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Ji J, Cui MK, Zou R, Wu MZ, Ge MX, Li J, Zhang ZR. An ATP13A1-assisted topogenesis pathway for folding multi-spanning membrane proteins. Mol Cell 2024; 84:1917-1931.e15. [PMID: 38723633 DOI: 10.1016/j.molcel.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 02/15/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Many multi-spanning membrane proteins contain poorly hydrophobic transmembrane domains (pTMDs) protected from phospholipid in mature structure. Nascent pTMDs are difficult for translocon to recognize and insert. How pTMDs are discerned and packed into mature, muti-spanning configuration remains unclear. Here, we report that pTMD elicits a post-translational topogenesis pathway for its recognition and integration. Using six-spanning protein adenosine triphosphate-binding cassette transporter G2 (ABCG2) and cultured human cells as models, we show that ABCG2's pTMD2 can pass through translocon into the endoplasmic reticulum (ER) lumen, yielding an intermediate with inserted yet mis-oriented downstream TMDs. After translation, the intermediate recruits P5A-ATPase ATP13A1, which facilitates TMD re-orientation, allowing further folding and the integration of the remaining lumen-exposed pTMD2. Depleting ATP13A1 or disrupting pTMD-characteristic residues arrests intermediates with mis-oriented and exposed TMDs. Our results explain how a "difficult" pTMD is co-translationally skipped for insertion and post-translationally buried into the final correct structure at the late folding stage to avoid excessive lipid exposure.
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Affiliation(s)
- Jia Ji
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Meng-Ke Cui
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Rong Zou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Ming-Zhi Wu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Man-Xi Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Jiqiang Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China.
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Karimova G, Ladant D. Defining Membrane Protein Topology Using pho-lac Reporter Fusions. Methods Mol Biol 2024; 2715:181-195. [PMID: 37930528 DOI: 10.1007/978-1-0716-3445-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Experimental determination of membrane protein topology can be achieved using various techniques. Here, we present the pho-lac dual reporter system, a simple, convenient, and reliable tool to analyze the topology of membrane protein in vivo. The system is based on the use of two topological markers with complementary properties: The Escherichia coli β-galactosidase, LacZ, which is active in the cytoplasm, and the E. coli alkaline phosphatase, PhoA, which is active in the bacterial periplasm. Specifically, in this pho-lac gene system, the reporter molecule is a chimera composed of the mature PhoA that is in-frame with the β-galactosidase α-peptide (LacZα). Hence, when targeted to the periplasm, the PhoA-LacZα dual reporter displays high alkaline phosphatase activity but no β-galactosidase activity. Conversely, when located in the cytoplasm, PhoA-LacZα has no phosphatase activity but exhibits high β-galactosidase activity in E. coli cells expressing the α-fragment of LacZ, LacZα (via the α-complementation phenomenon). The dual nature of the PhoA-LacZα reporter allows a simple way to normalize both enzymatic activities to obtain readily interpretable information about the subcellular location of the fusion site between the membrane protein under study and the reporter. In addition, the PhoA-LacZα reporter permits the utilization of dual indicator agar plates to easily discriminate between colonies bearing cytoplasmic fusions, periplasmic fusions, or out-of-frame fusions. In total, the phoA-lacZα fusion reporter approach is a direct and rather inexpensive method to characterize the topology of membrane proteins in vivo.
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Affiliation(s)
- Gouzel Karimova
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS, UMR 3528, Université Paris Cité, Paris, France.
| | - Daniel Ladant
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS, UMR 3528, Université Paris Cité, Paris, France
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3
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Bogdanov M. Exploring Uniform, Dual, and Dynamic Topologies of Membrane Proteins by Substituted Cysteine Accessibility Method (SCAM™). Methods Mol Biol 2024; 2715:121-157. [PMID: 37930526 PMCID: PMC10755806 DOI: 10.1007/978-1-0716-3445-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
A described simple and advanced protocol for Substituted Cysteine Accessibility Method as applied to transmembrane (TM) orientation (SCAM™) permits a topology analysis of proteins in their native state and can be universally adapted to any membrane system to either systematically map an uniform or identify and quantify the degree of mixed topology or establish transmembrane assembly dynamics from relatively static experimental data such as endpoint topologies of membrane proteins. In this approach, noncritical individual amino acids that are thought to reside in the putative extracellular or intracellular loops of a membrane protein are replaced one at the time by cysteine residue, and the orientation with respect to the membrane is evaluated by using a pair of membrane-impermeable non-detectable and detectable thiol-reactive labeling reagents. For the most water-exposed cysteine residues in proteins, the thiol pKa lies in the range of 8-9, and formation of cysteinyl thiolate ions is optimum in aqueous rather in a nonpolar environment. These features and the ease of specific chemical modification with thiol reagents are central to SCAM™. Membrane side-specific sulfhydryl labeling allows to discriminate "exposed, protected or dynamic" cysteines strategically "implanted" at desired positions throughout cysteine less target protein template. The strategy described is widely used to map the topology of membrane protein and establish its transmembrane dynamics in intact cells of both diderm (two-membraned) Gram-negative and monoderm (one-membraned) Gram-positive bacteria, cell-derived oriented membrane vesicles, and proteoliposomes.
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Affiliation(s)
- Mikhail Bogdanov
- Department of Biochemistry & Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA.
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4
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Chabalier M, Doan T, Cascales E. Probing Protein Topology and Conformation by Limited Proteolysis. Methods Mol Biol 2024; 2715:111-119. [PMID: 37930525 DOI: 10.1007/978-1-0716-3445-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Proteases are enzymes that catalyze the hydrolytic degradation of other proteins into peptides or amino acids through the digestion of the peptide bond. Promiscuous proteases that target a wide range of proteins are distinguished from specific proteases that have a narrow range of substrates. In terms of activity, endoproteases cleave their substrates at specific residues within the target proteins, whereas exoproteases cleave from one extremity and may have processive activities. Proteases are therefore very useful tools to study proteins, notably their structure or conformation. In addition, proteases can be used to probe the topology of bacterial membrane proteins. Here, we describe limited protease accessibility assays to define inner membrane protein topology and conformational changes based on digestion profiles.
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Affiliation(s)
- Maïalène Chabalier
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille, France
| | - Thierry Doan
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille, France.
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Desai M, Singh A, Pham D, Chowdhury SR, Sun B. Discovery and Visualization of the Hidden Relationships among N-Glycosylation, Disulfide Bonds, and Membrane Topology. Int J Mol Sci 2023; 24:16182. [PMID: 38003370 PMCID: PMC10671238 DOI: 10.3390/ijms242216182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Membrane proteins (MPs) are functionally important but structurally complex. In particular, MPs often carry three structural features, i.e., transmembrane domains (TMs), disulfide bonds (SSs), and N-glycosylation (N-GLYCO). All three features have been intensively studied; however, how the three features potentially correlate has been less addressed in the literature. With the growing accuracy from computational prediction, we used publicly available information on SSs and N-GLYCO and analyzed the potential relationships among post-translational modifications (PTMs) and the predicted membrane topology in the human proteome. Our results suggested a very close relationship between SSs and N-GLYCO that behaved similarly, whereas a complementary relation between the TMs and the two PTMs was also revealed, in which the high SS and/or N-GLYCO presence is often accompanied by a low TM occurrence in a protein. Furthermore, the occurrence of SSs and N-GLYCO in a protein heavily relies on the protein length; however, TMs seem not to possess such length dependence. Finally, SSs exhibits larger potential dynamics than N-GLYCO, which is confined by the presence of sequons. The special classes of proteins possessing extreme or unique patterns of the three structural features are comprehensively identified, and their structural features and potential dynamics help to identify their susceptibility to different physiological and pathophysiological insults, which could help drug development and protein engineering.
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Affiliation(s)
- Manthan Desai
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (A.S.); (D.P.); (S.R.C.)
| | - Amritpal Singh
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (A.S.); (D.P.); (S.R.C.)
| | - David Pham
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (A.S.); (D.P.); (S.R.C.)
| | - Syed Rafid Chowdhury
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (A.S.); (D.P.); (S.R.C.)
| | - Bingyun Sun
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Shakibaie MR, Modaresi F, Azizi O, Tadjrobehkar O, Ghaemi MM. Conformational changes in the AdeB transmembrane efflux pump by amphiphilic peptide Mastoparan-B, down-regulates expression of the adeB Gene and restores antibiotics Susceptibility.. [DOI: 10.1101/2023.01.03.522678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
ABSTRACTNo report exists on the role of Mastoparan B (MP-B) as an RND efflux pump inhibitor in multi-drug resistant (MDR)Acinetobacter baumannii. Here, we performed a series of in-silico experiments to predict the inhibition of the AdeB efflux pump by MP-B as a drug target agent. For this reason, an MDR strain ofA. baumanniiwas subjected to MICs against 12 antibiotics as well as MP-B. Expression of the adeB gene in the presence and absence of sub-MIC of MP-B was studied by qRT-PCR. It was found that MP-B had potent antimicrobial activity (MIC=1 μg/ml) associated with a 20-fold decrease in theadeB gene expression at the sub-MIC level. The stereochemical analysis using several automated servers confirmed that the AdeB protein is an inner membrane of the RND tripartite complex system with helix-turn-helix conformation and a pore rich in Phe, Ala, and Lys residue. Furthermore, 20 ligands were generated from the initial docked poses to create the correct protein-peptide complexes using the BioLiP pipeline. The pose showed high Z=1.2, C=1.41, TM=0.99, and RMSD=4.4 scores was selected for docking purposes. The molecular docking via AutoDock/Vina revealed that MP-B form H-bound with Val 499, Phe 454, Thr 474, Ser 461, Gly 465, and Tyr 468 residues of the AdeB helix-5 and caused a shift in the dihedral angle (Φ/Ψ) by distances of 9.0 Å, 9.3 Å, and 9.6 Å, respectively. This shift in folding was detected by AlphaFold 2 and influenced the overall druggability of the protein. From the above results, we concluded that MP-B can be a good candidate for bacterial efflux pump inhibition.
