1
|
Budhraja R, Karande S, Ding C, Ullrich MK, Wagner S, Reemtsma T, Adrian L. Characterization of membrane-bound metalloproteins in the anaerobic ammonium-oxidizing bacterium "Candidatus Kuenenia stuttgartiensis" strain CSTR1. Talanta 2020; 223:121711. [PMID: 33298257 DOI: 10.1016/j.talanta.2020.121711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 01/18/2023]
Abstract
Membrane-bound metalloproteins are the basis of biological energy conservation via respiratory processes, however, their biochemical characterization is difficult. Here, we followed a gel-based proteomics and metallomics approach to identify membrane-associated metalloproteins in the anaerobic ammonium-oxidizing "Candidatus Kuenenia stuttgartiensis" strain CSTR1. Membrane-associated protein complexes were separated by two dimensional Blue Native/SDS gel electrophoresis and subunits were identified by mass spectrometry; protein-bound metal ions were quantified from the gel by connecting either a desolvating nebulizer system or laser ablation to inductively coupled plasma triple quadrupole mass spectrometry (ICP-QqQ-MS). We identified most protein complexes predicted to be involved in anaerobic ammonium oxidation and carbon fixation. The ICP-QqQ-MS data showed the presence of Fe and Zn in a wide range of high molecular weight protein complexes (230-800 kDa). Mo was prominently found in gel slices with proteins of a size of 500-650 kDa, whereas Ni was only found using the desolvating nebulizer system in the protein range of 350-500 kDa. The detected protein complexes and their metal content were consistent with genome annotations. Gel-based metalloproteomics is a sensitive and reliable approach for the characterization of metalloproteins and could be used to characterize many multimeric metalloprotein complexes in biological systems.
Collapse
Affiliation(s)
- Rohit Budhraja
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Shubhangi Karande
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Leipzig, Germany
| | - Chang Ding
- Helmholtz Centre for Environmental Research - UFZ, Environmental Biotechnology, Leipzig, Germany
| | - Maria K Ullrich
- Helmholtz Centre for Environmental Research - UFZ, Analytical Chemistry, Leipzig, Germany
| | - Stephan Wagner
- Helmholtz Centre for Environmental Research - UFZ, Analytical Chemistry, Leipzig, Germany
| | - Thorsten Reemtsma
- Helmholtz Centre for Environmental Research - UFZ, Analytical Chemistry, Leipzig, Germany
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, Environmental Biotechnology, Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany.
| |
Collapse
|
2
|
Poole RK, Cozens AG, Shepherd M. The CydDC family of transporters. Res Microbiol 2019; 170:407-416. [PMID: 31279084 DOI: 10.1016/j.resmic.2019.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/12/2019] [Accepted: 06/25/2019] [Indexed: 12/23/2022]
Abstract
The CydDC family of ABC transporters export the low molecular weight thiols glutathione and cysteine to the periplasm of a variety of bacterial species. The CydDC complex has previously been shown to be important for disulfide folding, motility, respiration, and tolerance to nitric oxide and antibiotics. In addition, CydDC is thus far unique amongst ABC transporters in that it binds a haem cofactor that appears to modulate ATPase activity. CydDC has a diverse impact upon bacterial metabolism, growth, and virulence, and is of interest to those working on membrane transport mechanisms, redox biology, aerobic respiration, and stress sensing/tolerance during infection.
Collapse
Affiliation(s)
- Robert K Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Adam G Cozens
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Mark Shepherd
- School of Biosciences, University of Kent, Canterbury, United Kingdom.
