1
|
Marchetti M, Ronda L, Cozzi M, Bettati S, Bruno S. Genetically Encoded Biosensors for the Fluorescence Detection of O 2 and Reactive O 2 Species. SENSORS (BASEL, SWITZERLAND) 2023; 23:8517. [PMID: 37896609 PMCID: PMC10611200 DOI: 10.3390/s23208517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023]
Abstract
The intracellular concentrations of oxygen and reactive oxygen species (ROS) in living cells represent critical information for investigating physiological and pathological conditions. Real-time measurement often relies on genetically encoded proteins that are responsive to fluctuations in either oxygen or ROS concentrations. The direct binding or chemical reactions that occur in their presence either directly alter the fluorescence properties of the binding protein or alter the fluorescence properties of fusion partners, mostly consisting of variants of the green fluorescent protein. Oxygen sensing takes advantage of several mechanisms, including (i) the oxygen-dependent hydroxylation of a domain of the hypoxia-inducible factor-1, which, in turn, promotes its cellular degradation along with fluorescent fusion partners; (ii) the naturally oxygen-dependent maturation of the fluorophore of green fluorescent protein variants; and (iii) direct oxygen binding by proteins, including heme proteins, expressed in fusion with fluorescent partners, resulting in changes in fluorescence due to conformational alterations or fluorescence resonance energy transfer. ROS encompass a group of highly reactive chemicals that can interconvert through various chemical reactions within biological systems, posing challenges for their selective detection through genetically encoded sensors. However, their general reactivity, and particularly that of the relatively stable oxygen peroxide, can be exploited for ROS sensing through different mechanisms, including (i) the ROS-induced formation of disulfide bonds in engineered fluorescent proteins or fusion partners of fluorescent proteins, ultimately leading to fluorescence changes; and (ii) conformational changes of naturally occurring ROS-sensing domains, affecting the fluorescence properties of fusion partners. In this review, we will offer an overview of these genetically encoded biosensors.
Collapse
Affiliation(s)
- Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Monica Cozzi
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy;
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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]
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Liu Y, Chen Z, Shao Z, Guo R. Single gold nanoparticle-driven heme cofactor nanozyme as an unprecedented oxidase mimetic. Chem Commun (Camb) 2021; 57:3399-3402. [PMID: 33686388 DOI: 10.1039/d1cc00279a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The catalytic diversity of heme enzymes is a perpetuating pursuit for biomimetic chemistry, but heme nanozymes exhibit catalytic activity only reminiscent of peroxidases. Miraculously, the oxidase-like catalytic function of a heme cofactor is elicited with the help of gold nanoparticles (AuNPs) by maintaining heme with a low-valence state (ferrous) in a confined configuration.
Collapse
Affiliation(s)
- Yan Liu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, P. R. China.
| | | | | | | |
Collapse
|
7
|
Kostyuk AI, Kokova AD, Podgorny OV, Kelmanson IV, Fetisova ES, Belousov VV, Bilan DS. Genetically Encoded Tools for Research of Cell Signaling and Metabolism under Brain Hypoxia. Antioxidants (Basel) 2020; 9:E516. [PMID: 32545356 PMCID: PMC7346190 DOI: 10.3390/antiox9060516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 02/08/2023] Open
Abstract
Hypoxia is characterized by low oxygen content in the tissues. The central nervous system (CNS) is highly vulnerable to a lack of oxygen. Prolonged hypoxia leads to the death of brain cells, which underlies the development of many pathological conditions. Despite the relevance of the topic, different approaches used to study the molecular mechanisms of hypoxia have many limitations. One promising lead is the use of various genetically encoded tools that allow for the observation of intracellular parameters in living systems. In the first part of this review, we provide the classification of oxygen/hypoxia reporters as well as describe other genetically encoded reporters for various metabolic and redox parameters that could be implemented in hypoxia studies. In the second part, we discuss the advantages and disadvantages of the primary hypoxia model systems and highlight inspiring examples of research in which these experimental settings were combined with genetically encoded reporters.
Collapse
Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Koltzov Institute of Developmental Biology, 119334 Moscow, Russia
| | - Ilya V. Kelmanson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Elena S. Fetisova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| |
Collapse
|
8
|
Latham RD, Torrado M, Atto B, Walshe JL, Wilson R, Guss JM, Mackay JP, Tristram S, Gell DA. A heme-binding protein produced by Haemophilus haemolyticus inhibits non-typeable Haemophilus influenzae. Mol Microbiol 2019; 113:381-398. [PMID: 31742788 DOI: 10.1111/mmi.14426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 01/02/2023]
Abstract
Commensal bacteria serve as an important line of defense against colonisation by opportunisitic pathogens, but the underlying molecular mechanisms remain poorly explored. Here, we show that strains of a commensal bacterium, Haemophilus haemolyticus, make hemophilin, a heme-binding protein that inhibits growth of the opportunistic pathogen, non-typeable Haemophilus influenzae (NTHi) in culture. We purified the NTHi-inhibitory protein from H. haemolyticus and identified the hemophilin gene using proteomics and a gene knockout. An x-ray crystal structure of recombinant hemophilin shows that the protein does not belong to any of the known heme-binding protein folds, suggesting that it evolved independently. Biochemical characterisation shows that heme can be captured in the ferrous or ferric state, and with a variety of small heme-ligands bound, suggesting that hemophilin could function under a range of physiological conditions. Hemophilin knockout bacteria show a limited capacity to utilise free heme for growth. Our data suggest that hemophilin is a hemophore and that inhibition of NTHi occurs by heme starvation, raising the possibility that competition from hemophilin-producing H. haemolyticus could antagonise NTHi colonisation in the respiratory tract.