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Stella NA, Romanowski EG, Brothers KM, Calvario RC, Shanks RMQ. IgaA Protein, GumB, Has a Global Impact on the Transcriptome and Surface Proteome of Serratia marcescens. Infect Immun 2022; 90:e0039922. [PMID: 36317876 PMCID: PMC9671016 DOI: 10.1128/iai.00399-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
Bacterial stress response signaling systems, like the Rcs system are triggered by membrane and cell wall damaging compounds, including antibiotics and immune system factors. These regulatory systems help bacteria survive envelope stress by altering the transcriptome resulting in protective phenotypic changes that may also influence the virulence of the bacterium. This study investigated the role of the Rcs stress response system using a clinical keratitis isolate of Serratia marcescens with a mutation in the gumB gene. GumB, an IgaA ortholog, inhibits activation of the Rcs system, such that mutants have overactive Rcs signaling. Transcriptomic analysis indicated that approximately 15% of all S. marcescens genes were significantly altered with 2-fold or greater changes in expression in the ΔgumB mutant compared to the wild type, indicating a global transcriptional regulatory role for GumB. We further investigated the phenotypic consequences of two classes of genes with altered expression in the ΔgumB mutant expected to contribute to infections: serralysin metalloproteases PrtS, SlpB, and SlpE, and type I pili coded by fimABCD. Secreted fractions from the ΔgumB mutant had reduced cytotoxicity to a corneal cell line, and could be complemented by induced expression of prtS, but not cytolysin shlBA, phospholipase phlAB, or flagellar master regulator flhDC operons. Proteomic analysis, qRT-PCR, and type I pili-dependent yeast agglutination indicated an inhibitory role for the Rcs system in adhesin production. Together these data demonstrate GumB has a global impact on S. marcescens gene expression that had measurable effects on bacterial cytotoxicity and surface adhesin production.
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Affiliation(s)
- Nicholas A. Stella
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh Pennsylvania, USA
| | - Eric G. Romanowski
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh Pennsylvania, USA
| | - Kimberly M. Brothers
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh Pennsylvania, USA
| | - Rachel C. Calvario
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh Pennsylvania, USA
| | - Robert M. Q. Shanks
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh Pennsylvania, USA
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Enespa, Chandra P, Singh DP. Sources, purification, immobilization and industrial applications of microbial lipases: An overview. Crit Rev Food Sci Nutr 2022; 63:6653-6686. [PMID: 35179093 DOI: 10.1080/10408398.2022.2038076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Microbial lipase is looking for better attention with the fast growth of enzyme proficiency and other benefits like easy, cost-effective, and reliable manufacturing. Immobilized enzymes can be used repetitively and are incapable to catalyze the reactions in the system continuously. Hydrophobic supports are utilized to immobilize enzymes when the ionic strength is low. This approach allows for the immobilization, purification, stability, and hyperactivation of lipases in a single step. The diffusion of the substrate is more advantageous on hydrophobic supports than on hydrophilic supports in the carrier. These approaches are critical to the immobilization performance of the enzyme. For enzyme immobilization, synthesis provides a higher pH value as well as greater heat stability. Using a mixture of immobilization methods, the binding force between enzymes and the support rises, reducing enzyme leakage. Lipase adsorption produces interfacial activation when it is immobilized on hydrophobic support. As a result, in the immobilization process, this procedure is primarily used for a variety of industrial applications. Microbial sources, immobilization techniques, and industrial applications in the fields of food, flavor, detergent, paper and pulp, pharmaceuticals, biodiesel, derivatives of esters and amino groups, agrochemicals, biosensor applications, cosmetics, perfumery, and bioremediation are all discussed in this review.
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Affiliation(s)
- Enespa
- School for Agriculture, Sri Mahesh Prasad Post Graduate College, University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Prem Chandra
- Food Microbiology & Toxicology Laboratory, Department of Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, Uttar Pradesh, India
| | - Devendra Pratap Singh
- Department of Environmental Science, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, Uttar Pradesh, India
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Blackholly LR, Harris NJ, Findlay HE, Booth PJ. Cell-Free Expression to Probe Co-Translational Insertion of an Alpha Helical Membrane Protein. Front Mol Biosci 2022; 9:795212. [PMID: 35187078 PMCID: PMC8847741 DOI: 10.3389/fmolb.2022.795212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/11/2022] [Indexed: 01/23/2023] Open
Abstract
The majority of alpha helical membrane proteins fold co-translationally during their synthesis on the ribosome. In contrast, most mechanistic folding studies address refolding of full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation of membrane proteins is emerging as a useful tool to address folding during translation by a ribosome. We summarise the benefits of this approach and show how it can be successfully extended to a membrane protein with a complex topology. The bacterial leucine transporter, LeuT can be synthesised and inserted into lipid membranes using a variety of in vitro transcription translation systems. Unlike major facilitator superfamily transporters, where changes in lipids can optimise the amount of correctly inserted protein, LeuT insertion yields are much less dependent on the lipid composition. The presence of a bacterial translocon either in native membrane extracts or in reconstituted membranes also has little influence on the yield of LeuT incorporated into the lipid membrane, except at high reconstitution concentrations. LeuT is considered a paradigm for neurotransmitter transporters and possesses a knotted structure that is characteristic of this transporter family. This work provides a method in which to probe the formation of a protein as the polypeptide chain is being synthesised on a ribosome and inserting into lipids. We show that in comparison with the simpler major facilitator transporter structures, LeuT inserts less efficiently into membranes when synthesised cell-free, suggesting that more of the protein aggregates, likely as a result of the challenging formation of the knotted topology in the membrane.
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Affiliation(s)
| | | | | | - Paula J. Booth
- Department of Chemistry, King’s College London, London, United Kingdom
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O'Neil PT. A Limitation of Using Dithionite Quenching to Determine the Topology of Membrane-inserted Proteins. J Membr Biol 2021; 255:123-127. [PMID: 34694464 DOI: 10.1007/s00232-021-00199-6] [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: 08/11/2021] [Accepted: 08/21/2021] [Indexed: 10/20/2022]
Abstract
Determining the topology of membrane-inserted proteins and peptides often relies upon indirect fluorescent measurements. One such technique uses NBD, an environmentally sensitive fluorophore that can be covalently linked to proteins. Relative to a hydrophilic environment, NBD in a hydrophobic environment shows an increase in emission intensity and a shift to shorter wavelengths. To gain further insight, NBD fluorescence can be chemically quenched using dithionite. As dithionite is an anion, it is only expected to penetrate the outer leaflet interfacial region and should be excluded from the hydrocarbon core, the inner leaflet, and the lumen of LUV. This assumption holds at neutral pH, where a large number of NBD/dithionite experiments are carried out. Here, we report control experiments in which LUV were directly labeled with NBD-PE to assess dithionite quenching in acidic conditions. Results showed that at acidic pH, dithionite moved more freely across the bilayer to quench the inner leaflet. For the buffer conditions used, dithionite exhibited a sharp change in behavior between pH 5.5 and 6.0. Therefore, in acidic conditions, dithionite could not differentiate in which leaflet the NBD resided.
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Affiliation(s)
- Pierce T O'Neil
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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Fostering "Education": Do Extracellular Vesicles Exploit Their Own Delivery Code? Cells 2021; 10:cells10071741. [PMID: 34359911 PMCID: PMC8305232 DOI: 10.3390/cells10071741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs), comprising large microvesicles (MVs) and exosomes (EXs), play a key role in intercellular communication, both in physiological and in a wide variety of pathological conditions. However, the education of EV target cells has so far mainly been investigated as a function of EX cargo, while few studies have focused on the characterization of EV surface membrane molecules and the mechanisms that mediate the addressability of specific EVs to different cell types and tissues. Identifying these mechanisms will help fulfill the diagnostic, prognostic, and therapeutic promises fueled by our growing knowledge of EVs. In this review, we first discuss published studies on the presumed EV “delivery code” and on the combinations of the hypothesized EV surface membrane “sender” and “recipient” molecules that may mediate EV targeting in intercellular communication. Then we briefly review the main experimental approaches and techniques, and the bioinformatic tools that can be used to identify and characterize the structure and functional role of EV surface membrane molecules. In the final part, we present innovative techniques and directions for future research that would improve and deepen our understandings of EV-cell targeting.
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Current problems and future avenues in proteoliposome research. Biochem Soc Trans 2021; 48:1473-1492. [PMID: 32830854 DOI: 10.1042/bst20190966] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
Membrane proteins (MPs) are the gatekeepers between different biological compartments separated by lipid bilayers. Being receptors, channels, transporters, or primary pumps, they fulfill a wide variety of cellular functions and their importance is reflected in the increasing number of drugs that target MPs. Functional studies of MPs within a native cellular context, however, is difficult due to the innate complexity of the densely packed membranes. Over the past decades, detergent-based extraction and purification of MPs and their reconstitution into lipid mimetic systems has been a very powerful tool to simplify the experimental system. In this review, we focus on proteoliposomes that have become an indispensable experimental system for enzymes with a vectorial function, including many of the here described energy transducing MPs. We first address long standing questions on the difficulty of successful reconstitution and controlled orientation of MPs into liposomes. A special emphasis is given on coreconstitution of several MPs into the same bilayer. Second, we discuss recent progress in the development of fluorescent dyes that offer sensitive detection with high temporal resolution. Finally, we briefly cover the use of giant unilamellar vesicles for the investigation of complex enzymatic cascades, a very promising experimental tool considering our increasing knowledge of the interplay of different cellular components.
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Membrane Topology of Pestiviral Non-Structural Protein 2 and determination of the minimal autoprotease domain. J Virol 2021; 95:JVI.00154-21. [PMID: 33731461 PMCID: PMC8139697 DOI: 10.1128/jvi.00154-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pestiviruses like bovine viral diarrhea virus (BVDV) belong to the family Flaviviridae A distinctive feature of the Flaviviridae is the importance of non-structural (NS) proteins for RNA genome replication and virus morphogenesis. For pestiviruses, the NS2 protease-mediated release of NS3 is essential for RNA replication, whereas uncleaved NS2-3 is indispensable for producing viral progeny. Accordingly, in the pestiviral life cycle the switch from RNA replication to virion morphogenesis is temporally regulated by the extent of NS2-3 cleavage, which is catalyzed by the NS2 autoprotease. A detailed knowledge of the structural and functional properties of pestiviral NS2 and NS2-3 is mandatory for a better understanding of these processes.In the present study, we experimentally determined the membrane topology of NS2 of BVDV-1 strain NCP7 by the Substituted Cysteine Accessibility Method (SCAM) assay. According to the resulting model, the N terminus of NS2 resides in the ER lumen and is followed by three transmembrane segments (TM) and a cytoplasmic C-terminal protease domain. We used the resulting model for fine mapping of the minimal autoprotease domain. Only one TM segment was found to be essential for maintaining residual autoprotease activity. While the topology of pestiviral NS2 is overall comparable to the one of hepatitis C virus (HCV) NS2, our data also reveal potentially important differences between the two molecules. The improved knowledge about structural and functional properties of this protein will support future functional and structural studies on pestiviral NS2.ImportancePestiviral NS2 is central to the regulation of RNA replication and virion morphogenesis via its autoprotease activity. This activity is temporally regulated by the cellular DNAJC14 as a cofactor: while free NS3 is required for RNA replication as a component of the viral replicase, only uncleaved NS2-3 supports virion morphogenesis. For a better understanding of the underlying molecular interactions, topological and structural data are required. The topology-based determination of the minimal NS2-protease domain in the present study will facilitate future attempts to determine the structure of this unusual protease cofactor complex. In the hepatitis C virus system, NS2 functions as a hub in virion morphogenesis by interacting with structural as well as non-structural proteins. Our knowledge of the membrane topology will significantly support future detailed interaction studies for pestiviral NS2.
