globin domain suggest a mechanism for oxygen-dependent regulation. The structural information on the individual domains is combined into a model of the dimeric DosC holoprotein. These findings have direct implications for the oxygen-dependent regulation of the activity of the cyclase domain.
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Affiliation(s)
- Miroslaw Tarnawski
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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11
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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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12
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Roy J, Sen Santara S, Adhikari A, Mukherjee A, Adak S. Control of catalysis in globin coupled adenylate cyclase by a globin-B domain. Arch Biochem Biophys 2015; 579:85-90. [PMID: 26095616 DOI: 10.1016/j.abb.2015.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
The globin coupled heme containing adenylate cyclase from Leishmania major (HemAC-Lm) has two globin domains (globin-A and globin-B). Globin-B domain (210-360 amino acids) may guide the interaction between globin-A and adenylate cyclase domains for the regulation of catalysis. We investigated the role of globin-B domain in HemAC-Lm by constructing a series of mutants namely Δ209 (209 amino acids deleted), Δ360 (360 amino acids deleted), H161A, H311A and H311A-Δ209. Spectroscopic data suggest that the Δ209 and H311A-Δ209 proteins to be Fe(2+)-O2 form and apo form, respectively, indicating that His311 residue in the globin-B domain is crucial for heme binding in Δ209 protein. However, the H311A mutant is still of the Fe(2+)-O2 form whereas H161A mutant shows the apo form, indicating that only His161 residue in the globin-A domain is responsible for heme binding in full length enzyme. cAMP measurements suggest that the activities of Δ360 and Δ209 proteins were ∼10 and ∼1000 times lesser than full length enzyme, respectively, leading to the fact that globin-B domain inhibited catalysis rather than activation in absence of globin-A domain. These data suggest that the O2 bound globin-A domain in HemAC-Lm allows the best cooperation of the catalytic domain interactions to generate optimum cAMP.
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Affiliation(s)
- Jayasree Roy
- Division of Structural Biology and Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Sumit Sen Santara
- Division of Structural Biology and Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Ayan Adhikari
- Division of Structural Biology and Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Aditi Mukherjee
- Division of Structural Biology and Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Subrata Adak
- Division of Structural Biology and Bio-informatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India.
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13
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Pavlou A, Martínková M, Shimizu T, Kitanishi K, Stranava M, Loullis A, Pinakoulaki E. Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy. Phys Chem Chem Phys 2015; 17:17007-15. [DOI: 10.1039/c5cp01708d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present time-resolved step-scan FTIR evidence for the role of the distal Y43 and L65 residues in controlling the ligand dynamics in the signal transducer protein YddV.
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Affiliation(s)
- Andrea Pavlou
- Department of Chemistry
- University of Cyprus
- 1678 Nicosia
- Cyprus
| | - Markéta Martínková
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Toru Shimizu
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Kenichi Kitanishi
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Martin Stranava
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Andreas Loullis
- Department of Chemistry
- University of Cyprus
- 1678 Nicosia
- Cyprus
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14
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Stranava M, Martínková M, Stiborová M, Man P, Kitanishi K, Muchová L, Vítek L, Martínek V, Shimizu T. Introduction of water into the heme distal side by Leu65 mutations of an oxygen sensor, YddV, generates verdoheme and carbon monoxide, exerting the heme oxygenase reaction. J Inorg Biochem 2014; 140:29-38. [PMID: 25046385 DOI: 10.1016/j.jinorgbio.2014.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/21/2014] [Accepted: 06/16/2014] [Indexed: 12/26/2022]
Abstract
The globin-coupled oxygen sensor, YddV, is a heme-based oxygen sensor diguanylate cyclase. Oxygen binding to the heme Fe(II) complex in the N-terminal sensor domain of this enzyme substantially enhances its diguanylate cyclase activity which is conducted in the C-terminal functional domain. Leu65 is located on the heme distal side and is important for keeping the stability of the heme Fe(II)-O2 complex by preventing the entry of the water molecule to the heme complex. In the present study, it was found that (i) Escherichia coli-overexpressed and purified L65N mutant of the isolated heme-bound domain of YddV (YddV-heme) contained the verdoheme iron complex and other modified heme complexes as determined by optical absorption spectroscopy and mass spectrometry; (ii) CO was generated in the reconstituted system composed of heme-bound L65N and NADPH:cytochrome P450 reductase as confirmed by gas chromatography; (iii) CO generation of heme-bound L65N in the reconstituted system was inhibited by superoxide dismutase and catalase. In a concordance with the result, the reactive oxygen species increased the CO generation; (iv) the E. coli cells overexpressing the L65N protein of YddV-heme also formed significant amounts of CO compared to the cells overexpressing the wild type protein; (v) generation of verdoheme and CO was also observed for other mutants at Leu65 as well, but to a lesser extent. Since Leu65 mutations are assumed to introduce the water molecule into the heme distal side of YddV-heme, it is suggested that the water molecule would significantly contribute to facilitating heme oxygenase reactions for the Leu65 mutants.
