1
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Potter JR, Rivera S, Young PG, Patterson DC, Namitz KE, Yennawar N, Kincaid JR, Liu Y, Weinert EE. Heme pocket modulates protein conformation and diguanylate cyclase activity of a tetrameric globin coupled sensor. J Inorg Biochem 2024; 258:112638. [PMID: 38878680 DOI: 10.1016/j.jinorgbio.2024.112638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 07/01/2024]
Abstract
Bacteria use the second messenger cyclic dimeric guanosine monophosphate (c-di-GMP) to control biofilm formation and other key phenotypes in response to environmental signals. Changes in oxygen levels can alter c-di-GMP signaling through a family of proteins termed globin coupled sensors (GCS) that contain diguanylate cyclase domains. Previous studies have found that GCS diguanylate cyclase activity is controlled by ligand binding to the heme within the globin domain, with oxygen binding resulting in the greatest increase in catalytic activity. Herein, we present evidence that heme-edge residues control O2-dependent signaling in PccGCS, a GCS protein from Pectobacterium carotovorum, by modulating heme distortion. Using enzyme kinetics, resonance Raman spectroscopy, small angle X-ray scattering, and multi-wavelength analytical ultracentrifugation, we have developed an integrated model of the full-length PccGCS tetramer and have identified conformational changes associated with ligand binding, heme conformation, and cyclase activity. Taken together, these studies provide new insights into the mechanism by which O2 binding modulates activity of diguanylate cyclase-containing GCS proteins.
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Affiliation(s)
- Jacob R Potter
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Shannon Rivera
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Paul G Young
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Dayna C Patterson
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Kevin E Namitz
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Neela Yennawar
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA.
| | - Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA; Department of Chemistry, University of Akron, Akron, OH 44325, USA.
| | - Emily E Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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2
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Schuelke-Sanchez A, Yennawar NH, Weinert EE. Oxygen-selective regulation of cyclic di-GMP synthesis by a globin coupled sensor with a shortened linking domain modulates Shewanella sp. ANA-3 biofilm. J Inorg Biochem 2024; 252:112482. [PMID: 38218138 DOI: 10.1016/j.jinorgbio.2024.112482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Bacteria utilize heme proteins, such as globin coupled sensors (GCSs), to sense and respond to oxygen levels. GCSs are predicted in almost 2000 bacterial species and consist of a globin domain linked by a central domain to a variety of output domains, including diguanylate cyclase domains that synthesize c-di-GMP, a major regulator of biofilm formation. To investigate the effects of middle domain length and heme edge residues on GCS diguanylate cyclase activity and cellular function, a putative diguanylate cyclase-containing GCS from Shewanella sp. ANA-3 (SA3GCS) was characterized. Binding of O2 to the heme resulted in activation of diguanylate cyclase activity, while NO and CO binding had minimal effects on catalysis, demonstrating that SA3GCS exhibits greater ligand selectivity for cyclase activation than many other diguanylate cyclase-containing GCSs. Small angle X-ray scattering analysis of dimeric SA3GCS identified movement of the cyclase domains away from each other, while maintaining the globin dimer interface, as a potential mechanism for regulating cyclase activity. Comparison of the Shewanella ANA-3 wild type and SA3GCS deletion (ΔSA3GCS) strains identified changes in biofilm formation, demonstrating that SA3GCS diguanylate cyclase activity modulates Shewanella phenotypes.
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Affiliation(s)
- Ariel Schuelke-Sanchez
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Emily E Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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3
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Kitanishi K, Aoyama N, Shimonaka M. Gas-Selective Catalytic Regulation by a Newly Identified Globin-Coupled Sensor Phosphodiesterase Containing an HD-GYP Domain from the Human Pathogen Vibrio fluvialis. Biochemistry 2024; 63:523-532. [PMID: 38264987 PMCID: PMC10882959 DOI: 10.1021/acs.biochem.3c00484] [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: 09/12/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/25/2024]
Abstract
Globin-coupled sensors constitute an important family of heme-based gas sensors, an emerging class of heme proteins. In this study, we have identified and characterized a globin-coupled sensor phosphodiesterase containing an HD-GYP domain (GCS-HD-GYP) from the human pathogen Vibrio fluvialis, which is an emerging foodborne pathogen of increasing public health concern. The amino acid sequence encoded by the AL536_01530 gene from V. fluvialis indicated the presence of an N-terminal globin domain and a C-terminal HD-GYP domain, with HD-GYP domains shown previously to display phosphodiesterase activity toward bis(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP), a bacterial second messenger that regulates numerous important physiological functions in bacteria, including in bacterial pathogens. Optical absorption spectral properties of GCS-HD-GYP were found to be similar to those of myoglobin and hemoglobin and of other bacterial globin-coupled sensors. The binding of O2 to the Fe(II) heme iron complex of GCS-HD-GYP promoted the catalysis of the hydrolysis of c-di-GMP to its linearized product, 5'-phosphoguanylyl-(3',5')-guanosine (pGpG), whereas CO and NO binding did not enhance the catalysis, indicating a strict discrimination of these gaseous ligands. These results shed new light on the molecular mechanism of gas-selective catalytic regulation by globin-coupled sensors, with these advances apt to lead to a better understanding of the family of globin-coupled sensors, a still growing family of heme-based gas sensors. In addition, given the importance of c-di-GMP in infection and virulence, our results suggested that GCS-HD-GYP could play an important role in the ability of V. fluvialis to sense O2 and NO in the context of host-pathogen interactions.
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Affiliation(s)
- Kenichi Kitanishi
- Department
of Chemistry, Faculty of Science, Tokyo
University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Nao Aoyama
- Department
of Chemistry, Graduate School of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Motoyuki Shimonaka
- Department
of Chemistry, Faculty of Science, Tokyo
University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
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4
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Hoque NJ, Weinert EE. Control of bacterial second messenger signaling and motility by heme-based direct oxygen-sensing proteins. Curr Opin Microbiol 2023; 76:102396. [PMID: 37864983 DOI: 10.1016/j.mib.2023.102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
Bacteria sense and respond to their environment, allowing them to maximize their survival and growth under changing conditions, such as oxygen levels. Direct oxygen-sensing proteins allow bacteria to rapidly sense concentration changes and adapt by regulating signaling pathways and/or cellular machinery. Recent work has identified roles for direct oxygen-sensing proteins in controlling second messenger levels and motility machinery, as well as effects on biofilm formation, virulence, and motility. In this review, we discuss recent progress in understanding O2-dependent regulation of cyclic di-GMP signaling and motility and highlight the emerging importance in controlling bacterial physiology and behavior.
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Affiliation(s)
- Nushrat J Hoque
- Department of Chemistry, Penn State University, University Park, PA 16802, USA
| | - Emily E Weinert
- Department of Chemistry, Penn State University, University Park, PA 16802, USA; Department of Biochemistry & Molecular Biology, Penn State University, University Park, PA 16802, USA.