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14
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Bae Y, Lee SK, Chae YC, Park CY, Kang S. Accessibility-dependent topology studies of membrane proteins using a SpyTag/SpyCatcher protein-ligation system. Int J Biol Macromol 2021; 175:171-178. [PMID: 33549659 DOI: 10.1016/j.ijbiomac.2021.02.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/08/2023]
Abstract
Covalent protein-ligation methods were used not only to visualize the localization of proteins of interest in cells, but also to study the topology of plasma and subcellular organelle membrane proteins using fluorescent cell imaging. A 13-amino-acid SpyTag (ST) peptide was genetically introduced either into a variety of subcellular proteins of interest or into different positions of plasma or subcellular organelle membrane proteins individually. Conversely, a 15 kDa SpyCatcher (SC) protein was chemically conjugated with either fluorescent dyes or horseradish peroxidase (HRP) via a thiol-maleimide reaction. The extracellular ST-fused plasma membrane proteins were efficiently labeled with the fluorescent-dye-conjugated SC in both live and permeabilized cells, whereas the intracellularly localized ST-fused subcellular proteins were only labeled in permeabilized cells because of the limited accessibility of the fluorescent-dye-conjugated SC to the membrane. The fluorescent-dye-labeled SC together with selective membrane-permeabilizing agents successfully labeled the plasma or the subcellular organelle membrane proteins in a topology-dependent manner. Moreover, the HRP-conjugated SC not only successfully labeled the ST-fused plasma membrane proteins, thus significantly enhancing fluorescent signals in combination with the tyramide signal amplification agents, but also ligated with an external ST-fused target ligand, thus selectively binding to the endogenously expressed cellular receptors of the target cancer cells.
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Affiliation(s)
- Yoonji Bae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sang Kwon Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Young Chan Chae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Chan Young Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sebyung Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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15
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Mukherjee S, Bhattacharyya D, Bhunia A. Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain. Biophys Chem 2020; 266:106452. [PMID: 32818817 PMCID: PMC7418743 DOI: 10.1016/j.bpc.2020.106452] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/01/2020] [Accepted: 08/01/2020] [Indexed: 12/12/2022]
Abstract
The Envelope (E) protein in SARS Coronavirus (CoV) is a small structural protein, incorporated as part of the envelope. A major fraction of the protein has been known to be associated with the host membranes, particularly organelles related to intracellular trafficking, prompting CoV packaging and propagation. Studies have elucidated the central hydrophobic transmembrane domain of the E protein being responsible for much of the viroporin activity in favor of the virus. However, newer insights into the organizational principles at the membranous compartments within the host cells suggest further complexity of the system. The lesser hydrophobic Carboxylic-terminal of the protein harbors interesting amino acid sequences- suggesting at the prevalence of membrane-directed amyloidogenic properties that remains mostly elusive. These highly conserved segments indicate at several potential membrane-associated functional roles that can redefine our comprehensive understanding of the protein. This should prompt further studies in designing and characterizing of effective targeted therapeutic measures. The SARS CoV Envelope protein is a small structural protein of the virus, responsible for viroporin like activity. Membrane- E protein interaction provides an useful insight into gaining mechanistic insight into its viroporin functions. The central hydrophobic transmembrane domain of E protein, known to affect ion-channel formation. The C-terminal region of the protein show further potential host-membrane directed functional roles. The highly conserved amyloidogenic amino acid stretches of the C-terminal suggest for its contribution to CoV propagation.
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Affiliation(s)
- Shruti Mukherjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
| | - Dipita Bhattacharyya
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India.
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16
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Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation. Sci Rep 2020; 10:8880. [PMID: 32483232 PMCID: PMC7264363 DOI: 10.1038/s41598-020-65831-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/08/2020] [Indexed: 01/11/2023] Open
Abstract
Transmembrane proteins (TMP) play a crucial role in several physiological processes. Despite their importance and diversity, only a few TMP structures have been determined by high-resolution protein structure characterization methods so far. Due to the low number of determined TMP structures, the parallel development of various bioinformatics and experimental methods was necessary for their topological characterization. The combination of these methods is a powerful approach in the determination of TMP topology as in the Constrained Consensus TOPology prediction. To support the prediction, we previously developed a high-throughput topology characterization method based on primary amino group-labelling that is still limited in identifying all TMPs and their extracellular segments on the surface of a particular cell type. In order to generate more topology information, a new step, a partial proteolysis of the cell surface has been introduced to our method. This step results in new primary amino groups in the proteins that can be biotinylated with a membrane-impermeable agent while the cells still remain intact. Pre-digestion also promotes the emergence of modified peptides that are more suitable for MS/MS analysis. The modified sites can be utilized as extracellular constraints in topology predictions and may contribute to the refined topology of these proteins.
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17
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Sanguinetti M, Iriarte A, Amillis S, Marín M, Musto H, Ramón A. A pair of non-optimal codons are necessary for the correct biosynthesis of the Aspergillus nidulans urea transporter, UreA. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190773. [PMID: 31827830 PMCID: PMC6894576 DOI: 10.1098/rsos.190773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
In both prokaryotic and eukaryotic genomes, synonymous codons are unevenly used. Such differential usage of optimal or non-optimal codons has been suggested to play a role in the control of translation initiation and elongation, as well as at the level of transcription and mRNA stability. In the case of membrane proteins, codon usage has been proposed to assist in the establishment of a pause necessary for the correct targeting of the nascent chains to the translocon. By using as a model UreA, the Aspergillus nidulans urea transporter, we revealed that a pair of non-optimal codons encoding amino acids situated at the boundary between the N-terminus and the first transmembrane segment are necessary for proper biogenesis of the protein at 37°C. These codons presumably regulate the translation rate in a previously undescribed fashion, possibly contributing to the correct interaction of ureA-translating ribosome-nascent chain complexes with the signal recognition particle and/or other factors, while the polypeptide has not yet emerged from the ribosomal tunnel. Our results suggest that the presence of the pair of non-optimal codons would not be functionally important in all cellular conditions. Whether this mechanism would affect other proteins remains to be determined.
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Affiliation(s)
- Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay
- Laboratorio de Organización y Evolución del Genoma, Unidad de Genómica Evolutiva, Departamento de Evolución, Facultad de Ciencias, UdelaR, Montevideo, Uruguay
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Athens, Hellas, Greece
| | - Mónica Marín
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Organización y Evolución del Genoma, Unidad de Genómica Evolutiva, Departamento de Evolución, Facultad de Ciencias, UdelaR, Montevideo, Uruguay
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
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18
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Lin YH, Lin SY, Li GS, Weng SE, Tzeng SL, Hsiao YH, Hu NJ. Site-Directed Alkylation Detected by In-Gel Fluorescence (SDAF) to Determine the Topology Map and Probe the Solvent Accessibility of Membrane Proteins. Sci Rep 2019; 9:13171. [PMID: 31511541 PMCID: PMC6739316 DOI: 10.1038/s41598-019-49292-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/22/2019] [Indexed: 11/09/2022] Open
Abstract
The topology of helix-bundle membrane proteins provides low-resolution structural information with regard to the number and orientation of membrane-spanning helices, as well as the sidedness of intra/extra-cellular domains. In the past decades, several strategies have been developed to experimentally determine the topology of membrane proteins. However, generally, these methods are labour-intensive, time-consuming and difficult to implement for quantitative analysis. Here, we report a novel approach, site-directed alkylation detected by in-gel fluorescence (SDAF), which monitors the fluorescent band shift caused by alkylation of the EGFP-fused target membrane protein bearing one single introduced cysteine. In-gel fluorescence provides a unique readout of target membrane proteins with EGFP fusion from non-purified samples, revealing a distinct 5 kDa shift on SDS-PAGE gel due to conjugation with mPEG-MAL-5K. Using the structurally characterised bile acid transporter ASBTNM as an example, we demonstrate that SDAF generates a topology map consistent with the crystal structure. The efficiency of mPEG-MAL-5K modification at each introduced cysteine can easily be quantified and analysed, providing a useful tool for probing the solvent accessibility at a specific position of the target membrane protein.
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Affiliation(s)
- Yu-Hung Lin
- Graduate Institute of Biochemistry, National Chung Hsing University, 145 Xinda Rd., South Dist., Taichung City, 402, Taiwan, R.O.C
| | - Sung-Yao Lin
- Graduate Institute of Biochemistry, National Chung Hsing University, 145 Xinda Rd., South Dist., Taichung City, 402, Taiwan, R.O.C
| | - Guan-Syun Li
- Graduate Institute of Biochemistry, National Chung Hsing University, 145 Xinda Rd., South Dist., Taichung City, 402, Taiwan, R.O.C
| | - Shao-En Weng
- Graduate Institute of Biochemistry, National Chung Hsing University, 145 Xinda Rd., South Dist., Taichung City, 402, Taiwan, R.O.C
| | - Shu-Ling Tzeng
- Institute of Medicine, Chung Shan Medical University, No.110, Sec. 1, Jianguo N. Rd., Taichung City, 40201, Taiwan, R.O.C
| | - Yu-Hsuan Hsiao
- Graduate Institute of Biochemistry, National Chung Hsing University, 145 Xinda Rd., South Dist., Taichung City, 402, Taiwan, R.O.C
| | - Nien-Jen Hu
- Graduate Institute of Biochemistry, National Chung Hsing University, 145 Xinda Rd., South Dist., Taichung City, 402, Taiwan, R.O.C.. .,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, 145 Xinda Rd., South Dist., Taichung City, 402, Taiwan, R.O.C.. .,Ph.D. Program in Transnational Medicine, National Chung Hsing University, 145 Xinda Rd., South Dist., Taichung City, 402, Taiwan, R.O.C..
