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Chen Y, Sotomayor M, Capponi S, Hariharan B, Sahu ID, Haase M, Lorigan GA, Kuhn A, White SH, Dalbey RE. A hydrophilic microenvironment in the substrate-translocating groove of the YidC membrane insertase is essential for enzyme function. J Biol Chem 2022; 298:101690. [PMID: 35148995 PMCID: PMC8920935 DOI: 10.1016/j.jbc.2022.101690] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/27/2022] Open
Abstract
The YidC family of proteins are membrane insertases that catalyze the translocation of the periplasmic domain of membrane proteins via a hydrophilic groove located within the inner leaflet of the membrane. All homologs have a strictly conserved, positively charged residue in the center of this groove. In Bacillus subtilis, the positively charged residue has been proposed to be essential for interacting with negatively charged residues of the substrate, supporting a hypothesis that YidC catalyzes insertion via an early-step electrostatic attraction mechanism. Here, we provide data suggesting that the positively charged residue is important not for its charge but for increasing the hydrophilicity of the groove. We found that the positively charged residue is dispensable for Escherichia coli YidC function when an adjacent residue at position 517 was hydrophilic or aromatic, but was essential when the adjacent residue was apolar. Additionally, solvent accessibility studies support the idea that the conserved positively charged residue functions to keep the top and middle of the groove sufficiently hydrated. Moreover, we demonstrate that both the E. coli and Streptococcus mutans YidC homologs are functional when the strictly conserved arginine is replaced with a negatively charged residue, provided proper stabilization from neighboring residues. These combined results show that the positively charged residue functions to maintain a hydrophilic microenvironment in the groove necessary for the insertase activity, rather than to form electrostatic interactions with the substrates.
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Affiliation(s)
- Yuanyuan Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sara Capponi
- Department of Industrial and Applied Genomics, IBM AI and Cognitive Software Organization, IBM Almaden Research Center, San Jose, California, USA; NSF Center for Cellular Construction, University of California in San Francisco, San Francisco, California, USA
| | | | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA; Natural Science Division, Campbellsville University, Campbellsville, Kentucky, USA
| | - Maximilian Haase
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
| | - Stephen H White
- Department of Physiology and Biophysics, University of California, Irvine, California, USA
| | - Ross E Dalbey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.
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Kamel M, Löwe M, Schott-Verdugo S, Gohlke H, Kedrov A. Unsaturated fatty acids augment protein transport via the SecA:SecYEG translocon. FEBS J 2021; 289:140-162. [PMID: 34312977 DOI: 10.1111/febs.16140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/01/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022]
Abstract
The translocon SecYEG and the associated ATPase SecA form the primary protein secretion system in the cytoplasmic membrane of bacteria. The secretion is essentially dependent on the surrounding lipids, but the mechanistic understanding of their role in SecA : SecYEG activity is sparse. Here, we reveal that the unsaturated fatty acids (UFAs) of the membrane phospholipids, including tetraoleoyl-cardiolipin, stimulate SecA : SecYEG-mediated protein translocation up to ten-fold. Biophysical analysis and molecular dynamics simulations show that UFAs increase the area per lipid and cause loose packing of lipid head groups, where the N-terminal amphipathic helix of SecA docks. While UFAs do not affect the translocon folding, they promote SecA binding to the membrane, and the effect is enhanced up to fivefold at elevated ionic strength. Tight SecA : lipid interactions convert into the augmented translocation. Our results identify the fatty acid structure as a notable factor in SecA : SecYEG activity, which may be crucial for protein secretion in bacteria, which actively change their membrane composition in response to their habitat.