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5
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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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6
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Nitric Oxide Signaling for Aerial Mycelium Formation in Streptomyces coelicolor A3(2) M145. Appl Environ Microbiol 2022; 88:e0122222. [PMID: 36354316 PMCID: PMC9746327 DOI: 10.1128/aem.01222-22] [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: 11/12/2022] Open
Abstract
Nitric oxide (NO) is a well-known signaling molecule in various organisms. Streptomyces undergoes complex morphological differentiation, similar to that of fungi. A recent study revealed a nitrogen oxide metabolic cycle that forms NO in Streptomyces coelicolor A3(2) M145. Further, endogenously produced NO serves as a signaling molecule. Here, we report that endogenously produced NO regulates cyclic 3',5'-diguanylate (c-di-GMP) levels and controls aerial mycelium formation through the c-di-GMP-binding transcriptional regulator BldD in S. coelicolor A3(2) M145. These observations provide important insights into the mechanisms regulating morphological differentiation. This is the first study to demonstrate a link between NO and c-di-GMP in S. coelicolor A3(2) M145. Morphological differentiation is closely linked to the initiation of secondary metabolism in actinomycetes. Thus, the NO signaling-based regulation of aerial mycelium formation has potential applications in the fermentation industry employing useful actinomycetes. IMPORTANCE Eukaryotic and prokaryotic cells utilize nitric oxide (NO) to regulate physiological functions. Besides its role as a producer of different bioactive substances, Streptomyces is suggested to be involved in mycelial development regulated by endogenously produced NO. However, the regulatory mechanisms are unclear. In this study, we proposed that NO signaling is involved in aerial mycelium formation in S. coelicolor A3(2) M145. NO serves as a signaling molecule for the regulation of intracellular cyclic 3',5'-diguanylate (c-di-GMP) levels, resulting in aerial mycelium formation controlled by a c-di-GMP receptor, BldD. As the abundant production of valuable secondary metabolites is closely related to the initiation of morphological differentiation in Streptomyces, NO may provide value for application in industrial fermentation by serving as a tool for regulating secondary metabolism.
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7
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Kitanishi K, Shimonaka M, Unno M. Characterization of a Cobalt-Substituted Globin-Coupled Oxygen Sensor Histidine Kinase from Anaeromyxobacter sp. Fw109-5: Insights into Catalytic Regulation by Its Heme Coordination Structure. ACS OMEGA 2021; 6:34912-34919. [PMID: 34963974 PMCID: PMC8697598 DOI: 10.1021/acsomega.1c05564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/24/2021] [Indexed: 05/09/2023]
Abstract
Heme-based gas sensors are an emerging class of heme proteins. AfGcHK, a globin-coupled histidine kinase from Anaeromyxobacter sp. Fw109-5, is an oxygen sensor enzyme in which oxygen binding to Fe(II) heme in the globin sensor domain substantially enhances its autophosphorylation activity. Here, we reconstituted AfGcHK with cobalt protoporphyrin IX (Co-AfGcHK) in place of heme (Fe-AfGcHK) and characterized the spectral and catalytic properties of the full-length proteins. Spectroscopic analyses indicated that Co(III) and Co(II)-O2 complexes were in a 6-coordinated low-spin state in Co-AfGcHK, like Fe(III) and Fe(II)-O2 complexes of Fe-AfGcHK. Although both Fe(II) and Co(II) complexes were in a 5-coordinated state, Fe(II) and Co(II) complexes were in high-spin and low-spin states, respectively. The autophosphorylation activity of Co(III) and Co(II)-O2 complexes of Co-AfGcHK was fully active, whereas that of the Co(II) complex was moderately active. This contrasts with Fe-AfGcHK, where Fe(III) and Fe(II)-O2 complexes were fully active and the Fe(II) complex was inactive. Collectively, activity data and coordination structures of Fe-AfGcHK and Co-AfGcHK indicate that all fully active forms were in a 6-coordinated low-spin state, whereas the inactive form was in a 5-coordinated high-spin state. The 5-coordinated low-spin complex was moderately active-a novel finding of this study. These results suggest that the catalytic activity of AfGcHK is regulated by its heme coordination structure, especially the spin state of its heme iron. Our study presents the first successful preparation and characterization of a cobalt-substituted globin-coupled oxygen sensor enzyme and may lead to a better understanding of the molecular mechanisms of catalytic regulation in this family.
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Affiliation(s)
- Kenichi Kitanishi
- Department
of Chemistry, Faculty of Science, Tokyo
University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
- . Tel: +81-3-3260-4272 (ex. 5738)
| | - Motoyuki Shimonaka
- Department
of Chemistry, Faculty of Science, Tokyo
University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Masaki Unno
- Graduate
School of Science and Engineering, Ibaraki
University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
- Frontier
Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
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8
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Patterson DC, Liu Y, Das S, Yennawar NH, Armache JP, Kincaid JR, Weinert EE. Heme-Edge Residues Modulate Signal Transduction within a Bifunctional Homo-Dimeric Sensor Protein. Biochemistry 2021; 60:3801-3812. [PMID: 34843212 DOI: 10.1021/acs.biochem.1c00581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bifunctional enzymes, which contain two domains with opposing enzymatic activities, are widely distributed in bacteria, but the regulatory mechanism(s) that prevent futile cycling are still poorly understood. The recently described bifunctional enzyme, DcpG, exhibits unusual heme properties and is surprisingly able to differentially regulate its two cyclic dimeric guanosine monophosphate (c-di-GMP) metabolic domains in response to heme gaseous ligands. Mutagenesis of heme-edge residues was used to probe the heme pocket and resulted in decreased O2 dissociation kinetics, identifying roles for these residues in modulating DcpG gas sensing. In addition, the resonance Raman spectra of the DcpG wild type and heme-edge mutants revealed that the mutations alter the heme electrostatic environment, vinyl group conformations, and spin state population. Using small-angle X-ray scattering and negative stain electron microscopy, the heme-edge mutations were demonstrated to cause changes to the protein conformation, which resulted in altered signaling transduction and enzyme kinetics. These findings provide insights into molecular interactions that regulate DcpG gas sensing as well as mechanisms that have evolved to control multidomain bacterial signaling proteins.
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Affiliation(s)
- Dayna C Patterson
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Sayan Das
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Emily E Weinert
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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9
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Abstract
Cyclic diguanylate (c-di-GMP) signal transduction systems provide bacteria with the ability to sense changing cell status or environmental conditions and then execute suitable physiological and social behaviors in response. In this review, we provide a comprehensive census of the stimuli and receptors that are linked to the modulation of intracellular c-di-GMP. Emerging evidence indicates that c-di-GMP networks sense light, surfaces, energy, redox potential, respiratory electron acceptors, temperature, and structurally diverse biotic and abiotic chemicals. Bioinformatic analysis of sensory domains in diguanylate cyclases and c-di-GMP-specific phosphodiesterases as well as the receptor complexes associated with them reveals that these functions are linked to a diverse repertoire of protein domain families. We describe the principles of stimulus perception learned from studying these modular sensory devices, illustrate how they are assembled in varied combinations with output domains, and summarize a system for classifying these sensor proteins based on their complexity. Biological information processing via c-di-GMP signal transduction not only is fundamental to bacterial survival in dynamic environments but also is being used to engineer gene expression circuitry and synthetic proteins with à la carte biochemical functionalities.
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10
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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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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12
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Hagiwara S, Momotake A, Ogura T, Yanagisawa S, Suzuki A, Neya S, Yamamoto Y. Effects of Heme Electronic Structure and Local Heme Environment on Catalytic Activity of a Peroxidase-Mimicking Heme-DNAzyme. Inorg Chem 2021; 60:11206-11213. [PMID: 34289695 DOI: 10.1021/acs.inorgchem.1c01179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic cycle of a peroxidase-mimicking heme-DNAzyme involves an iron(IV)oxo porphyrin π-cation radical intermediate known as compound I formed through heterolytic O-O bond cleavage of an Fe3+-bound hydroperoxo ligand (Fe-OOH) in compound 0, like that of a heme enzyme such as horseradish peroxidase (HRP). Peroxidase assaying of complexes composed of chemically modified hemes possessing various electron densities of the heme iron atom (ρFe) and parallel-stranded tetrameric G-quadruplex DNAs of oligonucleotides d(TTAGGG), d(TTAGGGT), and d(TTAGGGA) was performed to elucidate the effects of the heme electronic structure and local heme environment on the catalytic activity of the heme-DNAzyme. The study revealed that the DNAzyme activity is enhanced through an increase in the ρFe and general base catalysis of the adenine base adjacent to the heme, which are reminiscent of the "push" and "pull" mechanisms in the catalytic cycle of HRP, respectively, and that the activity of the heme-DNAzyme can be independently controlled through the heme electronic structure and local heme environment. These findings allow a deeper understanding of the structure-function relationship of the peroxidase-mimicking heme-DNAzyme.
