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Hatano T, Palani S, Papatziamou D, Salzer R, Souza DP, Tamarit D, Makwana M, Potter A, Haig A, Xu W, Townsend D, Rochester D, Bellini D, Hussain HMA, Ettema TJG, Löwe J, Baum B, Robinson NP, Balasubramanian M. Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery. Nat Commun 2022; 13:3398. [PMID: 35697693 PMCID: PMC9192718 DOI: 10.1038/s41467-022-30656-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 05/10/2022] [Indexed: 11/23/2022] Open
Abstract
The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, in processes that include ubiquitin-mediated multivesicular body formation, membrane repair, cytokinetic abscission, and virus exit from host cells. This ESCRT system appears to have simpler, ancient origins, since many archaeal species possess homologues of ESCRT-III and Vps4, the components that execute the final membrane scission reaction, where they have been shown to play roles in cytokinesis, extracellular vesicle formation and viral egress. Remarkably, metagenome assemblies of Asgard archaea, the closest known living relatives of eukaryotes, were recently shown to encode homologues of the entire cascade involved in ubiquitin-mediated membrane remodelling, including ubiquitin itself, components of the ESCRT-I and ESCRT-II subcomplexes, and ESCRT-III and Vps4. Here, we explore the phylogeny, structure, and biochemistry of Asgard homologues of the ESCRT machinery and the associated ubiquitylation system. We provide evidence for the ESCRT-I and ESCRT-II subcomplexes being involved in ubiquitin-directed recruitment of ESCRT-III, as it is in eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin for the ubiquitin-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.
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Affiliation(s)
- Tomoyuki Hatano
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Saravanan Palani
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Dimitra Papatziamou
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Ralf Salzer
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Diorge P Souza
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Daniel Tamarit
- Laboratory of Microbiology, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Mehul Makwana
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Antonia Potter
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Alexandra Haig
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Wenjue Xu
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - David Townsend
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - David Rochester
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - Dom Bellini
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Hamdi M A Hussain
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Nicholas P Robinson
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK.
| | - Mohan Balasubramanian
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
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2
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Salzer R, Clark JJ, Vaysburd M, Chang VT, Albecka A, Kiss L, Sharma P, Gonzalez Llamazares A, Kipar A, Hiscox JA, Owen A, Aricescu AR, Stewart JP, James LC, Löwe J. Single-dose immunisation with a multimerised SARS-CoV-2 receptor binding domain (RBD) induces an enhanced and protective response in mice. FEBS Lett 2021; 595:2323-2340. [PMID: 34331769 PMCID: PMC8426897 DOI: 10.1002/1873-3468.14171] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022]
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, has triggered a worldwide health emergency. Here, we show that ferritin-like Dps from hyperthermophilic Sulfolobus islandicus, covalently coupled with SARS-CoV-2 antigens via the SpyCatcher system, forms stable multivalent dodecameric vaccine nanoparticles that remain intact even after lyophilisation. Immunisation experiments in mice demonstrated that the SARS-CoV-2 receptor binding domain (RBD) coupled to Dps (RBD-S-Dps) elicited a higher antibody titre and an enhanced neutralising antibody response compared to monomeric RBD. A single immunisation with RBD-S-Dps completely protected hACE2-expressing mice from serious illness and led to viral clearance from the lungs upon SARS-CoV-2 infection. Our data highlight that multimerised SARS-CoV-2 subunit vaccines are a highly efficacious modality, particularly when combined with an ultra-stable scaffold.
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Affiliation(s)
- Ralf Salzer
- MRC Laboratory of Molecular BiologyCambridgeUK
| | - Jordan J. Clark
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
| | | | | | | | - Leo Kiss
- MRC Laboratory of Molecular BiologyCambridgeUK
| | - Parul Sharma
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
| | | | - Anja Kipar
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
- Laboratory for Animal Model PathologyInstitute of Veterinary PathologyVetsuisse FacultyUniversity of ZurichSwitzerland
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
| | - Andrew Owen
- Department of Pharmacology and TherapeuticsCentre of Excellence in Long‐acting Therapeutics (CELT)University of LiverpoolUK
| | | | - James P. Stewart
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolUK
| | | | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUK
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Neuhaus A, Selvaraj M, Salzer R, Langer JD, Kruse K, Kirchner L, Sanders K, Daum B, Averhoff B, Gold VAM. Cryo-electron microscopy reveals two distinct type IV pili assembled by the same bacterium. Nat Commun 2020; 11:2231. [PMID: 32376942 PMCID: PMC7203116 DOI: 10.1038/s41467-020-15650-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). Here, we use cryo-electron microscopy and mass spectrometry to show that the bacterium Thermus thermophilus produces two forms of type IV pilus ('wide' and 'narrow'), differing in structure and protein composition. Wide pili are composed of the major pilin PilA4, while narrow pili are composed of a so-far uncharacterized pilin which we name PilA5. Functional experiments indicate that PilA4 is required for natural transformation, while PilA5 is important for twitching motility.
