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Zhang YL, Peng B, Li H, Yan F, Wu HK, Zhao XL, Lin XM, Min SY, Gao YY, Wang SY, Li YY, Peng XX. C-Terminal Domain of Hemocyanin, a Major Antimicrobial Protein from Litopenaeus vannamei: Structural Homology with Immunoglobulins and Molecular Diversity. Front Immunol 2017; 8:611. [PMID: 28659912 PMCID: PMC5468459 DOI: 10.3389/fimmu.2017.00611] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2017] [Indexed: 11/24/2022] Open
Abstract
Invertebrates rely heavily on immune-like molecules with highly diversified variability so as to counteract infections. However, the mechanisms and the relationship between this variability and functionalities are not well understood. Here, we showed that the C-terminal domain of hemocyanin (HMC) from shrimp Litopenaeus vannamei contained an evolutionary conserved domain with highly variable genetic sequence, which is structurally homologous to immunoglobulin (Ig). This domain is responsible for recognizing and binding to bacteria or red blood cells, initiating agglutination and hemolysis. Furthermore, when HMC is separated into three fractions using anti-human IgM, IgG, or IgA, the subpopulation, which reacted with anti-human IgM (HMC-M), showed the most significant antimicrobial activity. The high potency of HMC-M is a consequence of glycosylation, as it contains high abundance of α-d-mannose relative to α-d-glucose and N-acetyl-d-galactosamine. Thus, the removal of these glycans abolished the antimicrobial activity of HMC-M. Our results present a comprehensive investigation of the role of HMC in fighting against infections through genetic variability and epigenetic modification.
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Affiliation(s)
- Yue-Ling Zhang
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, School of Sciences, Shantou University, Shantou, China
| | - Bo Peng
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, China
| | - Hui Li
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, China
| | - Fang Yan
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, School of Sciences, Shantou University, Shantou, China
| | - Hong-Kai Wu
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, China
| | - Xian-Liang Zhao
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, School of Sciences, Shantou University, Shantou, China
| | - Xiang-Min Lin
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, China
| | - Shao-Ying Min
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, School of Sciences, Shantou University, Shantou, China
| | - Yuan-Yuan Gao
- School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - San-Ying Wang
- School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yuan-You Li
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, School of Sciences, Shantou University, Shantou, China
| | - Xuan-Xian Peng
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, China
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52
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Can't you hear me knocking: contact-dependent competition and cooperation in bacteria. Emerg Top Life Sci 2017; 1:75-83. [PMID: 29085916 DOI: 10.1042/etls20160019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Microorganisms are in constant competition for growth niches and environmental resources. In Gram-negative bacteria, contact-dependent growth inhibition (CDI) systems link the fate of one cell with its immediate neighbor through touch-dependent, receptor-mediated toxin delivery. Though discovered for their ability to confer a competitive growth advantage, CDI systems also play significant roles in inter-sibling cooperation, promoting both auto-aggregation and biofilm formation. In this review, we detail the mechanisms of CDI toxin delivery and consider how toxin exchange between isogenic sibling cells could regulate gene expression.
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53
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Mass spectrometric identification of intermediates in the O 2-driven [4Fe-4S] to [2Fe-2S] cluster conversion in FNR. Proc Natl Acad Sci U S A 2017; 114:E3215-E3223. [PMID: 28373574 DOI: 10.1073/pnas.1620987114] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The iron-sulfur cluster containing protein Fumarate and Nitrate Reduction (FNR) is the master regulator for the switch between anaerobic and aerobic respiration in Escherichia coli and many other bacteria. The [4Fe-4S] cluster functions as the sensory module, undergoing reaction with O2 that leads to conversion to a [2Fe-2S] form with loss of high-affinity DNA binding. Here, we report studies of the FNR cluster conversion reaction using time-resolved electrospray ionization mass spectrometry. The data provide insight into the reaction, permitting the detection of cluster conversion intermediates and products, including a [3Fe-3S] cluster and persulfide-coordinated [2Fe-2S] clusters [[2Fe-2S](S) n , where n = 1 or 2]. Analysis of kinetic data revealed a branched mechanism in which cluster sulfide oxidation occurs in parallel with cluster conversion and not as a subsequent, secondary reaction to generate [2Fe-2S](S) n species. This methodology shows great potential for broad application to studies of protein cofactor-small molecule interactions.
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54
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Liu Y, Cong X, Liu W, Laganowsky A. Characterization of Membrane Protein-Lipid Interactions by Mass Spectrometry Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:579-586. [PMID: 27924494 DOI: 10.1007/s13361-016-1555-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/06/2016] [Accepted: 11/03/2016] [Indexed: 05/21/2023]
Abstract
Lipids in the biological membrane can modulate the structure and function of integral and peripheral membrane proteins. Distinguishing individual lipids that bind selectively to membrane protein complexes from an ensemble of lipid-bound species remains a daunting task. Recently, ion mobility mass spectrometry (IM-MS) has proven to be invaluable for interrogating the interactions between protein and individual lipids, where the complex undergoes collision induced unfolding followed by quantification of the unfolding pathway to assess the effect of these interactions. However, gas-phase unfolding experiments for membrane proteins are typically performed on the entire ensemble (apo and lipid bound species), raising uncertainty to the contribution of individual lipids and the species that are ejected in the unfolding process. Here, we describe the application of mass spectrometry ion mobility mass spectrometry (MS-IM-MS) for isolating ions corresponding to lipid-bound states of a model integral membrane protein, ammonia channel (AmtB) from Escherichia coli. Free of ensemble effects, MS-IM-MS reveals that bound lipids are ejected as neutral species; however, no correlation was found between the lipid-induced stabilization of complex and their equilibrium binding constants. In comparison to data obtained by IM-MS, there are surprisingly limited differences in stability measurements from IM-MS and MS-IM-MS. The approach described here to isolate ions of membrane protein complexes will be useful for other MS methods, such as surface induced dissociation or collision induced dissociation to determine the stoichiometry of hetero-oligomeric membrane protein complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Yang Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Xiao Cong
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Wen Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Arthur Laganowsky
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX, 77807, USA.
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55
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Ionescu SA, Lee S, Housden NG, Kaminska R, Kleanthous C, Bayley H. Orientation of the OmpF Porin in Planar Lipid Bilayers. Chembiochem 2017; 18:554-562. [PMID: 28094462 DOI: 10.1002/cbic.201600644] [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] [Received: 11/28/2016] [Indexed: 12/27/2022]
Abstract
The outer-membrane protein OmpF is an abundant trimeric general diffusion porin that plays a central role in the transport of antibiotics and colicins across the outer membrane of E. coli. Individual OmpF trimers in planar lipid bilayers (PLBs) show one of two current-voltage asymmetries, thus implying that insertion occurs with either the periplasmic or the extracellular end first. A method for establishing the orientation of OmpF in PLB was developed, based on targeted covalent modification with membrane-impermeant reagents of peripheral cysteine residues introduced near the periplasmic or the extracellular entrance. By correlating the results of the modification experiments with measurements of current asymmetry or the sidedness of binding of the antibiotic enrofloxacin, OmpF orientation could be quickly determined in subsequent experiments under a variety of conditions. Our work will allow the precise interpretation of past and future studies of antibiotic permeation and protein translocation through OmpF and related porins.