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Affiliation(s)
- Shota Hagiwara
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Sachiko Yanagisawa
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Akihiro Suzuki
- Department of Material Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan.,Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
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13
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Kobayashi K, Kim J, Fukuda Y, Kozawa T, Inoue T. Fields, biochemistry fast autooxidation of a Bis-Histidyl-ligated globin from the anhydrobiotic tardigrade, ramazzottius varieornatus, by molecular oxygen. J Biochem 2021; 169:663-673. [PMID: 33479760 DOI: 10.1093/jb/mvab003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/27/2020] [Indexed: 01/11/2023] Open
Abstract
Tardigrades, a phylum of meiofaunal organisms, exhibit extraordinary tolerance to various environmental conditions, including extreme temperatures (-272 to 151 °C) and exposure to ionizing radiation. Proteins from anhydrobiotic tardigrades with homology to known proteins from other organisms are new potential targets for structural genomics. Recently, we reported spectroscopic and structural characterization of a hexacoordinated hemoglobin (Kumaglobin [Kgb]) found in an anhydrobiotic tardigrade. In the absence of its exogenous ligand, Kgb displays hexacoordination with distal and proximal histidines. In this work, we analyzed binding of the molecular oxygen ligand following reduction of heme in Kgb using a pulse radiolysis technique. Radiolytically generated hydrated electrons (eaq-) reduced the heme iron of Kgb within 20 µs. Subsequently, ferrous heme reacted with O2 to form a ferrous-dioxygen intermediate with a second-order rate constant of 3.0 × 106 M-1 s-1. The intermediate was rapidly (within 0.1 s) autooxidized to the ferric form. Redox potential measurements revealed an E'0 of -400 mV (vs. SHE) in the ferric/ferrous couple. Our results suggest that Kgb may serve as a physiological generator of O2·- via redox signaling and/or electron transfer.
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - JeeEun Kim
- Graduate School of Pharmaceutical Science, Osaka University, Suita, Japan
| | - Yohta Fukuda
- Graduate School of Pharmaceutical Science, Osaka University, Suita, Japan
| | - Takahiro Kozawa
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Suita, Japan
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14
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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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15
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Sousa EH, Carepo MS, Moura JJ. Nitrate-nitrite fate and oxygen sensing in dormant Mycobacterium tuberculosis: A bioinorganic approach highlighting the importance of transition metals. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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16
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Cyclic di-GMP cyclase SSFG_02181 from Streptomyces ghanaensis ATCC14672 regulates antibiotic biosynthesis and morphological differentiation in streptomycetes. Sci Rep 2020; 10:12021. [PMID: 32694623 PMCID: PMC7374567 DOI: 10.1038/s41598-020-68856-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
Streptomycetes are filamentous bacteria famous for their ability to produce a vast majority of clinically important secondary metabolites. Both complex morphogenesis and onset of antibiotic biosynthesis are tightly linked in streptomycetes and require series of specific signals for initiation. Cyclic dimeric 3′–5′ guanosine monophosphate, c-di-GMP, one of the well-known bacterial second messengers, has been recently shown to govern morphogenesis and natural product synthesis in Streptomyces by altering the activity of the pleiotropic regulator BldD. Here we report a role of the heme-binding diguanylate cyclase SSFG_02181 from Streptomyces ghanaensis in the regulation of the peptidoglycan glycosyltransferase inhibitor moenomycin A biosynthesis. Deletion of ssfg_02181 reduced the moenomycin A accumulation and led to a precocious sporulation, while the overexpression of the gene blocked sporogenesis and remarkably improved antibiotic titer. We also demonstrate that BldD negatively controls the expression of ssfg_02181, which stems from direct binding of BldD to the ssfg_02181 promoter. Notably, the heterologous expression of ssfg_02181 in model Streptomyces spp. arrested morphological progression at aerial mycelium level and strongly altered the production of secondary metabolites. Altogether, our work underscores the significance of c-di-GMP-mediated signaling in natural product biosynthesis and pointed to extensively applicable approach to increase antibiotic production levels in streptomycetes.
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17
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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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18
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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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19
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Barreto GA, Carepo MSP, Gondim ACS, Guimarães WG, Lopes LGF, Bernhardt PV, Paulo TF, Sousa EHS, Diógenes ICN. A spectroelectrochemical investigation of the heme-based sensor DevS from Mycobacterium tuberculosis: a redox versus oxygen sensor. FEBS J 2019; 286:4278-4293. [PMID: 31254441 DOI: 10.1111/febs.14974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/10/2019] [Accepted: 06/27/2019] [Indexed: 01/09/2023]
Abstract
Tuberculosis is one of the oldest known infectious diseases, responsible for millions of deaths annually around the world. The ability of Mycobacterium tuberculosis (Mtb) to enter into a dormant state has been considered integral to the success of this bacterium as a human pathogen. One of the key systems involved in regulating the entrance into dormancy is the differentially expressed in virulent strain sensor protein (DevS) [(dormancy survival sensor protein (DosS)]. However, the physiological signal for DevS has remained unclear since it was first shown to be a heme-based sensor with conflicting reports on whether it is a redox or an oxygen sensor. To address this question and provide a better understanding of the electronic properties of this protein, we present here, for the first time, a series of spectroelectrochemistry measurements of the full-length holo DevS in anaerobic conditions as well as bound to CO, NO, imidazole (Imz), cyanide, and O2 . An interesting feature of this protein is its ability to bind Imz even in the ferrous state, implying small-molecule analogues could be designed as potential regulators. Nonetheless, a midpoint potential (Em ) value of +10 mV [vs normal hydrogen electrode (NHE)] for DevS as measured under anaerobic conditions is much higher than the expected cytosolic potential for Mtb or even within stimulated macrophages (~ -270 mV vs NHE), indicating this sensor works in a reduced ferrous state. These data, along with the high oxygen affinity and very slow auto-oxidation rate of DevS, provides evidence that it is not a redox sensor. Overall, this study validates the biological function of DevS as an oxygen sensor directly involved in the dormancy/latency of Mtb.
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Affiliation(s)
- Giamwemberg A Barreto
- Laboratório de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Marta S P Carepo
- Laboratório de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil.,UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana C S Gondim
- Laboratório de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Wellinson G Guimarães
- Laboratório de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Luiz G F Lopes
- Laboratório de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Tércio F Paulo
- Laboratório de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Eduardo H S Sousa
- Laboratório de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Izaura C N Diógenes
- Laboratório de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
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20
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Kuang S, Yuan Y, Wu Z, Peng R. Expression, purification and characterization of diguanylate cyclase from Rhodococcus ruber. Protein Expr Purif 2019; 163:105441. [PMID: 31195084 DOI: 10.1016/j.pep.2019.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
Abstract
Diguanylate cyclases (DGCs) were responsible for the synthesis of second messenger cyclic di-guanosine monophosphate (c-di-GMP), which were involved in various physiological activities of bacterial species. Here, a full-length DGC from Rhodococcus ruber SD3 fused with glutathione-S-transferase (GST) was expressed in E. coli and purified by glutathione agarose resin. The apparent molecular mass of one subunit of the purified diguanylate cyclase with GST tag (GST-DGC) was estimated to be 71.9 kDa by SDS-PAGE, which was approximately in accordance with the theoretical value of 73.0 kDa. The sequence of GST-DGC was confirmed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The blue native PAGE indicated that GST-DGC formed octamer. The optimum pH and temperature for GST-DGC activity were 8.0 and 47 °C, respectively. The fusion protein exhibited high thermostability, and 94% of activity was retained when the protein was incubated at 87 °C for 1 h. Moreover, the fusion protein showed pH stability. The Km, Vmax and Kcat values for GST-DGC enzyme were 9.8 μM, 0.7 μM/min and 1.3 S-1. Some ions such as Zn2+, Mn2+, Fe2+, Ni2+ and Co2+ had inhibitory effects on the activity of the protein, while other ions such as Mg2+, K+ and Na+ slightly activated the protein. The fusion protein also showed rather high stability in the presence of toluene, cyclohexane and n-hexane.