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19
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Ge Y, Gu Y, Wang J, Zhang Z. Membrane topology of rat sodium-coupled neutral amino acid transporter 2 (SNAT2). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1460-1469. [PMID: 29678469 DOI: 10.1016/j.bbamem.2018.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/24/2018] [Accepted: 04/15/2018] [Indexed: 11/19/2022]
Abstract
Sodium-coupled neutral amino acid transporter 2 (SNAT2) is a subtype of the amino acid transport system A that is widely expressed in mammalian tissues. It plays critical roles in glutamic acid-glutamine circulation, liver gluconeogenesis and other biological pathway. However, the topology of the SNAT2 amino acid transporter is unknown. Here we identified the topological structure of SNAT2 using bioinformatics analysis, Methoxy-polyethylene glycol maleimide (mPEG-Mal) chemical modification, protease cleavage assays, immunofluorescence and examination of glycosylation. Our results show that SNAT2 contains 11 transmembrane domains (TMDs) with an intracellular N terminus and an extracellular C terminus. Three N-glycosylation sites were verified at the largest extracellular loop. This model is consistent with the previous model of SNAT2 with the exception of a difference in number of glycosylation sites. This is the first time to confirm the SNAT2 membrane topology using experimental methods. Our study on SNAT2 topology provides valuable structural information of one of the solute carrier family 38 (SLC38) members.
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Affiliation(s)
- Yudan Ge
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Yanting Gu
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Jiahong Wang
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Zhou Zhang
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China.
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20
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Predicting Alpha Helical Transmembrane Proteins Using HMMs. Methods Mol Biol 2018; 1552:63-82. [PMID: 28224491 DOI: 10.1007/978-1-4939-6753-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Alpha helical transmembrane (TM) proteins constitute an important structural class of membrane proteins involved in a wide variety of cellular functions. The prediction of their transmembrane topology, as well as their discrimination in newly sequenced genomes, is of great importance for the elucidation of their structure and function. Several methods have been applied for the prediction of the transmembrane segments and the topology of alpha helical transmembrane proteins utilizing different algorithmic techniques. Hidden Markov Models (HMMs) have been efficiently used in the development of several computational methods used for this task. In this chapter we give a brief review of different available prediction methods for alpha helical transmembrane proteins pointing out sequence and structural features that should be incorporated in a prediction method. We then describe the procedure of the design and development of a Hidden Markov Model capable of predicting the transmembrane alpha helices in proteins and discriminating them from globular proteins.
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21
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Lindsey ML, Jung M, Hall ME, DeLeon-Pennell KY. Proteomic analysis of the cardiac extracellular matrix: clinical research applications. Expert Rev Proteomics 2018; 15:105-112. [PMID: 29285949 DOI: 10.1080/14789450.2018.1421947] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The cardiac extracellular matrix (ECM) provides anatomical, biochemical, and physiological support to the left ventricle. ECM proteins are difficult to detect using unbiased proteomic approaches due to solubility issues and a relatively low abundance compared to cytoplasmic and mitochondrial proteins present in highly prevalent cardiomyocytes. Areas covered: Proteomic capabilities have dramatically improved over the past 20 years, due to enhanced sample preparation protocols and increased capabilities in mass spectrometry (MS), database searching, and bioinformatics analysis. This review summarizes technological advancements made in proteomic applications that make ECM proteomics highly feasible. Expert commentary: Proteomic analysis of the ECM provides an important contribution to our understanding of the molecular and cellular processes associated with cardiovascular disease. Using results generated from proteomics approaches in basic science applications and integrating proteomics templates into clinical research protocols will aid in efforts to personalize medicine.
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Affiliation(s)
- Merry L Lindsey
- a Research Service , G.V. (Sonny) Montgomery Veterans Affairs Medical Center , Jackson , MS , USA.,b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA
| | - Mira Jung
- b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA
| | - Michael E Hall
- b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA.,c Division of Cardiology , University of Mississippi Medical Center , Jackson , MS , USA
| | - Kristine Y DeLeon-Pennell
- a Research Service , G.V. (Sonny) Montgomery Veterans Affairs Medical Center , Jackson , MS , USA.,b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA
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22
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Jia B, Jeon CO. High-throughput recombinant protein expression in Escherichia coli: current status and future perspectives. Open Biol 2017; 6:rsob.160196. [PMID: 27581654 PMCID: PMC5008019 DOI: 10.1098/rsob.160196] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/03/2016] [Indexed: 12/26/2022] Open
Abstract
The ease of genetic manipulation, low cost, rapid growth and number of previous studies have made Escherichia coli one of the most widely used microorganism species for producing recombinant proteins. In this post-genomic era, challenges remain to rapidly express and purify large numbers of proteins for academic and commercial purposes in a high-throughput manner. In this review, we describe several state-of-the-art approaches that are suitable for the cloning, expression and purification, conducted in parallel, of numerous molecules, and we discuss recent progress related to soluble protein expression, mRNA folding, fusion tags, post-translational modification and production of membrane proteins. Moreover, we address the ongoing efforts to overcome various challenges faced in protein expression in E. coli, which could lead to an improvement of the current system from trial and error to a predictable and rational design.
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Affiliation(s)
- Baolei Jia
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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23
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Desikan R, Maiti PK, Ayappa KG. Assessing the Structure and Stability of Transmembrane Oligomeric Intermediates of an α-Helical Toxin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11496-11510. [PMID: 28930630 DOI: 10.1021/acs.langmuir.7b02277] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Protein membrane interactions play an important role in our understanding of diverse phenomena ranging from membrane-assisted protein aggregation to oligomerization and folding. Pore-forming toxins (PFTs) are the primary vehicle for infection by several strains of bacteria. These proteins which are expressed in a water-soluble form (monomers) bind to the target membrane and conformationally transform (protomers) and self-assemble to form a multimer transmembrane pore complex through a process of oligomerization. On the basis of the structure of the transmembrane domains, PFTs are broadly classified into β or α toxins. In contrast to β-PFTs, the paucity of available crystal structures coupled with the amphipathic nature of the transmembrane domains has hindered our understanding of α-PFT pore formation. In this article, we use molecular dynamics (MD) simulations to examine the process of pore formation of the bacterial α-PFT, cytolysin A from Escherichia coli (ClyA) in lipid bilayer membranes. Using atomistic MD simulations ranging from 50 to 500 ns, we show that transmembrane oligomeric intermediates or "arcs" form stable proteolipidic complexes consisting of protein arcs with toroidal lipids lining the free edges. By creating initial conditions where the lipids are contained within the arcs, we study the dynamics of spontaneous lipid evacuation and toroidal edge formation. This process occurs on the time scale of tens of nanoseconds, suggesting that once protomers oligomerize, transmembrane arcs are rapidly stabilized to form functional water channels capable of leakage. Using umbrella sampling with a coarse-grained molecular model, we obtain the free energy of insertion of a single protomer into the membrane. A single inserted protomer has a stabilization free energy of -52.9 ± 1.2 kJ/mol and forms a stable transmembrane water channel capable of leakage. Our simulations reveal that arcs are stable and viable intermediates that can occur during the pore-formation pathway for ClyA.
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Affiliation(s)
- Rajat Desikan
- Department of Chemical Engineering, ‡Centre for Condensed Matter Theory, Department of Physics, and §Centre for Biosystems Science and Engineering, Indian Institute of Science , Bengaluru, India 560012
| | - Prabal K Maiti
- Department of Chemical Engineering, ‡Centre for Condensed Matter Theory, Department of Physics, and §Centre for Biosystems Science and Engineering, Indian Institute of Science , Bengaluru, India 560012
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, ‡Centre for Condensed Matter Theory, Department of Physics, and §Centre for Biosystems Science and Engineering, Indian Institute of Science , Bengaluru, India 560012
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24
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Probing Inner Membrane Protein Topology by Proteolysis. Methods Mol Biol 2017. [PMID: 28667606 DOI: 10.1007/978-1-4939-7033-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Inner membrane proteins are inserted into the membrane via α-helices. These helices do not only constitute membrane anchors but may mediate specific interactions with membrane protein partners or participate in energetic processes. The number, location, and orientation of these helices is referred to as topology. Bitopic membrane proteins that consist of a single membrane-embedded domain connecting two soluble domains are distinguished from polytopic ones that consist of multiple membrane-spanning helices connected by extramembrane domains. Defining inner membrane protein topology could be achieved by different methods. Here we describe a protease accessibility assay that makes it possible to define topology based on digestion profiles.
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25
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The two transmembrane regions of Candida albicans Dfi1 contribute to its biogenesis. Biochem Biophys Res Commun 2017; 488:153-158. [PMID: 28483525 DOI: 10.1016/j.bbrc.2017.04.158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 11/22/2022]
Abstract
The opportunistic pathogen Candida albicans forms invasive filaments that grow into host tissues during disease. The glycosylated, integral plasma membrane protein Dfi1 is important for invasive filamentation in a laboratory model, and for lethality in murine disseminated candidiasis. However, Dfi1 topology and essential domains for Dfi1 biogenesis were undefined. Sequence analysis predicted that Dfi1 contains two transmembrane regions, located near the N- and C-termini. In this communication, we show that Dfi1 remains an integral membrane protein despite deletion of either predicted transmembrane region, whereas deletion of both regions results in a soluble protein. Additionally, Dfi1 that was properly oriented in the membrane, as indicated by N-linked glycosylation, was observed when either transmembrane region was deleted, but was absent when both transmembrane regions were deleted. Interestingly, deletion of the N-terminal transmembrane region resulted in production of two forms of Dfi1. Most of the protein molecules acquired normal N-linked glycosylation and a smaller population failed to become normally N-linked glycosylated. This defect was reversed by replacement of the N-terminal hydrophobic sequence with one synthetic transmembrane sequence but not another. Finally, microscopy studies revealed that Dfi1 lacking the N-terminal transmembrane region was observed at the cell periphery, where full-length Dfi1 normally localizes, whereas the double-truncation mutant was diffusely intracellular. Therefore, mature Dfi1 protein contains two transmembrane domains which contribute to its biogenesis.