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Affiliation(s)
- Alexander Neuhaus
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Muniyandi Selvaraj
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Laboratory of Structural Biology, Helsinki Institute of Life Science, 00014 University of Helsinki, Helsinki, Finland
| | - Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
- Structural Studies Division, Medical Research Council-Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Julian D Langer
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Max-von-Laue Str. 4, 60438, Frankfurt am Main, Germany
| | - Kerstin Kruse
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Lennart Kirchner
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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Kruse K, Salzer R, Averhoff B. The traffic ATPase PilF interacts with the inner membrane platform of the DNA translocator and type IV pili from Thermus thermophilus. FEBS Open Bio 2018; 9:4-17. [PMID: 30652069 PMCID: PMC6325625 DOI: 10.1002/2211-5463.12548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/10/2018] [Accepted: 10/25/2018] [Indexed: 12/20/2022] Open
Abstract
A major driving force for the adaptation of bacteria to changing environments is the uptake of naked DNA from the environment by natural transformation, which allows the acquisition of new capabilities. Uptake of the high molecular weight DNA is mediated by a complex transport machinery that spans the entire cell periphery. This DNA translocator catalyzes the binding and splitting of double‐stranded DNA and translocation of single‐stranded DNA into the cytoplasm, where it is recombined with the chromosome. The thermophilic bacterium Thermus thermophilus exhibits the highest transformation frequencies reported and is a model system to analyze the structure and function of this macromolecular transport machinery. Transport activity is powered by the traffic ATPase PilF, a soluble protein that forms hexameric complexes. Here, we demonstrate that PilF physically binds to an inner membrane assembly platform of the DNA translocator, comprising PilMNO, via the ATP‐binding protein PilM. Binding to PilMNO or PilMN stimulates the ATPase activity of PilF ~ 2‐fold, whereas there is no stimulation when binding to PilM or PilN alone. A PilMK26A variant defective in ATP binding still binds PilF and, together with PilN, stimulates PilF‐mediated ATPase activity. PilF is unique in having three conserved GSPII (general secretory pathway II) domains (A–C) at its N terminus. Deletion analyses revealed that none of the GSPII domains is essential for binding PilMN, but GSPIIC is essential for PilMN‐mediated stimulation of ATP hydrolysis by PilF. Our data suggest that PilM is a coupling protein that physically and functionally connects the soluble motor ATPase PilF to the DNA translocator via the PilMNO assembly platform.
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Affiliation(s)
- Kerstin Kruse
- Molecular Microbiology & Bioenergetics Institute of Molecular Biosciences Goethe University Frankfurt Germany
| | - Ralf Salzer
- Molecular Microbiology & Bioenergetics Institute of Molecular Biosciences Goethe University Frankfurt Germany.,Present address: Structural Studies Division Medical Research Council - Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave Cambridge CB2 OQH UK
| | - Beate Averhoff
- Molecular Microbiology & Bioenergetics Institute of Molecular Biosciences Goethe University Frankfurt Germany
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5
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D'Imprima E, Salzer R, Bhaskara RM, Sánchez R, Rose I, Kirchner L, Hummer G, Kühlbrandt W, Vonck J, Averhoff B. Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus. eLife 2017; 6. [PMID: 29280731 PMCID: PMC5745081 DOI: 10.7554/elife.30483] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/13/2017] [Indexed: 11/13/2022] Open
Abstract
Secretins form multimeric channels across the outer membrane of Gram-negative bacteria that mediate the import or export of substrates and/or extrusion of type IV pili. The secretin complex of Thermus thermophilus is an oligomer of the 757-residue PilQ protein, essential for DNA uptake and pilus extrusion. Here, we present the cryo-EM structure of this bifunctional complex at a resolution of ~7 Å using a new reconstruction protocol. Thirteen protomers form a large periplasmic domain of six stacked rings and a secretin domain in the outer membrane. A homology model of the PilQ protein was fitted into the cryo-EM map. A crown-like structure outside the outer membrane capping the secretin was found not to be part of PilQ. Mutations in the secretin domain disrupted the crown and abolished DNA uptake, suggesting a central role of the crown in natural transformation.