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Affiliation(s)
- Martin Stranava
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
| | - Markéta Martínková
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic.
| | - Marie Stiborová
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
| | - Petr Man
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic; Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, Prague 4, Czech Republic
| | - Kenichi Kitanishi
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
| | - Lucie Muchová
- Institute of Medical Biochemistry and Laboratory Diagnostics, 1(st) Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Libor Vítek
- Institute of Medical Biochemistry and Laboratory Diagnostics, 1(st) Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Václav Martínek
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
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15
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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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16
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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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17
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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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18
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Gardner PR. Hemoglobin: a nitric-oxide dioxygenase. SCIENTIFICA 2012; 2012:683729. [PMID: 24278729 PMCID: PMC3820574 DOI: 10.6064/2012/683729] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/04/2012] [Indexed: 05/09/2023]
Abstract
Members of the hemoglobin superfamily efficiently catalyze nitric-oxide dioxygenation, and when paired with native electron donors, function as NO dioxygenases (NODs). Indeed, the NOD function has emerged as a more common and ancient function than the well-known role in O2 transport-storage. Novel hemoglobins possessing a NOD function continue to be discovered in diverse life forms. Unique hemoglobin structures evolved, in part, for catalysis with different electron donors. The mechanism of NOD catalysis by representative single domain hemoglobins and multidomain flavohemoglobin occurs through a multistep mechanism involving O2 migration to the heme pocket, O2 binding-reduction, NO migration, radical-radical coupling, O-atom rearrangement, nitrate release, and heme iron re-reduction. Unraveling the physiological functions of multiple NODs with varying expression in organisms and the complexity of NO as both a poison and signaling molecule remain grand challenges for the NO field. NOD knockout organisms and cells expressing recombinant NODs are helping to advance our understanding of NO actions in microbial infection, plant senescence, cancer, mitochondrial function, iron metabolism, and tissue O2 homeostasis. NOD inhibitors are being pursued for therapeutic applications as antibiotics and antitumor agents. Transgenic NOD-expressing plants, fish, algae, and microbes are being developed for agriculture, aquaculture, and industry.
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Affiliation(s)
- Paul R. Gardner
- Miami Valley Biotech, 1001 E. 2nd Street, Suite 2445, Dayton, OH 45402, USA
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19
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Nakajima K, Kitanishi K, Kobayashi K, Kobayashi N, Igarashi J, Shimizu T. Leu65 in the heme distal side is critical for the stability of the Fe(II)–O2 complex of YddV, a globin-coupled oxygen sensor diguanylate cyclase. J Inorg Biochem 2012; 108:163-70. [DOI: 10.1016/j.jinorgbio.2011.09.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/12/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
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20
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Giordano D, Russo R, Ciaccio C, Howes BD, di Prisco G, Marden MC, Hui Bon Hoa G, Smulevich G, Coletta M, Verde C. Ligand- and proton-linked conformational changes of the ferrous 2/2 hemoglobin of Pseudoalteromonas haloplanktis TAC125. IUBMB Life 2012; 63:566-73. [PMID: 21698762 DOI: 10.1002/iub.492] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The spectroscopic and ligand-binding properties of a 2/2 globin from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 have been studied in the ferrous state. It displays two major conformations characterized by CO-association rates that differ by a factor of 20, with relative fractions that depend on pH. A dynamic equilibrium is found between the two conformations, as indicated by an enhanced slower phase when lower CO levels were used to allow a longer time to facilitate the transition. The deoxy form, in the absence of external ligands, is a mixture of a predominant six-coordinate low spin form and a five-coordinate high-spin state; the proportion of low spin increasing at alkaline pH. In addition, at temperatures above the physiological temperature of 1 °C, an enhanced tendency of the protein to oxidize is observed.