| |
Collapse
|
3
|
Quantitative Assessment of the Effects of Reducing Agents on Biological Macromolecules and on the Possible Repair of Oxidative Damage. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5704016. [PMID: 30175134 PMCID: PMC6098912 DOI: 10.1155/2018/5704016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022]
Abstract
Objective To quantitatively assess the influence of reducing agents on biological macromolecules and on the possible repair of oxidative damage. Methods Samples (antibody, enzyme, DNA, and diluted serum) were treated with reducing agents (ammonium ferrous sulfate, ascorbic acid, potassium iodide, and sodium hyposulfite) in the experimental group and with NaCl in the control group. Enzyme-linked immunosorbent assay and quantitative PCR were used to determine the activity of antibody, enzyme, and DNA. Native gel electrophoresis (Native-PAGE) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were used to determine protein structure. Reducing agents that had no inhibitory effect on biological macromolecules were selected. Antibodies were treated with oxidants to caused oxidative damage and then treated with reducing agents, and the possible repair of oxidative damage was assessed. Results Certain concentrations of ammonium ferrous sulfate resulted in significant inhibition of antibody, enzyme, DNA, and diluted serum. Certain concentrations of ascorbic acid resulted in significant inhibition of antibody. Sodium hyposulfite and potassium iodide had no effect on antibody, enzyme, DNA, and diluted serum. The OD values in group A (in which HBsAb was treated by oxidation and then a reductant) were significantly higher than those in group B (HBsAb treated by oxidation). Conclusion Ammonium ferrous sulfate, ascorbic acid, sodium hyposulfite, and potassium iodide had different effects on antibody, enzyme, DNA, and diluted serum. The reduction in antibody activity due to an oxidant was partially repaired by a reductant.
Collapse
|
4
|
Rudashevskaya EL, Sickmann A, Markoutsa S. Global profiling of protein complexes: current approaches and their perspective in biomedical research. Expert Rev Proteomics 2016; 13:951-964. [PMID: 27602509 DOI: 10.1080/14789450.2016.1233064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Despite the rapid evolution of proteomic methods, protein interactions and their participation in protein complexes - an important aspect of their function - has rarely been investigated on the proteome-wide level. Disease states, such as muscular dystrophy or viral infection, are induced by interference in protein-protein interactions within complexes. The purpose of this review is to describe the current methods for global complexome analysis and to critically discuss the challenges and opportunities for the application of these methods in biomedical research. Areas covered: We discuss advancements in experimental techniques and computational tools that facilitate profiling of the complexome. The main focus is on the separation of native protein complexes via size exclusion chromatography and gel electrophoresis, which has recently been combined with quantitative mass spectrometry, for a global protein-complex profiling. The development of this approach has been supported by advanced bioinformatics strategies and fast and sensitive mass spectrometers that have allowed the analysis of whole cell lysates. The application of this technique to biomedical research is assessed, and future directions are anticipated. Expert commentary: The methodology is quite new, and has already shown great potential when combined with complementary methods for detection of protein complexes.
Collapse
Affiliation(s)
- Elena L Rudashevskaya
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany
| | - Albert Sickmann
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany.,b Medizinisches Proteom-Center , Ruhr-Universität Bochum , Bochum , Germany.,c School of Natural & Computing Sciences, Department of Chemistry , University of Aberdeen , Aberdeen , UK
| | - Stavroula Markoutsa
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany
| |
Collapse
|
5
|
Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
Collapse
Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
| |
Collapse
|
6
|
Polyclonal Antibody Production for Membrane Proteins via Genetic Immunization. Sci Rep 2016; 6:21925. [PMID: 26908053 PMCID: PMC4764931 DOI: 10.1038/srep21925] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/02/2016] [Indexed: 01/08/2023] Open
Abstract
Antibodies are essential for structural determinations and functional studies of membrane proteins, but antibody generation is limited by the availability of properly-folded and purified antigen. We describe the first application of genetic immunization to a structurally diverse set of membrane proteins to show that immunization of mice with DNA alone produced antibodies against 71% (n = 17) of the bacterial and viral targets. Antibody production correlated with prior reports of target immunogenicity in host organisms, underscoring the efficiency of this DNA-gold micronanoplex approach. To generate each antigen for antibody characterization, we also developed a simple in vitro membrane protein expression and capture method. Antibody specificity was demonstrated upon identifying, for the first time, membrane-directed heterologous expression of the native sequences of the FopA and FTT1525 virulence determinants from the select agent Francisella tularensis SCHU S4. These approaches will accelerate future structural and functional investigations of therapeutically-relevant membrane proteins.