Collapse
Affiliation(s)
- Roger D Latham
- School of Medicine, University of Tasmania, Hobart, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, Australia
| | - James L Walshe
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Australia
| | - J Mitchell Guss
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Stephen Tristram
- School of Health Sciences, University of Tasmania, Launceston, Australia
| | - David A Gell
- School of Medicine, University of Tasmania, Hobart, Australia
| |
Collapse
|
9
|
Salman M, Villamil Franco C, Ramodiharilafy R, Liebl U, Vos MH. Interaction of the Full-Length Heme-Based CO Sensor Protein RcoM-2 with Ligands. Biochemistry 2019; 58:4028-4034. [PMID: 31502443 DOI: 10.1021/acs.biochem.9b00623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The heme-based and CO-responsive RcoM transcriptional regulators from Burkholderia xenovorans are known to display an extremely high affinity for CO while being insensitive to O2. We have quantitatively characterized the heme-CO interaction in full-length RcoM-2 and compared it with the isolated heme domain RcoMH-2 to establish the origin of these characteristics. Whereas the CO binding rates are similar to those of other heme-based sensor proteins, the dissociation rates are two to three orders of magnitude lower. The latter property is tuned by the yield of CO escape from the heme pocket after disruption of the heme-CO bond, as determined by ultrafast spectroscopy. For the full-length protein this yield is ∼0.5%, and for the isolated heme domain it is even lower, associated with correspondingly faster CO rebinding kinetics, leading to Kd values of 4 and 0.25 nM, respectively. These differences imply that the presence of the DNA-binding domain influences the ligand-binding properties of the heme domain, thus abolishing the observed quasi-irreversibility of CO binding to the isolated heme domain. RcoM-2 binds target DNA with high affinity (Kd < 2 nM) when CO is bound to the heme, and the presence of DNA also influences the heme-CO rebinding kinetics. The functional implications of our findings are discussed.
Collapse
Affiliation(s)
- Mayla Salman
- LOB, CNRS, INSERM, Ecole Polytechnique , Institut Polytechnique de Paris , 91128 Palaiseau , France
| | - Carolina Villamil Franco
- LOB, CNRS, INSERM, Ecole Polytechnique , Institut Polytechnique de Paris , 91128 Palaiseau , France
| | - Rivo Ramodiharilafy
- LOB, CNRS, INSERM, Ecole Polytechnique , Institut Polytechnique de Paris , 91128 Palaiseau , France
| | - Ursula Liebl
- LOB, CNRS, INSERM, Ecole Polytechnique , Institut Polytechnique de Paris , 91128 Palaiseau , France
| | - Marten H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique , Institut Polytechnique de Paris , 91128 Palaiseau , France
| |
Collapse
|
10
|
Recent Advances and Current Trends in Nucleotide Second Messenger Signaling in Bacteria. J Mol Biol 2019; 431:908-927. [PMID: 30668970 DOI: 10.1016/j.jmb.2019.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/05/2019] [Accepted: 01/07/2019] [Indexed: 02/01/2023]
Abstract
The "International Symposium on Nucleotide Second Messenger Signaling in Bacteria" (September 30-October 3, 2018, Berlin), which was organized within the framework of DFG Priority Programme 1879 (www.spp1879.de), brought together 125 participants from 20 countries to discuss recent progress and future trends in this field. Even 50 years after its discovery, (p)ppGpp is venturing into exciting new fields, especially in gram-positive bacteria. After triggering the current renaissance in bacterial second messenger research, c-di-GMP is becoming ever more global with abounding new molecular mechanisms of action and physiological functions. The more recently discovered c-di-AMP is rapidly catching up and has now been found even in archaea, with its function in osmotic homeostasis being conserved across kingdom boundaries. Small modules associated with mobile genetic elements, which make and react to numerous novel mixed cyclic dinucleotides, seem to roam around rather freely in the bacterial world. Finally, many novel and old nucleotide molecules are still lurking around in search of a function. Across many talks it became apparent that (p)ppGpp, c-di-GMP and GTP/ATP can share and compete for binding sites (e.g., the Walker A motif in GTP/ATPases) with intriguing regulatory consequences, thus contributing to the emergent trend of systemwide networks that interconnect diverse signaling nucleotides. Overall, this inspiring conference made it clear that second messenger signaling is currently one of the most dynamic and exciting areas in microbial molecular biology and physiology, with major impacts ranging from microbial systems biology and ecology to infection biology.
Collapse
|
11
|
Development of heme protein based oxygen sensing indicators. Sci Rep 2018; 8:11849. [PMID: 30087408 PMCID: PMC6081431 DOI: 10.1038/s41598-018-30329-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/27/2018] [Indexed: 12/16/2022] Open
Abstract
Oxygen is essential for aerobic life and is required for various oxygen-dependent biochemical reactions. In addition, oxygen plays important roles in multiple intracellular signaling pathways. Thus, to investigate oxygen homeostasis in living cells, we developed a genetically encoded oxygen sensor protein using the oxygen sensor domain of bacterial phosphodiesterase direct oxygen sensor protein (DosP), which was connected to yellow fluorescence protein (YFP) using an optimized antiparallel coiled-coil linker. The resulting ANA-Y (Anaerobic/aerobic sensing yellow fluorescence protein) was highly sensitive to oxygen and had a half saturation concentration of 18 μM. The ANA-Y reacts with dissolved oxygen within 10 s and the resulting increases in fluorescence are reversed with decreases in oxygen concentrations. This sensitivity of the ANA-Y enabled direct determinations of initial photosynthetic oxygen production by cyanobacteria. ANA-Y exhibits reversible fluorescence change of donor YFP following reversible absorbance change of acceptor DosH, and the operating mechanism of this ANA-Y could be used to develop various protein sensor probes for intracellular signaling molecules using natural sensor proteins.