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Affiliation(s)
- Sufang Kuang
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China
| | - Yuan Yuan
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China
| | - Zhonghao Wu
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China
| | - Ren Peng
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China.
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21
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Itoh T, Matsuura SI, Chuong TT, Tanaike O, Hamakawa S, Shimizu T. Successful Mesoporous Silica Encapsulation of Optimally Functional EcDOS (E. coli Direct Oxygen Sensor), a Heme-based O 2-Sensing Phosphodiesterase. ANAL SCI 2019; 35:329-335. [PMID: 30449836 DOI: 10.2116/analsci.18p449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The heme-based O2 sensor from Escherichia coli, EcDOS, exerts phosphodiesterase activity towards cyclic-di-GMP (c-di-GMP), an important second messenger that regulates biofilm formation, virulence, and other important functions necessary for bacterial survival. EcDOS is a two-domain protein composed of an N-terminal heme-bound O2-sensing domain and a C-terminal functional domain. O2 binding to the heme Fe(II) complex in the O2-sensing domain substantially enhances the catalytic activity of the functional domain, a property with potentially promising medical applications. Mesoporous silica is a useful material with finite-state machine-like features suitable for mediating numerous enzymatic functions. Here, we successfully encapsulated EcDOS into mesoporous silica, and demonstrated that encapsulated EcDOS was substantially activated by CO, an alternative signaling molecule used in place of O2, exhibiting the same activity as the native enzyme in aqueous solution. Encapsulated EcDOS was sufficiently stable to exert its enzymatic function over several experimental cycles under aerobic conditions at room temperature. Thus, the present study demonstrates the successful encapsulation of the heme-based O2 sensor EcDOS into mesoporous silica and shows that the native gas-stimulated function of EcDOS is well conserved. As such, this represents the first application of mesoporous silica to an oxygen-sensing-or any gas-sensing-enzyme.
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Affiliation(s)
- Tetsuji Itoh
- National Institute of Advanced Industrial Science and Technology (AIST)
| | | | - Tracy T Chuong
- National Institute of Advanced Industrial Science and Technology (AIST)
| | - Osamu Tanaike
- National Institute of Advanced Industrial Science and Technology (AIST)
| | - Satoshi Hamakawa
- National Institute of Advanced Industrial Science and Technology (AIST)
| | - Toru Shimizu
- National Institute of Advanced Industrial Science and Technology (AIST)
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22
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Rivera S, Young PG, Hoffer ED, Vansuch GE, Metzler CL, Dunham CM, Weinert EE. Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled Sensors. Inorg Chem 2018; 57:14386-14395. [PMID: 30378421 DOI: 10.1021/acs.inorgchem.8b02584] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In order to respond to external stimuli, bacteria have evolved sensor proteins linking external signals to intracellular outputs that can then regulate downstream pathways and phenotypes. Globin coupled sensor proteins (GCSs) serve to link environmental O2 levels to cellular processes by coupling a heme-containing sensor globin domain to a catalytic output domain. However, the mechanism by which O2 binding activates these proteins is currently unknown. To provide insights into the signaling mechanism, two distinct dimeric complexes of the isolated globin domain of the GCS from Bordetella pertussis ( BpeGlobin) were solved via X-ray crystallography in which differences in ligand-bound states were observed. Both monomers of one dimer contain Fe(II)-O2 states, while the other dimer consists of the Fe(III)-H2O and Fe(II)-O2 states. These data provide the first molecular insights into the heme pocket conformation of the active Fe(II)-O2 form of these enzymes. In addition, heme distortion modes and heme-protein interactions were found to correlate with the ligation state of the globin, suggesting that these conformational changes play a role in O2-dependent signaling. Fourier transform infrared spectroscopy (FTIR) of the full-length GCS from B. pertussis ( BpeGReg) and the closely related GCS from Pectobacterium carotovorum ssp. carotovorum ( PccGCS) confirmed the importance of an ordered water within the heme pocket and two distal residues (Tyr43 and Ser68) as hydrogen-bond donors. Taken together, this work provides mechanistic insights into BpeGReg O2 sensing and the signaling mechanisms of diguanylate cyclase-containing GCS proteins.
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Affiliation(s)
- Shannon Rivera
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Paul G Young
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Eric D Hoffer
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Gregory E Vansuch
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Carmen L Metzler
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Christine M Dunham
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Emily E Weinert
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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23
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Shinomiya R, Katahira Y, Araki H, Shibata T, Momotake A, Yanagisawa S, Ogura T, Suzuki A, Neya S, Yamamoto Y. Characterization of Catalytic Activities and Heme Coordination Structures of Heme-DNA Complexes Composed of Some Chemically Modified Hemes and an All Parallel-Stranded Tetrameric G-Quadruplex DNA Formed from d(TTAGGG). Biochemistry 2018; 57:5930-5937. [PMID: 30207701 DOI: 10.1021/acs.biochem.8b00793] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Heme binds selectively to the 3'-terminal G-quartet (G6 G-quartet) of an all parallel-stranded tetrameric G-quadruplex DNA, [d(TTAGGG)]4, to form a heme-DNA complex. Complexes between [d(TTAGGG)]4 and a series of chemically modified hemes possessing a heme Fe atom with a variety of electron densities were characterized in terms of their peroxidase activities to evaluate the effect of a change in the electron density of the heme Fe atom (ρFe) on their activities. The peroxidase activity of a complex decreased with a decreasing ρFe, supporting the idea that the activity of the complex is elicited through a reaction mechanism similar to that of a peroxidase. In the ferrous heme-DNA complex, carbon monoxide (CO) can bind to the heme Fe atom on the side of the heme opposite the G6 G-quartet, and a water molecule (H2O) is coordinated to the Fe atom as another axial ligand, trans to the CO. The stretching frequencies of Fe-bound CO (νCO) and the Fe-C bond (νFe-C) of CO adducts of the heme-DNA complexes were determined to investigate the structural and electronic natures of the axial ligands coordinated to the heme Fe atom. Comparison of the νCO and νFe-C values of the heme-DNA complexes with those of myoglobin (Mb) revealed that the donor strength of the axial ligation trans to the CO in a complex is considerably weaker than that of the proximal histidine in Mb, as expected from the coordination of H2O trans to the CO in the complex.