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Affiliation(s)
- Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Sejeong Lee
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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The Colicin E1 TolC Box: Identification of a Domain Required for Colicin E1 Cytotoxicity and TolC Binding. J Bacteriol 2016; 199:JB.00412-16. [PMID: 27795317 DOI: 10.1128/jb.00412-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/17/2016] [Indexed: 11/20/2022] Open
Abstract
Colicins are protein toxins made by Escherichia coli to kill related bacteria that compete for scarce resources. All colicins must cross the target cell outer membrane in order to reach their intracellular targets. Normally, the first step in the intoxication process is the tight binding of the colicin to an outer membrane receptor protein via its central receptor-binding domain. It is shown here that for one colicin, E1, that step, although it greatly increases the efficiency of killing, is not absolutely necessary. For colicin E1, the second step, translocation, relies on the outer membrane/transperiplasmic protein TolC. The normal role of TolC in bacteria is as an essential component of a family of tripartite drug and toxin exporters, but for colicin E1, it is essential for its import. Colicin E1 and some N-terminal translocation domain peptides had been shown previously to bind in vitro to TolC and occlude channels made by TolC in planar lipid bilayer membranes. Here, a set of increasingly shorter colicin E1 translocation domain peptides was shown to bind to Escherichia coli in vivo and protect them from subsequent challenge by colicin E1. A segment of only 21 residues, the "TolC box," was thereby defined; that segment is essential for colicin E1 cytotoxicity and for binding of translocation domain peptides to TolC. IMPORTANCE The Escherichia coli outer membrane/transperiplasmic protein TolC is normally an essential component of the bacterium's tripartite drug and toxin export machinery. The protein toxin colicin E1 instead uses TolC for its import into the cells that it kills, thereby subverting its normal role. Increasingly shorter constructs of the colicin's N-terminal translocation domain were used to define an essential 21-residue segment that is required for both colicin cytotoxicity and for binding of the colicin's translocation domain to bacteria, in order to protect them from subsequent challenge by active colicin E1. Thus, an essential TolC binding sequence of colicin E1 was identified and may ultimately lead to the development of drugs to block the bacterial drug export pathway.
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57
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CdiA Effectors from Uropathogenic Escherichia coli Use Heterotrimeric Osmoporins as Receptors to Recognize Target Bacteria. PLoS Pathog 2016; 12:e1005925. [PMID: 27723824 PMCID: PMC5056734 DOI: 10.1371/journal.ppat.1005925] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/10/2016] [Indexed: 12/28/2022] Open
Abstract
Many Gram-negative bacterial pathogens express contact-dependent growth inhibition (CDI) systems that promote cell-cell interaction. CDI+ bacteria express surface CdiA effector proteins, which transfer their C-terminal toxin domains into susceptible target cells upon binding to specific receptors. CDI+ cells also produce immunity proteins that neutralize the toxin domains delivered from neighboring siblings. Here, we show that CdiAEC536 from uropathogenic Escherichia coli 536 (EC536) uses OmpC and OmpF as receptors to recognize target bacteria. E. coli mutants lacking either ompF or ompC are resistant to CDIEC536-mediated growth inhibition, and both porins are required for target-cell adhesion to inhibitors that express CdiAEC536. Experiments with single-chain OmpF fusions indicate that the CdiAEC536 receptor is heterotrimeric OmpC-OmpF. Because the OmpC and OmpF porins are under selective pressure from bacteriophages and host immune systems, their surface-exposed loops vary between E. coli isolates. OmpC polymorphism has a significant impact on CDIEC536 mediated competition, with many E. coli isolates expressing alleles that are not recognized by CdiAEC536. Analyses of recombinant OmpC chimeras suggest that extracellular loops L4 and L5 are important recognition epitopes for CdiAEC536. Loops L4 and L5 also account for much of the sequence variability between E. coli OmpC proteins, raising the possibility that CDI contributes to the selective pressure driving OmpC diversification. We find that the most efficient CdiAEC536 receptors are encoded by isolates that carry the same cdi gene cluster as E. coli 536. Thus, it appears that CdiA effectors often bind preferentially to "self" receptors, thereby promoting interactions between sibling cells. As a consequence, these effector proteins cannot recognize nor suppress the growth of many potential competitors. These findings suggest that self-recognition and kin selection are important functions of CDI. Bacterial pathogens often live in crowded communities where cells reside in close contact with one another. Many of these bacteria possess contact-dependent growth inhibition (CDI) systems, which allow cells to touch and inhibit each other using toxic CdiA proteins. CDI+ bacteria also produce immunity proteins that specifically protect the cell from the CdiA toxins of neighboring sibling cells. The CDI system from Escherichia coli EC93 was the first to be characterized and its CdiA toxin recognizes a receptor (BamA) that is identical in virtually all E. coli isolates. Here, we describe a different CDI system from uropathogenic E. coli 536, which causes urinary tract infections. In contrast to E. coli EC93, CdiA from E. coli 536 binds to receptor proteins (OmpC/OmpF) that vary widely between different E. coli isolates. Thus, uropathogenic E. coli preferentially bind and deliver toxins into sibling cells and other closely related E. coli strains. These results suggest that CDI systems distinguish between "self" and "non-self" cells. Moreover, because sibling cells are immune to CdiA-mediated growth inhibition, these findings raise the possibility that toxin exchange may be used for communication and cooperative behavior between genetically identical bacteria.
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58
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Donnarumma D, Faleri A, Costantino P, Rappuoli R, Norais N. The role of structural proteomics in vaccine development: recent advances and future prospects. Expert Rev Proteomics 2016; 13:55-68. [PMID: 26714563 DOI: 10.1586/14789450.2016.1121113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Vaccines are the most effective way to fight infectious diseases saving countless lives since their introduction. Their evolution during the last century made use of the best technologies available to continuously increase their efficacy and safety. Mass spectrometry (MS) and proteomics are already playing a central role in the identification and characterization of novel antigens. Over the last years, we have been witnessing the emergence of structural proteomics in vaccinology, as a major tool for vaccine candidate discovery, antigen design and life cycle management of existing products. In this review, we describe the MS techniques associated to structural proteomics and we illustrate the contribution of structural proteomics to vaccinology discussing potential applications.
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59
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Zakharov SD, Wang XS, Cramer WA. The Colicin E1 TolC-Binding Conformer: Pillar or Pore Function of TolC in Colicin Import? Biochemistry 2016; 55:5084-94. [PMID: 27536862 DOI: 10.1021/acs.biochem.6b00621] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The mechanism by which the drug export protein TolC is utilized for import of the cytotoxin colicin E1 across the outer membrane and periplasmic space is addressed. Studies of the initial binding of colicin E1 with TolC, occlusion of membrane-incorporated TolC ion channels, and the structure underlying the colicin-TolC complex were based on the interactions with TolC of individual colicin translocation domain (T-domain) peptides from a set of 19 that span different segments of the T-domain. These studies led to identification of a short 20-residue segment 101-120, a "TolC box", located near the center of the colicin T-domain, which is necessary for binding of colicin to TolC. Omission of this segment eliminated the ability of the T-domain to occlude TolC channels and to co-elute with TolC on a size-exclusion column. Far-ultraviolet circular dichroism spectral and thermal stability analysis of the structure of T-domain peptides implies (i) a helical hairpin conformation of the T-domain, (ii) the overlap of the TolC-binding site with a hinge of the helical hairpin, and (iii) a TolC-dependent stage of colicin import in which a central segment of the T-domain in a helical hairpin conformation binds to the TolC entry port following initial binding to the BtuB receptor. These studies provide the first structure-based information about the interaction of colicin E1 with the unique TolC protein. The model inferred for binding of the T-domain to TolC implies reservations about the traditional model for colicin import in which TolC functions to provide a channel for translocation of the colicin in an unfolded state across the bacterial outer membrane and a large part of the periplasmic space.