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21
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Moura A, Pereira C, Henriques I, Correia A. Novel gene cassettes and integrons in antibiotic-resistant bacteria isolated from urban wastewaters. Res Microbiol 2011; 163:92-100. [PMID: 22127350 DOI: 10.1016/j.resmic.2011.10.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 10/21/2011] [Indexed: 11/26/2022]
Abstract
In this study, the occurrence and diversity of integrons were evaluated in 697 isolates belonging to Enterobacteriaceae and Aeromonas spp. isolated from urban wastewaters. Screening of integrons was performed by dot blot hybridization and intI-positive strains were further characterized. The global prevalence of integrons was 3.73%. Three new gene cassettes were identified: a novel aadA variant (aadA17), a gene putatively involved in cell signaling (dcyA) and an open reading frame of unknown function interrupted by a novel insertion sequence (orfER.17::ISAs12). In total, thirteen different gene cassette arrays were detected, 4 representing novel integrons: intI1-dcyA-tniC, intI1-orfER.1.7::ISAs12-aadA13-qacEΔ1-sul1, intI1-aacA4-catB3-bla(OxA-10)-aadA1-qacEΔ1-sul1 and intI1-catB8-aadA17-qacEΔ1-sul1. Approximately 80% of strains were resistant to at least 3 antibiotics of different classes. The presence of novel integron structures in treated effluents suggests that domestic wastewaters may favor the formation of novel combinations of gene cassettes. Moreover, the high prevalence of multiresistant strains highlights the urgent need to employ effective means of effluent disinfection to avoid dissemination of antibiotic-resistant bacteria.
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Affiliation(s)
- Alexandra Moura
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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22
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Kitanishi K, Kobayashi K, Uchida T, Ishimori K, Igarashi J, Shimizu T. Identification and functional and spectral characterization of a globin-coupled histidine kinase from Anaeromyxobacter sp. Fw109-5. J Biol Chem 2011; 286:35522-35534. [PMID: 21852234 PMCID: PMC3195594 DOI: 10.1074/jbc.m111.274811] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/04/2011] [Indexed: 12/13/2022] Open
Abstract
Two-component signal transduction systems regulate numerous important physiological functions in bacteria. In this study we have identified, cloned, overexpressed, and characterized a dimeric full-length heme-bound (heme:protein, 1:1 stoichiometry) globin-coupled histidine kinase (AfGcHK) from Anaeromyxobacter sp. strain Fw109-5 for the first time. The Fe(III), Fe(II)-O(2), and Fe(II)-CO complexes of the protein displayed autophosphorylation activity, whereas the Fe(II) complex had no significant activity. A H99A mutant lost heme binding ability, suggesting that this residue is the heme proximal ligand. Moreover, His-183 was proposed as the autophosphorylation site based on the finding that the H183A mutant protein was not phosphorylated. The phosphate group of autophosphorylated AfGcHK was transferred to Asp-52 and Asp-169 of a response regulator, as confirmed from site-directed mutagenesis experiments. Based on the amino acid sequences and crystal structures of other globin-coupled oxygen sensor enzymes, Tyr-45 was assumed to be the O(2) binding site at the heme distal side. The O(2) dissociation rate constant, 0.10 s(-1), was substantially increased up to 8.0 s(-1) upon Y45L mutation. The resonance Raman frequencies representing ν(Fe-O2) (559 cm(-1)) and ν(O-O) (1149 cm(-1)) of the Fe(II)-O(2) complex of Y45F mutant AfGcHK were distinct from those of the wild-type protein (ν(Fe-O2), 557 cm(-1); ν(O-O), 1141 cm(-1)), supporting the proposal that Tyr-45 is located at the distal side and forms hydrogen bonds with the oxygen molecule bound to the Fe(II) complex. Thus, we have successfully identified and characterized a novel heme-based globin-coupled oxygen sensor histidine kinase, AfGcHK, in this study.
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Affiliation(s)
- Kenichi Kitanishi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kazuo Kobayashi
- Institute of Scientific and Industrial Research, Osaka University, Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Jotaro Igarashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Toru Shimizu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan.