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26
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Langó T, Róna G, Hunyadi-Gulyás É, Turiák L, Varga J, Dobson L, Várady G, Drahos L, Vértessy BG, Medzihradszky KF, Szakács G, Tusnády GE. Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins. Sci Rep 2017; 7:42610. [PMID: 28211907 PMCID: PMC5304180 DOI: 10.1038/srep42610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/11/2017] [Indexed: 01/17/2023] Open
Abstract
Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins.
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Affiliation(s)
- Tamás Langó
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary
| | - Gergely Róna
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest, H-1111, Hungary.,Department of Biochemistry and Molecular Pharmacology, Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Center of the Hungarian Academy of Sciences, Temesvari krt. 62, Szeged, H-6726, Hungary
| | - Lilla Turiák
- Institute of Organic Chemistry, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary
| | - Julia Varga
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary
| | - László Dobson
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary
| | - György Várady
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary
| | - László Drahos
- Institute of Organic Chemistry, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary
| | - Beáta G Vértessy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest, H-1111, Hungary
| | - Katalin F Medzihradszky
- Laboratory of Proteomics Research, Biological Research Center of the Hungarian Academy of Sciences, Temesvari krt. 62, Szeged, H-6726, Hungary
| | - Gergely Szakács
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary
| | - Gábor E Tusnády
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary
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27
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Hausner J, Hartmann N, Jordan M, Büttner D. The Predicted Lytic Transglycosylase HpaH from Xanthomonas campestris pv. vesicatoria Associates with the Type III Secretion System and Promotes Effector Protein Translocation. Infect Immun 2017; 85:e00788-16. [PMID: 27895129 PMCID: PMC5278175 DOI: 10.1128/iai.00788-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/20/2016] [Indexed: 02/08/2023] Open
Abstract
The pathogenicity of the Gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria depends on a type III secretion (T3S) system, which spans both bacterial membranes and translocates effector proteins into plant cells. The assembly of the T3S system presumably involves the predicted lytic transglycosylase (LT) HpaH, which is encoded adjacent to the T3S gene cluster. Bacterial LTs degrade peptidoglycan and often promote the formation of membrane-spanning macromolecular protein complexes. In the present study, we show that HpaH localizes to the bacterial periplasm and binds to peptidoglycan as well as to components of the T3S system, including the predicted periplasmic inner rod proteins HrpB1 and HrpB2 as well as the pilus protein HrpE. In vivo translocation assays revealed that HpaH promotes the translocation of various effector proteins and of early substrates of the T3S system, suggesting a general contribution of HpaH to type III-dependent protein export. Mutant studies and the analysis of reporter fusions showed that the N-terminal region of HpaH contributes to protein function and is proteolytically cleaved. The N-terminally truncated HpaH cleavage product is secreted into the extracellular milieu by a yet-unknown transport pathway, which is independent of the T3S system.
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Affiliation(s)
- Jens Hausner
- Institute of Biology, Genetics Department, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Nadine Hartmann
- Institute of Biology, Genetics Department, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Jordan
- Institute of Biology, Genetics Department, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Daniela Büttner
- Institute of Biology, Genetics Department, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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28
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Bogdanov M. Mapping of Membrane Protein Topology by Substituted Cysteine Accessibility Method (SCAM™). Methods Mol Biol 2017; 1615:105-128. [PMID: 28667607 DOI: 10.1007/978-1-4939-7033-9_9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A described simple and advanced protocol for the substituted-cysteine accessibility method as applied to transmembrane (TM) orientation (SCAM™) permits a topology analysis of proteins in their native state and can be universally adapted to any membrane system to either systematically map an uniform topology or identify and quantify the degree of mixed topology. In this approach, noncritical individual amino acids that are thought to reside in the putative extracellular or intracellular loops of a membrane protein are replaced one at a time by cysteine residue, and the orientation with respect to the membrane is evaluated using a pair of membrane-impermeable nondetectable and detectable thiol-reactive labeling reagents.
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Affiliation(s)
- Mikhail Bogdanov
- Department of Biochemistry & Molecular Biology, University of Texas Health Science Center at Houston, McGovern Medical School, UT-GSBS, P.O. Box 20334, Houston, TX, 77030, USA.
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29
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Yan R, Wang X, Huang L, Tian Y, Cai W. Transmembrane region prediction by using sequence-derived features and machine learning methods. RSC Adv 2017. [DOI: 10.1039/c7ra03883f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Membrane proteins are central to carrying out impressive biological functions.
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Affiliation(s)
- Renxiang Yan
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
| | - Xiaofeng Wang
- College of Mathematics and Computer Science
- Shanxi Normal University
- Linfen 041004
- China
| | - Lanqing Huang
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
| | - Yarong Tian
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
| | - Weiwen Cai
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
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30
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Abstract
Experimental determination of membrane protein topology can be achieved using various techniques. Here we present the pho-lac dual reporter system, a simple, convenient, and reliable tool to analyze the topology of membrane proteins in vivo. The system is based on the use of two topological markers with complementary properties, the Escherichia coli β-galactosidase LacZ, which is active in the cytoplasm, and the E. coli alkaline phosphatase PhoA, which is active in the bacterial periplasm. Specifically, in this pho-lac gene system, the reporter molecule is a chimera composed of the mature PhoA that is in frame with the β-galactosidase α-peptide, LacZα. Hence, when targeted to the periplasm, the PhoA-LacZα dual reporter displays high alkaline phosphatase activity but no β-galactosidase activity. Conversely, when located in the cytoplasm, PhoA-LacZα has no phosphatase activity but exhibits high β-galactosidase activity in E. coli cells expressing the ω fragment of LacZ, LacZω (via the α-complementation phenomenon). The dual nature of the PhoA-LacZα reporter allows a simple way to normalize both enzymatic activities to obtain readily interpretable information about the subcellular location of the fusion site between the membrane protein under study and the reporter. In addition, the PhoA-LacZα reporter permits utilization of dual-indicator agar plates to easily discriminate between colonies bearing cytoplasmic fusions, periplasmic fusions, or out-of-frame fusions. In total, the phoA-lacZα fusion reporter approach is a straightforward and rather inexpensive method of characterizing the topology of membrane proteins in vivo.
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Affiliation(s)
- Gouzel Karimova
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS, UMR 3528, 28 rue du Dr. Roux, Paris, 75015, France.
| | - Daniel Ladant
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS, UMR 3528, 28 rue du Dr. Roux, Paris, 75015, France
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31
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Shen G, Cui W, Zhang H, Zhou F, Huang W, Liu Q, Yang Y, Li S, Bowman GR, Sadler JE, Gross ML, Li W. Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer. Nat Struct Mol Biol 2016; 24:69-76. [PMID: 27918545 DOI: 10.1038/nsmb.3333] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/24/2016] [Indexed: 01/25/2023]
Abstract
Although warfarin is the most widely used anticoagulant worldwide, the mechanism by which warfarin inhibits its target, human vitamin K epoxide reductase (hVKOR), remains unclear. Here we show that warfarin blocks a dynamic electron-transfer process in hVKOR. A major fraction of cellular hVKOR is in an intermediate redox state containing a Cys51-Cys132 disulfide, a characteristic accommodated by a four-transmembrane-helix structure of hVKOR. Warfarin selectively inhibits this major cellular form of hVKOR, whereas disruption of the Cys51-Cys132 disulfide impairs warfarin binding and causes warfarin resistance. Relying on binding interactions identified by cysteine alkylation footprinting and mass spectrometry coupled with mutagenesis analysis, we conducted structure simulations, which revealed a closed warfarin-binding pocket stabilized by the Cys51-Cys132 linkage. Understanding the selective warfarin inhibition of a specific redox state of hVKOR should enable the rational design of drugs that exploit the redox chemistry and associated conformational changes in hVKOR.
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Affiliation(s)
- Guomin Shen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Fengbo Zhou
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Wei Huang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA.,School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yihu Yang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Shuang Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - J Evan Sadler
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
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32
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Lindsey ML, Hall ME, Harmancey R, Ma Y. Adapting extracellular matrix proteomics for clinical studies on cardiac remodeling post-myocardial infarction. Clin Proteomics 2016; 13:19. [PMID: 27651752 PMCID: PMC5024439 DOI: 10.1186/s12014-016-9120-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/15/2016] [Indexed: 01/16/2023] Open
Abstract
Following myocardial infarction (MI), the left ventricle (LV) undergoes a series of cardiac wound healing responses that involve stimulation of robust inflammation to clear necrotic myocytes and tissue debris and induction of extracellular matrix (ECM) protein synthesis to generate a scar. Proteomic strategies provide us with a means to index the ECM proteins expressed in the LV, quantify amounts, determine functions, and explore interactions. This review will focus on the efforts taken in the proteomics research field that have expanded our understanding of post-MI LV remodeling, concentrating on the strengths and limitations of different proteomic approaches to glean information that is specific to ECM turnover in the post-MI setting. We will discuss how recent advances in sample preparation and labeling protocols increase our successes at detecting components of the cardiac ECM proteome. We will summarize how proteomic approaches, focusing on the ECM compartment, have progressed over time to current gel-free methods using decellularized fractions or labeling strategies that will be useful for clinical applications. This review will provide an overview of how cardiac ECM proteomics has evolved over the last decade and will provide insight into future directions that will drive forward our understanding of cardiac ECM turnover in the post-MI LV.
