1
|
Mokdad A, Ang E, Desciak M, Ott C, Vilbert A, Beddow O, Butuc A, Larsen RW, Reynolds MF. Photoacoustic Calorimetry Studies of O 2-Sensing FixL and (R200, I209) Variants from Sinorhizobium meliloti Reveal Conformational Changes Coupled to Ligand Photodissociation from the Heme-PAS Domain. Biochemistry 2024; 63:116-127. [PMID: 38127721 PMCID: PMC10765370 DOI: 10.1021/acs.biochem.3c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
FixL is an oxygen-sensing heme-PAS protein that regulates nitrogen fixation in the root nodules of plants. In this paper, we present the first photothermal studies of the full-length wild-type FixL protein from Sinorhizobium meliloti and the first thermodynamic profile of a full-length heme-PAS protein. Photoacoustic calorimetry studies reveal a quadriphasic relaxation for SmFixL*WT and the five variant proteins (SmFixL*R200H, SmFixL*R200Q, SmFixL*R200E, SmFixL*R200A, and SmFixL*I209M) with four intermediates from <20 ns to ∼1.5 μs associated with the photodissociation of CO from the heme. The altered thermodynamic profiles of the full-length SmFixL* variant proteins confirm that the conserved heme domain residues R200 and I209 are important for signal transduction. In contrast, the truncated heme domain, SmFixLH128-264, shows only a single, fast monophasic relaxation at <50 ns associated with the fast disruption of a salt bridge and release of CO to the solvent, suggesting that the full-length protein is necessary to observe the conformational changes that propagate the signal from the heme domain to the kinase domain.
Collapse
Affiliation(s)
- Audrey Mokdad
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue SCA 400, Tampa, Florida 33620, United States
| | - EuTchen Ang
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Michael Desciak
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Christine Ott
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Avery Vilbert
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Olivia Beddow
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Artiom Butuc
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Randy W. Larsen
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue SCA 400, Tampa, Florida 33620, United States
| | - Mark F. Reynolds
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| |
Collapse
|
2
|
The Treponema denticola PAS Domain-Containing Histidine Kinase Hpk2 Is a Heme Binding Sensor of Oxygen Levels. J Bacteriol 2018; 200:JB.00116-18. [PMID: 29986942 DOI: 10.1128/jb.00116-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 07/04/2018] [Indexed: 12/29/2022] Open
Abstract
Periodontal disease (PD) results from a shift in the composition of the microbial community of the subgingival crevice. As the bacterial population transitions from Gram-positive bacteria to predominantly Gram-negative anaerobes and spirochetes, dramatic changes occur in the physiological and immunological environment at diseased sites. Treponema denticola thrives in periodontal pockets, indicating that it has a unique ability to adapt to changing environmental conditions. Hpk2 (tde1970), a Per-Arnt-Sim motif (PAS) domain-containing histidine kinase (HK), is part of the T. denticola Hpk2-Rrp2 (tde1969) two-component regulatory (TCR) system. This TCR system is growth phase regulated and has been postulated to play a key role in adaptive responses. In this study, we employ predictive structural analyses and site-directed mutagenesis to investigate the functional role of specific amino acid residues located within the Hpk2 PAS domain. Specific substitutions impacted autophosphorylation (AP), phosphotransfer (PT), oligomerization, and hemin binding. The AP, PT, hemin binding, and oligomerization potential of some mutated Hpk2 proteins differed under aerobic versus anaerobic reaction conditions. The data presented here suggest that the regulatory activity of Hpk2 is linked to diatomic gas levels. In a broader sense, this study highlights the importance of studying proteins produced by anaerobes under conditions that approximate the environment in which they thrive.IMPORTANCE Periodontal disease affects nearly 60% of the global adult population. Its costs to individuals, and to society as a whole, are enormous. As periodontal disease develops, there is a shift in the composition of the oral microbial community. The bacteria that become dominant are able to cause significant damage to the tissues that support the teeth, leading to tooth loss. Treponema denticola is one of the keystone pathogens associated with periodontal disease. An earlier study demonstrated that the Hpk2 and Rrp2 proteins play an important role in adaptive responses. Here, we explore the role of specific Hpk2 amino acids in environmental sensing and function, using structural analyses and site-directed mutagenesis.