Collapse
|
12
|
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]
|
13
|
Bouzhir-Sima L, Motterlini R, Gross J, Vos MH, Liebl U. Unusual Dynamics of Ligand Binding to the Heme Domain of the Bacterial CO Sensor Protein RcoM-2. J Phys Chem B 2016; 120:10686-10694. [DOI: 10.1021/acs.jpcb.6b08160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Latifa Bouzhir-Sima
- LOB,
Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau Cedex, France
| | - Roberto Motterlini
- Faculté
de Médicine, Université Paris-Est, Créteil 94000, France
- INSERM, U955, Equipe 12, Créteil 94000, France
| | - Julia Gross
- LOB,
Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau Cedex, France
| | - Marten H. Vos
- LOB,
Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau Cedex, France
| | - Ursula Liebl
- LOB,
Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau Cedex, France
| |
Collapse
|
14
|
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.
Collapse
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
| | | | | | | | | | | | | | | |
Collapse
|
15
|
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
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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
| |
Collapse
|
18
|
Du Y, Liu G, Yan Y, Huang D, Luo W, Martinkova M, Man P, Shimizu T. Conversion of a heme-based oxygen sensor to a heme oxygenase by hydrogen sulfide: effects of mutations in the heme distal side of a heme-based oxygen sensor phosphodiesterase (Ec DOS). Biometals 2013; 26:839-52. [PMID: 23736976 DOI: 10.1007/s10534-013-9640-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/27/2013] [Indexed: 02/05/2023]
Abstract
The heme-based oxygen-sensor phosphodiesterase from Escherichia coli (Ec DOS), is composed of an N-terminal heme-bound oxygen sensing domain and a C-terminal catalytic domain. Oxygen (O2) binding to the heme Fe(II) complex in Ec DOS substantially enhances catalysis. Addition of hydrogen sulfide (H2S) to the heme Fe(III) complex in Ec DOS also remarkably stimulates catalysis in part due to the heme Fe(III)-SH and heme Fe(II)-O2 complexes formed by H2S. In this study, we examined the roles of the heme distal amino acids, M95 (the axial ligand of the heme Fe(II) complex) and R97 (the O2 binding site in the heme Fe(II)-O2 complex) of the isolated heme-binding domain of Ec DOS (Ec DOS-PAS) in the binding of H2S under aerobic conditions. Interestingly, R97A and R97I mutant proteins formed an oxygen-incorporated modified heme, verdoheme, following addition of H2S combined with H2O2 generated by the reactions. Time-dependent mass spectroscopic data corroborated the findings. In contrast, H2S did not interact with the heme Fe(III) complex of M95H and R97E mutants. Thus, M95 and/or R97 on the heme distal side in Ec DOS-PAS significantly contribute to the interaction of H2S with the Fe(III) heme complex and also to the modification of the heme Fe(III) complex with reactive oxygen species. Importantly, mutations of the O2 binding site of the heme protein converted its function from oxygen sensor to that of a heme oxygenase. This study establishes the novel role of H2S in modifying the heme iron complex to form verdoheme with the aid of reactive oxygen species.
Collapse
Affiliation(s)
- Yongming Du
- Department of Cell Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Martínková M, Kitanishi K, Shimizu T. Heme-based globin-coupled oxygen sensors: linking oxygen binding to functional regulation of diguanylate cyclase, histidine kinase, and methyl-accepting chemotaxis. J Biol Chem 2013; 288:27702-11. [PMID: 23928310 DOI: 10.1074/jbc.r113.473249] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
An emerging class of novel heme-based oxygen sensors containing a globin fold binds and senses environmental O2 via a heme iron complex. Structure-function relationships of oxygen sensors containing a heme-bound globin fold are different from those containing heme-bound PAS and GAF folds. It is thus worth reconsidering from an evolutionary perspective how heme-bound proteins with a globin fold similar to that of hemoglobin and myoglobin could act as O2 sensors. Here, we summarize the molecular mechanisms of heme-based oxygen sensors containing a globin fold in an effort to shed light on the O2-sensing properties and O2-stimulated catalytic enhancement observed for these proteins.
Collapse
Affiliation(s)
- Markéta Martínková
- From the Department of Biochemistry, Faculty of Science, Charles University in Prague, 128 43 Prague 2, Czech Republic
| | | | | |
Collapse
|
20
|
Shimizu T. The Heme-Based Oxygen-Sensor Phosphodiesterase Ec DOS (DosP): Structure-Function Relationships. BIOSENSORS 2013; 3:211-37. [PMID: 25586128 PMCID: PMC4263535 DOI: 10.3390/bios3020211] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/24/2013] [Accepted: 06/13/2013] [Indexed: 02/05/2023]
Abstract
Escherichia coli Direct Oxygen Sensor (Ec DOS, also known as Ec DosP) is a heme-based O2-sensing phosphodiesterase from Escherichia coli that catalyzes the conversion of cyclic-di-GMP to linear di-GMP. Cyclic-di-GMP is an important second messenger in bacteria, highlighting the importance of understanding structure-function relationships of Ec DOS. Ec DOS is composed of an N-terminal heme-bound O2-sensing PAS domain and a C-terminal phosphodiesterase catalytic domain. Notably, its activity is markedly enhanced by O2 binding to the heme Fe(II) complex in the PAS sensor domain. X-ray crystal structures and spectroscopic and catalytic characterization of the wild-type and mutant proteins have provided important structural and functional clues to understanding the molecular mechanism of intramolecular catalytic regulation by O2 binding. This review summarizes the intriguing findings that have obtained for Ec DOS.