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Affiliation(s)
- Michael Kamel
- Synthetic Membrane Systems, Institute for Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Maryna Löwe
- Synthetic Membrane Systems, Institute for Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Stephan Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Bioinformatics), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Bioinformatics), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Germany
| | - Alexej Kedrov
- Synthetic Membrane Systems, Institute for Biochemistry, Heinrich Heine University Düsseldorf, Germany
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Prabudiansyah I, Kusters I, Caforio A, Driessen AJ. Characterization of the annular lipid shell of the Sec translocon. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2050-6. [DOI: 10.1016/j.bbamem.2015.06.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/24/2015] [Accepted: 06/26/2015] [Indexed: 11/16/2022]
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Ge Y, Draycheva A, Bornemann T, Rodnina MV, Wintermeyer W. Lateral opening of the bacterial translocon on ribosome binding and signal peptide insertion. Nat Commun 2014; 5:5263. [PMID: 25314960 PMCID: PMC4218953 DOI: 10.1038/ncomms6263] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/12/2014] [Indexed: 01/05/2023] Open
Abstract
Proteins are co-translationally inserted into the bacterial plasma membrane via the SecYEG translocon by lateral release of hydrophobic transmembrane segments into the phospholipid bilayer. The trigger for lateral opening of the translocon is not known. Here we monitor lateral opening by photo-induced electron transfer (PET) between two fluorophores attached to the two SecY helices at the rim of the gate. In the resting translocon, the fluorescence is quenched, consistent with a closed conformation. Ribosome binding to the translocon diminishes PET quenching, indicating opening of the gate. The effect is larger with ribosomes exposing hydrophobic transmembrane segments and vanishes at low temperature. We propose a temperature-dependent dynamic equilibrium between closed and open conformations of the translocon that is shifted towards partially and fully open by ribosome binding and insertion of a hydrophobic peptide, respectively. The combined effects of ribosome and peptide binding allow for co-translational membrane insertion of successive transmembrane segments. Integral membrane proteins laterally partition from the SecYEG translocon into the phospholipid bilayer. Here, the authors use photo-induced electron transfer to show that ribosome binding induces the opening of the lateral gate, and demonstrate that lateral opening does not happen at low temperature.
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Affiliation(s)
- Yan Ge
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Albena Draycheva
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Thomas Bornemann
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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Bauer BW, Shemesh T, Chen Y, Rapoport TA. A "push and slide" mechanism allows sequence-insensitive translocation of secretory proteins by the SecA ATPase. Cell 2014; 157:1416-1429. [PMID: 24906156 DOI: 10.1016/j.cell.2014.03.063] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/22/2014] [Accepted: 03/31/2014] [Indexed: 11/16/2022]
Abstract
In bacteria, most secretory proteins are translocated across the plasma membrane by the interplay of the SecA ATPase and the SecY channel. How SecA moves a broad range of polypeptide substrates is only poorly understood. Here we show that SecA moves polypeptides through the SecY channel by a "push and slide" mechanism. In its ATP-bound state, SecA interacts through a two-helix finger with a subset of amino acids in a substrate, pushing them into the channel. A polypeptide can also passively slide back and forth when SecA is in the predominant ADP-bound state or when SecA encounters a poorly interacting amino acid in its ATP-bound state. SecA performs multiple rounds of ATP hydrolysis before dissociating from SecY. The proposed push and slide mechanism is supported by a mathematical model and explains how SecA allows translocation of a wide range of polypeptides. This mechanism may also apply to hexameric polypeptide-translocating ATPases.