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Affiliation(s)
- Stanislav D Zakharov
- Department of Biological Sciences, Purdue University , Hockmeyer Building of Structural Biology, West Lafayette, Indiana 47907, United States
| | - Xin S Wang
- Department of Biological Sciences, Purdue University , Hockmeyer Building of Structural Biology, West Lafayette, Indiana 47907, United States
| | - William A Cramer
- Department of Biological Sciences, Purdue University , Hockmeyer Building of Structural Biology, West Lafayette, Indiana 47907, United States
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60
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Probing the dynamic regulation of peripheral membrane proteins using hydrogen deuterium exchange-MS (HDX-MS). Biochem Soc Trans 2016; 43:773-86. [PMID: 26517882 DOI: 10.1042/bst20150065] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many cellular signalling events are controlled by the selective recruitment of protein complexes to membranes. Determining the molecular basis for how lipid signalling complexes are recruited, assembled and regulated on specific membrane compartments has remained challenging due to the difficulty of working in conditions mimicking native biological membrane environments. Enzyme recruitment to membranes is controlled by a variety of regulatory mechanisms, including binding to specific lipid species, protein-protein interactions, membrane curvature, as well as post-translational modifications. A powerful tool to study the regulation of membrane signalling enzymes and complexes is hydrogen deuterium exchange-MS (HDX-MS), a technique that allows for the interrogation of protein dynamics upon membrane binding and recruitment. This review will highlight the theory and development of HDX-MS and its application to examine the molecular basis of lipid signalling enzymes, specifically the regulation and activation of phosphoinositide 3-kinases (PI3Ks).
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61
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De Geyter J, Tsirigotaki A, Orfanoudaki G, Zorzini V, Economou A, Karamanou S. Protein folding in the cell envelope of Escherichia coli. Nat Microbiol 2016; 1:16107. [PMID: 27573113 DOI: 10.1038/nmicrobiol.2016.107] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022]
Abstract
While the entire proteome is synthesized on cytoplasmic ribosomes, almost half associates with, localizes in or crosses the bacterial cell envelope. In Escherichia coli a variety of mechanisms are important for taking these polypeptides into or across the plasma membrane, maintaining them in soluble form, trafficking them to their correct cell envelope locations and then folding them into the right structures. The fidelity of these processes must be maintained under various environmental conditions including during stress; if this fails, proteases are called in to degrade mislocalized or aggregated proteins. Various soluble, diffusible chaperones (acting as holdases, foldases or pilotins) and folding catalysts are also utilized to restore proteostasis. These responses can be general, dealing with multiple polypeptides, with functional overlaps and operating within redundant networks. Other chaperones are specialized factors, dealing only with a few exported proteins. Several complex machineries have evolved to deal with binding to, integration in and crossing of the outer membrane. This complex protein network is responsible for fundamental cellular processes such as cell wall biogenesis; cell division; the export, uptake and degradation of molecules; and resistance against exogenous toxic factors. The underlying processes, contributing to our fundamental understanding of proteostasis, are a treasure trove for the development of novel antibiotics, biopharmaceuticals and vaccines.
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Affiliation(s)
- Jozefien De Geyter
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Alexandra Tsirigotaki
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Valentina Zorzini
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium.,Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Spyridoula Karamanou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
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62
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McCaughey LC, Ritchie ND, Douce GR, Evans TJ, Walker D. Efficacy of species-specific protein antibiotics in a murine model of acute Pseudomonas aeruginosa lung infection. Sci Rep 2016; 6:30201. [PMID: 27444885 PMCID: PMC4957109 DOI: 10.1038/srep30201] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 06/30/2016] [Indexed: 01/03/2023] Open
Abstract
Protein antibiotics, known as bacteriocins, are widely produced by bacteria for intraspecies competition. The potency and targeted action of bacteriocins suggests that they could be developed into clinically useful antibiotics against highly drug resistant Gram-negative pathogens for which there are few therapeutic options. Here we show that Pseudomonas aeruginosa specific bacteriocins, known as pyocins, show strong efficacy in a murine model of P. aeruginosa lung infection, with the concentration of pyocin S5 required to afford protection from a lethal infection at least 100-fold lower than the most commonly used inhaled antibiotic tobramycin. Additionally, pyocins are stable in the lung, poorly immunogenic at high concentrations and efficacy is maintained in the presence of pyocin specific antibodies after repeated pyocin administration. Bacteriocin encoding genes are frequently found in microbial genomes and could therefore offer a ready supply of highly targeted and potent antibiotics active against problematic Gram-negative pathogens.
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Affiliation(s)
- Laura C McCaughey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.,The ithree institute, University of Technology Sydney, Ultimo, New South Wales, Australia.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Neil D Ritchie
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Gillian R Douce
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Thomas J Evans
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
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63
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Structural and biophysical analysis of nuclease protein antibiotics. Biochem J 2016; 473:2799-812. [PMID: 27402794 PMCID: PMC5264503 DOI: 10.1042/bcj20160544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/07/2016] [Indexed: 01/28/2023]
Abstract
Protein antibiotics (bacteriocins) are a large and diverse family of multidomain toxins that kill specific Gram-negative bacteria during intraspecies competition for resources. Our understanding of the mechanism of import of such potent toxins has increased significantly in recent years, especially with the reporting of several structures of bacteriocin domains. Less well understood is the structural biochemistry of intact bacteriocins and how these compare across bacterial species. Here, we focus on endonuclease (DNase) bacteriocins that target the genomes of Escherichia coli and Pseudomonas aeruginosa, known as E-type colicins and S-type pyocins, respectively, bound to their specific immunity (Im) proteins. First, we report the 3.2 Å structure of the DNase colicin ColE9 in complex with its ultra-high affinity Im protein, Im9. In contrast with Im3, which when bound to the ribonuclease domain of the homologous colicin ColE3 makes contact with the translocation (T) domain of the toxin, we find that Im9 makes no such contact and only interactions with the ColE9 cytotoxic domain are observed. Second, we report small-angle X-ray scattering data for two S-type DNase pyocins, S2 and AP41, into which are fitted recently determined X-ray structures for isolated domains. We find that DNase pyocins and colicins are both highly elongated molecules, even though the order of their constituent domains differs. We discuss the implications of these architectural similarities and differences in the context of the translocation mechanism of protein antibiotics through the cell envelope of Gram-negative bacteria.
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64
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Horne JE, Radford SE. A growing toolbox of techniques for studying β-barrel outer membrane protein folding and biogenesis. Biochem Soc Trans 2016; 44:802-9. [PMID: 27284045 PMCID: PMC4900752 DOI: 10.1042/bst20160020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/21/2023]
Abstract
Great strides into understanding protein folding have been made since the seminal work of Anfinsen over 40 years ago, but progress in the study of membrane protein folding has lagged behind that of their water soluble counterparts. Researchers in these fields continue to turn to more advanced techniques such as NMR, mass spectrometry, molecular dynamics (MD) and single molecule methods to interrogate how proteins fold. Our understanding of β-barrel outer membrane protein (OMP) folding has benefited from these advances in the last decade. This class of proteins must traverse the periplasm and then insert into an asymmetric lipid membrane in the absence of a chemical energy source. In this review we discuss old, new and emerging techniques used to examine the process of OMP folding and biogenesis in vitro and describe some of the insights and new questions these techniques have revealed.
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Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, The University of Leeds, Leeds LS2 9JT, U.K
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, The University of Leeds, Leeds LS2 9JT, U.K.
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65
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Discovery, characterization and in vivo activity of pyocin SD2, a protein antibiotic from Pseudomonas aeruginosa. Biochem J 2016; 473:2345-58. [PMID: 27252387 PMCID: PMC4964976 DOI: 10.1042/bcj20160470] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/01/2016] [Indexed: 11/17/2022]
Abstract
Increasing rates of antibiotic resistance among Gram-negative pathogens such as Pseudomonas aeruginosa means alternative approaches to antibiotic development are urgently required. Pyocins, produced by P. aeruginosa for intraspecies competition, are highly potent protein antibiotics known to actively translocate across the outer membrane of P. aeruginosa. Understanding and exploiting the mechanisms by which pyocins target, penetrate and kill P. aeruginosa is a promising approach to antibiotic development. In this work we show the therapeutic potential of a newly identified tRNase pyocin, pyocin SD2, by demonstrating its activity in vivo in a murine model of P. aeruginosa lung infection. In addition, we propose a mechanism of cell targeting and translocation for pyocin SD2 across the P. aeruginosa outer membrane. Pyocin SD2 is concentrated at the cell surface, via binding to the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide (LPS), from where it can efficiently locate its outer membrane receptor FpvAI. This strategy of utilizing both the CPA and a protein receptor for cell targeting is common among pyocins as we show that pyocins S2, S5 and SD3 also bind to the CPA. Additional data indicate a key role for an unstructured N-terminal region of pyocin SD2 in the subsequent translocation of the pyocin into the cell. These results greatly improve our understanding of how pyocins target and translocate across the outer membrane of P. aeruginosa. This knowledge could be useful for the development of novel anti-pseudomonal therapeutics and will also support the development of pyocin SD2 as a therapeutic in its own right.