Collapse
Affiliation(s)
- Toru Shimizu
- Department of Cell Biology, Shantou University Medical College, Shantou 515041, China.
| |
Collapse
|
21
|
Abstract
Heme is a prosthetic group best known for roles in oxygen transport, oxidative catalysis, and respiratory electron transport. Recent years have seen the roles of heme extended to sensors of gases such as O2 and NO and cell redox state, and as mediators of cellular responses to changes in intracellular levels of these gases. The importance of heme is further evident from identification of proteins that bind heme reversibly, using it as a signal, e.g. to regulate gene expression in circadian rhythm pathways and control heme synthesis itself. In this minireview, we explore the current knowledge of the diverse roles of heme sensor proteins.
Collapse
Affiliation(s)
- Hazel M. Girvan
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Andrew W. Munro
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| |
Collapse
|
22
|
Aono S. The Dos family of globin-related sensors using PAS domains to accommodate haem acting as the active site for sensing external signals. Adv Microb Physiol 2013; 63:273-327. [PMID: 24054799 DOI: 10.1016/b978-0-12-407693-8.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sensor proteins play crucial roles in maintaining homeostasis of cells by sensing changes in extra- and intracellular chemical and physical conditions to trigger biological responses. It has recently become clear that gas molecules function as signalling molecules in these biological regulatory systems responsible for transcription, chemotaxis, synthesis/hydrolysis of nucleotide second messengers, and other complex physiological processes. Haem-containing sensor proteins are widely used to sense gas molecules because haem can bind gas molecules reversibly. Ligand binding to the haem in the sensor proteins triggers conformational changes around the haem, which results in their functional regulation. Spectroscopic and crystallographic studies are essential to understand how these sensor proteins function in these biological regulatory systems. In this chapter, I discuss structural and functional relationships of haem-containing PAS and PAS-related families of the sensor proteins.
Collapse
|
23
|
Farhana A, Saini V, Kumar A, Lancaster JR, Steyn AJ. Environmental heme-based sensor proteins: implications for understanding bacterial pathogenesis. Antioxid Redox Signal 2012; 17:1232-45. [PMID: 22494151 PMCID: PMC3430476 DOI: 10.1089/ars.2012.4613] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 04/11/2012] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE Heme is an important prosthetic group required in a wide array of functions, including respiration, photosynthesis, metabolism, O(2) transport, xenobiotic detoxification, and peroxide production and destruction, and is an essential cofactor in proteins such as catalases, peroxidases, and members of the cytochrome P450 superfamily. Importantly, bacterial heme-based sensor proteins exploit the redox chemistry of heme to sense environmental gases and the intracellular redox state of the cell. RECENT ADVANCES The bacterial proteins FixL (Rhizobium ssp.), CooA (Rhodospirillum rubrum), EcDos (Escherichia. coli), RcoM (Burkholderia xenovorans), and particularly Mycobacterium tuberculosis (Mtb) DosS and DosT have emerged as model paradigms of environmental heme-based sensors capable of detecting multiple gases including NO, CO, and O(2). CRITICAL ISSUES How the diatomic gases NO, CO, or O(2) bind to heme iron to generate Fe-NO, Fe-CO, and Fe-O(2) bonds, respectively, and how the oxidation of heme iron by O(2) serves as a sensing mechanism that controls the activity of key proteins is complex and largely unclear. This is particularly important as many bacterial pathogens, including Mtb, encounters three overlapping host gases (NO, CO, and O(2)) during human infection. FUTURE DIRECTIONS Heme is an important prosthetic group that monitors the microbe's internal and external surroundings to alter signal transduction or enzymatic activation. Modern expression, metabolomic and biochemical technologies combined with in vivo pathogenesis studies should provide fresh insights into the mechanism of action of heme-based redox sensors.
