1
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Hoque NJ, Rivera S, Young PG, Weinert EE, Liu Y. Heme pocket hydrogen bonding residue interactions within the Pectobacterium Diguanylate cyclase-containing globin coupled sensor: A resonance Raman study. J Inorg Biochem 2024; 260:112686. [PMID: 39106644 DOI: 10.1016/j.jinorgbio.2024.112686] [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: 03/30/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/09/2024]
Abstract
Heme-based sensor proteins are used by organisms to control signaling and physiological effects in response to their gaseous environment. Globin-coupled sensors (GCS) are oxygen-sensing proteins that are widely distributed in bacteria. These proteins consist of a heme globin domain linked by a middle domain to various output domains, including diguanylate cyclase domains, which are responsible for synthesizing c-di-GMP, a bacterial second messenger crucial for regulating biofilm formation. To understand the roles of heme pocket residues in controlling activity of the diguanylate cyclase domain, variants of the Pectobacterium carotovorum GCS (PccGCS) were characterized by enzyme kinetics and resonance Raman (rR) spectroscopy. Results of these studies have identified roles for hydrogen bonding and heme edge residues in modulating heme pocket conformation and flexibility. Better understanding of the ligand-dependent GCS signaling mechanism and the residues involved may allow for future development of methods to control O2-dependent c-di-GMP production.
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Affiliation(s)
- Nushrat J Hoque
- Department of Chemistry, 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
| | - Emily E Weinert
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Yilin Liu
- Department of Chemistry, University of Akron, Akron, OH 44325, USA.
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2
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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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3
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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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4
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Zhan X, Zhang K, Wang C, Fan Q, Tang X, Zhang X, Wang K, Fu Y, Liang H. A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa. Nat Commun 2024; 15:1860. [PMID: 38424057 PMCID: PMC10904736 DOI: 10.1038/s41467-024-46149-3] [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: 10/28/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a bacterial second messenger that modulates various processes including biofilm formation, motility, and host-microbe symbiosis. Numerous studies have conducted comprehensive analysis of c-di-GMP. However, the mechanisms by which certain environmental signals such as iron control intracellular c-di-GMP levels are unclear. Here, we show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein, IsmP, and a diguanylate cyclase, ImcA. Binding of iron to the CHASE4 domain of IsmP inhibits the IsmP-ImcA interaction, which leads to increased c-di-GMP synthesis by ImcA, thus promoting biofilm formation and reducing bacterial motility. Structural characterization of the apo-CHASE4 domain and its binding to iron allows us to pinpoint residues defining its specificity. In addition, the cryo-electron microscopy structure of ImcA in complex with a c-di-GMP analog (GMPCPP) suggests a unique conformation in which the compound binds to the catalytic pockets and to the membrane-proximal side located at the cytoplasm. Thus, our results indicate that a CHASE4 domain directly senses iron and modulates the crosstalk between c-di-GMP metabolic enzymes.
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Affiliation(s)
- Xueliang Zhan
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Kuo Zhang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Chenchen Wang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Qiao Fan
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Xiujia Tang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xi Zhang
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Ke Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yang Fu
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Haihua Liang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China.
- University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China.
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5
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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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6
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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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7
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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: 8] [Impact Index Per Article: 8.0] [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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8
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Hengge R, Pruteanu M, Stülke J, Tschowri N, Turgay K. Recent advances and perspectives in nucleotide second messenger signaling in bacteria. MICROLIFE 2023; 4:uqad015. [PMID: 37223732 PMCID: PMC10118264 DOI: 10.1093/femsml/uqad015] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
Nucleotide second messengers act as intracellular 'secondary' signals that represent environmental or cellular cues, i.e. the 'primary' signals. As such, they are linking sensory input with regulatory output in all living cells. The amazing physiological versatility, the mechanistic diversity of second messenger synthesis, degradation, and action as well as the high level of integration of second messenger pathways and networks in prokaryotes has only recently become apparent. In these networks, specific second messengers play conserved general roles. Thus, (p)ppGpp coordinates growth and survival in response to nutrient availability and various stresses, while c-di-GMP is the nucleotide signaling molecule to orchestrate bacterial adhesion and multicellularity. c-di-AMP links osmotic balance and metabolism and that it does so even in Archaea may suggest a very early evolutionary origin of second messenger signaling. Many of the enzymes that make or break second messengers show complex sensory domain architectures, which allow multisignal integration. The multiplicity of c-di-GMP-related enzymes in many species has led to the discovery that bacterial cells are even able to use the same freely diffusible second messenger in local signaling pathways that can act in parallel without cross-talking. On the other hand, signaling pathways operating with different nucleotides can intersect in elaborate signaling networks. Apart from the small number of common signaling nucleotides that bacteria use for controlling their cellular "business," diverse nucleotides were recently found to play very specific roles in phage defense. Furthermore, these systems represent the phylogenetic ancestors of cyclic nucleotide-activated immune signaling in eukaryotes.