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66
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Gault J, Donlan JAC, Liko I, Hopper JTS, Gupta K, Housden NG, Struwe WB, Marty MT, Mize T, Bechara C, Zhu Y, Wu B, Kleanthous C, Belov M, Damoc E, Makarov A, Robinson CV. High-resolution mass spectrometry of small molecules bound to membrane proteins. Nat Methods 2016; 13:333-6. [PMID: 26901650 PMCID: PMC4856209 DOI: 10.1038/nmeth.3771] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/13/2016] [Indexed: 12/24/2022]
Abstract
Small molecules are known to stabilize membrane proteins and to modulate their function and oligomeric state, but such interactions are often hard to precisely define. Here we develop and apply a high-resolution, Orbitrap mass spectrometry-based method for analyzing intact membrane protein-ligand complexes. Using this platform, we resolve the complexity of multiple binding events, quantify small molecule binding and reveal selectivity for endogenous lipids that differ only in acyl chain length.
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Affiliation(s)
- Joseph Gault
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Joseph A C Donlan
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Idlir Liko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Jonathan T S Hopper
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Kallol Gupta
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | | | - Weston B Struwe
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Michael T Marty
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Todd Mize
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Cherine Bechara
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Ya Zhu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, China
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, China
| | | | | | | | | | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
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67
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Burger VM, Nolasco DO, Stultz CM. Expanding the Range of Protein Function at the Far End of the Order-Structure Continuum. J Biol Chem 2016; 291:6706-13. [PMID: 26851282 PMCID: PMC4807258 DOI: 10.1074/jbc.r115.692590] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The traditional view of the structure-function paradigm is that a protein's function is inextricably linked to a well defined, three-dimensional structure, which is determined by the protein's primary amino acid sequence. However, it is now accepted that a number of proteins do not adopt a unique tertiary structure in solution and that some degree of disorder is required for many proteins to perform their prescribed functions. In this review, we highlight how a number of protein functions are facilitated by intrinsic disorder and introduce a new protein structure taxonomy that is based on quantifiable metrics of a protein's disorder.
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Affiliation(s)
- Virginia M Burger
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and
| | - Diego O Nolasco
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and
| | - Collin M Stultz
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and the Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138
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68
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Choi H, Chakraborty S, Liu R, Gellman SH, Weisshaar JC. Single-Cell, Time-Resolved Antimicrobial Effects of a Highly Cationic, Random Nylon-3 Copolymer on Live Escherichia coli. ACS Chem Biol 2016; 11:113-20. [PMID: 26493221 DOI: 10.1021/acschembio.5b00547] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Synthetic random copolymers based on the nylon-3 (β-peptide) backbone show promise as inexpensive antimicrobial agents resistant to proteolysis. We present a time-resolved observational study of the attack of a particular copolymer MM63:CHx37 on single, live Escherichia coli cells. The composition and chain length of MM63:CHx37 (63% cationic subunits, 37% hydrophobic subunits, 35-subunit average length) were optimized to enhance antibacterial activity while minimizing lysis of human red blood cells. For E. coli cells that export GFP to the periplasm, we obtain alternating phase-contrast and green fluorescence images with a time resolution of 12 s over 60 min following initiation of copolymer flow. Within seconds, cells shrink and exhibit the same plasmolysis spaces that occur following abrupt external osmotic upshift. The osmoprotection machinery attempts to replenish cytoplasmic water, but recovery is interrupted by permeabilization of the cytoplasmic membrane (CM) to GFP. Evidently, the highly cationic copolymer and its counterions rapidly translocate across the outer membrane without permeabilizing it to GFP. The CM permeabilization event is spatially localized. Cells whose CM has been permeabilized never recover growth. The minimum inhibitory concentration (MIC) for cells lacking the osmolyte importer ProP is 4-fold smaller than for normal cells, suggesting that osmoprotection is an important survival strategy. In addition, at the time of CM permeabilization, we observe evidence of oxidative stress. The MIC under anaerobic conditions is at least 8-fold larger than under aerobic conditions, further implicating oxidative damage as an important bacteriostatic effect. Once the copolymer reaches the periplasm, multiple growth-halting mechanisms proceed in parallel.
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Affiliation(s)
- Heejun Choi
- Department of Chemistry and ‡Molecular Biophysics
Program, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Saswata Chakraborty
- Department of Chemistry and ‡Molecular Biophysics
Program, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Runhui Liu
- Department of Chemistry and ‡Molecular Biophysics
Program, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry and ‡Molecular Biophysics
Program, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - James C. Weisshaar
- Department of Chemistry and ‡Molecular Biophysics
Program, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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69
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Kay KL, Hamilton CJ, Le Brun NE. Mass spectrometry of B. subtilis CopZ: Cu(i)-binding and interactions with bacillithiol. Metallomics 2016; 8:709-19. [DOI: 10.1039/c6mt00036c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mass spectrometry reveals a high resolution overview of species formed by CopZ and Cu(i), and the effects of the physiological low molecular weight thiol bacillithiol.
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Affiliation(s)
- Kristine L. Kay
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich, UK
| | | | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich, UK
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70
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Marcoux J, Cianférani S. Towards integrative structural mass spectrometry: Benefits from hybrid approaches. Methods 2015; 89:4-12. [DOI: 10.1016/j.ymeth.2015.05.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/06/2015] [Accepted: 05/25/2015] [Indexed: 01/10/2023] Open
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71
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Chong ZS, Woo WF, Chng SS. Osmoporin OmpC forms a complex with MlaA to maintain outer membrane lipid asymmetry in Escherichia coli. Mol Microbiol 2015; 98:1133-46. [PMID: 26314242 DOI: 10.1111/mmi.13202] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2015] [Indexed: 12/21/2022]
Abstract
Gram-negative bacteria can survive in harsh environments in part because the asymmetric outer membrane (OM) hinders the entry of toxic compounds. Lipid asymmetry is established by having phospholipids (PLs) confined to the inner leaflet of the membrane and lipopolysaccharides (LPS) to the outer leaflet. Perturbation of OM lipid asymmetry, characterized by PL accumulation in the outer leaflet, disrupts proper LPS packing and increases membrane permeability. The multi-component Mla system prevents PL accumulation in the outer leaflet of the OM via an unknown mechanism. Here, we demonstrate that in Escherichia coli, the Mla system maintains OM lipid asymmetry with the help of osmoporin OmpC. We show that the OM lipoprotein MlaA interacts specifically with OmpC and OmpF. This interaction is sufficient to localize MlaA lacking its lipid anchor to the OM. Removing OmpC, but not OmpF, causes accumulation of PLs in the outer leaflet of the OM in stationary phase, as was previously observed for MlaA. We establish that OmpC is an additional component of the Mla system; the OmpC-MlaA complex may function to remove PLs directly from the outer leaflet to maintain OM lipid asymmetry. Our work reveals a novel function for the general diffusion channel OmpC in lipid transport.