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Kitanishi K, Kobayashi K, Kawamura Y, Ishigami I, Ogura T, Nakajima K, Igarashi J, Tanaka A, Shimizu T. Important Roles of Tyr43 at the Putative Heme Distal Side in the Oxygen Recognition and Stability of the Fe(II)−O2 Complex of YddV, a Globin-Coupled Heme-Based Oxygen Sensor Diguanylate Cyclase. Biochemistry 2010; 49:10381-93. [DOI: 10.1021/bi100733q] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kenichi Kitanishi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kazuo Kobayashi
- Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Yuriko Kawamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Izumi Ishigami
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Kyosuke Nakajima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Jotaro Igarashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Atsunari Tanaka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Toru Shimizu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
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Carbon monoxide in biology and microbiology: surprising roles for the "Detroit perfume". Adv Microb Physiol 2009; 56:85-167. [PMID: 20943125 DOI: 10.1016/s0065-2911(09)05603-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbon monoxide (CO) is a colorless, odorless gas with a reputation for being an anthropogenic poison; there is extensive documentation of the modes of human exposure, toxicokinetics, and health effects. However, CO is also generated endogenously by heme oxygenases (HOs) in mammals and microbes, and its extraordinary biological activities are now recognized and increasingly utilized in medicine and physiology. This review introduces recent advances in CO biology and chemistry and illustrates the exciting possibilities that exist for a deeper understanding of its biological consequences. However, the microbiological literature is scant and is currently restricted to: 1) CO-metabolizing bacteria, CO oxidation by CO dehydrogenase (CODH) and the CO-sensing mechanisms that enable CO oxidation; 2) the use of CO as a heme ligand in microbial biochemistry; and 3) very limited information on how microbes respond to CO toxicity. We demonstrate how our horizons in CO biology have been extended by intense research activity in recent years in mammalian and human physiology and biochemistry. CO is one of several "new" small gas molecules that are increasingly recognized for their profound and often beneficial biological activities, the others being nitric oxide (NO) and hydrogen sulfide (H2S). The chemistry of CO and other heme ligands (oxygen, NO, H2S and cyanide) and the implications for biological interactions are briefly presented. An important advance in recent years has been the development of CO-releasing molecules (CO-RMs) for aiding experimental administration of CO as an alternative to the use of CO gas. The chemical principles of CO-RM design and mechanisms of CO release from CO-RMs (dissociation, association, reduction and oxidation, photolysis, and acidification) are reviewed and we present a survey of the most commonly used CO-RMs. Amongst the most important new applications of CO in mammalian physiology and medicine are its vasoactive properties and the therapeutic potentials of CO-RMs in vascular disease, anti-inflammatory effects, CO-mediated cell signaling in apoptosis, applications in organ preservation, and the effects of CO on mitochondrial function. The very limited literature on microbial growth responses to CO and CO-RMs in vitro, and the transcriptomic and physiological consequences of microbial exposure to CO and CO-RMs are reviewed. There is current interest in CO and CO-RMs as antimicrobial agents, particularly in the control of bacterial infections. Future prospects are suggested and unanswered questions posed.
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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: 176] [Impact Index Per Article: 11.7] [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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26
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Sawai H, Yoshioka S, Uchida T, Hyodo M, Hayakawa Y, Ishimori K, Aono S. Molecular oxygen regulates the enzymatic activity of a heme-containing diguanylate cyclase (HemDGC) for the synthesis of cyclic di-GMP. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:166-72. [PMID: 19818878 DOI: 10.1016/j.bbapap.2009.09.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 09/24/2009] [Accepted: 09/29/2009] [Indexed: 12/27/2022]
Abstract
We have studied the structural and enzymatic properties of a diguanylate cyclase from an obligatory anaerobic bacterium Desulfotalea psychrophila, which consists of the N-terminal sensor domain and the C-terminal diguanylate cyclase domain. The sensor domain shows an amino acid sequence homology and spectroscopic properties similar to those of the sensor domains of the globin-coupled sensor proteins containing a protoheme. This heme-containing diguanylate cyclase catalyzes the formation of cyclic di-GMP from GTP only when the heme in the sensor domain binds molecular oxygen. When the heme is in the ferric, deoxy, CO-bound, or NO-bound forms, no enzymatic activity is observed. Resonance Raman spectroscopy reveals that Tyr55 forms a hydrogen bond with the heme-bound O(2), but not with CO. Instead, Gln81 interacts with the heme-bound CO. These differences of a hydrogen bonding network will play a crucial role for the selective O(2) sensing responsible for the regulation of the enzymatic activity.