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Affiliation(s)
- Ryosuke Shinomiya
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Yuya Katahira
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Haruka Araki
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Tomokazu Shibata
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Atsuya Momotake
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science , University of Hyogo , Hyogo 678-1297 , Japan
| | - Takashi Ogura
- Graduate School of Life Science , University of Hyogo , Hyogo 678-1297 , Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, National Institute of Technology , Nagaoka College , Nagaoka 940-8532 , Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences , Chiba University , Chuoh-Inohana , Chiba 260-8675 , Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan.,Tsukuba Research Center for Energy Materials Science (TREMS) , University of Tsukuba , Tsukuba 305-8571 , Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA) , University of Tsukuba , Tsukuba 305-8577 , Japan
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24
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Tsutsui Y, Kobayashi K, Takeuchi F, Tsubaki M, Kozawa T. Reaction Intermediates of Nitric Oxide Synthase from Deinococcus radiodurans as Revealed by Pulse Radiolysis: Evidence for Intramolecular Electron Transfer from Biopterin to Fe II-O 2 Complex. Biochemistry 2018; 57:1611-1619. [PMID: 29320163 DOI: 10.1021/acs.biochem.7b00887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nitric oxide synthase (NOS) is a cytochrome P450-type mono-oxygenase that catalyzes the oxidation of l-arginine (Arg) to nitric oxide (NO) through a reaction intermediate N-hydroxy-l-arginine (NHA). The mechanism underlying the reaction catalyzed by NOS from Deinococcus radiodurans was investigated using pulse radiolysis. Radiolytically generated hydrated electrons reduced the heme iron of NOS within 2 μs. Subsequently, ferrous heme reacted with O2 to form a ferrous-dioxygen intermediate with a second-order rate constant of 2.8 × 108 M-1 s-1. In the tetrahydrofolate (H4F)-bound enzyme, the ferrous-dioxygen intermediate was found to decay an another intermediate with a first-order rate constant of 2.2 × 103 s-1. The spectrum of the intermediate featured an absorption maximum at 440 nm and an absorption minimum at 390 nm. In the absence of H4F, this step did not proceed, suggesting that H4F was reduced with the ferrous-dioxygen intermediate to form a second intermediate. The intermediate further converted to the original ferric form with a first-order rate constant of 4 s-1. A similar intermediate could be detected after pulse radiolysis in the presence of NHA, although the intermediate decayed more slowly (0.5 s-1). These data suggested that a common catalytically active intermediate involved in the substrate oxidation of both Arg and NHA may be formed during catalysis. In addition, we investigated the solvent isotope effects on the kinetics of the intermediate after pulse radiolysis. Our experiments revealed dramatic kinetic solvent isotope effects on the conversion of the intermediate to the ferric form, of 10.5 and 2.5 for Arg and NHA, respectively, whereas the faster phases were not affected. These data suggest that the proton transfer in DrNOS is the rate-limiting reaction of the intermediate with the substrates.
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Affiliation(s)
- Yuko Tsutsui
- The Institute of Scientific and Industrial Research , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan
| | - Kazuo Kobayashi
- The Institute of Scientific and Industrial Research , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan
| | - Fusako Takeuchi
- Institute for Promotion of Higher Education , Kobe University , 1-2-1 Tsurukabuto , Nada-ku, Kobe , Hyogo 657-8501 , Japan
| | - Motonari Tsubaki
- Graduate School of Science, Department of Chemistry , Kobe University , 1-1 Rokkodai-cho , Nada-ku, Kobe , Hyogo 657-8501 , Japan
| | - Takahiro Kozawa
- The Institute of Scientific and Industrial Research , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan
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25
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Burns JL, Jariwala PB, Rivera S, Fontaine BM, Briggs L, Weinert EE. Oxygen-Dependent Globin Coupled Sensor Signaling Modulates Motility and Virulence of the Plant Pathogen Pectobacterium carotovorum. ACS Chem Biol 2017; 12:2070-2077. [PMID: 28612602 DOI: 10.1021/acschembio.7b00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial pathogens utilize numerous signals to identify the presence of their host and coordinate changes in gene expression that allow for infection. Within plant pathogens, these signals typically include small molecules and/or proteins from their plant hosts and bacterial quorum sensing molecules to ensure sufficient bacterial cell density for successful infection. In addition, bacteria use environmental signals to identify conditions when the host defenses are weakened and potentially to signal entry into an appropriate host/niche for infection. A globin coupled sensor protein (GCS), termed PccGCS, within the soft rot bacterium Pectobacterium carotovorum ssp. carotovorum WPP14 has been identified as an O2 sensor and demonstrated to alter virulence factor excretion and control motility, with deletion of PccGCS resulting in decreased rotting of a potato host. Using small molecules that modulate bacterial growth and quorum sensing, PccGCS signaling also has been shown to modulate quorum sensing pathways, resulting in the PccGCS deletion strain being more sensitive to plant-derived phenolic acids, which can function as quorum sensing inhibitors, and exhibiting increased N-acylhomoserine lactone (AHL) production. These findings highlight a role for GCS proteins in controlling key O2-dependent phenotypes of pathogenic bacteria and suggest that modulating GCS signaling to limit P. carotovorum motility may provide a means to decrease rotting of plant hosts.
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Affiliation(s)
- Justin L. Burns
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Parth B. Jariwala
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Shannon Rivera
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Benjamin M. Fontaine
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Laura Briggs
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Emily E. Weinert
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
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26
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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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27
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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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28
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Burns JL, Rivera S, Deer DD, Joynt SC, Dvorak D, Weinert EE. Oxygen and Bis(3',5')-cyclic Dimeric Guanosine Monophosphate Binding Control Oligomerization State Equilibria of Diguanylate Cyclase-Containing Globin Coupled Sensors. Biochemistry 2016; 55:6642-6651. [PMID: 27933792 DOI: 10.1021/acs.biochem.6b00526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria sense their environment to alter phenotypes, including biofilm formation, to survive changing conditions. Heme proteins play important roles in sensing the bacterial gaseous environment and controlling the switch between motile and sessile (biofilm) states. Globin coupled sensors (GCS), a family of heme proteins consisting of a globin domain linked by a central domain to an output domain, are often found with diguanylate cyclase output domains that synthesize c-di-GMP, a major regulator of biofilm formation. Characterization of diguanylate cyclase-containing GCS proteins from Bordetella pertussis and Pectobacterium carotovorum demonstrated that cyclase activity is controlled by ligand binding to the heme within the globin domain. Both O2 binding to the heme within the globin domain and c-di-GMP binding to a product-binding inhibitory site (I-site) within the cyclase domain control oligomerization states of the enzymes. Changes in oligomerization state caused by c-di-GMP binding to the I-site also affect O2 kinetics within the globin domain, suggesting that shifting the oligomer equilibrium leads to broad rearrangements throughout the protein. In addition, mutations within the I-site that eliminate product inhibition result in changes to the accessible oligomerization states and decreased catalytic activity. These studies provide insight into the mechanism by which ligand binding to the heme and I-site controls activity of GCS proteins and suggests a role for oligomerization-dependent activity in vivo.
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Affiliation(s)
- Justin L Burns
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - Shannon Rivera
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - D Douglas Deer
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - Shawnna C Joynt
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - David Dvorak
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - Emily E Weinert
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
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29
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Honorio-Felício N, Carepo MS, de F. Paulo T, de França Lopes LG, Sousa EH, Diógenes IC, Bernhardt PV. The Heme-Based Oxygen Sensor Rhizobium etli FixL: Influence of Auxiliary Ligands on Heme Redox Potential and Implications on the Enzyme Activity. J Inorg Biochem 2016; 164:34-41. [DOI: 10.1016/j.jinorgbio.2016.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/05/2016] [Accepted: 08/22/2016] [Indexed: 12/09/2022]
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30
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Rivera S, Burns JL, Vansuch GE, Chica B, Weinert EE. Globin domain interactions control heme pocket conformation and oligomerization of globin coupled sensors. J Inorg Biochem 2016; 164:70-76. [PMID: 27614715 DOI: 10.1016/j.jinorgbio.2016.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/24/2022]
Abstract
Globin coupled sensors (GCS) are O2-sensing proteins used by bacteria to monitor the surrounding gaseous environment. To investigate the biphasic O2 dissociation kinetics observed for full-length GCS proteins, isolated globin domains from Pectobacterium carotovorum ssp. carotovorum (PccGlobin), and Bordetella pertussis (BpeGlobin), have been characterized. PccGlobin is found to be dimeric, while BpeGlobin is monomeric, indicating key differences in the globin domain dimer interface. Through characterization of wild type globin domains and globin variants with mutations at the dimer interface and within the distal pocket, dimerization of the globin domain is demonstrated to correlate with biphasic dissociation kinetics. Furthermore, a distal pocket tyrosine is identified as the primary hydrogen bond donor, while a secondary hydrogen bond donor within the distal heme pocket is involved in conformation(s) that lead to the second O2 dissociation rate. These findings highlight the role of the globin dimer interface in controlling properties of both the heme pocket and full-length GCS proteins.
