Dos, a Heme-Binding PAS Protein from <i>Escherichia coli</i>, Is a Direct Oxygen Sensor

Delgado-Nixon, Vondolee M.; González, Gonzalo; Gilles-Gonzalez, Marie Alda

doi:10.1021/bi991911s

Cited by 252 publications

(341 citation statements)

References 42 publications

(81 reference statements)

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“…The O 2 -sensing proteins identified so far include FixL (7), phosphodiesterase A 1 from Acetobacter xylinum (8), Escherichia coli direct oxygen sensor (DOS) 3 (9), and HemAT (10). FixL, A. xylinum phosphodiesterase A1, and E. coli DOS belong to the PAS (PER/ ARNT/SIM) family and contain a heme-bound PAS domain as a sensor, but HemAT is globin-like, belonging to the methyl-accepting chemotaxis protein (MCP) family.…”

mentioning

confidence: 99%

Protein Conformation Changes of HemAT-Bs upon Ligand Binding Probed by Ultraviolet Resonance Raman Spectroscopy

El-Mashtoly¹,

Yoshimura

et al. 2008

Journal of Biological Chemistry

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confidence: 99%

Protein Conformation Changes of HemAT-Bs upon Ligand Binding Probed by Ultraviolet Resonance Raman Spectroscopy

El-Mashtoly¹,

Yoshimura

et al. 2008

Journal of Biological Chemistry

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“…It is conserved in all known FixL proteins, AxPDEA1, and EcDos (3,6,7). It is the only polar residue in the heme pockets of FixL proteins (8,9).…”

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confidence: 99%

A Distal Arginine in Oxygen-Sensing Heme-PAS Domains Is Essential to Ligand Binding, Signal Transduction, and Structure

et al. 2003

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To evaluate the contributions of the Gβ-2 arginine to signal transduction in oxygen-sensing heme-PAS domains, we replaced this residue with alanine in Bradyrhizobium japonicum FixL and examined the results on heme-domain structure, ligand binding, and kinase regulation. In the isolated R220A BjFixL heme-PAS domain, the iron−histidine bond was increased in length by 0.31 Å, the heme flattened even without a ligand, and the interaction of a presumed regulatory loop (the FG loop) with the helix of heme attachment was weakened. Binding of carbon monoxide was similar for ferrous BjFixL and R220A BjFixL. In contrast, the level of binding of oxygen was dramatically lower (K d ∼ 1.5 mM) for R220A BjFixL, and this was manifested as 60- and 3-fold lower on- and off-rate constants, respectively. Binding of cyanide followed the same pattern as binding of oxygen. The catalytic activity was 3−4-fold higher in the “on-state” unliganded forms of R220A BjFixL than in the corresponding BjFixL species. Cyanide regulation of this activity was strongly impaired, but some inhibition was nevertheless preserved. Carbon monoxide and nitric oxide regulation, although weak in BjFixL, were abolished from R220A BjFixL. We conclude that the Gβ-2 arginine assists in the binding of oxygen to BjFixL but does not accomplish this by stabilizing the oxy form. This arginine is not absolutely required for regulation, although it is important for shifting a pre-existing kinase equilibrium toward the inactive state on binding of regulatory ligands. These findings support a regulatory model in which the heme-PAS domain operates as an ensemble that couples to the kinase rather than a mechanism driven by a single central switch.

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“…A role in O 2 /redox sensing for SO3389 coincides with the strong evidence that PAS domains can be sensors for gases (e.g., O 2 ) and/or intracellular redox potentials (53). For example, the PAS protein NifA has been shown to respond to O 2 via a flavin adenine dinucleotide (FAD) (6), and the E. coli Dos protein (EcDos) is a heme-containing gas sensor that has N-terminal PAS domains (12). PAS domain families comprise a protein clan with divergent sequences (15); however, a recent study characterized the structures of PAS domains with known and unknown cofactors and showed a broadly conserved structure that is comprised of a five-stranded antiparallel ␤-sheet and several ␣-helices for all PAS domains characterized to date (34).…”

Section: Resultsmentioning

confidence: 99%

Shewanella oneidensis MR-1 Sensory Box Protein Involved in Aerobic and Anoxic Growth

Sundararajan

Kurowski

Yan

et al. 2011

Appl Environ Microbiol

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Although little is known of potential function for conserved signaling proteins, it is hypothesized that such proteins play important roles to coordinate cellular responses to environmental stimuli. In order to elucidate the function of a putative sensory box protein (PAS domains) in Shewanella oneidensis MR-1, the physiological role of SO3389 was characterized. The predicted open reading frame (ORF) encodes a putative sensory box protein that has PAS, GGDEF, and EAL domains, and an in-frame deletion mutant was constructed (⌬SO3389) with approximately 95% of the ORF deleted. Under aerated conditions, wild-type and mutant cultures had similar growth rates, but the mutant culture had a lower growth rate under static, aerobic conditions. Oxygen consumption rates were lower for mutant cultures (1.5-fold), and wild-type cultures also maintained lower dissolved oxygen concentrations under aerated growth conditions. When transferred to anoxic conditions, the mutant did not grow with fumarate, iron(III), or dimethyl sulfoxide (DMSO) as electron acceptors. Biochemical assays demonstrated the expression of different c-type cytochromes as well as decreased fumarate reductase activity in the mutant transferred to anoxic growth conditions. Transcriptomic studies showed the inability of the mutant to up-express and down-express genes, including c-type cytochromes (e.g., SO4047/SO4048, SO3285/SO3286), reductases (e.g., SO0768, SO1427), and potential regulators (e.g., SO1329). The complemented strain was able to grow when transferred from aerobic to anoxic growth conditions with the tested electron acceptors. The modeled structure for the SO3389 PAS domains was highly similar to the crystal structures of FAD-binding PAS domains that are known O 2 /redox sensors. Based on physiological, genomic, and bioinformatic results, we suggest that the sensory box protein, SO3389, is an O 2 /redox sensor that is involved in optimization of aerobic growth and transitions to anoxia in S. oneidensis MR-1.In the postgenomic era, uncharacterized genes pose a major challenge in biology (16), and many sequenced genomes still contain a large fraction (up to 30 to 40%) of genes without defined physiological roles (13). In fact, many aspects of signaling and stress response most likely reside in this fraction of genes for a given organism and underlie the lack of understanding in physiological responses and control of metabolism. Many uncharacterized genes/proteins are classified as sensory box proteins based upon conserved domains, but signals and cellular responses for most presumptive sensory box proteins are not known.Shewanella oneidensis MR-1, a facultative anaerobe classified as a gammaproteobacterium, can utilize numerous inorganic compounds as electron acceptors (e.g., oxygen, nitrate, and metals). The S. oneidensis MR-1 genome sequence was determined (20), and the most recent annotation of the 5.1-Mb genome estimated 4,467 genes, of which 1,623 had hypothetical functions (28). Many bacteria considered to be "environmental" organisms typica...

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Dos, a Heme-Binding PAS Protein from Escherichia coli, Is a Direct Oxygen Sensor

Cited by 252 publications

References 42 publications

Protein Conformation Changes of HemAT-Bs upon Ligand Binding Probed by Ultraviolet Resonance Raman Spectroscopy

Protein Conformation Changes of HemAT-Bs upon Ligand Binding Probed by Ultraviolet Resonance Raman Spectroscopy

A Distal Arginine in Oxygen-Sensing Heme-PAS Domains Is Essential to Ligand Binding, Signal Transduction, and Structure

Shewanella oneidensis MR-1 Sensory Box Protein Involved in Aerobic and Anoxic Growth

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