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Affiliation(s)
- Merry L Lindsey
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA ; Division of Cardiology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS USA ; Research Service, G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, MS USA
| | - Michael E Hall
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA ; Division of Cardiology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS USA
| | - Romain Harmancey
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA
| | - Yonggang Ma
- Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 North State St., Jackson, MS 39216-4505 USA
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33
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N-linked glycosylation of N48 is required for equilibrative nucleoside transporter 1 (ENT1) function. Biosci Rep 2016; 36:BSR20160063. [PMID: 27480168 PMCID: PMC5006311 DOI: 10.1042/bsr20160063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/01/2016] [Indexed: 11/29/2022] Open
Abstract
Our study confirmed that Asn48 of hENT1 is the only N-glycosylated residue when expressed in HEK293 cells, and loss of the N-glycan resulted in less hENT1 at the plasma membrane, as well as a loss of function and protein–protein self-interaction. Human equilibrative nucleoside transporter 1 (hENT1) transports nucleosides and nucleoside analogue drugs across cellular membranes and is necessary for the uptake of many anti-cancer, anti-parasitic and anti-viral drugs. Previous work, and in silico prediction, suggest that hENT1 is glycosylated at Asn48 in the first extracellular loop of the protein and that glycosylation plays a role in correct localization and function of hENT1. Site-directed mutagenesis of wild-type (wt) hENT1 removed potential glycosylation sites. Constructs (wt 3xFLAG-hENT1, N48Q-3xFLAG-hENT1 or N288Q-3xFLAG-hENT2) were transiently transfected into HEK293 cells and cell lysates were treated with or without peptide–N-glycosidase F (PNGase-F), followed by immunoblotting analysis. Substitution of N48 prevents hENT1 glycosylation, confirming a single N-linked glycosylation site. N48Q-hENT1 protein is found at the plasma membrane in HEK293 cells but at lower levels compared with wt hENT1 based on S-(4-nitrobenzyl)-6-thioinosine (NBTI) binding analysis (wt 3xFLAG-ENT1 Bmax, 41.5±2.9 pmol/mg protein; N48Q-3xFLAG-ENT1 Bmax, 13.5±0.45 pmol/mg protein) and immunofluorescence microscopy. Although present at the membrane, chloroadenosine transport assays suggest that N48Q-hENT1 is non-functional (wt 3xFLAG-ENT1, 170.80±44.01 pmol/mg protein; N48Q-3xFLAG-ENT1, 57.91±17.06 pmol/mg protein; mock-transfected 74.31±19.65 pmol/mg protein). Co-immunoprecipitation analyses suggest that N48Q ENT1 is unable to interact with self or with wt hENT1. Based on these data we propose that glycosylation at N48 is critical for the localization, function and oligomerization of hENT1.
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34
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Zhang C, Ye Z, Xue P, Shu Q, Zhou Y, Ji Y, Fu Y, Wang J, Yang F. Evaluation of Different N-Glycopeptide Enrichment Methods for N-Glycosylation Sites Mapping in Mouse Brain. J Proteome Res 2016; 15:2960-8. [PMID: 27480293 DOI: 10.1021/acs.jproteome.6b00098] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-Glycosylation of proteins plays a critical role in many biological pathways. Because highly heterogeneous N-glycopeptides are present in biological sources, the enrichment procedure is a crucial step for mass spectrometry analysis. Five enrichment methods, including IP-ZIC-HILIC, hydrazide chemistry, lectin affinity, ZIC-HILIC-FA, and TiO2 affinity were evaluated and compared in the study of mapping N-glycosylation sites in mouse brain. On the basis of our results, the identified N-glycosylation sites were 1891, 1241, 891, 869, and 710 and the FDR values were 3.29, 5.62, 9.54, 9.54, and 20.02%, respectively. Therefore, IP-ZIC-HILIC enrichment method displayed the highest sensitivity and specificity. In this work, we identified a total of 3446 unique glycosylation sites conforming to the N-glycosylation consensus motif (N-X-T/S/C; X ≠ P) with (18)O labeling in 1597 N-glycoproteins. N-glycosylation site information was used to confirm or correct the transmembrane topology of the 57 novel transmembrane N-glycoproteins.
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Affiliation(s)
- Chengqian Zhang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Zilu Ye
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Peng Xue
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
| | - Qingbo Shu
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Yue Zhou
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Yanlong Ji
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Ying Fu
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
| | - Jifeng Wang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
| | - Fuquan Yang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.,University of Chinese Academy of Sciences , Beijing100049, China
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35
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Konovalova A, Silhavy TJ. Outer membrane lipoprotein biogenesis: Lol is not the end. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0030. [PMID: 26370942 DOI: 10.1098/rstb.2015.0030] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bacterial lipoproteins are lipid-anchored proteins that contain acyl groups covalently attached to the N-terminal cysteine residue of the mature protein. Lipoproteins are synthesized in precursor form with an N-terminal signal sequence (SS) that targets translocation across the cytoplasmic or inner membrane (IM). Lipid modification and SS processing take place at the periplasmic face of the IM. Outer membrane (OM) lipoproteins take the localization of lipoproteins (Lol) export pathway, which ends with the insertion of the N-terminal lipid moiety into the inner leaflet of the OM. For many lipoproteins, the biogenesis pathway ends here. We provide examples of lipoproteins that adopt complex topologies in the OM that include transmembrane and surface-exposed domains. Biogenesis of such lipoproteins requires additional steps beyond the Lol pathway. In at least one case, lipoprotein sequences reach the cell surface by being threaded through the lumen of a beta-barrel protein in an assembly reaction that requires the heteropentomeric Bam complex. The inability to predict surface exposure reinforces the importance of experimental verification of lipoprotein topology and we will discuss some of the methods used to study OM protein topology.
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Affiliation(s)
- Anna Konovalova
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, NJ 08544, USA
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36
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Li P, Rivera-Cancel G, Kinch LN, Salomon D, Tomchick DR, Grishin NV, Orth K. Bile salt receptor complex activates a pathogenic type III secretion system. eLife 2016; 5. [PMID: 27377244 PMCID: PMC4933562 DOI: 10.7554/elife.15718] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/07/2016] [Indexed: 11/26/2022] Open
Abstract
Bile is an important component of the human gastrointestinal tract with an essential role in food absorption and antimicrobial activities. Enteric bacterial pathogens have developed strategies to sense bile as an environmental cue to regulate virulence genes during infection. We discovered that Vibrio parahaemolyticus VtrC, along with VtrA and VtrB, are required for activating the virulence type III secretion system 2 in response to bile salts. The VtrA/VtrC complex activates VtrB in the presence of bile salts. The crystal structure of the periplasmic domains of the VtrA/VtrC heterodimer reveals a β-barrel with a hydrophobic inner chamber. A co-crystal structure of VtrA/VtrC with bile salt, along with biophysical and mutational analysis, demonstrates that the hydrophobic chamber binds bile salts and activates the virulence network. As part of a family of conserved signaling receptors, VtrA/VtrC provides structural and functional insights into the evolutionarily conserved mechanism used by bacteria to sense their environment. DOI:http://dx.doi.org/10.7554/eLife.15718.001 When we eat a meal, bile salts in the intestine help the body to absorb molecules of fat. Certain bacteria that cause food poisoning in humans, such as Vibrio parahaemolyticus, can also detect bile salts and use them to sense that they have reached the intestine of a suitable host. The bacteria then produce toxins that inflame the intestine; this can result in days of diarrhea. However, it was not clear how the bacteria detect the bile salt signal and how this triggers them to produce the toxins. Li, Rivera-Cancel et al. now discover that not one, but two, genes are required for this process. The genes encode two proteins, called VtrA and VtrC, that interact to form protein ‘complex’ on the surface of the membrane that surrounds the bacterial cell. The two proteins create a barrel-like structure that can bind to bile salts and trigger the cell to produce the toxins. Future experiments will aim to understand how the binding of bile salts to this protein complex causes an increase toxin production. A future challenge is to find out how other disease-causing bacteria sense environmental cues to produce toxins. With this knowledge, researchers might be able to design new drugs that could prevent the production of toxins to relieve symptoms of food poisoning and other illnesses. DOI:http://dx.doi.org/10.7554/eLife.15718.002
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Affiliation(s)
- Peng Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Giomar Rivera-Cancel
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Dor Salomon
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Diana R Tomchick
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
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37
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Baker JA, Simkovic F, Taylor HMC, Rigden DJ. Potential DNA binding and nuclease functions of ComEC domains characterized in silico. Proteins 2016; 84:1431-42. [PMID: 27318187 PMCID: PMC5031224 DOI: 10.1002/prot.25088] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/25/2016] [Accepted: 06/13/2016] [Indexed: 12/15/2022]
Abstract
Bacterial competence, which can be natural or induced, allows the uptake of exogenous double stranded DNA (dsDNA) into a competent bacterium. This process is known as transformation. A multiprotein assembly binds and processes the dsDNA to import one strand and degrade another yet the underlying molecular mechanisms are relatively poorly understood. Here distant relationships of domains in Competence protein EC (ComEC) of Bacillus subtilis (Uniprot: P39695) were characterized. DNA-protein interactions were investigated in silico by analyzing models for structural conservation, surface electrostatics and structure-based DNA binding propensity; and by data-driven macromolecular docking of DNA to models. Our findings suggest that the DUF4131 domain contains a cryptic DNA-binding OB fold domain and that the β-lactamase-like domain is the hitherto cryptic competence nuclease. Proteins 2016; 84:1431-1442. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
- James A Baker
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Felix Simkovic
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Helen M C Taylor
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Daniel J Rigden
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom.
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38
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Molnár J, Szakács G, Tusnády GE. Characterization of Disease-Associated Mutations in Human Transmembrane Proteins. PLoS One 2016; 11:e0151760. [PMID: 26986070 PMCID: PMC4795776 DOI: 10.1371/journal.pone.0151760] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 03/03/2016] [Indexed: 11/21/2022] Open
Abstract
Transmembrane protein coding genes are commonly associated with human diseases. We characterized disease causing mutations and natural polymorphisms in transmembrane proteins by mapping missense genetic variations from the UniProt database on the transmembrane protein topology listed in the Human Transmembrane Proteome database. We found characteristic differences in the spectrum of amino acid changes within transmembrane regions: in the case of disease associated mutations the non-polar to non-polar and non-polar to charged amino acid changes are equally frequent. In contrast, in the case of natural polymorphisms non-polar to charged amino acid changes are rare while non-polar to non-polar changes are common. The majority of disease associated mutations result in glycine to arginine and leucine to proline substitutions. Mutations to positively charged amino acids are more common in the center of the lipid bilayer, where they cause more severe structural and functional anomalies. Our analysis contributes to the better understanding of the effect of disease associated mutations in transmembrane proteins, which can help prioritize genetic variations in personal genomic investigations.