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Affiliation(s)
- Shannon Rivera
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Justin L Burns
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Gregory E Vansuch
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Bryant Chica
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Emily E Weinert
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA.
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31
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An O2-sensing stressosome from a Gram-negative bacterium. Nat Commun 2016; 7:12381. [PMID: 27488264 PMCID: PMC4976288 DOI: 10.1038/ncomms12381] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/28/2016] [Indexed: 12/16/2022] Open
Abstract
Bacteria have evolved numerous pathways to sense and respond to changing environmental conditions, including, within Gram-positive bacteria, the stressosome complex that regulates transcription of general stress response genes. However, the signalling molecules recognized by Gram-positive stressosomes have yet to be identified, hindering our understanding of the signal transduction mechanism within the complex. Furthermore, an analogous pathway has yet to be described in Gram-negative bacteria. Here we characterize a putative stressosome from the Gram-negative bacterium Vibrio brasiliensis. The sensor protein RsbR binds haem and exhibits ligand-dependent control of the stressosome complex activity. Oxygen binding to the haem decreases activity, while ferrous RsbR results in increased activity, suggesting that the V. brasiliensis stressosome may be activated when the bacterium enters anaerobic growth conditions. The findings provide a model system for investigating ligand-dependent signalling within stressosome complexes, as well as insights into potential pathways controlled by oxygen-dependent signalling within Vibrio species.
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32
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Kobayashi K, Nakagaki M, Ishikawa H, Iwai K, O’Brian MR, Ishimori K. Redox-Dependent Dynamics in Heme-Bound Bacterial Iron Response Regulator (Irr) Protein. Biochemistry 2016; 55:4047-54. [DOI: 10.1021/acs.biochem.6b00512] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuo Kobayashi
- The
Institute of Scientific and Industrial Research, Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Megumi Nakagaki
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Haruto Ishikawa
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Kazuhiro Iwai
- Molecular
and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8561, Japan
| | - Mark R. O’Brian
- Department
of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, New York 14214, United States
| | - Koichiro Ishimori
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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33
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Fojtikova V, Bartosova M, Man P, Stranava M, Shimizu T, Martinkova M. Effects of hydrogen sulfide on the heme coordination structure and catalytic activity of the globin-coupled oxygen sensor AfGcHK. Biometals 2016; 29:715-29. [PMID: 27395436 DOI: 10.1007/s10534-016-9947-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/01/2016] [Indexed: 12/13/2022]
Abstract
AfGcHK is a globin-coupled histidine kinase that is one component of a two-component signal transduction system. The catalytic activity of this heme-based oxygen sensor is due to its C-terminal kinase domain and is strongly stimulated by the binding of O2 or CO to the heme Fe(II) complex in the N-terminal oxygen sensing domain. Hydrogen sulfide (H2S) is an important gaseous signaling molecule and can serve as a heme axial ligand, but its interactions with heme-based oxygen sensors have not been studied as extensively as those of O2, CO, and NO. To address this knowledge gap, we investigated the effects of H2S binding on the heme coordination structure and catalytic activity of wild-type AfGcHK and mutants in which residues at the putative O2-binding site (Tyr45) or the heme distal side (Leu68) were substituted. Adding Na2S to the initial OH-bound 6-coordinate Fe(III) low-spin complexes transformed them into SH-bound 6-coordinate Fe(III) low-spin complexes. The Leu68 mutants also formed a small proportion of verdoheme under these conditions. Conversely, when the heme-based oxygen sensor EcDOS was treated with Na2S, the initially formed Fe(III)-SH heme complex was quickly converted into Fe(II) and Fe(II)-O2 complexes. Interestingly, the autophosphorylation activity of the heme Fe(III)-SH complex was not significantly different from the maximal enzyme activity of AfGcHK (containing the heme Fe(III)-OH complex), whereas in the case of EcDOS the changes in coordination caused by Na2S treatment led to remarkable increases in catalytic activity.
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Affiliation(s)
- Veronika Fojtikova
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Martina Bartosova
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Petr Man
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic.,Biotechnology and Biomedicine Centre (BioCeV), Institute of Microbiology of the Czech Academy of Science, v.v.i., Prumyslova 595, Vestec, 252 42, Czech Republic
| | - Martin Stranava
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Marketa Martinkova
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2, 128 43, Czech Republic.
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34
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Donné J, Van Kerckhoven M, Maes L, Cos P, Dewilde S. The role of the globin-coupled sensor YddV in a mature E. coli biofilm population. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:835-9. [PMID: 27083533 DOI: 10.1016/j.bbapap.2016.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 11/27/2022]
Abstract
Biofilm-associated infections are hard to treat because of their high antibiotic resistance and the presence of a very persistent subpopulation of bacteria. The second messenger molecule cyclic di-guanosine monophosphate (c-di-GMP) plays a very important role in this biofilm physiology. Here, we evaluated the role of YddV, an enzyme with a c-di-GMP synthesis function, in the formation and maturation of Escherichia coli biofilms. Our results suggest that YddV stimulates biofilm growth via its role in the production of c-di-GMP and this likely by influencing the production of matrix (e.g. poly-N-acetylglucosamine (PGA)). However, lowering the YddV expression did not alter the biofilm formation since there was no significant difference between the biofilm phenotypes of WT E. coli and YddV-knockout bacteria. Additionally, YddV expression had no significant influence on the amount of persister cells within the biofilm population, questioning the use of YddV as therapeutic target.
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Affiliation(s)
- Joke Donné
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Marian Van Kerckhoven
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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35
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Kanai Y, Nishimura R, Nishiyama K, Shibata T, Yanagisawa S, Ogura T, Matsuo T, Hirota S, Neya S, Suzuki A, Yamamoto Y. Effects of Heme Electronic Structure and Distal Polar Interaction on Functional and Vibrational Properties of Myoglobin. Inorg Chem 2016; 55:1613-22. [DOI: 10.1021/acs.inorgchem.5b02520] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuki Kanai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Kotaro Nishiyama
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Sachiko Yanagisawa
- Department of Life
Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Department of Life
Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Matsuo
- Graduate School of
Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of
Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life Science
Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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36
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Lambry JC, Stranava M, Lobato L, Martinkova M, Shimizu T, Liebl U, Vos MH. Ultrafast Spectroscopy Evidence for Picosecond Ligand Exchange at the Binding Site of a Heme Protein: Heme-Based Sensor YddV. J Phys Chem Lett 2016; 7:69-74. [PMID: 26651267 DOI: 10.1021/acs.jpclett.5b02517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An important question for the functioning of heme proteins is whether different ligands present within the protein moiety can readily exchange with heme-bound ligands. Studying the dynamics of the heme domain of the Escherichia coli sensor protein YddV upon dissociation of NO from the ferric heme by ultrafast spectroscopy, we demonstrate that when the hydrophobic leucine residue in the distal heme pocket is mutated to glycine, in a substantial fraction of the protein water replaces NO as an internal ligand in as fast as ∼4 ps. This process, which is near-barrierless and occurs orders of magnitude faster than the corresponding process in myoglobin, corresponds to a ligand swap of NO with a water molecule present in the heme pocket, as corroborated by molecular dynamics simulations. Our findings provide important new insight into ligand exchange in heme proteins that functionally interact with different external ligands.
