Unusual Dynamics of Ligand Binding to the Heme Domain of the Bacterial CO Sensor Protein RcoM-2

2016 ◽  
Vol 120 (41) ◽  
pp. 10686-10694 ◽  
Author(s):  
Latifa Bouzhir-Sima ◽  
Roberto Motterlini ◽  
Julia Gross ◽  
Marten H. Vos ◽  
Ursula Liebl
Keyword(s):  
Ligand Binding ◽  
Sensor Protein ◽  
Heme Domain ◽  
Co Sensor

scholarly journals Heme Ligand Binding Properties and Intradimer Interactions in the Full-length Sensor Protein Dos from Escherichia coli and Its Isolated Heme Domain

2009 ◽  
Vol 284 (52) ◽  
pp. 36146-36159 ◽  
Author(s):  
Christophe Lechauve ◽  
Latifa Bouzhir-Sima ◽  
Taku Yamashita ◽  
Michael C. Marden ◽  
Marten H. Vos ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ligand Binding ◽  
Full Length ◽  
Binding Properties ◽  
Sensor Protein ◽  
Heme Domain

Ligand Binding Dynamics to the Heme Domain of the Oxygen Sensor Dos fromEscherichia coli

Biochemistry ◽  
2003 ◽  
Vol 42 (21) ◽  
pp. 6527-6535 ◽  
Author(s):  
Ursula Liebl ◽  
Latifa Bouzhir-Sima ◽  
Laurent Kiger ◽  
Michael C. Marden ◽  
Jean-Christophe Lambry ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Oxygen Sensor ◽  
Fromescherichia Coli ◽  
Heme Domain

scholarly journals Interaction of the Full-Length Heme-Based CO Sensor Protein RcoM-2 with Ligands

Biochemistry ◽  
2019 ◽  
Vol 58 (39) ◽  
pp. 4028-4034 ◽  
Author(s):  
Mayla Salman ◽  
Carolina Villamil Franco ◽  
Rivo Ramodiharilafy ◽  
Ursula Liebl ◽  
Marten H. Vos
Keyword(s):  
Full Length ◽  
Sensor Protein ◽  
Co Sensor

scholarly journals Ligand Dynamics and Early Signaling Events in the Heme Domain of the Sensor Protein Dos fromEscherichia coli

2007 ◽  
Vol 283 (4) ◽  
pp. 2344-2352 ◽  
Author(s):  
Taku Yamashita ◽  
Latifa Bouzhir-Sima ◽  
Jean-Christophe Lambry ◽  
Ursula Liebl ◽  
Marten H. Vos
Keyword(s):  
Fromescherichia Coli ◽  
Sensor Protein ◽  
Signaling Events ◽  
Heme Domain

scholarly journals Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges

2018 ◽  
Vol 19 (12) ◽  
pp. 3755 ◽  
Author(s):  
David Martín-Mora ◽  
Matilde Fernández ◽  
Félix Velando ◽  
Álvaro Ortega ◽  
José Gavira ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Ligand Binding ◽  
Functional Annotation ◽  
Signal Molecules ◽  
Signal Molecule ◽  
Ligand Screening ◽  
Sensor Protein ◽  
Sensor Proteins ◽  
Screening Approaches ◽  
Signal Transduction Systems

Bacteria possess a large number of signal transduction systems that sense and respond to different environmental cues. Most frequently these are transcriptional regulators, two-component systems and chemosensory pathways. A major bottleneck in the field of signal transduction is the lack of information on signal molecules that modulate the activity of the large majority of these systems. We review here the progress made in the functional annotation of sensor proteins using high-throughput ligand screening approaches of purified sensor proteins or individual ligand binding domains. In these assays, the alteration in protein thermal stability following ligand binding is monitored using Differential Scanning Fluorimetry. We illustrate on several examples how the identification of the sensor protein ligand has facilitated the elucidation of the molecular mechanism of the regulatory process. We will also discuss the use of virtual ligand screening approaches to identify sensor protein ligands. Both approaches have been successfully applied to functionally annotate a significant number of bacterial sensor proteins but can also be used to study proteins from other kingdoms. The major challenge consists in the study of sensor proteins that do not recognize signal molecules directly, but that are activated by signal molecule-loaded binding proteins.

scholarly journals CO-dependent Activity-controlling Mechanism of Heme-containing CO-sensor Protein, Neuronal PAS Domain Protein 2

2005 ◽  
Vol 280 (22) ◽  
pp. 21358-21368 ◽  
Author(s):  
Takeshi Uchida ◽  
Emiko Sato ◽  
Akira Sato ◽  
Ikuko Sagami ◽  
Toru Shimizu ◽  
...  
Keyword(s):  
Pas Domain ◽  
Controlling Mechanism ◽  
Sensor Protein ◽  
Dependent Activity ◽  
Co Sensor ◽  
Domain Protein

scholarly journals Gas Sensing and Signaling in the PAS-Heme Domain of the Pseudomonas aeruginosa Aer2 Receptor