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Affiliation(s)
- Benedikt W Bauer
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom Shemesh
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Yu Chen
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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Traffic jam at the bacterial sec translocase: targeting the SecA nanomotor by small-molecule inhibitors. ACTA ACUST UNITED AC 2011; 18:685-98. [PMID: 21700205 DOI: 10.1016/j.chembiol.2011.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 04/27/2011] [Accepted: 04/28/2011] [Indexed: 11/20/2022]
Abstract
The rapid rise of drug-resistant bacteria is one of the most serious unmet medical needs facing the world. Despite this increasing problem of antibiotic resistance, the number of different antibiotics available for the treatment of serious infections is dwindling. Therefore, there is an urgent need for new antibacterial drugs, preferably with novel modes of action to potentially avoid cross-resistance with existing antibacterial agents. In recent years, increasing attention has been paid to bacterial protein secretion as a potential antibacterial target. Among the different protein secretion pathways that are present in bacterial pathogens, the general protein secretory (Sec) pathway is widely considered as an attractive target for antibacterial therapy. One of the key components of the Sec pathway is the peripheral membrane ATPase SecA, which provides the energy for the translocation of preproteins across the bacterial cytoplasmic membrane. In this review, we will provide an overview of research efforts on the discovery and development of small-molecule SecA inhibitors. Furthermore, recent advances on the structure and function of SecA and their potential impact on antibacterial drug discovery will be discussed.
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Perevoshchikova IV, Kotova EA, Antonenko YN. Fluorescence correlation spectroscopy in biology, chemistry, and medicine. BIOCHEMISTRY (MOSCOW) 2011; 76:497-516. [PMID: 21639831 DOI: 10.1134/s0006297911050014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science.
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Affiliation(s)
- I V Perevoshchikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
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Quaternary structure of SecA in solution and bound to SecYEG probed at the single molecule level. Structure 2011; 19:430-9. [PMID: 21397193 DOI: 10.1016/j.str.2010.12.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 12/17/2010] [Accepted: 12/22/2010] [Indexed: 11/20/2022]
Abstract
Dual-color fluorescence-burst analysis (DCFBA) was applied to measure the quaternary structure and high-affinity binding of the bacterial motor protein SecA to the protein-conducting channel SecYEG reconstituted into lipid vesicles. DCFBA is an equilibrium technique that enables the direct observation and quantification of protein-protein interactions at the single molecule level. SecA binds to SecYEG as a dimer with a nucleotide- and preprotein-dependent dissociation constant. One of the SecA protomers binds SecYEG in a salt-resistant manner, whereas binding of the second protomer is salt sensitive. Because protein translocation is salt sensitive, we conclude that the dimeric state of SecA is required for protein translocation. A structural model for the dimeric assembly of SecA while bound to SecYEG is proposed based on the crystal structures of the Thermotoga maritima SecA-SecYEG and the Escherichia coli SecA dimer.
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Kusters I, Mukherjee N, de Jong MR, Tans S, Koçer A, Driessen AJM. Taming membranes: functional immobilization of biological membranes in hydrogels. PLoS One 2011; 6:e20435. [PMID: 21655266 PMCID: PMC3105061 DOI: 10.1371/journal.pone.0020435] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 04/27/2011] [Indexed: 01/17/2023] Open
Abstract
Single molecule studies on membrane proteins embedded in their native environment are hampered by the intrinsic difficulty of immobilizing elastic and sensitive biological membranes without interfering with protein activity. Here, we present hydrogels composed of nano-scaled fibers as a generally applicable tool to immobilize biological membrane vesicles of various size and lipid composition. Importantly, membrane proteins immobilized in the hydrogel as well as soluble proteins are fully active. The triggered opening of the mechanosensitive channel of large conductance (MscL) reconstituted in giant unilamellar vesicles (GUVs) was followed in time on single GUVs. Thus, kinetic studies of vectorial transport processes across biological membranes can be assessed on single, hydrogel immobilized, GUVs. Furthermore, protein translocation activity by the membrane embedded protein conducting channel of bacteria, SecYEG, in association with the soluble motor protein SecA was quantitatively assessed in bulk and at the single vesicle level in the hydrogel. This technique provides a new way to investigate membrane proteins in their native environment at the single molecule level by means of fluorescence microscopy.
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Affiliation(s)
- Ilja Kusters
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, AG Groningen, the Netherlands
| | - Nobina Mukherjee
- Department of Membrane Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | | | | | - Armağan Koçer
- Department of Membrane Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, AG Groningen, the Netherlands
- * E-mail:
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