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Affiliation(s)
- Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ricardo Sánchez
- Sofja Kovalevskaja Group, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ilona Rose
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Lennart Kirchner
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany.,Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
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6
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Salzer R, Fruwert J, Köhler HJ. Zum Einfloß des Substituenten auf die Elektronendichteverteilung in geradkettigen Alkanderivaten. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/zpch-1974-255135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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7
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Salzer R, D'Imprima E, Gold VAM, Rose I, Drechsler M, Vonck J, Averhoff B. Topology and Structure/Function Correlation of Ring- and Gate-forming Domains in the Dynamic Secretin Complex of Thermus thermophilus. J Biol Chem 2016; 291:14448-56. [PMID: 27226590 DOI: 10.1074/jbc.m116.724153] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/06/2022] Open
Abstract
Secretins are versatile outer membrane pores used by many bacteria to secrete proteins, toxins, or filamentous phages; extrude type IV pili (T4P); or take up DNA. Extrusion of T4P and natural transformation of DNA in the thermophilic bacterium Thermus thermophilus requires a unique secretin complex comprising six stacked rings, a membrane-embedded cone structure, and two gates that open and close a central channel. To investigate the role of distinct domains in ring and gate formation, we examined a set of deletion derivatives by cryomicroscopy techniques. Here we report that maintaining the N0 ring in the deletion derivatives led to stable PilQ complexes. Analyses of the variants unraveled that an N-terminal domain comprising a unique βββαβ fold is essential for the formation of gate 2. Furthermore, we identified four βαββα domains essential for the formation of the N2 to N5 rings. Mutant studies revealed that deletion of individual ring domains significantly reduces piliation. The N1, N2, N4, and N5 deletion mutants were significantly impaired in T4P-mediated twitching motility, whereas the motility of the N3 mutant was comparable with that of wild-type cells. This indicates that the deletion of the N3 ring leads to increased pilus dynamics, thereby compensating for the reduced number of pili of the N3 mutant. All mutants exhibit a wild-type natural transformation phenotype, leading to the conclusion that DNA uptake is independent of functional T4P.
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Affiliation(s)
- Ralf Salzer
- From Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main and
| | - Edoardo D'Imprima
- the Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vicki A M Gold
- the Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Ilona Rose
- From Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main and
| | - Moritz Drechsler
- From Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main and
| | - Janet Vonck
- the Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Beate Averhoff
- From Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main and
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8
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Abstract
Proteins of the secretin family form large macromolecular complexes, which assemble in the outer membrane of Gram-negative bacteria. Secretins are major components of type II and III secretion systems and are linked to extrusion of type IV pili (T4P) and to DNA uptake. By electron cryo-tomography of whole Thermus thermophilus cells, we determined the in situ structure of a T4P molecular machine in the open and the closed state. Comparison reveals a major conformational change whereby the N-terminal domains of the central secretin PilQ shift by ∼30 Å, and two periplasmic gates open to make way for pilus extrusion. Furthermore, we determine the structure of the assembled pilus. DOI:http://dx.doi.org/10.7554/eLife.07380.001 Gram-negative bacteria can cause serious diseases in humans, such as cholera and bacterial meningitis. These bacteria are surrounded by two membranes: an inner membrane and an outer membrane. Proteins called secretins are components of several large molecular complexes that are embedded within the outer membrane. Some secretin-containing complexes form pores in the bacterial membranes and allow molecules to pass in or out of the cell. Some secretins also form part of the machinery that allow Gram-negative bacteria to grow fibre-like structures called type IV pili. These pili help bacteria that cause infections to move and stick to host cells, where they can also trigger massive changes in the host cells' architecture. Multiple copies of a secretin protein called PilQ form a channel in the outer membrane of the bacteria that allows a type IV pilus to grow out of the surface of the cell. The pilus can then hook the bacteria onto surfaces and other cells. There is evidence to suggest the type IV pilus machinery is involved in the uptake of DNA from other bacteria, an important but poorly understood process that has contributed to the spread of multi-drug resistance. Now, Gold et al. have used a cutting-edge technique called ‘electron cryo-tomography’ to analyse the three-dimensional structure of the machinery that builds the type IV pili in the membranes of a bacterium called Thermus thermophilus. This analysis revealed that, similar to many other channel complexes, the PilQ channel can be ‘open’ or ‘closed’. When pili are absent, the channel is closed, but the channel opens when pili are present. Further analysis also revealed the structure of an assembled pilus. Next, Gold et al. studied the open state of the type IV pilus in more detail and observed that a region of each of the PilQ proteins moves a considerable distance to make way for the pilus to enter the central pore. These results will pave the way for future studies of type IV pili and other secretin-containing complexes and underpin efforts to investigate new drug targets to combat bacterial infections. DOI:http://dx.doi.org/10.7554/eLife.07380.002
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Affiliation(s)
- Vicki A M Gold
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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Salzer R, Kern T, Joos F, Averhoff B. The Thermus thermophilus comEA/comEC operon is associated with DNA binding and regulation of the DNA translocator and type IV pili. Environ Microbiol 2015; 18:65-74. [PMID: 25727469 DOI: 10.1111/1462-2920.12820] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/20/2015] [Indexed: 11/30/2022]
Abstract
Natural transformation systems and type IV pili are linked in many naturally competent bacteria. In the Gram-negative bacterium Thermus thermophilus, a leading model organism for studies of DNA transporters in thermophilic bacteria, seven competence proteins play a dual role in both systems, whereas two competence genes, comEA and comEC, are suggested to represent unique DNA translocator proteins. Here we show that the T. thermophilus ComEA protein binds dsDNA and is anchored in the inner membrane. comEA is co-transcribed with the flanking comEC gene, and transcription of this operon is upregulated by nutrient limitation and low temperature. To our surprise, a comEC mutant was impaired in piliation. We followed this observation and uncovered that the impaired piliation of the comEC mutant is due to a transcriptional downregulation of pilA4 and the pilN both playing a dual role in piliation and natural competence. Moreover, the comEC mutation resulted in a dramatic decrease in mRNA levels of the pseudopilin gene pilA1, which is unique for the DNA transporter. We conclude that ComEC modulates transcriptional regulation of type IV pili and DNA translocator components thereby mediating a response to extracellular parameters.