2017 ◽  
Vol 199 (18) ◽  
Author(s):  
Darysbel Garcia ◽  
Emilie Orillard ◽  
Mark S. Johnson ◽  
Kylie J. Watts
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Ligand Binding ◽  
Cellular Response ◽  
Gas Sensing ◽  
Opportunistic Pathogen ◽  
Signaling Mechanism ◽  
Content Type ◽  
Environmental Bacterium ◽  
Heme Domain ◽  
Trp Mutant

ABSTRACT The Aer2 chemoreceptor from Pseudomonas aeruginosa contains a PAS sensing domain that coordinates b-type heme and signals in response to the binding of O2, CO, or NO. PAS-heme structures suggest that Aer2 uniquely coordinates heme via a His residue on a 310 helix (H234 on Eη), stabilizes O2 binding via a Trp residue (W283), and signals via both W283 and an adjacent Leu residue (L264). Ligand binding may displace L264 and reorient W283 for hydrogen bonding to the ligand. Here, we clarified the mechanisms by which Aer2-PAS binds heme, regulates ligand binding, and initiates conformational signaling. H234 coordinated heme, but additional hydrophobic residues in the heme cleft were also critical for stable heme binding. O2 appeared to be the native Aer2 ligand (dissociation constant [Kd ] of 16 μM). With one exception, mutants that bound O2 could signal, whereas many mutants that bound CO could not. W283 stabilized O2 binding but not CO binding, and it was required for signal initiation; W283 mutants that could not stabilize O2 were rapidly oxidized to Fe(III). W283F was the only Trp mutant that bound O2 with wild-type affinity. The size and nature of residue 264 was important for gas binding and signaling: L264W blocked O2 binding, L264A and L264G caused O2-mediated oxidation, and L264K formed a hexacoordinate heme. Our data suggest that when O2 binds to Aer2, L264 moves concomitantly with W283 to initiate the conformational signal. The signal then propagates from the PAS domain to regulate the C-terminal HAMP and kinase control domains, ultimately modulating a cellular response. IMPORTANCE Pseudomonas aeruginosa is a ubiquitous environmental bacterium and opportunistic pathogen that infects multiple body sites, including the lungs of cystic fibrosis patients. P. aeruginosa senses and responds to its environment via four chemosensory systems. Three of these systems regulate biofilm formation, twitching motility, and chemotaxis. The role of the fourth system, Che2, is unclear but has been implicated in virulence. The Che2 system contains a chemoreceptor called Aer2, which contains a PAS sensing domain that binds heme and senses oxygen. Here, we show that Aer2 uses unprecedented mechanisms to bind O2 and initiate signaling. These studies provide both the first functional corroboration of the Aer2-PAS signaling mechanism previously proposed from structure as well as a signaling model for Aer2-PAS receptors.

CarR, a MarR-family regulator from Corynebacterium glutamicum, modulated antibiotic and aromatic compound resistance

2019 ◽  
Vol 476 (21) ◽  
pp. 3141-3159 ◽  
Author(s):  
Meiru Si ◽  
Can Chen ◽  
Zengfan Wei ◽  
Zhijin Gong ◽  
GuiZhi Li ◽  
...  
Keyword(s):  
Stress Response ◽  
Ligand Binding ◽  
Corynebacterium Glutamicum ◽  
Conformational Changes ◽  
Cysteine Oxidation ◽  
Transcriptional Regulatory ◽  
Ligand Free ◽  
Redox Sensing

Abstract MarR (multiple antibiotic resistance regulator) proteins are a family of transcriptional regulators that is prevalent in Corynebacterium glutamicum. Understanding the physiological and biochemical function of MarR homologs in C. glutamicum has focused on cysteine oxidation-based redox-sensing and substrate metabolism-involving regulators. In this study, we characterized the stress-related ligand-binding functions of the C. glutamicum MarR-type regulator CarR (C. glutamicum antibiotic-responding regulator). We demonstrate that CarR negatively regulates the expression of the carR (ncgl2886)–uspA (ncgl2887) operon and the adjacent, oppositely oriented gene ncgl2885, encoding the hypothetical deacylase DecE. We also show that CarR directly activates transcription of the ncgl2882–ncgl2884 operon, encoding the peptidoglycan synthesis operon (PSO) located upstream of carR in the opposite orientation. The addition of stress-associated ligands such as penicillin and streptomycin induced carR, uspA, decE, and PSO expression in vivo, as well as attenuated binding of CarR to operator DNA in vitro. Importantly, stress response-induced up-regulation of carR, uspA, and PSO gene expression correlated with cell resistance to β-lactam antibiotics and aromatic compounds. Six highly conserved residues in CarR were found to strongly influence its ligand binding and transcriptional regulatory properties. Collectively, the results indicate that the ligand binding of CarR induces its dissociation from the carR–uspA promoter to derepress carR and uspA transcription. Ligand-free CarR also activates PSO expression, which in turn contributes to C. glutamicum stress resistance. The outcomes indicate that the stress response mechanism of CarR in C. glutamicum occurs via ligand-induced conformational changes to the protein, not via cysteine oxidation-based thiol modifications.

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