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Affiliation(s)
- Zhi-Soon Chong
- Department of Chemistry, National University of Singapore, Singapore, 117543
| | - Wei-Fen Woo
- Department of Chemistry, National University of Singapore, Singapore, 117543
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore, 117543.,Singapore Center on Environmental Life Sciences Engineering (SCELSE), National University of Singapore, Singapore, 117456
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72
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Rassam P, Copeland NA, Birkholz O, Tóth C, Chavent M, Duncan AL, Cross SJ, Housden NG, Kaminska R, Seger U, Quinn DM, Garrod TJ, Sansom MSP, Piehler J, Baumann CG, Kleanthous C. Supramolecular assemblies underpin turnover of outer membrane proteins in bacteria. Nature 2015; 523:333-6. [PMID: 26061769 PMCID: PMC4905513 DOI: 10.1038/nature14461] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 04/08/2015] [Indexed: 12/24/2022]
Abstract
Gram-negative bacteria inhabit a broad range of ecological niches. For Escherichia coli, this includes river water as well as humans and animals, where it can be both a commensal and a pathogen. Intricate regulatory mechanisms ensure that bacteria have the right complement of β-barrel outer membrane proteins (OMPs) to enable adaptation to a particular habitat. Yet no mechanism is known for replacing OMPs in the outer membrane, an issue that is further confounded by the lack of an energy source and the high stability and abundance of OMPs. Here we uncover the process underpinning OMP turnover in E. coli and show it to be passive and binary in nature, in which old OMPs are displaced to the poles of growing cells as new OMPs take their place. Using fluorescent colicins as OMP-specific probes, in combination with ensemble and single-molecule fluorescence microscopy in vivo and in vitro, as well as molecular dynamics simulations, we established the mechanism for binary OMP partitioning. OMPs clustered to form ∼0.5-μm diameter islands, where their diffusion is restricted by promiscuous interactions with other OMPs. OMP islands were distributed throughout the cell and contained the Bam complex, which catalyses the insertion of OMPs in the outer membrane. However, OMP biogenesis occurred as a gradient that was highest at mid-cell but largely absent at cell poles. The cumulative effect is to push old OMP islands towards the poles of growing cells, leading to a binary distribution when cells divide. Hence, the outer membrane of a Gram-negative bacterium is a spatially and temporally organized structure, and this organization lies at the heart of how OMPs are turned over in the membrane.
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Affiliation(s)
- Patrice Rassam
- 1] Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK [2] Department of Biology, University of York, York YO10 5DD, UK
| | | | - Oliver Birkholz
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Csaba Tóth
- Department of Biology, University of York, York YO10 5DD, UK
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stephen J Cross
- Department of Biology, University of York, York YO10 5DD, UK
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Urban Seger
- Department of Biology, University of York, York YO10 5DD, UK
| | - Diana M Quinn
- Department of Biology, University of York, York YO10 5DD, UK
| | - Tamsin J Garrod
- Department of Biology, University of York, York YO10 5DD, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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73
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Bonome EL, Lepore R, Raimondo D, Cecconi F, Tramontano A, Chinappi M. Multistep Current Signal in Protein Translocation through Graphene Nanopores. J Phys Chem B 2015; 119:5815-23. [DOI: 10.1021/acs.jpcb.5b02172] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emma Letizia Bonome
- Dipartimento
di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Roma, Italy
| | - Rosalba Lepore
- Dipartimento
di Fisica, Sapienza Università di Roma, 00185 Rome, Italy
| | - Domenico Raimondo
- Dipartimento
di Fisica, Sapienza Università di Roma, 00185 Rome, Italy
| | - Fabio Cecconi
- CNR-Istituto dei Sistemi Complessi UoS Sapienza, Via dei Taurini 19, 00185 Roma, Italy
| | - Anna Tramontano
- Dipartimento
di Fisica, Sapienza Università di Roma, 00185 Rome, Italy
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Viale Regina Elena, 291 Rome 00185, Italy
| | - Mauro Chinappi
- Center
for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Via Regina Elena 291, 00161 Roma, Italy
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74
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Papadakos G, Sharma A, Lancaster LE, Bowen R, Kaminska R, Leech AP, Walker D, Redfield C, Kleanthous C. Consequences of Inducing Intrinsic Disorder in a High-Affinity Protein–Protein Interaction. J Am Chem Soc 2015; 137:5252-5. [DOI: 10.1021/ja512607r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Grigorios Papadakos
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Amit Sharma
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna E. Lancaster
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
| | - Rebecca Bowen
- Department of Biology, University of York, Heslington Road, York YO10 5DD, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Andrew P. Leech
- Department of Biology, University of York, Heslington Road, York YO10 5DD, United Kingdom
| | - Daniel Walker
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, University of Glasgow, Glasgow G12 8AT, United Kingdom
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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75
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Bechara C, Robinson CV. Different Modes of Lipid Binding to Membrane Proteins Probed by Mass Spectrometry. J Am Chem Soc 2015; 137:5240-7. [DOI: 10.1021/jacs.5b00420] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Chérine Bechara
- Department of Chemistry,
Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry,
Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
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76
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Relating sequence encoded information to form and function of intrinsically disordered proteins. Curr Opin Struct Biol 2015; 32:102-12. [PMID: 25863585 DOI: 10.1016/j.sbi.2015.03.008] [Citation(s) in RCA: 281] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) showcase the importance of conformational plasticity and heterogeneity in protein function. We summarize recent advances that connect information encoded in IDP sequences to their conformational properties and functions. We focus on insights obtained through a combination of atomistic simulations and biophysical measurements that are synthesized into a coherent framework using polymer physics theories.
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77
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Mehmood S, Allison TM, Robinson CV. Mass Spectrometry of Protein Complexes: From Origins to Applications. Annu Rev Phys Chem 2015; 66:453-74. [DOI: 10.1146/annurev-physchem-040214-121732] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Timothy M. Allison
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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78
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Boeri Erba E, Petosa C. The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes. Protein Sci 2015; 24:1176-92. [PMID: 25676284 DOI: 10.1002/pro.2661] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called "native conditions" (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein-ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes.
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Affiliation(s)
- Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
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79
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Cho SH, Szewczyk J, Pesavento C, Zietek M, Banzhaf M, Roszczenko P, Asmar A, Laloux G, Hov AK, Leverrier P, Van der Henst C, Vertommen D, Typas A, Collet JF. Detecting envelope stress by monitoring β-barrel assembly. Cell 2015; 159:1652-64. [PMID: 25525882 DOI: 10.1016/j.cell.2014.11.045] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/06/2014] [Accepted: 11/24/2014] [Indexed: 01/29/2023]
Abstract
The cell envelope protects bacteria from their surroundings. Defects in its integrity or assembly are sensed by signal transduction systems, allowing cells to rapidly adjust. The Rcs phosphorelay responds to outer membrane (OM)- and peptidoglycan-related stress in enterobacteria. We elucidated how the OM lipoprotein RcsF, the upstream Rcs component, senses envelope stress and activates the signaling cascade. RcsF interacts with BamA, the major component of the β-barrel assembly machinery. In growing cells, BamA continuously funnels RcsF through the β-barrel OmpA, displaying RcsF on the cell surface. This process spatially separates RcsF from the downstream Rcs component, which we show is the inner membrane protein IgaA. The Rcs system is activated when BamA fails to bind RcsF and funnel it to OmpA. Newly synthesized RcsF then remains periplasmic, interacting with IgaA to activate the cascade. Thus RcsF senses envelope damage by monitoring the activity of the Bam machinery.
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Affiliation(s)
- Seung-Hyun Cho
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Joanna Szewczyk
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Christina Pesavento
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Matylda Zietek
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Manuel Banzhaf
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Paula Roszczenko
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Abir Asmar
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Géraldine Laloux
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Ann-Kristin Hov
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Pauline Leverrier
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Charles Van der Henst
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Didier Vertommen
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Jean-François Collet
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium.