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Affiliation(s)
- Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Timo Kern
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Friederike Joos
- Department of Structural Biology, Max-Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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10
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Salzer R, Joos F, Averhoff B. Different effects of MglA and MglB on pilus-mediated functions and natural competence in Thermus thermophilus. Extremophiles 2014; 19:261-7. [PMID: 25472010 DOI: 10.1007/s00792-014-0711-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/16/2014] [Indexed: 02/02/2023]
Abstract
The thermophilic bacterium Thermus thermophilus is known for its high natural competence. Uptake of DNA is mediated by a DNA translocator that shares components with type IV pili. Localization and function of type IV pili in other bacteria depend on the cellular localization at the poles of the bacterium, a process that involves MglA and MglB. T. thermophilus contains homologs of MglA and MglB. The genes encoding MglA and MglB were deleted and the physiology of the mutants was studied. Deletion of the genes individually or in tandem had no effect on pili formation but pili lost their localization at the poles. The mutants abolished pilus-mediated functions such as twitching motility and adherence but had no effect on uptake of DNA by natural competence. These data demonstrate that MglA and MglB are dispensable for natural transformation and are consistent with the hypothesis that uptake of DNA does not depend on type IV pili or their cellular localization.
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Affiliation(s)
- Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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11
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Salzer R, Herzberg M, Nies DH, Joos F, Rathmann B, Thielmann Y, Averhoff B. Zinc and ATP binding of the hexameric AAA-ATPase PilF from Thermus thermophilus: role in complex stability, piliation, adhesion, twitching motility, and natural transformation. J Biol Chem 2014; 289:30343-30354. [PMID: 25202014 DOI: 10.1074/jbc.m114.598656] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The traffic AAA-ATPase PilF is essential for pilus biogenesis and natural transformation of Thermus thermophilus HB27. Recently, we showed that PilF forms hexameric complexes containing six zinc atoms coordinated by conserved tetracysteine motifs. Here we report that zinc binding is essential for complex stability. However, zinc binding is neither required for pilus biogenesis nor natural transformation. A number of the mutants did not exhibit any pili during growth at 64 °C but still were transformable. This leads to the conclusion that type 4 pili and the DNA translocator are distinct systems. At lower growth temperatures (55 °C) the zinc-depleted multiple cysteine mutants were hyperpiliated but defective in pilus-mediated twitching motility. This provides evidence that zinc binding is essential for the role of PilF in pilus dynamics. Moreover, we found that zinc binding is essential for complex stability but dispensable for ATPase activity. In contrast to many polymerization ATPases from mesophilic bacteria, ATP binding is not required for PilF complex formation; however, it significantly increases complex stability. These data suggest that zinc and ATP binding increase complex stability that is important for functionality of PilF under extreme environmental conditions.
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Affiliation(s)
- Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin Luther University, 06120 Halle-Wittenberg, Germany
| | - Dietrich H Nies
- Molecular Microbiology, Institute for Biology/Microbiology, Martin Luther University, 06120 Halle-Wittenberg, Germany
| | - Friederike Joos
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany, and
| | - Barbara Rathmann
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Yvonne Thielmann
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany,.
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Salzer R, Kern T, Joos F, Averhoff B. Environmental factors affecting the expression of type IV pilus genes as well as piliation of Thermus thermophilus. FEMS Microbiol Lett 2014; 357:56-62. [PMID: 24935261 DOI: 10.1111/1574-6968.12506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/06/2014] [Indexed: 11/30/2022] Open
Abstract
The thermophilic bacterium Thermus thermophilus HB27 is known for its highly efficient natural transformation system, which has become a model system to study the structure and function of DNA transporter in thermophilic bacteria. The DNA transporter is functionally linked to type IV pili (T4P), which are essential for twitching motility and adhesion to solid surfaces. However, the pilus structures themselves are dispensable for natural transformation. Here, we report that the cellular mRNA levels of the major structural subunit of the T4P, PilA4, are regulated by environmental factors. Growth of T. thermophilus in minimal medium or low temperature (55 °C) leads to a significant increase in pilA4 transcripts. In contrast, the transcript levels of the minor pilin pilA1 as well as other T4P genes are nearly unaffected. The elevated pilA4 mRNA levels are accompanied by an increase in piliation of the cells but not by elevated natural transformation frequencies. Hyperpiliation leads to increased adhesion to plastic surfaces. The increased cell-surface interactions are suggested to represent an adaptive response to temperature stress and may be advantageous for survival of T. thermophilus.