Collapse
Affiliation(s)
- Aisha Farhana
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Vikram Saini
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ashwani Kumar
- Institute of Microbial Technology, Chandigarh, India
| | - Jack R. Lancaster
- Department of Anesthesiology, Physiology and Biophysics, and Environmental Sciences, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Adrie J.C. Steyn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Centers for AIDS Research, University of Alabama at Birmingham, Birmingham, Alabama
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Durban, South Africa
- Department of Pathology, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
24
|
Rinaldo S, Castiglione N, Giardina G, Caruso M, Arcovito A, Longa SD, D'Angelo P, Cutruzzolà F. Unusual heme binding properties of the dissimilative nitrate respiration regulator, a bacterial nitric oxide sensor. Antioxid Redox Signal 2012; 17:1178-89. [PMID: 22424265 DOI: 10.1089/ars.2011.4226] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AIMS In the opportunistic pathogen Pseudomonas aeruginosa, nitric oxide (NO) triggers the respiration of nitrate (denitrification), thus allowing survival in chronic infection sites as a microaerobic-anaerobic biofilm. The NO-dependent induction of denitrification is mediated by the dissimilative nitrate respiration regulator (DNR), a transcription factor forming a stable complex with heme, which is required to sense the physiological messenger (i.e., NO). The molecular details of NO sensing in DNR and, more in general, in this class of sensors are largely unknown, and a study aimed at integrating microbiology and biochemistry is needed. RESULTS Here we present a comprehensive study, including in vivo results and spectroscopy, kinetics, and protein engineering, that demonstrates the direct involvement of a histidine residue in heme iron coordination. Moreover, a peculiar phenomenon of ligand switching around heme iron, which hampers the identification of the second heme axial ligand, is also suggested. These results indicate that DNR is characterized by a remarkable flexibility in solution, as observed for other cAMP receptor protein/fumarate and nitrate reductase regulators (CRP-FNR) to which DNR belongs. INNOVATION The present work represents one of the few studies focused on the biochemistry of NO sensing by bacterial transcriptional regulators. The data presented demonstrate that structural plasticity of DNR is crucial for the sensing activity and confers to the protein unusual heme binding properties. CONCLUSIONS Protein flexibility and dynamics is a key structural feature essential to explain the evolutionary success and adaptability of CRP-FNR, and may represent a common strategy employed by heme-based redox sensors, which presents features deeply different from those of canonical hemeproteins.
Collapse
Affiliation(s)
- Serena Rinaldo
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Smith AT, Marvin KA, Freeman KM, Kerby RL, Roberts GP, Burstyn JN. Identification of Cys94 as the distal ligand to the Fe(III) heme in the transcriptional regulator RcoM-2 from Burkholderia xenovorans. J Biol Inorg Chem 2012; 17:1071-82. [PMID: 22855237 PMCID: PMC3484680 DOI: 10.1007/s00775-012-0920-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/03/2012] [Indexed: 10/28/2022]
Abstract
The CO-responsive transcriptional regulator RcoM from Burkholderia xenovorans (BxRcoM) was recently identified as a Cys(thiolate)-ligated heme protein that undergoes a redox-mediated ligand switch; however, the Cys bound to the Fe(III) heme was not identified. To that end, we generated and purified three Cys-to-Ser variants of BxRcoM-2--C94S, C127S, and C130S--and examined their spectroscopic properties in order to identify the native Cys(thiolate) ligand. Electronic absorption, resonance Raman, and electron paramagnetic resonance (EPR) spectroscopies demonstrate that the C127S and C130S variants, like wild-type BxRcoM-2, bind a six-coordinate low-spin Fe(III) heme using a Cys/His ligation motif. In contrast, electronic absorption and resonance Raman spectra of the C94S variant are most consistent with a mixture of five-coordinate high-spin and six-coordinate low-spin Fe(III) heme, neither of which are ligated by a Cys(thiolate) ligand. The EPR spectrum of C94S is dominated by a large, axial high-spin Fe(III) signal, confirming that the native ligation motif is not maintained in this variant. Together, these data reveal that Cys(94) is the distal Fe(III) heme ligand in BxRcoM-2; by sequence alignment, Cys(94) is also implicated as the distal Fe(III) heme ligand in BxRcoM-1, another homologue found in the same organism.
Collapse
Affiliation(s)
- Aaron T. Smith
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Katherine A. Marvin
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Katherine M. Freeman
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Robert L. Kerby
- Department of Bacteriology, University of Wisconsin–Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Gary P. Roberts
- Department of Bacteriology, University of Wisconsin–Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
| |
Collapse
|
26
|
Nakajima K, Kitanishi K, Kobayashi K, Kobayashi N, Igarashi J, Shimizu T. Leu65 in the heme distal side is critical for the stability of the Fe(II)–O2 complex of YddV, a globin-coupled oxygen sensor diguanylate cyclase. J Inorg Biochem 2012; 108:163-70. [DOI: 10.1016/j.jinorgbio.2011.09.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/12/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
|
27
|
Kitanishi K, Kobayashi K, Uchida T, Ishimori K, Igarashi J, Shimizu T. Identification and functional and spectral characterization of a globin-coupled histidine kinase from Anaeromyxobacter sp. Fw109-5. J Biol Chem 2011; 286:35522-35534. [PMID: 21852234 PMCID: PMC3195594 DOI: 10.1074/jbc.m111.274811] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/04/2011] [Indexed: 12/13/2022] Open
Abstract
Two-component signal transduction systems regulate numerous important physiological functions in bacteria. In this study we have identified, cloned, overexpressed, and characterized a dimeric full-length heme-bound (heme:protein, 1:1 stoichiometry) globin-coupled histidine kinase (AfGcHK) from Anaeromyxobacter sp. strain Fw109-5 for the first time. The Fe(III), Fe(II)-O(2), and Fe(II)-CO complexes of the protein displayed autophosphorylation activity, whereas the Fe(II) complex had no significant activity. A H99A mutant lost heme binding ability, suggesting that this residue is the heme proximal ligand. Moreover, His-183 was proposed as the autophosphorylation site based on the finding that the H183A mutant protein was not phosphorylated. The phosphate group of autophosphorylated AfGcHK was transferred to Asp-52 and Asp-169 of a response regulator, as confirmed from site-directed mutagenesis experiments. Based on the amino acid sequences and crystal structures of other globin-coupled oxygen sensor enzymes, Tyr-45 was assumed to be the O(2) binding site at the heme distal side. The O(2) dissociation rate constant, 0.10 s(-1), was substantially increased up to 8.0 s(-1) upon Y45L mutation. The resonance Raman frequencies representing ν(Fe-O2) (559 cm(-1)) and ν(O-O) (1149 cm(-1)) of the Fe(II)-O(2) complex of Y45F mutant AfGcHK were distinct from those of the wild-type protein (ν(Fe-O2), 557 cm(-1); ν(O-O), 1141 cm(-1)), supporting the proposal that Tyr-45 is located at the distal side and forms hydrogen bonds with the oxygen molecule bound to the Fe(II) complex. Thus, we have successfully identified and characterized a novel heme-based globin-coupled oxygen sensor histidine kinase, AfGcHK, in this study.