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80
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Calabrese AN, Watkinson TG, Henderson PJF, Radford SE, Ashcroft AE. Amphipols outperform dodecylmaltoside micelles in stabilizing membrane protein structure in the gas phase. Anal Chem 2014; 87:1118-26. [PMID: 25495802 PMCID: PMC4636139 DOI: 10.1021/ac5037022] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Noncovalent mass spectrometry (MS) is emerging as an invaluable technique to probe the structure, interactions, and dynamics of membrane proteins (MPs). However, maintaining native-like MP conformations in the gas phase using detergent solubilized proteins is often challenging and may limit structural analysis. Amphipols, such as the well characterized A8-35, are alternative reagents able to maintain the solubility of MPs in detergent-free solution. In this work, the ability of A8-35 to retain the structural integrity of MPs for interrogation by electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is compared systematically with the commonly used detergent dodecylmaltoside. MPs from the two major structural classes were selected for analysis, including two β-barrel outer MPs, PagP and OmpT (20.2 and 33.5 kDa, respectively), and two α-helical proteins, Mhp1 and GalP (54.6 and 51.7 kDa, respectively). Evaluation of the rotationally averaged collision cross sections of the observed ions revealed that the native structures of detergent solubilized MPs were not always retained in the gas phase, with both collapsed and unfolded species being detected. In contrast, ESI-IMS-MS analysis of the amphipol solubilized MPs studied resulted in charge state distributions consistent with less gas phase induced unfolding, and the presence of lowly charged ions which exhibit collision cross sections comparable with those calculated from high resolution structural data. The data demonstrate that A8-35 can be more effective than dodecylmaltoside at maintaining native MP structure and interactions in the gas phase, permitting noncovalent ESI-IMS-MS analysis of MPs from the two major structural classes, while gas phase dissociation from dodecylmaltoside micelles leads to significant gas phase unfolding, especially for the α-helical MPs studied.
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Affiliation(s)
- Antonio N Calabrese
- School of Molecular and Cellular Biology and ‡School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
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81
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Ridley H, Lakey JH. Antibacterial toxin colicin N and phage protein G3p compete with TolB for a binding site on TolA. MICROBIOLOGY-SGM 2014; 161:503-15. [PMID: 25536997 PMCID: PMC4339652 DOI: 10.1099/mic.0.000024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Most colicins kill Escherichia coli cells by membrane pore formation or nuclease activity and, superficially, the mechanisms are similar: receptor binding, translocon recruitment, periplasmic receptor binding and membrane insertion. However, in detail, they employ a wide variety of molecular interactions that reveal a high degree of evolutionary diversification. Group A colicins bind to members of the TolQRAB complex in the periplasm and heterotrimeric complexes of colicin–TolA–TolB have been observed for both ColA and ColE9. ColN, the smallest and simplest pore-forming colicin, binds only to TolA and we show here that it uses the binding site normally used by TolB, effectively preventing formation of the larger complex used by other colicins. ColN binding to TolA was by β-strand addition with a KD of 1 µM compared with 40 µM for the TolA–TolB interaction. The β-strand addition and ColN activity could be abolished by single proline point mutations in TolA, which each removed one backbone hydrogen bond. By also blocking TolA–TolB binding these point mutations conferred a complete tol phenotype which destabilized the outer membrane, prevented both ColA and ColE9 activity, and abolished phage protein binding to TolA. These are the only point mutations known to have such pleiotropic effects and showed that the TolA–TolB β-strand addition is essential for Tol function. The formation of this simple binary ColN–TolA complex provided yet more evidence of a distinct translocation route for ColN and may help to explain the unique toxicity of its N-terminal domain.
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Affiliation(s)
- Helen Ridley
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jeremy H Lakey
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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82
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Konovalova A, Perlman DH, Cowles CE, Silhavy TJ. Transmembrane domain of surface-exposed outer membrane lipoprotein RcsF is threaded through the lumen of β-barrel proteins. Proc Natl Acad Sci U S A 2014; 111:E4350-8. [PMID: 25267629 PMCID: PMC4205638 DOI: 10.1073/pnas.1417138111] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RcsF (regulator of capsule synthesis) is an outer membrane (OM) lipoprotein that functions to sense defects such as changes in LPS. However, LPS is found in the outer leaflet, and RcsF was thought to be tethered to the inner leaflet by its lipidated N terminus, raising the question of how it monitors LPS. We show that RcsF has a transmembrane topology with the lipidated N terminus on the cell surface and the C-terminal signaling domain in the periplasm. Strikingly, the short, unstructured, charged transmembrane domain is threaded through the lumen of β-barrel OM proteins where it is protected from the hydrophobic membrane interior. We present evidence that these unusual complexes, which contain one protein inside another, are formed by the Bam complex that assembles all β-barrel proteins in the OM. The ability of the Bam complex to expose lipoproteins at the cell surface underscores the mechanistic versatility of the β-barrel assembly machine.
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Affiliation(s)
- Anna Konovalova
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544
| | - David H Perlman
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544
| | - Charles E Cowles
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544
| | - Thomas J Silhavy
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544
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83
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Gurnev PA, Yap TL, Pfefferkorn CM, Rostovtseva TK, Berezhkovskii AM, Lee JC, Parsegian VA, Bezrukov SM. Alpha-synuclein lipid-dependent membrane binding and translocation through the α-hemolysin channel. Biophys J 2014; 106:556-65. [PMID: 24507596 DOI: 10.1016/j.bpj.2013.12.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/30/2013] [Accepted: 12/16/2013] [Indexed: 11/19/2022] Open
Abstract
Gauging the interactions of a natively unfolded Parkinson disease-related protein, alpha-synuclein (α-syn) with membranes and its pathways between and within cells is important for understanding its pathogenesis. Here, to address these questions, we use a robust β-barrel channel, α-hemolysin, reconstituted into planar lipid bilayers. Transient, ~95% blockage of the channel current by α-syn was observed when 1), α-syn was added from the membrane side where the shorter (stem) part of the channel is exposed; and 2), the applied potential was lower on the side of α-syn addition. While the on-rate of α-syn binding to the channel strongly increased with the applied field, the off-rate displayed a turnover behavior. Statistical analysis suggests that at voltages >50 mV, a significant fraction of the α-syn molecules bound to the channel undergoes subsequent translocation. The observed on-rate varied by >100 times depending on the bilayer lipid composition. Removal of the last 25 amino acids from the highly negatively charged C-terminal of α-syn resulted in a significant decrease in the binding rates. Taken together, these results demonstrate that β-barrel channels may serve as sensitive probes of α-syn interactions with membranes as well as model systems for studies of channel-assisted protein transport.