Collapse
|
3
|
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
|
4
|
Helms G, Satterlee JD. Keeping PASE with WEFT: SHWEFT-PASE pulse sequences for 1H NMR spectra of highly paramagnetic molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:222-229. [PMID: 23401036 DOI: 10.1002/mrc.3929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/14/2012] [Accepted: 01/04/2013] [Indexed: 06/01/2023]
Abstract
Metalloproteins are a category of biomolecules in which the metal site is usually the locus of activity or function. In many cases, the metal ions are paramagnetic or have accessible paramagnetic states, many of which can be studied using NMR spectroscopy. Extracting useful information from (1)H NMR spectra of highly paramagnetic proteins can be difficult because the paramagnetism leads to large resonance shifts (~400 ppm), extremely broad lines, extreme baseline nonlinearity, and peak shape distortion. It is demonstrated that employing polychromatic and adiabatic shaped pulses in simple pulse sequences, then combining existing sequences, leads to significant spectral improvement for highly paramagnetic proteins. These sequences employ existing technology, with available hardware, and are of short duration to accommodate short nuclear T1 and T2. They are shown to display uniform excitation over large spectral widths (~75 kHz), accommodate high repetition rates, produce flat baselines over 75 kHz while maintaining peak shape fidelity, and can be used to reduce spectral dynamic range. High-spin (S = 5/2) metmyoglobin, a prototypical highly paramagnetic protein, was used as the test molecule. The resulting one-dimensional (1D) pulse sequences combine shaped pulses with super-water elimination Fourier transform, which can be further combined with paramagnetic spectroscopy to give shaped pulses with super-water elimination Fourier transform-paramagnetic spectroscopy. These sequences require, at most, direct current offset correction and minimal phasing. The performance of these sequences in simple (1)H 1D, 1D NOE, and two-dimensional NOESY experiments is demonstrated for metmyoglobin and Paracoccus denitrificans Co(2+)-amicyanin (S = 3/2), and employed to make new heme hyperfine resonance assignments for high-spin metBjFixLH(151-256), the heme sensing domain of Bradyrhizobium japonicum FixL.
Collapse
Affiliation(s)
- Gregory Helms
- Center for NMR Spectroscopy, Washington State University, Pullman, WA 99164-4630, USA
| | | |
Collapse
|
5
|
Murthy UMN, Wecker MSA, Posewitz MC, Gilles-Gonzalez MA, Ghirardi ML. Novel FixL homologues in Chlamydomonas reinhardtii bind heme and O(2). FEBS Lett 2012; 586:4282-8. [PMID: 22801216 DOI: 10.1016/j.febslet.2012.06.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/26/2012] [Accepted: 06/28/2012] [Indexed: 11/17/2022]
Abstract
Genome inspection revealed nine putative heme-binding, FixL-homologous proteins in Chlamydomonas reinhardtii. The heme-binding domains from two of these proteins, FXL1 and FXL5 were cloned, expressed in Escherichia coli, purified and characterized. The recombinant FXL1 and FXL5 domains stained positively for heme, while mutations in the putative ligand-binding histidine FXL1-H200S and FXL5-H200S resulted in loss of heme binding. The FXL1 and FXL5 [Fe(II), bound O(2)] had Soret absorption maxima around 415 nm, and weaker absorptions at longer wavelengths, in concurrence with the literature. Ligand-binding measurements showed that FXL1 and FXL5 bind O(2) with moderate affinity, 135 and 222 μM, respectively. This suggests that Chlamydomonas may use the FXL proteins in O(2)-sensing mechanisms analogous to that reported in nitrogen-fixing bacteria to regulate gene expression.
Collapse
Affiliation(s)
- U M Narayana Murthy
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | | | | | | | | |
Collapse
|
6
|
Origins of aging mass loss in recombinant N-terminus and C-terminus deletion mutants of the heme-PAS biosensor domain BjFixLH(140-270). J Inorg Biochem 2011; 105:609-15. [PMID: 21443850 DOI: 10.1016/j.jinorgbio.2011.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 01/20/2011] [Accepted: 01/21/2011] [Indexed: 11/22/2022]
Abstract
Nine recombinant FixL heme domains from Bradyrhizobium japonicum previously were shown to exhibit mass instability independent of many environmental factors (J.D. Satterlee, C. Suquet, A. Bidwai, J. Erman, L. Schwall, R. Jimenez, Biochemistry 47 (2008) 1540-1553). Two of those recombinant proteins were produced in remote laboratories. Mass losses begin appearing at completion of isolation and comprise a substantial proportion of samples within 1-3 days of storage and handling. Thus, degradation occurs during the time frame of experiments and crystallization. Detailed understanding of this instability is desired in order to formulate stable heme-PAS sensor domains for experimentation and for a mechanistic interpretation. However, mass spectra of the full length heme-PAS domain, BjFixLH(140-270), are complex by 1-3 days following isolation due to broad features and a high density of overlapping peaks, so that individual peak assignments are at present ambiguous. This stymies direct, quantitative interpretation of the source of the observed mass losses. To solve this dilemma amino-terminal primary sequencing and MALDI-TOF (Matrix Assisted Laser Desorption Ionization-Time of Flight) mass spectrometry monitoring of three terminal variants of BjFixLH(140-270) have been achieved. The working hypothesis, that the experimentally observed mass losses originate in the PAS protein sequence termini, has been substantiated. This establishes a basis for interpreting the more complex results from aging full length BjFixLH(140-270).