Collapse
Affiliation(s)
- Kenichi Kitanishi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kazuo Kobayashi
- Institute of Scientific and Industrial Research, Osaka University, Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Jotaro Igarashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Toru Shimizu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan.
| |
Collapse
|
28
|
A hydrogen-bonding network formed by the B10–E7–E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification. J Biol Inorg Chem 2011; 16:599-609. [DOI: 10.1007/s00775-011-0761-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Accepted: 01/17/2011] [Indexed: 10/18/2022]
|
29
|
Gupta N, Ragsdale SW. Thiol-disulfide redox dependence of heme binding and heme ligand switching in nuclear hormone receptor rev-erb{beta}. J Biol Chem 2010; 286:4392-403. [PMID: 21123168 DOI: 10.1074/jbc.m110.193466] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Rev-erbβ is a heme-binding nuclear hormone receptor that represses a broad spectrum of target genes involved in regulating metabolism, the circadian cycle, and proinflammatory responses. Here, we demonstrate that a thiol-disulfide redox switch controls the interaction between heme and the ligand-binding domain of Rev-erbβ. The reduced dithiol state of Rev-erbβ binds heme 5-fold more tightly than the oxidized disulfide state. By means of site-directed mutagenesis and by UV-visible and EPR spectroscopy, we also show that the ferric heme of reduced (dithiol) Rev-erbβ can undergo a redox-triggered switch from imidazole/thiol ligation (via His-568 and Cys-384, based on a prior crystal structure) to His/neutral residue ligation upon oxidation to the disulfide form. On the other hand, we find that change in the redox state of iron has no effect on heme binding to the ligand-binding domain of the protein. The low dissociation constant for the complex between Fe(3+)- or Fe(2+)-heme and the reduced dithiol state of the protein (K(d) = ∼ 20 nM) is in the range of the intracellular free heme concentration. We also determined that the Fe(2+)-heme bound to the ligand-binding domain of Rev-erbβ has high affinity for CO (K(d) = 60 nM), which replaces one of the internal ligands when bound. We suggest that this thiol-disulfide redox switch is one mechanism by which oxidative stress is linked to circadian and/or metabolic imbalance. Heme dissociation from Rev-erbβ has been shown to derepress the expression of target genes in response to changes in intracellular redox conditions. We propose that oxidative stress leads to oxidation of cysteine(s), thus releasing heme from Rev-erbβ and altering its transcriptional activity.
Collapse
Affiliation(s)
- Nirupama Gupta
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA
| | | |
Collapse
|
30
|
Lukat-Rodgers GS, Correia C, Botuyan MV, Mer G, Rodgers KR. Heme-based sensing by the mammalian circadian protein CLOCK. Inorg Chem 2010; 49:6349-65. [PMID: 20666392 DOI: 10.1021/ic902388q] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Heme is emerging as a key player in the synchrony of circadian-coupled transcriptional regulation. Current evidence suggests that levels of circadian-linked transcription are regulated in response to both the availability of intracellular heme and heme-based sensing of carbon monoxide (CO) and possibly nitric oxide (NO). The protein CLOCK is central to the regulation and maintenance of circadian rhythms in mammals. CLOCK comprises two PAS domains, each with a heme binding site. Our studies focus on the functionality of the murine CLOCK PAS-A domain (residues 103-265). We show that CLOCK PAS-A binds iron(III) protoporhyrin IX to form a complex with 1:1 stoichiometry. Optical absorbance and resonance Raman studies reveal that the heme of ferric CLOCK PAS-A is a six-coordinate, low-spin complex whose resonance Raman signature is insensitive to pH over the range of protein stability. Ferrous CLOCK PAS-A is a mixture of five-coordinate, high-spin and six-coordinate, low-spin complexes. Ferrous CLOCK PAS-A forms complexes with CO and NO. Ferric CLOCK PAS-A undergoes reductive nitrosylation in the presence of NO to generate a CLOCK PAS-A-NO, which is a five-coordinate {FeNO}(7) complex. Formation of the highly stable {FeNO}(7) heme complex from either ferrous or ferric heme makes possible the binding of NO at very low concentration, a characteristic of NO sensors. Comparison of the spectroscopic properties and CO-binding kinetics of CLOCK PAS-A with other CO sensor proteins reveals that CLOCK PAS-A exhibits chemical properties consistent with a heme-based gas sensor protein.