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Affiliation(s)
| | - Martin Stranava
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Hlavova (Albertov) 2030/8, Prague 4, Czech Republic
| | - Laura Lobato
- LOB, Ecole Polytechnique, CNRS, INSERM, 91128 Palaiseau Cedex, France
| | - Marketa Martinkova
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Hlavova (Albertov) 2030/8, Prague 4, Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Hlavova (Albertov) 2030/8, Prague 4, Czech Republic
| | - Ursula Liebl
- LOB, Ecole Polytechnique, CNRS, INSERM, 91128 Palaiseau Cedex, France
| | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM, 91128 Palaiseau Cedex, France
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37
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Abstract
Worldwide, infectious diseases are one of the leading causes of death among children. At least 65% of all infections are caused by the biofilm mode of bacterial growth. Bacteria colonise surfaces and grow as multicellular biofilm communities surrounded by a polymeric matrix as a common survival strategy. These sessile communities endow bacteria with high tolerance to antimicrobial agents and hence cause persistent and chronic bacterial infections, such as dental caries, periodontitis, otitis media, cystic fibrosis and pneumonia. The highly complex nature and the rapid adaptability of the biofilm population impede our understanding of the process of biofilm formation, but an important role for oxygen-binding proteins herein is clear. Much research on this bacterial lifestyle is already performed, from genome/proteome analysis to in vivo antibiotic susceptibility testing, but without significant progress in biofilm treatment or eradication. This review will present the multiple challenges of biofilm research and discuss possibilities to cross these barriers in future experimental studies.
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Affiliation(s)
- Joke Donné
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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38
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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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39
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Fojtikova V, Stranava M, Vos MH, Liebl U, Hranicek J, Kitanishi K, Shimizu T, Martinkova M. Kinetic Analysis of a Globin-Coupled Histidine Kinase, AfGcHK: Effects of the Heme Iron Complex, Response Regulator, and Metal Cations on Autophosphorylation Activity. Biochemistry 2015. [PMID: 26212354 DOI: 10.1021/acs.biochem.5b00517] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The globin-coupled histidine kinase, AfGcHK, is a part of the two-component signal transduction system from the soil bacterium Anaeromyxobacter sp. Fw109-5. Activation of its sensor domain significantly increases its autophosphorylation activity, which targets the His183 residue of its functional domain. The phosphate group of phosphorylated AfGcHK is then transferred to the cognate response regulator. We investigated the effects of selected variables on the autophosphorylation reaction's kinetics. The kcat values of the heme Fe(III)-OH(-), Fe(III)-cyanide, Fe(III)-imidazole, and Fe(II)-O2 bound active AfGcHK forms were 1.1-1.2 min(-1), and their Km(ATP) values were 18.9-35.4 μM. However, the active form bearing a CO-bound Fe(II) heme had a kcat of 1.0 min(-1) but a very high Km(ATP) value of 357 μM, suggesting that its active site structure differs strongly from the other active forms. The Fe(II) heme-bound inactive form had kcat and Km(ATP) values of 0.4 min(-1) and 78 μM, respectively, suggesting that its low activity reflects a low affinity for ATP relative to that of the Fe(III) form. The heme-free form exhibited low activity, with kcat and Km(ATP) values of 0.3 min(-1) and 33.6 μM, respectively, suggesting that the heme iron complex is essential for high catalytic activity. Overall, our results indicate that the coordination and oxidation state of the sensor domain heme iron profoundly affect the enzyme's catalytic activity because they modulate its ATP binding affinity and thus change its kcat/Km(ATP) value. The effects of the response regulator and different divalent metal cations on the autophosphorylation reaction are also discussed.
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Affiliation(s)
| | | | - Marten H Vos
- §Laboratoire d'Optique et Biosciences, INSERM U1182-CNRS UMR7645, Ecole Polytechnique, 91128 Palaiseau Cedex, France
| | - Ursula Liebl
- §Laboratoire d'Optique et Biosciences, INSERM U1182-CNRS UMR7645, Ecole Polytechnique, 91128 Palaiseau Cedex, France
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40
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Yan F, Fojtikova V, Man P, Stranava M, Martínková M, Du Y, Huang D, Shimizu T. Catalytic enhancement of the heme-based oxygen-sensing phosphodiesterase EcDOS by hydrogen sulfide is caused by changes in heme coordination structure. Biometals 2015; 28:637-52. [PMID: 25804428 DOI: 10.1007/s10534-015-9847-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 03/13/2015] [Indexed: 02/05/2023]
Abstract
EcDOS is a heme-based O2-sensing phosphodiesterase in which O2 binding to the heme iron complex in the N-terminal domain substantially enhances catalysis toward cyclic-di-GMP, which occurs in the C-terminal domain. Here, we found that hydrogen sulfide enhances the catalytic activity of full-length EcDOS, possibly owing to the admixture of 6-coordinated heme Fe(III)-SH(-) and Fe(II)-O2 complexes generated during the reaction. Alanine substitution at Met95, the axial ligand for the heme Fe(II) complex, converted the heme Fe(III) complex into the heme Fe(III)-SH(-) complex, but the addition of Na2S did not further reduce it to the heme Fe(II) complex of the Met95Ala mutant, and no subsequent formation of the heme Fe(II)-O2 complex was observed. In contrast, a Met95His mutant formed a stable heme Fe(II)-O2 complex in response to the same treatment. An Arg97Glu mutant, containing a glutamate substitution at the amino acid that interacts with O2 in the heme Fe(II)-O2 complex, formed a stable heme Fe(II) complex in response to Na2S, but this complex failed to bind O2. Interestingly, the addition of Na2S promoted formation of verdoheme (oxygen-incorporated, modified protoporphyrin IX) in an Arg97Ile mutant. Catalytic enhancement by Na2S was similar for Met95 mutants and the wild type, but significantly lower for the Arg97 mutants. Thus, this study shows the first isolation of spectrometrically separated, stable heme Fe(III)-SH(-), heme Fe(II) and heme Fe(II)-O2 complexes of full-length EcDOS with Na2S, and confirms that external-ligand-bound, 6-coordinated heme Fe(III)-SH(-) or heme Fe(II)-O2 complexes critically contribute to the Na2S-induced catalytic enhancement of EcDOS.
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Affiliation(s)
- 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, 515041, Guangdong, China
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41
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Liang ZX. The expanding roles of c-di-GMP in the biosynthesis of exopolysaccharides and secondary metabolites. Nat Prod Rep 2015; 32:663-83. [PMID: 25666534 DOI: 10.1039/c4np00086b] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The cyclic dinucleotide c-di-GMP has emerged in the last decade as a prevalent intracellular messenger that orchestrates the transition between the motile and sessile lifestyles of many bacterial species. The motile-to-sessile transition is often associated with the formation of extracellular matrix-encased biofilm, an organized community of bacterial cells that often contributes to antibiotic resistance and host-pathogen interaction. It is increasingly clear that c-di-GMP controls motility, biofilm formation and bacterial pathogenicity partially through regulating the production of exopolysaccharides (EPS) and small-molecule secondary metabolites. This review summarizes our current understanding of the regulation of EPS biosynthesis by c-di-GMP in a diversity of bacterial species and highlights the emerging role of c-di-GMP in the biosynthesis of small-molecule secondary metabolites.