Collapse
|
7
|
Rowe HM, Huntley JF. From the Outside-In: The Francisella tularensis Envelope and Virulence. Front Cell Infect Microbiol 2015; 5:94. [PMID: 26779445 PMCID: PMC4688374 DOI: 10.3389/fcimb.2015.00094] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/07/2015] [Indexed: 12/20/2022] Open
Abstract
Francisella tularensis is a highly-infectious bacterium that causes the rapid, and often lethal disease, tularemia. Many studies have been performed to identify and characterize the virulence factors that F. tularensis uses to infect a wide variety of hosts and host cell types, evade immune defenses, and induce severe disease and death. This review focuses on the virulence factors that are present in the F. tularensis envelope, including capsule, LPS, outer membrane, periplasm, inner membrane, secretion systems, and various molecules in each of aforementioned sub-compartments. Whereas, no single bacterial molecule or molecular complex single-handedly controls F. tularensis virulence, we review here how diverse bacterial systems work in conjunction to subvert the immune system, attach to and invade host cells, alter phagosome/lysosome maturation pathways, replicate in host cells without being detected, inhibit apoptosis, and induce host cell death for bacterial release and infection of adjacent cells. Given that the F. tularensis envelope is the outermost layer of the bacterium, we highlight herein how many of these molecules directly interact with the host to promote infection and disease. These and future envelope studies are important to advance our collective understanding of F. tularensis virulence mechanisms and offer targets for future vaccine development efforts.
Collapse
Affiliation(s)
- Hannah M Rowe
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences Toledo, OH, USA
| | - Jason F Huntley
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences Toledo, OH, USA
| |
Collapse
|
8
|
Chandler JC, Sutherland MD, Harton MR, Molins CR, Anderson RV, Heaslip DG, Bosio CM, Belisle JT. Francisella tularensis LVS surface and membrane proteins as targets of effective post-exposure immunization for tularemia. J Proteome Res 2014; 14:664-75. [PMID: 25494920 PMCID: PMC4324441 DOI: 10.1021/pr500628k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Francisella tularensis causes disease (tularemia)
in a large number of mammals, including man. We previously demonstrated
enhanced efficacy of conventional antibiotic therapy for tularemia
by postexposure passive transfer of immune sera developed against
a F. tularensis LVS membrane protein fraction (MPF).
However, the protein composition of this immunogenic fraction was
not defined. Proteomic approaches were applied to define the protein
composition and identify the immunogens of MPF. MPF consisted of at
least 299 proteins and 2-D Western blot analyses using sera from MPF-immunized
and F. tularensis LVS-vaccinated mice coupled to
liquid chromatography–tandem mass spectrometry identified 24
immunoreactive protein spots containing 45 proteins. A reverse vaccinology
approach that applied labeling of F. tularensis LVS
surface proteins and bioinformatics was used to reduce the complexity
of potential target immunogens. Bioinformatics analyses of the immunoreactive
proteins reduced the number of immunogen targets to 32. Direct surface
labeling of F. tularensis LVS resulted in the identification
of 31 surface proteins. However, only 13 of these were reactive with
MPF and/or F. tularensis LVS immune sera. Collectively,
this use of orthogonal proteomic approaches reduced the complexity
of potential immunogens in MPF by 96% and allowed for prioritization
of target immunogens for antibody-based immunotherapies against tularemia.
Collapse
Affiliation(s)
- Jeffrey C Chandler
- Rocky Mountain Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Department of Microbiology, Immunology, and Pathology, Colorado State University , Campus Delivery 0922, Fort Collins 80523, Colorado, United States
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Glew MD, Veith PD, Chen D, Seers CA, Chen YY, Reynolds EC. Blue native-PAGE analysis of membrane protein complexes in Porphyromonas gingivalis. J Proteomics 2014; 110:72-92. [DOI: 10.1016/j.jprot.2014.07.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/01/2014] [Accepted: 07/20/2014] [Indexed: 11/30/2022]
|
10
|
Diéguez-Casal E, Freixeiro P, Costoya L, Criado MT, Ferreirós C, Sánchez S. High resolution clear native electrophoresis is a good alternative to blue native electrophoresis for the characterization of the Escherichia coli membrane complexes. J Microbiol Methods 2014; 102:45-54. [PMID: 24845470 DOI: 10.1016/j.mimet.2014.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 10/25/2022]
Abstract
Blue native electrophoresis (BNE) has become the most popular method for the global analysis of membrane protein complexes. Although it has been shown to be very useful for that purpose, it can produce the dissociation of complexes with weak interactions and, due to the use of Coomassie Brilliant Blue, does not allow the subsequent application of fluorimetric and/or enzymatic techniques. Recently, we have successfully used the high resolution clear native electrophoresis (hrCNE) for the analysis of Neisseria meningitidis outer membrane porin complexes. The aim of this study was to determine the composition of the complexome of the Escherichia coli envelope by using hrCNE and to compare our results with those previously obtained using BNE. The bidimensional electrophoresis approaches used, hrCN/hrCNE and hrCN/SDS-PAGE, coupled to mass spectrometry allowed a detailed analysis of the complexome of E. coli membranes. For the first time, the three subunits of the formate dehydrogenase FDH-O were identified forming a single complex and hrCNE also allowed the identification of both the HflK and HflC proteins as components of the HflA complex. This technique also allowed us to suggest a relationship between OmpF and DLDH and, although OmpA is considered to be monomeric in vivo, we found this protein structured as homodimers. Thus hrCNE provides a good tool for future analyses of bacterial membrane proteins and complexes and is an important alternative to the commonly used BNE.