Collapse
Affiliation(s)
- Gudrun S Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
| | | | | | | | | |
Collapse
|
31
|
Kitanishi K, Kobayashi K, Kawamura Y, Ishigami I, Ogura T, Nakajima K, Igarashi J, Tanaka A, Shimizu T. Important Roles of Tyr43 at the Putative Heme Distal Side in the Oxygen Recognition and Stability of the Fe(II)−O2 Complex of YddV, a Globin-Coupled Heme-Based Oxygen Sensor Diguanylate Cyclase. Biochemistry 2010; 49:10381-93. [DOI: 10.1021/bi100733q] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kenichi Kitanishi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kazuo Kobayashi
- Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Yuriko Kawamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Izumi Ishigami
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Kyosuke Nakajima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Jotaro Igarashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Atsunari Tanaka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Toru Shimizu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
| |
Collapse
|
32
|
Kobayashi K, Tanaka A, Takahashi H, Igarashi J, Ishitsuka Y, Yokota N, Shimizu T. Catalysis and oxygen binding of Ec DOS: a haem-based oxygen-sensor enzyme from Escherichia coli. ACTA ACUST UNITED AC 2010; 148:693-703. [DOI: 10.1093/jb/mvq103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
33
|
Affiliation(s)
- Taku YAMASHITA
- Laboratory of Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University
| |
Collapse
|
34
|
Yan H, Chen W. 3',5'-Cyclic diguanylic acid: a small nucleotide that makes big impacts. Chem Soc Rev 2010; 39:2914-24. [PMID: 20577685 DOI: 10.1039/b914942m] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
3',5'-Cyclic diguanylic acid (c-di-GMP) is a naturally occurring small cyclic dinucleotide found in bacteria. There has been a recent surge of interest in the two-component signalling networks involving this molecule. This tutorial review introduces the biosynthesis of c-di-GMP, particularly the conserved domain features involved in its enzymatic synthesis and degradation, cellular functions and phenotypes regulated by c-di-GMP through c-di-GMP-binding proteins. The chemical synthesis and structural studies of c-di-GMP are also summarized. Two potential applications of c-di-GMP, i.e. bacterial biofilm formation and immunostimulation, are surveyed. Recent observations on c-di-GMP-binding riboswitches are also introduced.
Collapse
Affiliation(s)
- Hongbin Yan
- Department of Chemistry, Brock University, 500 Glenridge Ave., St. Catharines, Ontario, L2S 3A1, Canada.
| | | |
Collapse
|
35
|
Lechauve C, Bouzhir-Sima L, Yamashita T, Marden MC, Vos MH, Liebl U, Kiger L. Heme ligand binding properties and intradimer interactions in the full-length sensor protein dos from Escherichia coli and its isolated heme domain. J Biol Chem 2009; 284:36146-36159. [PMID: 19864414 DOI: 10.1074/jbc.m109.066811] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dos from Escherichia coli is a bacterial gas sensor protein comprising a heme-containing gas sensor domain and a phosphodiesterase catalytic domain. Using a combination of static light scattering and gel filtration experiments, we established that, as are many other sensor proteins, the full-length protein is dimeric. The full-length dimer (association constant <10 nm) is more stable than the dimeric heme domain (association constant approximately 1 mum), and the dimer interface presumably includes both sensor and catalytic domains. Ultrafast spectroscopic studies showed little influence of the catalytic domain on kinetic processes in the direct vicinity of the heme. By contrast, the properties of ligand (CO and O(2)) binding to the heme in the sensor domain, occurring on a microsecond to second time scale, were found to be influenced by (i) the presence of the catalytic domain, (ii) the dimerization state, and in dimers, (iii) the ligation state of the other subunit. These results imply allosteric interactions within dimers. Steady-state titrations demonstrated marked cooperativity in oxygen binding to both the full-length protein and the isolated heme domain, a feature not reported to date for any dimeric sensor protein. Analysis of a variety of time-resolved experiments showed that Met-95 plays a major role in the intradimer interactions. The intrinsic binding and dissociation rates of Met-95 to the heme were modulated approximately 10-fold by intradimer and sensor-catalytic domain interactions. Dimerization effects were also observed for cyanide binding to the ferric heme domains, suggesting a similar role for Met-95 in ferric proteins.
Collapse
Affiliation(s)
| | - Latifa Bouzhir-Sima
- Laboratory of Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France; INSERM U696, 91228 Palaiseau, France
| | - Taku Yamashita
- Laboratory of Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France; INSERM U696, 91228 Palaiseau, France
| | - Michael C Marden
- INSERM U779, Universités Paris VI et XI, 94276 Le Kremlin-Bicêtre, France
| | - Marten H Vos
- Laboratory of Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France; INSERM U696, 91228 Palaiseau, France.
| | - Ursula Liebl
- Laboratory of Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France; INSERM U696, 91228 Palaiseau, France
| | - Laurent Kiger
- INSERM U779, Universités Paris VI et XI, 94276 Le Kremlin-Bicêtre, France.
| |
Collapse
|
36
|
Ito S, Igarashi J, Shimizu T. The FG loop of a heme-based gas sensor enzyme, Ec DOS, functions in heme binding, autoxidation and catalysis. J Inorg Biochem 2009; 103:1380-5. [PMID: 19712978 DOI: 10.1016/j.jinorgbio.2009.07.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2009] [Revised: 07/14/2009] [Accepted: 07/15/2009] [Indexed: 12/01/2022]
Abstract
Ec DOS is a heme-based gas sensor enzyme that catalyzes conversion from cyclic-di-GMP to linear-di-GMP in response to gas molecules, such as oxygen, CO and NO. Ec DOS contains an N-terminal heme-binding PAS domain and C-terminal phosphodiesterase domain. Based on crystal structures of the isolated heme-binding domain, it is suggested that the FG loop is involved in intra-molecular signal transduction to the catalytic domain. We generated nine full-length proteins mutated at ionic and non-ionic polar residues between positions 83 and 96 corresponding to the F-helix and FG loop, and examined the heme binding properties, autoxidation rates, and catalytic activities of mutant proteins. N84A and R85A mutant proteins displayed lower heme binding affinities, consistent with the finding that Asn84 interacts with propionate of protoporphyrin IX, and Arg85 with Asp40 on the heme proximal side. Autoxidation rates (0.058-0.54 min(-1)) of R91A, S96A and K89A/R91A/E93A mutant proteins were significantly higher than that (0.0053 min(-1)) of wild-type protein, suggesting that these residues in the FG loop form heme distal architecture conferring stability to the Fe(II)-O(2) complex. Catalytic activities of N84A and R85A mutant proteins with low heme affinity were significantly higher than those of wild-type protein in the absence of gas molecules. Accordingly, we propose that loss of heme binding enhances basal catalysis without the gas molecule, consistent with previous reports on heme inhibition of Ec DOS catalysis.