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Affiliation(s)
- Ralf Salzer
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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Salzer R, Herzberg M, Nies DH, Biuković G, Grüber G, Müller V, Averhoff B. The DNA uptake ATPase PilF of Thermus thermophilus: a reexamination of the zinc content. Extremophiles 2013; 17:697-8. [PMID: 23712905 DOI: 10.1007/s00792-013-0544-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
The DNA-translocator ATPase PilF of Thermus thermophilus HB27 is a hexamer built by six identical subunits. Despite the presence of a conserved zinc-binding site in every subunit, only one zinc atom per hexamer was found. Re-examination of the zinc content of PilF purified from cells grown in complex media with different lots of yeast extract revealed six zinc atoms per hexamer. These data demonstrate that the low zinc content reported before was most likely a result of zinc depletion of the yeast extract used.
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Affiliation(s)
- Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
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Genest S, Salzer R, Steiner G. Molecular imaging of paper cross sections by FT-IR spectroscopy and principal component analysis. Anal Bioanal Chem 2013; 405:5421-30. [DOI: 10.1007/s00216-013-6967-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 02/27/2013] [Accepted: 04/02/2013] [Indexed: 10/26/2022]
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Burkhardt J, Vonck J, Langer JD, Salzer R, Averhoff B. Unusual N-terminal ααβαββα fold of PilQ from Thermus thermophilus mediates ring formation and is essential for piliation. J Biol Chem 2012; 287:8484-94. [PMID: 22253437 DOI: 10.1074/jbc.m111.334912] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA translocators of natural transformation systems are complex systems critical for the uptake of free DNA and provide a powerful mechanism for adaptation to changing environmental conditions. In natural transformation machineries, outer membrane secretins are suggested to form a multimeric pore for the uptake of external DNA. Recently, we reported on a novel structure of the DNA translocator secretin complex, PilQ, in Thermus thermophilus HB27 comprising a stable cone and cup structure and six ring structures with a large central channel. Here, we report on structural and functional analyses of a set of N-terminal PilQ deletion derivatives in T. thermophilus HB27. We identified 136 N-terminal residues exhibiting an unusual ααβαββα fold as a ring-building domain. Deletion of this domain had a dramatic effect on twitching motility, adhesion, and piliation but did not abolish natural transformation. These findings provide clear evidence that the pilus structures of T. thermophilus are not essential for natural transformation. The truncated complex was not affected in inner and outer membrane association, indicating that the 136 N-terminal residues are not essential for membrane targeting. Analyses of complex formation of the truncated PilQ monomers revealed that the region downstream of residue 136 is required for multimerization, and the region downstream of residue 207 is essential for monomer stability. Possible implications of our findings for the mechanism of DNA uptake are discussed.
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Affiliation(s)
- Janin Burkhardt
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
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Kiehntopf M, Mönch B, Salzer R, Kupfer M, Hartmann M. Quality control of cytotoxic drug preparations by means of Raman spectroscopy. Pharmazie 2012; 67:95-96. [PMID: 22393839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- M Kiehntopf
- Institute for Clinical Chemistry and Laboratory Medicine, Jena University Hospital, Jena, Germany.
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Steller L, Kreir M, Salzer R. Natural and artificial ion channels for biosensing platforms. Anal Bioanal Chem 2011; 402:209-30. [PMID: 22080413 DOI: 10.1007/s00216-011-5517-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 10/14/2011] [Accepted: 10/18/2011] [Indexed: 10/15/2022]
Abstract
The single-molecule selectivity and specificity of the binding process together with the expected intrinsic gain factor obtained when utilizing flow through a channel have attracted the attention of analytical chemists for two decades. Sensitive and selective ion channel biosensors for high-throughput screening are having an increasing impact on modern medical care, drug screening, environmental monitoring, food safety, and biowarefare control. Even virus antigens can be detected by ion channel biosensors. The study of ion channels and other transmembrane proteins is expected to lead to the development of new medications and therapies for a wide range of illnesses. From the first attempts to use membrane proteins as the receptive part of a sensor, ion channels have been engineered as chemical sensors. Several other types of peptidic or nonpeptidic channels have been investigated. Various gating mechanisms have been implemented in their pores. Three technical problems had to be solved to achieve practical biosensors based on ion channels: the fabrication of stable lipid bilayer membranes, the incorporation of a receptor into such a structure, and the marriage of the modified membrane to a transducer. The current status of these three areas of research, together with typical applications of ion-channel biosensors, are discussed in this review.
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Affiliation(s)
- L Steller
- Department of Magnetic and Acoustic Resonances, Leibniz Institute for Solid State and Materials Research, Dresden, Germany.