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Affiliation(s)
- Philip A Gurnev
- Physics Department, University of Massachusetts, Amherst, Massachusetts; Section on Molecular Transport, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - Thai Leong Yap
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Candace M Pfefferkorn
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Tatiana K Rostovtseva
- Section on Molecular Transport, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Alexander M Berezhkovskii
- Mathematical and Statistical Computing Laboratory, Division for Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland
| | - Jennifer C Lee
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Sergey M Bezrukov
- Section on Molecular Transport, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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84
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Ruhe ZC, Nguyen JY, Beck CM, Low DA, Hayes CS. The proton-motive force is required for translocation of CDI toxins across the inner membrane of target bacteria. Mol Microbiol 2014; 94:466-81. [PMID: 25174572 DOI: 10.1111/mmi.12779] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2014] [Indexed: 01/09/2023]
Abstract
Contact-dependent growth inhibition (CDI) is a mode of bacterial competition orchestrated by the CdiB/CdiA family of two-partner secretion proteins. The CdiA effector extends from the surface of CDI(+) inhibitor cells, binds to receptors on neighbouring bacteria and delivers a toxin domain derived from its C-terminal region (CdiA-CT). Here, we show that CdiA-CT toxin translocation requires the proton-motive force (pmf) within target bacteria. The pmf is also critical for the translocation of colicin toxins, which exploit the energized Ton and Tol systems to cross the outer membrane. However, CdiA-CT translocation is clearly distinct from known colicin-import pathways because ΔtolA ΔtonB target cells are fully sensitive to CDI. Moreover, we provide evidence that CdiA-CT toxins can be transferred into the periplasm of de-energized target bacteria, indicating that transport across the outer membrane is independent of the pmf. Remarkably, CDI toxins transferred under de-energized conditions remain competent to enter the target-cell cytoplasm once the pmf is restored. Collectively, these results indicate that outer- and inner-membrane translocation steps can be uncoupled, and that the pmf is required for CDI toxin transport from the periplasm to the target-cell cytoplasm.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106-9625, USA
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85
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Grinter R, Josts I, Zeth K, Roszak AW, McCaughey LC, Cogdell RJ, Milner JJ, Kelly SM, Byron O, Walker D. Structure of the atypical bacteriocin pectocin M2 implies a novel mechanism of protein uptake. Mol Microbiol 2014; 93:234-46. [PMID: 24865810 PMCID: PMC4671253 DOI: 10.1111/mmi.12655] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2014] [Indexed: 01/08/2023]
Abstract
The colicin-like bacteriocins are potent protein antibiotics that have evolved to efficiently cross the outer membrane of Gram-negative bacteria by parasitizing nutrient uptake systems. We have structurally characterized the colicin M-like bacteriocin, pectocin M2, which is active against strains of Pectobacterium spp. This unusual bacteriocin lacks the intrinsically unstructured translocation domain that usually mediates translocation of these bacteriocins across the outer membrane, containing only a single globular ferredoxin domain connected to its cytotoxic domain by a flexible α-helix, which allows it to adopt two distinct conformations in solution. The ferredoxin domain of pectocin M2 is homologous to plant ferredoxins and allows pectocin M2 to parasitize a system utilized by Pectobacterium to obtain iron during infection of plants. Furthermore, we identify a novel ferredoxin-containing bacteriocin pectocin P, which possesses a cytotoxic domain homologous to lysozyme, illustrating that the ferredoxin domain acts as a generic delivery module for cytotoxic domains in Pectobacterium.
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Affiliation(s)
- Rhys Grinter
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, UK
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86
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Different subunits belonging to the same protein complex often exhibit discordant expression levels and evolutionary properties. Curr Opin Struct Biol 2014; 26:113-20. [DOI: 10.1016/j.sbi.2014.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/27/2014] [Accepted: 06/04/2014] [Indexed: 11/21/2022]
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87
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Futai K. Attenuated colicin-based screening to discover and create novel resistance genes. J Microbiol Methods 2014; 100:128-36. [DOI: 10.1016/j.mimet.2014.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 03/06/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
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88
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Mathavan I, Zirah S, Mehmood S, Choudhury HG, Goulard C, Li Y, Robinson CV, Rebuffat S, Beis K. Structural basis for hijacking siderophore receptors by antimicrobial lasso peptides. Nat Chem Biol 2014; 10:340-2. [PMID: 24705590 PMCID: PMC3992131 DOI: 10.1038/nchembio.1499] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 03/13/2014] [Indexed: 11/09/2022]
Abstract
The lasso peptide microcin J25 is known to hijack the siderophore receptor FhuA for initiating internalization. Here, we provide what is to our knowledge the first structural evidence on the recognition mechanism, and our biochemical data show that another closely related lasso peptide cannot interact with FhuA. Our work provides an explanation on the narrow activity spectrum of lasso peptides and opens the path to the development of new antibacterials.
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Affiliation(s)
- Indran Mathavan
- 1] Department of Life Sciences, Imperial College London, London, UK. [2] Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Oxfordshire, UK. [3] Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, UK
| | - Séverine Zirah
- Communication Molecules and Adaptation of Microorganisms Laboratory, UMR 7245 CNRS-Muséum National d'Histoire Naturelle, Paris, France
| | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Hassanul G Choudhury
- 1] Department of Life Sciences, Imperial College London, London, UK. [2] Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Oxfordshire, UK. [3] Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, UK
| | - Christophe Goulard
- Communication Molecules and Adaptation of Microorganisms Laboratory, UMR 7245 CNRS-Muséum National d'Histoire Naturelle, Paris, France
| | - Yanyan Li
- Communication Molecules and Adaptation of Microorganisms Laboratory, UMR 7245 CNRS-Muséum National d'Histoire Naturelle, Paris, France
| | | | - Sylvie Rebuffat
- Communication Molecules and Adaptation of Microorganisms Laboratory, UMR 7245 CNRS-Muséum National d'Histoire Naturelle, Paris, France
| | - Konstantinos Beis
- 1] Department of Life Sciences, Imperial College London, London, UK. [2] Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Oxfordshire, UK. [3] Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, UK
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89
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Kim YC, Tarr AW, Penfold CN. Colicin import into E. coli cells: a model system for insights into the import mechanisms of bacteriocins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1717-31. [PMID: 24746518 DOI: 10.1016/j.bbamcr.2014.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/04/2014] [Accepted: 04/06/2014] [Indexed: 01/03/2023]
Abstract
Bacteriocins are a diverse group of ribosomally synthesized protein antibiotics produced by most bacteria. They range from small lanthipeptides produced by lactic acid bacteria to much larger multi domain proteins of Gram negative bacteria such as the colicins from Escherichia coli. For activity bacteriocins must be released from the producing cell and then bind to the surface of a sensitive cell to instigate the import process leading to cell death. For over 50years, colicins have provided a working platform for elucidating the structure/function studies of bacteriocin import and modes of action. An understanding of the processes that contribute to the delivery of a colicin molecule across two lipid membranes of the cell envelope has advanced our knowledge of protein-protein interactions (PPI), protein-lipid interactions and the role of order-disorder transitions of protein domains pertinent to protein transport. In this review, we provide an overview of the arrangement of genes that controls the synthesis and release of the mature protein. We examine the uptake processes of colicins from initial binding and sequestration of binding partners to crossing of the outer membrane, and then discuss the translocation of colicins through the cell periplasm and across the inner membrane to their cytotoxic site of action. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Young Chan Kim
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK
| | - Alexander W Tarr
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK
| | - Christopher N Penfold
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK.
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90
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Johnson CL, Ridley H, Marchetti R, Silipo A, Griffin DC, Crawford L, Bonev B, Molinaro A, Lakey JH. The antibacterial toxin colicin N binds to the inner core of lipopolysaccharide and close to its translocator protein. Mol Microbiol 2014; 92:440-52. [PMID: 24589252 PMCID: PMC4114557 DOI: 10.1111/mmi.12568] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2014] [Indexed: 12/03/2022]
Abstract
Colicins are a diverse family of large antibacterial protein toxins, secreted by and active against Escherichia coli and must cross their target cell's outer membrane barrier to kill. To achieve this, most colicins require an abundant porin (e.g. OmpF) plus a low‐copy‐number, high‐affinity, outer membrane protein receptor (e.g. BtuB). Recently, genetic screens have suggested that colicin N (ColN), which has no high‐affinity receptor, targets highly abundant lipopolysaccharide (LPS) instead. Here we reveal the details of this interaction and demonstrate that the ColN receptor‐binding domain (ColN‐R) binds to a specific region of LPS close to the membrane surface. Data from in vitro studies using calorimetry and both liquid‐ and solid‐state NMR reveal the interactions behind the in vivo requirement for a defined oligosaccharide region of LPS. Delipidated LPS (LPSΔLIPID) shows weaker binding; and thus full affinity requires the lipid component. The site of LPS binding means that ColN will preferably bind at the interface and thus position itself close to the surface of its translocon component, OmpF. ColN is, currently, unique among colicins in requiring LPS and, combined with previous data, this implies that the ColN translocon is distinct from those of other known colicins.