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Affiliation(s)
- Regine Hengge
- Corresponding author. Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany. Tel: +49-30-2093-49686; Fax: +49-30-2093-49682; E-mail:
| | | | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Natalia Tschowri
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
| | - Kürşad Turgay
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
- Max Planck Unit for the Science of Pathogens, 10115 Berlin, Germany
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9
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Koppenhöfer S, Lang AS. Patterns of abundance, chromosomal localization, and domain organization among c-di-GMP-metabolizing genes revealed by comparative genomics of five alphaproteobacterial orders. BMC Genomics 2022; 23:834. [PMID: 36522693 PMCID: PMC9756655 DOI: 10.1186/s12864-022-09072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/17/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a bacterial second messenger that affects diverse processes in different bacteria, including the cell cycle, motility, and biofilm formation. Its cellular levels are controlled by the opposing activities of two types of enzymes, with synthesis by diguanylate cyclases containing a GGDEF domain and degradation by phosphodiesterases containing either an HD-GYP or an EAL domain. These enzymes are ubiquitous in bacteria with up to 50 encoded in some genomes, the specific functions of which are mostly unknown. RESULTS We used comparative analyses to identify genomic patterns among genes encoding proteins with GGDEF, EAL, and HD-GYP domains in five orders of the class Alphaproteobacteria. GGDEF-containing sequences and GGDEF-EAL hybrids were the most abundant and had the highest diversity of co-occurring auxiliary domains while EAL and HD-GYP containing sequences were less abundant and less diverse with respect to auxiliary domains. There were striking patterns in the chromosomal localizations of the genes found in two of the orders. The Rhodobacterales' EAL-encoding genes and Rhizobiales' GGDEF-EAL-encoding genes showed opposing patterns of distribution compared to the GGDEF-encoding genes. In the Rhodobacterales, the GGDEF-encoding genes showed a tri-modal distribution with peaks mid-way between the origin (ori) and terminus (ter) of replication and at ter while the EAL-encoding genes peaked near ori. The patterns were more complex in the Rhizobiales, but the GGDEF-encoding genes were biased for localization near ter. CONCLUSIONS The observed patterns in the chromosomal localizations of these genes suggest a coupling of synthesis and hydrolysis of c-di-GMP with the cell cycle. Moreover, the higher proportions and diversities of auxiliary domains associated with GGDEF domains and GGDEF-EAL hybrids compared to EAL or HD-GYP domains could indicate that more stimuli affect synthesis compared to hydrolysis of c-di-GMP.
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Affiliation(s)
- Sonja Koppenhöfer
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada.
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10
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Vávra J, Sergunin A, Jeřábek P, Shimizu T, Martínková M. Signal transduction mechanisms in heme-based globin-coupled oxygen sensors with a focus on a histidine kinase ( AfGcHK) and a diguanylate cyclase (YddV or EcDosC). Biol Chem 2022; 403:1031-1042. [PMID: 36165459 DOI: 10.1515/hsz-2022-0185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/08/2022] [Indexed: 01/19/2023]
Abstract
Heme is a vital cofactor of proteins with roles in oxygen transport (e.g. hemoglobin), storage (e.g. myoglobin), and activation (e.g. P450) as well as electron transfer (e.g. cytochromes) and many other functions. However, its structural and functional role in oxygen sensing proteins differs markedly from that in most other enzymes, where it serves as a catalytic or functional center. This minireview discusses the mechanism of signal transduction in two heme-based oxygen sensors: the histidine kinase AfGcHK and the diguanylate cyclase YddV (EcDosC), both of which feature a heme-binding domain containing a globin fold resembling that of hemoglobin and myoglobin.
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Affiliation(s)
- Jakub Vávra
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Artur Sergunin
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Petr Jeřábek
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Markéta Martínková
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
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11
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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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