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Doucette TA, Kong LY, Yang Y, Wei J, Wang J, Fuller GN, Heimberger AB, Rao G, Ajewung N, Kamnasaran D, Katz AM, Amankulor N, Squatrito M, Hambardzumyan D, Holland EC, Poschl J, Lorenz A, Von Bueren A, Li S, Peraud A, Tonn JC, Herms J, Xiang M, Rutkowski S, Kretzschmar H, Schuller U, Studebaker A, Raffel C, Aoki Y, Hashizume R, Ozawa T, Gupta N, James CD, Navis AC, Hamans BC, Claes A, Heerschap A, Wesseling P, Jeuken JW, Leenders WP, Agudelo PA, Williams S, Nowicki MO, Johnson J, Li PK, Chiocca EA, Lannutti JJ, Lawler SE, Viapiano MS, Bergeron J, Aliaga A, Bedell B, Soderquist C, Sonabend A, Lei L, Crisman C, Yun JP, Sisti J, Castelli M, Bruce JN, Canoll P, Kirsch M, Stelling A, Salzer R, Krafft C, Schackert G, Steiner G, Balvers RK, van den Hengel SK, Wakimoto H, Hoeben RC, Leenstra S, Dirven CM, Lamfers ML, Sabha NS, Agnihotri S, Wolf A, von Deimling A, Croul S, Guha A, Trojahn US, Lenferink A, Bedell B, O'Connor-McCourt M, Wakimoto H, Kanai R, Curry WT, Yip S, Barnard ZR, Mohapatra G, Stemmer-Rachamimov AO, Martuza RL, Rabkin SD, Binder ZA, Salmasi V, Lim M, Weingart J, Brem H, Olivi A, Riggins GJ, Gallia GL, Rong Y, Zhang Z, Gang C, Tucker-Burden C, Van Meir E, Brat DJ, Balvers RK, Kloezeman JJ, Kleijn A, French PJ, Dirven CM, Leenstra S, Lamfers ML, Balvers RK, Kloezeman JJ, Spoor JK, Dirven CM, Lamfers ML, Leenstra S, Bazzoli E, Fomchenko EI, Schultz N, Brennan C, DeAngelis LM, Holland EC, Nimer SD, Squatrito M, Mohyeldin A, Hsu W, Shah SR, Adams H, Shah P, Katuri L, Kosztowski T, Loeb DM, Wolinsky JP, Gokaskan ZL, Quinones-Hinojosa A, Daphu IK, Immervoll H, Bjerkvig R, Thorsen F, Caretti V, Idema S, Zondervan I, Meijer DH, Lagerweij T, Barazas M, Vos W, Hamans B, van der Stoop P, Hulleman E, van der Valk P, Bugiani M, Wesseling P, Vandertop WP, Noske D, Kaspers GJ, Molthoff C, Wurdinger T, Chow LM, Endersby R, Zhu X, Rankin S, Qu C, Zhang J, Ellison DW, Baker SJ, Tabar V, LaFaille F, Studer L. Tumor Models (In Vivo/In Vitro). Neuro Oncol 2010. [DOI: 10.1093/neuonc/noq116.s20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Tasdemiroglu E, Kaya M, Yildirim CH, Lucas KG, Bao L, Bruggeman R, Specht C, Murray JC, Donahue DJ, Galliani CA, Blondin NA, Hui P, Vortmeyer A, Hasbani J, Baehring J, Jensen RL, Lee J, Lake WB, Baskaya MK, Salamat MS, Kennedy T, Abraham S, Jensen RL, Lusis EA, Scheithauer B, Yachnis AT, Chicoine MR, Paulus W, Perry A, Chan DT, Kam MK, Ma BB, Ng SC, Siu DY, Ng HK, Poon WS, Dunbar EM, Dong HJ, Liu C, Chi YY, Keeling C, Yachnis AT, Stephen JH, Sievert AJ, Resnick AC, Storm PB, Judkins AR, Santi M, Kirsch M, Stelling A, Koch E, Salzer R, Schackert G, Steiner G, Pollo B, Maderna E, Valletta L, Guzzetti S, Eoli M, Calatozzolo C, Nunziata R, Salmaggi A, Finocchiaro G, Kastenhuber ER, Campos C, Brennan CW, Mellinghoff IK, Huse JT, Zhang H, Sergey M, Estrada DK, Kay AB, Wagner AS, Khanlou N, Vinters HV, Cloughesy TF, Yong WH. Pathology. Neuro Oncol 2010. [DOI: 10.1093/neuonc/noq116.s10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gróf M, Gatial A, Milata V, Prónayová N, Sümmchen L, Salzer R. Conformational studies of 3-aminomethylene-2,4-pentanedione using vibrational and NMR spectra, and ab initio calculations. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.12.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Husaru L, Schulze R, Steiner G, Wolff T, Habicher WD, Salzer R. Potential analytical applications of gated artificial ion channels. Anal Bioanal Chem 2005; 382:1882-8. [PMID: 16052346 DOI: 10.1007/s00216-005-3380-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Revised: 05/25/2005] [Accepted: 06/03/2005] [Indexed: 11/29/2022]
Abstract
Biosensors based on natural ion channels combine a biological recognition mechanism with a physical transduction technique in a very selective and sensitive manner. This kind of molecular sensor will contribute to drug screening and environmental screening. Key information about channel gating, ion transport, and molecular mechanism is provided by the patch-clamp technique, commonly used for electrophysiological analysis. Here we report the synthesis of light-gated artificial ion channels, necessary constituents for construction of biosensors based on natural ion channels. The artificial gated ion channels described here are based on calix[4]resorcinarene. Opening and closing of the artificial ion channel is achieved by azo groups, which work like a lid. Azo groups alter their conformation on irradiation with light, and are chemically quite stable. Addition of a gate function will enhance the potential of synthetic channels to be used in sensors as molecular switches.