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Affiliation(s)
- János Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Gábor E. Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
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39
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Sivanesan D, Beauchamp C, Quinou C, Lee J, Lesage S, Chemtob S, Rioux JD, Michnick SW. IL23R (Interleukin 23 Receptor) Variants Protective against Inflammatory Bowel Diseases (IBD) Display Loss of Function due to Impaired Protein Stability and Intracellular Trafficking. J Biol Chem 2016; 291:8673-85. [PMID: 26887945 DOI: 10.1074/jbc.m116.715870] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Indexed: 01/19/2023] Open
Abstract
Genome-wide association studies as well as murine models have shown that the interleukin 23 receptor (IL23R) pathway plays a pivotal role in chronic inflammatory diseases such as Crohn disease (CD), ulcerative colitis, psoriasis, and type 1 diabetes. Genome-wide association studies and targeted re-sequencing studies have revealed the presence of multiple potentially causal variants of the IL23R. Specifically the G149R, V362I, and R381Q IL23Rα chain variants are linked to protection against the development of Crohn disease and ulcerative colitis in humans. Moreover, the exact mechanism of action of these receptor variants has not been elucidated. We show that all three of these IL23Rα variants cause a reduction in IL23 receptor activation-mediated phosphorylation of the signal-transducing activator of transcription 3 (STAT3) and phosphorylation of signal transducing activator of transcription 4 (STAT4). The reduction in signaling is due to lower levels of cell surface receptor expression. For G149R, the receptor retention in the endoplasmic reticulum is due to an impairment of receptor maturation, whereas the R381Q and V362I variants have reduced protein stability. Finally, we demonstrate that the endogenous expression of IL23Rα protein from V362I and R381Q variants in human lymphoblastoid cell lines exhibited lower expression levels relative to susceptibility alleles. Our results suggest a convergent cause of IL23Rα variant protection against chronic inflammatory disease.
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Affiliation(s)
- Durga Sivanesan
- From the Department of Biochemistry, University of Montreal, Montreal, Quebec H3C 3J7, Canada, University of Ottawa, Department of Biochemistry, Microbiology, and Immunology, Ottawa, Ontario K1H 8M5, Canada
| | - Claudine Beauchamp
- University of Montreal and the Montreal Heart Institute, Research Center, Montreal, Quebec H1T 1C8, Canada
| | - Christiane Quinou
- CHU Sainte-Justine, Research Centre, Montreal, Quebec H3T 1C5, Canada, and
| | - Jonathan Lee
- University of Ottawa, Department of Biochemistry, Microbiology, and Immunology, Ottawa, Ontario K1H 8M5, Canada
| | - Sylvie Lesage
- Centre of Recherche Hospital Maisonneuve-Rosemont, Department of Microbiology, Infection, and Immunology, University of Montreal, Montreal, Quebec H1T 2M4, Canada
| | - Sylvain Chemtob
- CHU Sainte-Justine, Research Centre, Montreal, Quebec H3T 1C5, Canada, and
| | - John D Rioux
- University of Montreal and the Montreal Heart Institute, Research Center, Montreal, Quebec H1T 1C8, Canada
| | - Stephen W Michnick
- From the Department of Biochemistry, University of Montreal, Montreal, Quebec H3C 3J7, Canada,
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40
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Martins IJ. Overnutrition Determines LPS Regulation of Mycotoxin Induced Neurotoxicity in Neurodegenerative Diseases. Int J Mol Sci 2015; 16:29554-73. [PMID: 26690419 PMCID: PMC4691133 DOI: 10.3390/ijms161226190] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/19/2015] [Accepted: 12/01/2015] [Indexed: 12/11/2022] Open
Abstract
Chronic neurodegenerative diseases are now associated with obesity and diabetes and linked to the developing and developed world. Interests in healthy diets have escalated that may prevent neurodegenerative diseases such as Parkinson's and Alzheimer's disease. The global metabolic syndrome involves lipoprotein abnormalities and insulin resistance and is the major disorder for induction of neurological disease. The effects of bacterial lipopolysaccharides (LPS) on dyslipidemia and NAFLD indicate that the clearance and metabolism of fungal mycotoxins are linked to hypercholesterolemia and amyloid beta oligomers. LPS and mycotoxins are associated with membrane lipid disturbances with effects on cholesterol interacting proteins, lipoprotein metabolism, and membrane apo E/amyloid beta interactions relevant to hypercholesterolemia with close connections to neurological diseases. The influence of diet on mycotoxin metabolism has accelerated with the close association between mycotoxin contamination from agricultural products such as apple juice, grains, alcohol, and coffee. Cholesterol efflux in lipoproteins and membrane cholesterol are determined by LPS with involvement of mycotoxin on amyloid beta metabolism. Nutritional interventions such as diets low in fat/carbohydrate/cholesterol have become of interest with relevance to low absorption of lipophilic LPS and mycotoxin into lipoproteins with rapid metabolism of mycotoxin to the liver with the prevention of neurodegeneration.
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Affiliation(s)
- Ian James Martins
- Centre of Excellence in Alzheimer's Disease Research and Care, School of Medical Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup 6027, Australia.
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Nedlands 6009, Australia.
- McCusker Alzheimer's Research Foundation, Hollywood Medical Centre, 85 Monash Avenue, Suite 22, Nedlands 6009, Australia.
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Determining the N-terminal orientations of recombinant transmembrane proteins in the Escherichia coli plasma membrane. Sci Rep 2015; 5:15086. [PMID: 26462555 PMCID: PMC4604451 DOI: 10.1038/srep15086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/11/2015] [Indexed: 11/08/2022] Open
Abstract
In silico algorithms have been the common approach for transmembrane (TM) protein topology prediction. However, computational tools may produce questionable results and experimental validation has proven difficult. Although biochemical strategies are available to determine the C-terminal orientation of TM proteins, experimental strategies to determine the N-terminal orientation are still limited but needed because the N-terminal end is essential for membrane targeting. Here, we describe a new and easy method to effectively determine the N-terminal orientation of the target TM proteins in Escherichia coli plasma membrane environment. D94N, the mutant of bacteriorhodopsin from Haloarcula marismortui, can be a fusion partner to increase the production of the target TM proteins if their N-termini are in cytoplasm (Nin orientation). To create a suitable linker for orientating the target TM proteins with the periplasmic N-termini (Nout orientation) correctly, we designed a three-TM-helix linker fused at the C-terminus of D94N fusion partner (termed D94N-3TM) and found that D94N-3TM can specifically improve the production of the Nout target TM proteins. In conclusion, D94N and D94N-3TM fusion partners can be applied to determine the N-terminal end of the target TM proteins oriented either Nin or Nout by evaluating the net expression of the fusion proteins.
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42
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Glycosylation of solute carriers: mechanisms and functional consequences. Pflugers Arch 2015; 468:159-76. [PMID: 26383868 DOI: 10.1007/s00424-015-1730-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/19/2015] [Accepted: 08/21/2015] [Indexed: 12/21/2022]
Abstract
Solute carriers (SLCs) are one of the largest groups of multi-spanning membrane proteins in mammals and include ubiquitously expressed proteins as well as proteins with highly restricted tissue expression. A vast number of studies have addressed the function and organization of SLCs as well as their posttranslational regulation, but only relatively little is known about the role of SLC glycosylation. Glycosylation is one of the most abundant posttranslational modifications of animal proteins and through recent advances in our understanding of protein-glycan interactions, the functional roles of SLC glycosylation are slowly emerging. The purpose of this review is to provide a concise overview of the aspects of glycobiology most relevant to SLCs, to discuss the roles of glycosylation in the regulation and function of SLCs, and to outline the major open questions in this field, which can now be addressed given major technical advances in this and related fields of study in recent years.
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43
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White C, Nixon A, Bradbury NA. Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP). J Vis Exp 2015. [PMID: 25939013 DOI: 10.3791/52509] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The correct topology and orientation of integral membrane proteins are essential for their proper function, yet such information has not been established for many membrane proteins. A simple technique called fluorescence protease protection (FPP) is presented, which permits the determination of membrane protein topology in living cells. This technique has numerous advantages over other methods for determining protein topology, in that it does not require the availability of multiple antibodies against various domains of the membrane protein, does not require large amounts of protein, and can be performed on living cells. The FPP method employs the spatially confined actions of proteases on the degradation of green fluorescent protein (GFP) tagged membrane proteins to determine their membrane topology and orientation. This simple approach is applicable to a wide variety of cell types, and can be used to determine membrane protein orientation in various subcellular organelles such as the mitochondria, Golgi, endoplasmic reticulum and components of the endosomal/recycling system. Membrane proteins, tagged on either the N-termini or C-termini with a GFP fusion, are expressed in a cell of interest, which is subject to selective permeabilization using the detergent digitonin. Digitonin has the ability to permeabilize the plasma membrane, while leaving intracellular organelles intact. GFP moieties exposed to the cytosol can be selectively degraded through the application of protease, whereas GFP moieties present in the lumen of organelles are protected from the protease and remain intact. The FPP assay is straightforward, and results can be obtained rapidly.
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Affiliation(s)
- Carl White
- Department of Physiology and Biophysics, Chicago Medical School
| | - Alex Nixon
- Department of Physiology and Biophysics, Chicago Medical School
| | - Neil A Bradbury
- Department of Physiology and Biophysics, Chicago Medical School;
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44
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Wright FA, Lu JP, Sliter DA, Dupré N, Rouleau GA, Wojcikiewicz RJH. A Point Mutation in the Ubiquitin Ligase RNF170 That Causes Autosomal Dominant Sensory Ataxia Destabilizes the Protein and Impairs Inositol 1,4,5-Trisphosphate Receptor-mediated Ca2+ Signaling. J Biol Chem 2015; 290:13948-57. [PMID: 25882839 DOI: 10.1074/jbc.m115.655043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Indexed: 12/11/2022] Open
Abstract
RNF170 is an endoplasmic reticulum membrane ubiquitin ligase that contributes to the ubiquitination of activated inositol 1,4,5-trisphosphate (IP3) receptors, and also, when point mutated (arginine to cysteine at position 199), causes autosomal dominant sensory ataxia (ADSA), a disease characterized by neurodegeneration in the posterior columns of the spinal cord. Here we demonstrate that this point mutation inhibits RNF170 expression and signaling via IP3 receptors. Inhibited expression of mutant RNF170 was seen in cells expressing exogenous RNF170 constructs and in ADSA lymphoblasts, and appears to result from enhanced RNF170 autoubiquitination and proteasomal degradation. The basis for these effects was probed via additional point mutations, revealing that ionic interactions between charged residues in the transmembrane domains of RNF170 are required for protein stability. In ADSA lymphoblasts, platelet-activating factor-induced Ca(2+) mobilization was significantly impaired, whereas neither Ca(2+) store content, IP3 receptor levels, nor IP3 production were altered, indicative of a functional defect at the IP3 receptor locus, which may be the cause of neurodegeneration. CRISPR/Cas9-mediated genetic deletion of RNF170 showed that RNF170 mediates the addition of all of the ubiquitin conjugates known to become attached to activated IP3 receptors (monoubiquitin and Lys(48)- and Lys(63)-linked ubiquitin chains), and that wild-type and mutant RNF170 have apparently identical ubiquitin ligase activities toward IP3 receptors. Thus, the Ca(2+) mobilization defect seen in ADSA lymphoblasts is apparently not due to aberrant IP3 receptor ubiquitination. Rather, the defect likely reflects abnormal ubiquitination of other substrates, or adaptation to the chronic reduction in RNF170 levels.