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Affiliation(s)
- Christopher L Johnson
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK
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91
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Thalassinos K, Pandurangan AP, Xu M, Alber F, Topf M. Conformational States of macromolecular assemblies explored by integrative structure calculation. Structure 2014; 21:1500-8. [PMID: 24010709 PMCID: PMC3988990 DOI: 10.1016/j.str.2013.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 08/10/2013] [Accepted: 08/12/2013] [Indexed: 12/22/2022]
Abstract
A detailed description of macromolecular assemblies in multiple conformational states can be very valuable for understanding cellular processes. At present, structural determination of most assemblies in different biologically relevant conformations cannot be achieved by a single technique and thus requires an integrative approach that combines information from multiple sources. Different techniques require different computational methods to allow efficient and accurate data processing and analysis. Here, we summarize the latest advances and future challenges in computational methods that help the interpretation of data from two techniques—mass spectrometry and three-dimensional cryo-electron microscopy (with focus on alignment and classification of heterogeneous subtomograms from cryo-electron tomography). We evaluate how new developments in these two broad fields will lead to further integration with atomic structures to broaden our picture of the dynamic behavior of assemblies in their native environment.
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Affiliation(s)
- Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
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92
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Twenty years of gas phase structural biology. Structure 2014; 21:1541-50. [PMID: 24010713 DOI: 10.1016/j.str.2013.08.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 01/01/2023]
Abstract
Over the past two decades, mass spectrometry (MS) of protein complexes from their native state has made inroads into structural biology. To coincide with the 20(th) anniversary of Structure, and given that it is now approximately 20 years since the first mass spectra of noncovalent protein complexes were reported, it is timely to consider progress of MS as a structural biology tool. Early reports focused on soluble complexes, contributing to ligand binding studies, subunit interaction maps, and topological models. Recent discoveries have enabled delivery of membrane complexes, encapsulated in detergent micelles, prompting new opportunities. By maintaining interactions between membrane and cytoplasmic subunits in the gas phase, it is now possible to investigate the effects of lipids, nucleotides, and drugs on intact membrane assemblies. These investigations reveal allosteric and synergistic effects of small molecule binding and expose the consequences of posttranslational modifications. In this review, we consider recent progress in the study of protein complexes, focusing particularly on complexes extracted from membranes, and outline future prospects for gas phase structural biology.
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93
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Jakes KS. Daring to be different: colicin N finds another way. Mol Microbiol 2014; 92:435-9. [PMID: 24589284 DOI: 10.1111/mmi.12569] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2014] [Indexed: 11/28/2022]
Abstract
The mechanisms by which colicins, protein toxins produced by Escherichia coli, kill other E. coli, have become much better understood in recent years. Most colicins initially bind to an outer membrane protein receptor, and then search for a separate nearby outer membrane protein translocator that serves as a pathway into target cells. Many colicins use the outer membrane porin, OmpF, as that translocator, while using a different primary receptor. Colicin N is unique among known colicins in that only OmpF had been identified as being required for uptake of the colicin and it was presumed to somehow serve as both receptor and translocator. Genetic screens also identified a number of genes required for lipopolysaccharide (LPS) synthesis as uniquely required for killing by colicin N, but not by other colicins. Johnson et al. show that the receptor-binding domain of colicin N binds to LPS, and does not require OmpF for that binding. LPS of a minimal length is required for binding, explaining the requirement for specific elements of the LPS biosynthetic pathway. For colicin N, the receptor-binding domain does not recognize a protein, but rather the most abundant component of the outer membrane itself, LPS.
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Affiliation(s)
- Karen S Jakes
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
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94
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Ghale G, Lanctôt AG, Kreissl HT, Jacob MH, Weingart H, Winterhalter M, Nau WM. Chemosensorische Ensembles zur Echtzeitdetektion von Transportprozessen durch Biomembranen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309583] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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95
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Ghale G, Lanctôt AG, Kreissl HT, Jacob MH, Weingart H, Winterhalter M, Nau WM. Chemosensing Ensembles for Monitoring Biomembrane Transport in Real Time. Angew Chem Int Ed Engl 2014; 53:2762-5. [DOI: 10.1002/anie.201309583] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Indexed: 12/27/2022]
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96
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Schmidt C, Robinson CV. Dynamic protein ligand interactions--insights from MS. FEBS J 2014; 281:1950-64. [PMID: 24393119 PMCID: PMC4154455 DOI: 10.1111/febs.12707] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/19/2013] [Accepted: 12/30/2013] [Indexed: 12/31/2022]
Abstract
Proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form catalytic cores, fine‐tuned for different cellular actions. The study of dynamic interactions between proteins and their cognate ligands is therefore fundamental to the understanding of biological systems. During the last two decades MS, and its associated techniques, has become accepted as a method for the study of protein–ligand interactions, not only for covalent complexes, where the use of MS is well established, but also, and significantly for protein–ligand interactions, for noncovalent assemblies. In this review, we employ a broad definition of a ligand to encompass protein subunits, drug molecules, oligonucleotides, carbohydrates, and lipids. Under the appropriate conditions, MS can reveal the composition, heterogeneity and dynamics of these protein–ligand interactions, and in some cases their structural arrangements and binding affinities. Herein, we highlight MS approaches for studying protein–ligand complexes, including those containing integral membrane subunits, and showcase examples from recent literature. Specifically, we tabulate the myriad of methodologies, including hydrogen exchange, proteomics, hydroxyl radical footprinting, intact complexes, and crosslinking, which, when combined with MS, provide insights into conformational changes and subtle modifications in response to ligand‐binding interactions.
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97
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Konermann L, Vahidi S, Sowole MA. Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules. Anal Chem 2013; 86:213-32. [DOI: 10.1021/ac4039306] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Modupeola A. Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
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98
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Vankemmelbeke M, Housden NG, James R, Kleanthous C, Penfold CN. Immunity protein release from a cell-bound nuclease colicin complex requires global conformational rearrangement. Microbiologyopen 2013; 2:853-61. [PMID: 24039240 PMCID: PMC3831645 DOI: 10.1002/mbo3.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 07/12/2013] [Accepted: 07/21/2013] [Indexed: 11/24/2022] Open
Abstract
Nuclease colicins bind their target receptor BtuB in the outer membrane of sensitive Escherichia coli cells in the form of a high-affinity complex with their cognate immunity proteins. The release of the immunity protein from the colicin complex is a prerequisite for cell entry of the colicin and occurs via a process that is still relatively poorly understood. We have previously shown that an energy input in the form of the cytoplasmic membrane proton motive force is required to promote immunity protein (Im9) release from the colicin E9/Im9 complex and colicin cell entry. We report here that engineering rigidity in the structured part of the colicin translocation domain via the introduction of disulfide bonds prevents immunity protein release from the colicin complex. Reduction of the disulfide bond by the addition of DTT leads to immunity protein release and resumption of activity. Similarly, the introduction of a disulfide bond in the DNase domain previously shown to abolish channel formation in planar bilayers also prevented immunity protein release. Importantly, all disulfide bonds, in the translocation as well as the DNase domain, also abolished the biological activity of the Im9-free colicin E9, the reduction of which led to a resumption of activity. Our results show, for the first time, that conformational flexibility in the structured translocation and DNase domains of a nuclease colicin is essential for immunity protein release, providing further evidence for the hypothesis that global structural rearrangement of the colicin molecule is required for disassembly of this high-affinity toxin-immunity protein complex prior to outer membrane translocation.
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Affiliation(s)
- Mireille Vankemmelbeke
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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DeForte S, Reddy KD, Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (April-May-June, 2013). INTRINSICALLY DISORDERED PROTEINS 2013; 1:e27454. [PMID: 28516028 PMCID: PMC5424790 DOI: 10.4161/idp.27454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 01/18/2023]
Abstract
The current literature on intrinsically disordered proteins is overwhelming. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a series of reader's digest type articles objectively representing the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the period of April, May, and June of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA.,USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
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