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Affiliation(s)
- L Husaru
- Institute of Analytical Chemistry, Dresden University of Technology, 01062 Dresden, Germany
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Affiliation(s)
- R Salzer
- Institute of Analytical Chemistry, Dresden University of Technology, 01062 Dresden, Germany.
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Thomas H, Paasch S, Machill S, Thiele S, Herzog K, Hemmer M, Gasteiger J, Salzer R. Internet-assisted exercises in structural analysis. Fresenius J Anal Chem 2001; 371:4-10. [PMID: 11605756 DOI: 10.1007/s002160100842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this report we describe our experience in the analytical chemistry curriculum of teaching spectrometer principles and preparing spectroscopy laboratory exercises by means of virtual instruments. The benefits of the intensified preparation of laboratory exercises by virtual instruments will be evaluated with respect to the subsequent handling of real instruments. The utilization of in-house electronic media with Internet resources for elucidation and verification of a structural assignment will also be considered.
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Affiliation(s)
- H Thomas
- Institute of Analytical Chemistry, Dresden University of Technology, Germany
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Abstract
CuMoO4 crystals reversibly change their color from green to brown upon heating, accompanied by a loss in transmittance. UV/VIS spectroscopic analysis revealed that these changes are due to particular electronic properties of the crystal instead of its chemical decomposition or structural change. Investigations were carried out in the temperature range 23-400 degrees C. The intensive green color of the crystal at room temperature is caused by a small transmission window between two absorption bands, the band gap of the crystal in the blue and the 3d9-->4p absorption of the Cu2+ ions in the red. With increasing temperature the band gap shifts towards longer wavelengths, and the crystal changes both color and transmittance. Spectroscopic features of the crystal are discussed together with the temperature dependence of its electrical resistance. Resistance measurements were performed simultaneously to the optical measurements.
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Affiliation(s)
- G Steiner
- Institute for Analytical Chemistry, Dresden University of Technology, Germany
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Steiner G, Möller H, Savchuk O, Ferse D, Adler H, Salzer R. Characterisation of ultra-thin polymer films by polarisation modulation FTIR spectroscopy. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(01)00438-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Recovery as well as appearance and abundance (in percent) of different fractions of humic substances are found to depend on injected sample amounts in reversed phase HPLC. Sample amounts have been varied both by varying sample concentration and sample volume. In case of lowest amounts injected only two fractions were obtained for a commercial humic acid sodium salt, i.e. one for excluded molecules and one for hydrophobic components. The abundance of excluded molecules decreases upon increasing amounts injected. Another three fractions are obtained upon increasing amount injected: a hydrophilic fraction and two hydrophobic ones. This behavior is explained by auxiliary equilibria between excluded components and humic molecules previously adsorbed on the stationary phase.
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Affiliation(s)
- G Preusse
- Dresden University of Technology, Institute of Analytical Chemistry, Germany
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Selzer P, Gasteiger J, Thomas H, Salzer R. Rapid access to infrared reference spectra of arbitrary organic compounds: scope and limitations of an approach to the simulation of infrared spectra by neural networks. Chemistry 2000; 6:920-7. [PMID: 10826615 DOI: 10.1002/(sici)1521-3765(20000303)6:5<920::aid-chem920>3.0.co;2-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Substance identification by infrared spectroscopy is performed by comparison of the experimental spectrum with a reference spectrum from a printed compilation or a database. If the analyzed compound can not be found in a database the corresponding reference spectrum has to be simulated. In order to achieve this, several reasonable candidates of structures for the compound at hand have to be conceived and for all these, infrared spectra have to be developed. The simulated spectrum that is most similar to the experimental suggests the correct structure. A rapid spectrum prediction method based on neural networks has been developed that supplies reference spectra for any organic compound. The scope and limitations of this method will be discussed on a test set of 16 compounds representing a broad range of organic chemistry.
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Affiliation(s)
- P Selzer
- Computer-Chemie-Centrum, Institut fur Organische Chemie, Universitat Erlangen-Nurnberg, Germany
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Salzer R, Steiner G, Mantsch HH, Mansfield J, Lewis EN. Infrared and Raman imaging of biological and biomimetic samples. Fresenius J Anal Chem 2000; 366:712-6. [PMID: 11225782 DOI: 10.1007/s002160051565] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Established methods for imaging of biological or biomimetic samples, such as fluorescence and optical microscopy, magnetic resonance imaging (MRI), X-ray tomography or positron emission tomography (PET) are currently complemented by infrared (both near-IR and mid-IR) as well as Raman spectroscopic imaging, whether it be on a microscopic or macroscopic scale. These vibrational spectroscopic techniques provide a wealth of information without a priori knowledge of either the spectral data or the composition of the sample. Infrared radiation does not harm the organism, no electric potential needs to be applied, and the measurements are not influenced by electromagnetic fields. In addition, no extrinsic labeling or staining, which may perturb the system under investigation, has to be added. The immense volume of information contained in spectroscopic images requires multivariate analysis methodologies in order to effectively mine the chemical and spatial information contained within the data as well as to analyze a time-series of images in order to reveal the origin of a chemical or biochemical process. The promise and limitations of this new analytical tool are surveyed in this review.