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Affiliation(s)
- Forrest A Wright
- From the Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Justine P Lu
- From the Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York 13210
| | | | - Nicolas Dupré
- the Neuromuscular and Neurogenetic Disease Clinic, CHU de Québec, Laval University, Quebec City, Quebec G1J 1Z4, Canada, and
| | - Guy A Rouleau
- the Montreal Neurological Institute and Hospital and Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada
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45
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Tian Y, Koganti T, Yao Z, Cannon P, Shah P, Pietrovito L, Modesti A, Aiyetan P, DeLeon-Pennell K, Ma Y, Halade GV, Hicks C, Zhang H, Lindsey ML. Cardiac extracellular proteome profiling and membrane topology analysis using glycoproteomics. Proteomics Clin Appl 2015; 8:595-602. [PMID: 24920555 DOI: 10.1002/prca.201400009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/23/2014] [Accepted: 06/06/2014] [Indexed: 01/23/2023]
Abstract
PURPOSE Extracellular proteins are easily accessible, which presents a subproteome of molecular targets that have high diagnostic and therapeutic potential. Efforts have been made to catalog the cardiac extracellular matridome and analyze the topology of identified proteins for the design of therapeutic targets. Although many bioinformatics tools have been developed to predict protein topology, topology has been experimentally validated for only a very small portion of membrane proteins. The aim of this study was to use a glycoproteomics and MS approach to identify glycoproteins in the extracellular matridome of the infarcted left ventricle (LV) and provide experimental evidence for topological determination. EXPERIMENTAL DESIGN Glycoproteomics analysis was performed on eight biological replicates of LV samples from wild-type mice at 7 days following myocardial infarction using SPE of glycopeptides, followed by mass spectrometric identification of N-linked glycosylation sites for topology assessment. RESULTS We identified hundreds of glycoproteins, and the identified N-glycosylation sites provide novel information on the correct topology for membrane proteins present in the infarct setting. CONCLUSIONS AND CLINICAL RELEVANCE Our data provide the foundation for future studies of the LV infarct extracellular matridome, which may facilitate the discovery of drug targets and biomarkers.
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Affiliation(s)
- Yuan Tian
- San Antonio Cardiovascular Proteomics Center, San Antonio, TX, USA; Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Gahl RF, Tekle E, Zhu GA, Taraska JW, Tjandra N. Acquiring snapshots of the orientation of trans-membrane protein domains using a hybrid FRET pair. FEBS Lett 2015; 589:885-9. [PMID: 25747388 DOI: 10.1016/j.febslet.2015.02.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/14/2015] [Accepted: 02/21/2015] [Indexed: 01/24/2023]
Abstract
One challenge in studying the function of membrane-embedded proteins is determining the orientation of key domains in the context of the changing and dynamic membrane environment. We describe a confocal microscopy setup that utilizes external electric field pulses to direct dipicrylamine (DPA) to a membrane leaflet. The detection of FRET between DPA and a fluorescent probe attributes it to the inner or outer leaflet of a membrane. By utilizing short acquisition times and confocal imaging, this attribution could be made even in changing membrane environments. Our setup adds versatility to the study of the biological activity of membrane-embedded proteins.
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Affiliation(s)
- Robert F Gahl
- Biochemistry and Biophysics Center, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
| | - Ephrem Tekle
- Biochemistry and Biophysics Center, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
| | - Gefei Alex Zhu
- Biochemistry and Biophysics Center, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
| | - Nico Tjandra
- Biochemistry and Biophysics Center, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA.
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The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3. J Bacteriol 2015; 197:1792-806. [PMID: 25777671 DOI: 10.1128/jb.02626-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/06/2015] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED In Sinorhizobium meliloti, three NodD transcriptional regulators activate bacterial nodulation (nod) gene expression. NodD1 and NodD2 require plant compounds to activate nod genes. The NodD3 protein does not require exogenous compounds to activate nod gene expression; instead, another transcriptional regulator, SyrM, activates nodD3 expression. In addition, NodD3 can activate syrM expression. SyrM also activates expression of another gene, syrA, which when overexpressed causes a dramatic increase in exopolysaccharide production. In a previous study, we identified more than 200 genes with altered expression in a strain overexpressing nodD3. In this work, we define the transcriptomes of strains overexpressing syrM or syrA. The syrM, nodD3, and syrA overexpression transcriptomes share similar gene expression changes; analyses imply that nodD3 and syrA are the only targets directly activated by SyrM. We propose that most of the gene expression changes observed when nodD3 is overexpressed are due to NodD3 activation of syrM expression, which in turn stimulates SyrM activation of syrA expression. The subsequent increase in SyrA abundance results in broad changes in gene expression, most likely mediated by the ChvI-ExoS-ExoR regulatory circuit. IMPORTANCE Symbioses with bacteria are prevalent across the animal and plant kingdoms. Our system of study, the rhizobium-legume symbiosis (Sinorhizobium meliloti and Medicago spp.), involves specific host-microbe signaling, differentiation in both partners, and metabolic exchange of bacterial fixed nitrogen for host photosynthate. During this complex developmental process, both bacteria and plants undergo profound changes in gene expression. The S. meliloti SyrM-NodD3-SyrA and ChvI-ExoS-ExoR regulatory circuits affect gene expression and are important for optimal symbiosis. In this study, we defined the transcriptomes of S. meliloti overexpressing SyrM or SyrA. In addition to identifying new targets of the SyrM-NodD3-SyrA regulatory circuit, our work further suggests how it is linked to the ChvI-ExoS-ExoR regulatory circuit.
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48
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Kappes MA, Miller CL, Faaberg KS. Porcine reproductive and respiratory syndrome virus nonstructural protein 2 (nsp2) topology and selective isoform integration in artificial membranes. Virology 2015; 481:51-62. [PMID: 25768891 DOI: 10.1016/j.virol.2015.01.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/15/2015] [Accepted: 01/30/2015] [Indexed: 11/28/2022]
Abstract
The membrane insertion and topology of nonstructural protein 2 (nsp2) of porcine reproductive and respiratory syndrome virus (PRRSV) strain VR-2332 was assessed using a cell free translation system in the presence or absence of artificial membranes. Expression of PRRSV nsp2 in the absence of all other viral factors resulted in the genesis of both full-length nsp2 as well as a select number of C-terminal nsp2 isoforms. Addition of membranes to the translation stabilized the translation reaction, resulting in predominantly full-length nsp2 as assessed by immunoprecipitation. Analysis further showed full-length nsp2 strongly associates with membranes, along with two additional large nsp2 isoforms. Membrane integration of full-length nsp2 was confirmed through high-speed density fractionation, protection from protease digestion, and immunoprecipitation. The results demonstrated that nsp2 integrated into the membranes with an unexpected topology, where the amino (N)-terminal (cytoplasmic) and C-terminal (luminal) domains were orientated on opposite sides of the membrane surface.
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Affiliation(s)
- Matthew A Kappes
- Virus and Prion Research Unit, USDA-ARS-National Animal Disease Center, Ames, IA, USA; Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Cathy L Miller
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Kay S Faaberg
- Virus and Prion Research Unit, USDA-ARS-National Animal Disease Center, Ames, IA, USA.
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Lhor M, Méthot M, Horchani H, Salesse C. Structure of the N-terminal segment of human retinol dehydrogenase 11 and its preferential lipid binding using model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:878-85. [DOI: 10.1016/j.bbamem.2014.12.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 12/09/2014] [Accepted: 12/15/2014] [Indexed: 11/25/2022]
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The lipid-modifying multiple peptide resistance factor is an oligomer consisting of distinct interacting synthase and flippase subunits. mBio 2015; 6:mBio.02340-14. [PMID: 25626904 PMCID: PMC4324311 DOI: 10.1128/mbio.02340-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
UNLABELLED Phospholipids are synthesized at the inner leaflet of the bacterial cytoplasmic membrane but have to be translocated to the outer leaflet to maintain membrane lipid bilayer composition and structure. Even though phospholipid flippases have been proposed to exist in bacteria, only one such protein, MprF, has been described. MprF is a large integral membrane protein found in several prokaryotic phyla, whose C terminus modifies phosphatidylglycerol (PG), the most common bacterial phospholipid, with lysine or alanine to modulate the membrane surface charge and, as a consequence, confer resistance to cationic antimicrobial agents such as daptomycin. In addition, MprF is a flippase for the resulting lipids, Lys-PG or Ala-PG. Here we demonstrate that the flippase activity resides in the N-terminal 6 to 8 transmembrane segments of the Staphylococcus aureus MprF and that several conserved, charged amino acids and a proline residue are crucial for flippase function. MprF protects S. aureus against the membrane-active antibiotic daptomycin only when both domains are present, but the two parts do not need to be covalently linked and can function in trans. The Lys-PG synthase and flippase domains were each found to homo-oligomerize and also to interact with each other, which illustrates how the two functional domains may act together. Moreover, full-length MprF proteins formed oligomers, indicating that MprF functions as a dimer or larger oligomer. Together our data reveal how bacterial phospholipid flippases may function in the context of lipid biosynthetic processes. IMPORTANCE Bacterial cytoplasmic membranes are crucial for maintaining and protecting cellular integrity. For instance, they have to cope with membrane-damaging agents such as cationic antimicrobial peptides (CAMPs) produced by competing bacteria (bacteriocins), secreted by eukaryotic host cells (defensins), or used as antimicrobial therapy (daptomycin). The MprF protein is found in many Gram-positive, Gram-negative, and even archaeal commensals or pathogens and confers resistance to CAMPs by modifying anionic phospholipids with amino acids, thereby compromising the membrane interaction of CAMPs. Here we describe how MprF does not only modify phospholipids but uses an additional, distinct domain for translocating the resulting lysinylated phospholipids to the outer leaflet of the membrane. We reveal critical details for the structure and function of MprF, the first dedicated prokaryotic phospholipid flippase, which may pave the way for targeting MprF with new antimicrobials that would not kill bacteria but sensitize them to antibiotics and innate host defense molecules.
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