Collapse
Affiliation(s)
- Shinya Ito
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Sendai 980-8577, Japan
| | | | | |
Collapse
|
37
|
Ioanoviciu A, Meharenna YT, Poulos TL, Ortiz de Montellano PR. DevS oxy complex stability identifies this heme protein as a gas sensor in Mycobacterium tuberculosis dormancy. Biochemistry 2009; 48:5839-48. [PMID: 19463006 DOI: 10.1021/bi802309y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DevS is one of the two sensing kinases responsible for DevR activation and the subsequent entry of Mycobacterium tuberculosis into dormancy. Full-length wild-type DevS forms a stable oxy-ferrous complex. The DevS autoxidation rates are extremely low (half-lives of >24 h) in the presence of cations such as K(+), Na(+), Mg(2+), and Ca(2+). At relatively high concentrations (100 mM), Cu(2+) accelerates autoxidation more than 1500-fold. Contrary to expectations, removal of the key hydrogen bond between the iron-coordinated oxygen and Tyr171 in the Y171F mutant provides a protein of comparable stability to autoxidation and similar oxygen dissociation rate. This correlates with our earlier finding that the Y171F mutant and wild-type kinase activities are similarly regulated by the binding of oxygen: namely, the ferrous five-coordinate complex is active, whereas the oxy-ferrous six-coordinate species is inactive. Our results indicate that DevS is a gas sensor in vivo rather than a redox sensor and that the stability of its ferrous-oxy complex is enhanced by interdomain interactions.
Collapse
Affiliation(s)
- Alexandra Ioanoviciu
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94158-2517, USA
| | | | | | | |
Collapse
|
38
|
Role of Phe113 at the distal side of the heme domain of an oxygen-sensor (Ec DOS) in the characterization of the heme environment. J Inorg Biochem 2009; 103:989-96. [DOI: 10.1016/j.jinorgbio.2009.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 04/17/2009] [Accepted: 04/20/2009] [Indexed: 11/18/2022]
|
39
|
Green J, Crack JC, Thomson AJ, LeBrun NE. Bacterial sensors of oxygen. Curr Opin Microbiol 2009; 12:145-51. [DOI: 10.1016/j.mib.2009.01.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 01/19/2009] [Accepted: 01/22/2009] [Indexed: 12/23/2022]
|
40
|
Tanaka A, Shimizu T. Ligand binding to the Fe(III)-protoporphyrin IX complex of phosphodiesterase from Escherichia coli (Ec DOS) markedly enhances catalysis of cyclic di-GMP: roles of Met95, Arg97, and Phe113 of the putative heme distal side in catalytic regulation and ligand binding. Biochemistry 2009; 47:13438-46. [PMID: 19053256 DOI: 10.1021/bi8012017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphodiesterase (Ec DOS) from Escherichia coli is a gas-sensor enzyme in which binding of gas molecules, such as O(2), CO, and NO, to the Fe(II)-protoporphyrin IX complex in the sensor domain stimulates phosphodiesterase activity toward cyclic-di-GMP. In this study, we report that external axial ligands, such as cyanide or imidazole, bind to Fe(III)-protoporphyrin IX in the sensor domain and induce a 10- to 11-fold increase (from 8.1 up to 86 min(-1)) in catalysis, which is more substantial than that (6.3 to 7.2-fold) observed for other gas-stimulated Fe(II) heme-bound enzymes. Catalytic activity (50 min(-1)) of the heme-free mutant, H77A, was comparable to that of the ligand-stimulated enzymes. Accordingly, we propose that the heme at the sensor domain inhibits catalysis and that ligand binding to the heme iron complex releases this catalytic suppression. Furthermore, mutations of Met95, Arg97, and Phe113 at the putative heme distal side suppressed the ligand effects on catalysis. The rate constants (19,000 x 10(-5) microM(-1)min(-1)) for cyanide binding to the M95A and M95L mutants of the full-length enzyme were 633-fold higher than that to wild-type Ec DOS (30 x 10(-5) microM(-1)min(-1)). The absorption spectrum of the F113Y mutant suggests that the Tyr O(-) group directly coordinates to the Fe(III) complex and that the cyanide binding rate to the mutant is very slow, compared with those of the wild-type and other mutant proteins. We observed a similar trend in the binding behavior of imidazole to full-length mutant enzymes. Therefore, while Met95 and Phe113 are not direct axial ligands for the Fe(III) complex, catalytic, spectroscopic, and ligand binding evidence suggests that these residues are located in the vicinity of the heme.
Collapse
Affiliation(s)
- Atsunari Tanaka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | | |
Collapse
|