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Affiliation(s)
- R Salzer
- Technische Universität Dresden, Institut für Analytische Chemie, Germany
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Gatial A, Sklenák Š, Milata V, Biskupič S, Salzer R, Scheller D, Woelki G. The vibrational and NMR spectra, conformations and ab initio calculations of 1-aminoethylidene propanedinitrile and its N -methyl derivatives. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(99)00212-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gatial A, Milata V, Zalibera L, Biskupič S, Salzer R. The vibrational and NMR spectra, conformations and ab initio calculations of phenylaminomethylene- and 1-phenylaminoethylidene-propanedinitrile. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(98)00889-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gatial A, Herzog K, Milata V, Zalibera L, Biskupic S, Salzer R. The vibrational and NMR spectra, conformations and ab initio calculations of 3-methoxymethylene-2,4-pentanedione. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(98)00888-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gatial A, Sklenák Š, Milata V, Biskupič S, Zalibera L, Salzer R. The vibrational and NMR spectra, conformations and ab initio calculations of methoxymethylene- and 1-methoxyethylidene- propanedinitrile. J Mol Struct 1997. [DOI: 10.1016/s0022-2860(96)09504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Roland U, Henssge E, Sümmchen L, Salzer R. Fluoreszenzeffekte bei Raman-spektroskopischen Untersuchungen am Titandioxid — Einfluß von Temperung und Adsorption. ACTA ACUST UNITED AC 1995. [DOI: 10.1524/zpch.1995.191.part_2.197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Salzer R, Roland U, Drummer H, Sümmchen L, Kolitsch A, Drescher D. Charakterisierung dünner Kohlenstoffschichten durch Ramanspektroskopie. ACTA ACUST UNITED AC 1995. [DOI: 10.1524/zpch.1995.191.part_1.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Gatial A, Sklenak S, Klaeboe P, Nielsen C, Priebe H, Salzer R, Kurkova D. The infrared and Raman spectra, conformations and ab initio calculations of 4-azidobut-1-yne. J Mol Struct 1995. [DOI: 10.1016/0022-2860(95)08731-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Ziegler B, Herzog K, Salzer R. In-situ investigations of thermal processes in polymers by simultaneous differential scanning calorimetry and infrared spectroscopy. J Mol Struct 1995. [DOI: 10.1016/0022-2860(95)08687-q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Quapp W, Ferner S, Salzer R. Bestimmung des Bandenformindex mittels Voigtfunktion. Z PHYS CHEM 1989. [DOI: 10.1515/zpch-1989-270156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Quapp W, Ferner S, Salzer R. Bestimmung des Bandenformindex mittels Voigtfunktion. Z PHYS CHEM 1989. [DOI: 10.1515/zpch-1989-01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Michel D, Gergs M, Schlemmbach H, Windsch W, Fruwert S, Salzer R, Rosenberger H, Scheler G. Study of H/D substitution in solid solutions of tris-sarcosine calcium chloride by infrared and NMR spectroscopy. Chem Phys Lett 1986. [DOI: 10.1016/0009-2614(86)85032-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
Aztreozam was evaluated in the treatment of a variety of orthopedic infections. Included were 17 patients with osteomyelitis, three with purulent arthropathy with prostheses, and 16 with superficial infections secondary to trauma or surgical procedure. Pathogens were gram-negative bacilli sensitive to aztreonam. Concomitant antibiotics were administered for gram-positive cocci that were present initially or by superinfection. Infecting organisms included Pseudomonas aeruginosa (minimal inhibitory concentration 4 to 16 micrograms/ml), Serratia marcescens, Enterobacter cloacae, Enterobacter sakazakii, Morganella morganii, Citrobacter freundii, Proteus vulgaris, Proteus rettgeri, Acinetobacter calcoaceticus and others (all with minimal inhibitory concentrations less than 1.0 microgram/ml). Dosage of aztreonam was 2 to 8 g per day administered intravenously or intramuscularly for five to 52 days. Clinical and bacteriologic responses were adequate in all instances. Recurrences were observed in two individuals with osteomyelitis and one with purulent arthropathy. Adverse clinical or laboratory observations were infrequent and inconsequential.
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Ferner S, Salzer R, Borsdorf R. Bestimmung des Bandenformindex an konformativ unterschiedlichen C-Halogen-Valenzschwingungen. Z PHYS CHEM 1983. [DOI: 10.1515/zpch-1983-0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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50
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