Collapse
Affiliation(s)
- Ernesto Diéguez-Casal
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Paula Freixeiro
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Liliana Costoya
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M Teresa Criado
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carlos Ferreirós
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Sandra Sánchez
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| |
Collapse
|
11
|
Martin-Garcia JM, Hansen DT, Zook J, Loskutov AV, Robida MD, Craciunescu FM, Sykes KF, Wachter RM, Fromme P, Allen JP. Purification and biophysical characterization of the CapA membrane protein FTT0807 from Francisella tularensis. Biochemistry 2014; 53:1958-70. [PMID: 24593131 PMCID: PMC3985703 DOI: 10.1021/bi401644s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
The capA gene (FTT0807)
from Francisella
tularensis subsp. tularensis SCHU S4 encodes a 44.4
kDa integral membrane protein composed of 403 amino acid residues
that is part of an apparent operon that encodes at least two other
membrane proteins, CapB, and CapC, which together play a critical
role in the virulence and pathogenesis of this bacterium. The capA gene was overexpressed in Escherichia
coli as a C-terminal His6-tagged fusion
with a folding reporter green fluorescent protein (frGFP). Purification
procedures using several detergents were developed for the fluorescing
and membrane-bound product, yielding approximately 30 mg of pure protein
per liter of bacterial culture. Dynamic light scattering indicated
that CapA-frGFP was highly monodisperse, with a size that was dependent
upon both the concentration and choice of detergent. Circular dichroism
showed that CapA-frGFP was stable over the range of 3–9 for
the pH, with approximately half of the protein having well-defined
α-helical and β-sheet secondary structure. The addition
of either sodium chloride or calcium chloride at concentrations producing
ionic strengths above 0.1 M resulted in a small increase of the α-helical
content and a corresponding decrease in the random-coil content. Secondary-structure
predictions on the basis of the analysis of the sequence indicate
that the CapA membrane protein has two transmembrane helices with
a substantial hydrophilic domain. The hydrophilic domain is predicted
to contain a long disordered region of 50–60 residues, suggesting
that the increase of α-helical content at high ionic strength
could arise because of electrostatic interactions involving the disordered
region. CapA is shown to be an inner-membrane protein and is predicted
to play a key cellular role in the assembly of polysaccharides.
Collapse
Affiliation(s)
- Jose M Martin-Garcia
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Salzano AM, Novi G, Arioli S, Corona S, Mora D, Scaloni A. Mono-dimensional blue native-PAGE and bi-dimensional blue native/urea-PAGE or/SDS-PAGE combined with nLC–ESI-LIT-MS/MS unveil membrane protein heteromeric and homomeric complexes in Streptococcus thermophilus. J Proteomics 2013; 94:240-61. [DOI: 10.1016/j.jprot.2013.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/04/2013] [Accepted: 09/14/2013] [Indexed: 02/06/2023]
|
13
|
Low abundance of respiratory nitrate reductase is essential for Escherichia coli in resistance to aminoglycoside and cephalosporin. J Proteomics 2013; 87:78-88. [DOI: 10.1016/j.jprot.2013.05.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 05/06/2013] [Accepted: 05/16/2013] [Indexed: 11/19/2022]
|