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Affiliation(s)
- Zhao-Xun Liang
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551.
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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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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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Burns JL, Deer DD, Weinert EE. Oligomeric state affects oxygen dissociation and diguanylate cyclase activity of globin coupled sensors. MOLECULAR BIOSYSTEMS 2015; 10:2823-6. [PMID: 25174604 DOI: 10.1039/c4mb00366g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial biofilm formation is regulated by enzymes, such as diguanylate cyclases, that respond to environmental signals and alter c-di-GMP levels. Diguanylate cyclase activity of two globin coupled sensors is shown to be regulated by gaseous ligands, with cyclase activity and O2 dissociation affected by protein oligomeric state.
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Affiliation(s)
- Justin L Burns
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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45
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Townsley L, Yildiz FH. Temperature affects c-di-GMP signalling and biofilm formation in Vibrio cholerae. Environ Microbiol 2015; 17:4290-305. [PMID: 25684220 DOI: 10.1111/1462-2920.12799] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/19/2015] [Accepted: 01/31/2015] [Indexed: 02/04/2023]
Abstract
Biofilm formation is crucial to the environmental survival and transmission of Vibrio cholerae, the facultative human pathogen responsible for the disease cholera. During its infectious cycle, V. cholerae experiences fluctuations in temperature within the aquatic environment and during the transition between human host and aquatic reservoirs. In this study, we report that biofilm formation is induced at low temperatures through increased levels of the signalling molecule, cyclic diguanylate (c-di-GMP). Strains harbouring in frame deletions of all V. cholerae genes that are predicted to encode diguanylate cyclases (DGCs) or phosphodiesterases (PDEs) were screened for their involvement in low-temperature-induced biofilm formation and Vibrio polysaccharide gene expression. Of the 52 mutants tested, deletions of six DGCs and three PDEs were found to affect these phenotypes at low temperatures. Unlike wild type, a strain lacking all six DGCs did not exhibit a low-temperature-dependent increase in c-di-GMP, indicating that these DGCs are required for temperature modulation of c-di-GMP levels. We also show that temperature modulates c-di-GMP levels in a similar fashion in the Gram-negative pathogen Pseudomonas aeruginosa but not in the Gram-positive pathogen Listeria monocytogenes. This study uncovers the role of temperature in environmental regulation of biofilm formation and c-di-GMP signalling.
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Affiliation(s)
- Loni Townsley
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
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46
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Castro M, Deane SM, Ruiz L, Rawlings DE, Guiliani N. Diguanylate cyclase null mutant reveals that C-Di-GMP pathway regulates the motility and adherence of the extremophile bacterium Acidithiobacillus caldus. PLoS One 2015; 10:e0116399. [PMID: 25689133 PMCID: PMC4331095 DOI: 10.1371/journal.pone.0116399] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/09/2014] [Indexed: 01/06/2023] Open
Abstract
An understanding of biofilm formation is relevant to the design of biological strategies to improve the efficiency of the bioleaching process and to prevent environmental damages caused by acid mine/rock drainage. For this reason, our laboratory is focused on the characterization of the molecular mechanisms involved in biofilm formation in different biomining bacteria. In many bacteria, the intracellular levels of c-di-GMP molecules regulate the transition from the motile planktonic state to sessile community-based behaviors, such as biofilm development, through different kinds of effectors. Thus, we recently started a study of the c-di-GMP pathway in several biomining bacteria including Acidithiobacillus caldus. C-di-GMP molecules are synthesized by diguanylate cyclases (DGCs) and degraded by phosphodiesterases (PDEs). We previously reported the existence of intermediates involved in c-di-GMP pathway from different Acidithiobacillus species. Here, we report our work related to At. caldus ATCC 51756. We identified several putative-ORFs encoding DGC and PDE and effector proteins. By using total RNA extracted from At. caldus cells and RT-PCR, we demonstrated that these genes are expressed. We also demonstrated the presence of c-di-GMP by mass spectrometry and showed that genes for several of the DGC enzymes were functional by heterologous genetic complementation in Salmonella enterica serovar Typhimurium mutants. Moreover, we developed a DGC defective mutant strain (Δc1319) that strongly indicated that the c-di-GMP pathway regulates the swarming motility and adherence to sulfur surfaces by At. caldus. Together, our results revealed that At. caldus possesses a functional c-di-GMP pathway which could be significant for ores colonization during the bioleaching process.
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Affiliation(s)
- Matías Castro
- Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Shelly M. Deane
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Lina Ruiz
- Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Douglas E. Rawlings
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Nicolas Guiliani
- Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- * E-mail:
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47
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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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48
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Anzenbacher P, Marchal S, Palacký J, Anzenbacherová E, Domaschke T, Lange R, Shimizu T, Kitanishi K, Stranava M, Stiborová M, Martinkova M. Pressure effects reveal that changes in the redox states of the heme iron complexes in the sensor domains of two heme-based oxygen sensor proteins,EcDOS and YddV, have profound effects on their flexibility. FEBS J 2014; 281:5208-19. [DOI: 10.1111/febs.13060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 09/01/2014] [Accepted: 09/16/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Pavel Anzenbacher
- Institute of Pharmacology; Faculty of Medicine; Palacky University; Olomouc Czech Republic
| | - Stéphane Marchal
- INSERM U710; Place Eugène Bataillon; Montpellier France
- INSERM U1046; Centre Hospitalier Universitaire Arnaud de Villeneuve; Montpellier France
| | - Jan Palacký
- Institute of Pharmacology; Faculty of Medicine; Palacky University; Olomouc Czech Republic
| | - Eva Anzenbacherová
- Institute of Medical Chemistry and Biochemistry; Faculty of Medicine; Palacky University; Olomouc Czech Republic
| | | | - Reinhard Lange
- INSERM U710; Place Eugène Bataillon; Montpellier France
- INRA; UMR 1208 IATE; Equipe Biochimie et Technologie Alimentaires; Université Montpellier 2; Montpellier France
| | - Toru Shimizu
- Department of Biochemistry; Faculty of Science; Charles University in Prague; Prague 2 Czech Republic
| | - Kenichi Kitanishi
- Department of Biochemistry; Faculty of Science; Charles University in Prague; Prague 2 Czech Republic
| | - Martin Stranava
- Department of Biochemistry; Faculty of Science; Charles University in Prague; Prague 2 Czech Republic
| | - Marie Stiborová
- Department of Biochemistry; Faculty of Science; Charles University in Prague; Prague 2 Czech Republic
| | - Marketa Martinkova
- Department of Biochemistry; Faculty of Science; Charles University in Prague; Prague 2 Czech Republic
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49
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Nishimura R, Shibata T, Tai H, Ishigami I, Yanagisawa S, Ogura T, Neya S, Suzuki A, Yamamoto Y. Effect of the Electron Density of the Heme Fe Atom on the Fe–Histidine Coordination Bond in Deoxy Myoglobin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20130331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | - Hulin Tai
- Department of Chemistry, University of Tsukuba
| | - Izumi Ishigami
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Sachiko Yanagisawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Akihiro Suzuki
- Department of Materials Engineering, Nagaoka National College of Technology
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50
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Nishimura R, Matsumoto D, Shibata T, Yanagisawa S, Ogura T, Tai H, Matsuo T, Hirota S, Neya S, Suzuki A, Yamamoto Y. Electronic Control of Ligand-Binding Preference of a Myoglobin Mutant. Inorg Chem 2014; 53:9156-65. [DOI: 10.1021/ic5011924] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Daichi Matsumoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Sachiko Yanagisawa
- Department of Life
Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Department of Life
Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hulin Tai
- Graduate School of
Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takashi Matsuo
- Graduate School of
Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of
Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life Science
Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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