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Affiliation(s)
- Hitomi Sawai
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi 444-8787, Japan
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Green J, Crack JC, Thomson AJ, LeBrun NE. Bacterial sensors of oxygen. Curr Opin Microbiol 2009; 12:145-51. [DOI: 10.1016/j.mib.2009.01.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 01/19/2009] [Accepted: 01/22/2009] [Indexed: 12/23/2022]
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Pesce A, Thijs L, Nardini M, Desmet F, Sisinni L, Gourlay L, Bolli A, Coletta M, Van Doorslaer S, Wan X, Alam M, Ascenzi P, Moens L, Bolognesi M, Dewilde S. HisE11 and HisF8 provide bis-histidyl heme hexa-coordination in the globin domain of Geobacter sulfurreducens globin-coupled sensor. J Mol Biol 2008; 386:246-60. [PMID: 19109973 DOI: 10.1016/j.jmb.2008.12.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 12/05/2008] [Accepted: 12/09/2008] [Indexed: 02/08/2023]
Abstract
Among heme-based sensors, recent phylogenomic and sequence analyses have identified 34 globin coupled sensors (GCS), to which an aerotactic or gene-regulating function has been tentatively ascribed. Here, the structural and biochemical characterization of the globin domain of the GCS from Geobacter sulfurreducens (GsGCS(162)) is reported. A combination of X-ray crystallography (crystal structure at 1.5 A resolution), UV-vis and resonance Raman spectroscopy reveals the ferric GsGCS(162) as an example of bis-histidyl hexa-coordinated GCS. In contrast to the known hexa-coordinated globins, the distal heme-coordination in ferric GsGCS(162) is provided by a His residue unexpectedly located at the E11 topological site. Furthermore, UV-vis and resonance Raman spectroscopy indicated that ferrous deoxygenated GsGCS(162) is a penta-/hexa-coordinated mixture, and the heme hexa-to-penta-coordination transition does not represent a rate-limiting step for carbonylation kinetics. Lastly, electron paramagnetic resonance indicates that ferrous nitrosylated GsGCS(162) is a penta-coordinated species, where the proximal HisF8-Fe bond is severed.
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Affiliation(s)
- Alessandra Pesce
- Department of Physics, CNISM and Center for Excellence in Biomedical Research, University of Genova, Via Dodecaneso, 33, I-16146 Genova, Italy
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Finlay BJ, Esteban GF. Oxygen sensing drives predictable migrations in a microbial community. Environ Microbiol 2008; 11:81-5. [PMID: 18803645 DOI: 10.1111/j.1462-2920.2008.01742.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Oxygen sensing is widely practised by aerobic organisms ranging from bacteria to vertebrates, and a dominant oxygen-sensing mechanism may persist among all aerobes. We traced population migrations of 10 species of the larger aerobic ciliated protozoa living in lake sediment, and in the 15 m water column of Esthwaite Water in the English Lake District (UK). In so doing, we discovered that the character and dynamics of the lake sediment and water column were remarkably predictable in performance over a continuous period of almost 2 years. Increasing warming of the lake sediment, coupled with low oxygen tension, resulted in the emergence of aerobic ciliates out of the sediment and their migration into the water column. And with the annual collapse of thermal stratification in the water column, the whole annual cycle was repeated. In an unusual discovery, we found that particular ciliate species seemed to be 'linked' to other (functionally different) ciliate species partners via the ambient oxygen tension. The favoured hypothesis is that all ciliate species in a particular body-size range seek out a particular, preferred oxygen tension. If that is the case, the 'cement' providing the cohesion of the ciliate community might actually be the preferred oxygen tension. The principal aim of our study is to clarify the microbial migration itself, not the response of the different ciliate species to oxygen gradients once they have established themselves in the water column. The latter happens once the organisms have migrated out of the sediment together, driven by the ambient oxygen tension.
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Affiliation(s)
- Bland J Finlay
- Queen Mary University of London, School of Biological and Chemical Sciences, The River Laboratory, Wareham BH20 6BB, UK.
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