Collapse
|
7
|
Reynolds MF, Ackley L, Blizman A, Lutz Z, Manoff D, Miles M, Pace M, Patterson J, Pozzessere N, Saia K, Sato R, Smith D, Tarves P, Weaver M, Sieg K, Lukat-Rodgers GS, Rodgers KR. Role of conserved F(alpha)-helix residues in the native fold and stability of the kinase-inhibited oxy state of the oxygen-sensing FixL protein from Sinorhizobium meliloti. Arch Biochem Biophys 2009; 485:150-9. [PMID: 19254684 DOI: 10.1016/j.abb.2009.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 02/11/2009] [Accepted: 02/12/2009] [Indexed: 10/21/2022]
Abstract
The oxygen-sensing FixL protein from Sinorhizobium meliloti is part of the heme-PAS family of gas sensors that regulate many important signal transduction pathways in a wide variety of organisms. We examined the role of the conserved F(alpha)-9 arginine 200 and several other conserved residues on the proximal F(alpha)-helix in the heme domain of SmFixL* using site-directed mutagenesis in conjunction with UV-visible, EPR, and resonance Raman spectroscopy. The F(alpha)-helix variants R200A, E, Q, H, Y197A, and D195A were expressed at reasonable levels and purified to homogeneity. The R200I and Y201A variants did not express in observable quantities. Tyrosine 201 is crucial for forming the native protein fold of SmFixL* while Y197 and R200 are important for stabilizing the kinase-inhibited oxy state. Our results show a clear correlation between H-bond donor ability of the F(alpha)-9 side chain and the rate of heme autoxidation. This trend in conjunction with crystal structures of liganded BjFixL heme domains, show that H-bonding between the conserved F(alpha)-9 arginine and the heme-6-propionate group contributes to the kinetic stability of the kinase-inactivated, oxy state of SmFixL*.
Collapse
Affiliation(s)
- Mark F Reynolds
- Department of Chemistry, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Bidwai AK, Ok EY, Erman JE. pH dependence of cyanide binding to the ferric heme domain of the direct oxygen sensor from Escherichia coli and the effect of alkaline denaturation. Biochemistry 2008; 47:10458-70. [PMID: 18771281 DOI: 10.1021/bi800872d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The spectrum of the ferric heme domain of the direct oxygen sensor protein from Escherichia coli ( EcDosH) has been measured between pH 3.0 and 12.6. EcDosH undergoes acid denaturation with an apparent p K a of 4.24 +/- 0.05 and a Hill coefficient of 3.1 +/- 0.6 and reversible alkaline denaturation with a p K a of 9.86 +/- 0.04 and a Hill coefficient of 1.1 +/- 0.1. Cyanide binding to EcDosH has been investigated between pH 4 and 11. The EcDosH-cyanide complex is most stable at pH 9 with a K D of 0.29 +/- 0.06 microM. The kinetics of cyanide binding are monophasic between pH 4 and 8. At pH >or=8.5, the reaction is biphasic with the fast phase dependent upon the cyanide concentration and the slow phase independent of cyanide. The slow phase is attributed to conversion of denatured EcDosH to the native state, with a pH-independent rate of 0.052 +/- 0.006 s (-1). The apparent association rate constant for cyanide binding to EcDosH increases from 3.6 +/- 0.1 M (-1) s (-1) at pH 4 to 520 +/- 20 M (-1) s (-1) at pH 11. The dissociation rate constant averages (8.6 +/- 1.3) x 10 (-5) s (-1) between pH 5 and 9, increasing to (1.4 +/- 0.1) x 10 (-3) s (-1) at pH 4 and (2.5 +/- 0.1) x 10 (-3) s (-1) at pH 12.2. The mechanism of cyanide binding is consistent with preferential binding of the cyanide anion to native EcDosH. The reactions of imidazole and H 2O 2 with ferric EcDosH were also investigated and show little reactivity.
Collapse
Affiliation(s)
- Anil K Bidwai
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, USA
| | | | | |
Collapse
|
9
|
Landfried DA, Vuletich DA, Pond MP, Lecomte JTJ. Structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins. Gene 2007; 398:12-28. [PMID: 17550789 PMCID: PMC2394511 DOI: 10.1016/j.gene.2007.02.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Accepted: 02/05/2007] [Indexed: 01/09/2023]
Abstract
The binding of a cofactor to a protein matrix often involves a reorganization of the polypeptide structure. b Hemoproteins provide multiple examples of this behavior. In this minireview, selected monomeric and single b heme proteins endowed with distinct topological properties are inspected for the extent of induced refolding upon heme binding. To complement the data reported in the literature, original results are presented on a two-on-two globin of cyanobacterial origin (Synechococcus sp. PCC 7002 GlbN) and on the heme-containing module of FixL, an oxygen-sensing protein with the mixed alpha/beta topology of PAS domains. GlbN had a stable apoprotein that was further stabilized and locally refolded by heme binding; in contrast, apoFixLH presented features of a molten globule. Sequence analyses (helicity, disorder, and polarity) and solvent accessibility calculations were performed to identify trends in the architecture of b hemoproteins. In several cases, the primary structure appeared biased toward a partially disordered binding pocket in the absence of the cofactor.
Collapse
Affiliation(s)
- Daniel A Landfried
- The Pennsylvania State University, Department of Chemistry, University Park, PA 16802, USA
| | | | | | | |
Collapse
|