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Immadisetty K, Polasa A, Shelton R, Moradi M. Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel. Comput Struct Biotechnol J 2022; 20:2539-2550. [PMID: 35685356 PMCID: PMC9156883 DOI: 10.1016/j.csbj.2022.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/11/2022] Open
Abstract
Mechanosensitive channel of large conductance (MscL) detects and responds to changes in the pressure profile of cellular membranes and transduces the mechanical energy into electrical and/or chemical signals. MscL can be activated using ultrasonic or chemical activation methods to improve the absorption of medicines and bioactive compounds into cells. However, re-engineering chemical signals such as pH change can trigger channel activation in MscL. This study elucidates the activation mechanism of an engineered MscL at an atomic level through a combination of equilibrium and non-equilibrium (NE) molecular dynamics (MD) simulations. Comparing the wild-type (WT) and engineered MscL activation processes suggests that the two systems are likely associated with different active states and different transition pathways. These findings indicate that (1) periplasmic loops play a key role in the activation process of MscL, (2) the loss of various backbone-backbone hydrogen bonds and salt bridge interactions in the engineered MscL channel causes the spontaneous opening of the channel, and (3) the most significant interactions lost during the activation process are between the transmembrane helices 1 and 2 in engineered MscL channel. The orientation-based biasing approach for producing and optimizing an open MscL model used in this work is a promising way to characterize unknown protein functional states and investigate the activation processes in ion channels and transmembrane proteins in general. This work paves the way for a computational framework for engineering more efficient pH-sensing mechanosensitive channels.
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Affiliation(s)
- Kalyan Immadisetty
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Reid Shelton
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
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2
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Hegde RS, Keenan RJ. The mechanisms of integral membrane protein biogenesis. Nat Rev Mol Cell Biol 2022; 23:107-124. [PMID: 34556847 DOI: 10.1038/s41580-021-00413-2] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2021] [Indexed: 02/08/2023]
Abstract
Roughly one quarter of all genes code for integral membrane proteins that are inserted into the plasma membrane of prokaryotes or the endoplasmic reticulum membrane of eukaryotes. Multiple pathways are used for the targeting and insertion of membrane proteins on the basis of their topological and biophysical characteristics. Multipass membrane proteins span the membrane multiple times and face the additional challenges of intramembrane folding. In many cases, integral membrane proteins require assembly with other proteins to form multi-subunit membrane protein complexes. Recent biochemical and structural analyses have provided considerable clarity regarding the molecular basis of membrane protein targeting and insertion, with tantalizing new insights into the poorly understood processes of multipass membrane protein biogenesis and multi-subunit protein complex assembly.
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Affiliation(s)
- Ramanujan S Hegde
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Robert J Keenan
- Gordon Center for Integrative Science, The University of Chicago, Chicago, IL, USA.
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3
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Haylock S, Friddin MS, Hindley JW, Rodriguez E, Charalambous K, Booth PJ, Barter LMC, Ces O. Membrane protein mediated bilayer communication in networks of droplet interface bilayers. Commun Chem 2020; 3:77. [PMID: 34113722 PMCID: PMC7610947 DOI: 10.1038/s42004-020-0322-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Droplet interface bilayers (DIBs) are model membranes formed between lipid monolayer-encased water droplets in oil. Compared to conventional methods, one of the most unique properties of DIBs is that they can be connected together to generate multi-layered ‘tissue-like’ networks, however introducing communication pathways between these compartments typically relies on water-soluble pores that are unable to gate. Here, we show that network connectivity can instead be achieved using a water-insoluble membrane protein by successfully reconstituting a chemically activatable mutant of the mechanosensitive channel MscL into a network of DIBs. Moreover, we also show how the small molecule activator can diffuse through an open channel and across the neighbouring droplet to activate MscL present in an adjacent bilayer. This demonstration of membrane protein mediated bilayer communication could prove key toward developing the next generation of responsive bilayer networks capable of defining information flow inside a minimal tissue.
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Affiliation(s)
- Stuart Haylock
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - Mark S Friddin
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - James W Hindley
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,fabriCELL, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - Enrique Rodriguez
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - Kalypso Charalambous
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Laura M C Barter
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
| | - Oscar Ces
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London W12 0BZ, UK.,fabriCELL, Imperial College London, 80 Wood Lane, London W12 0BZ, UK
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4
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Physicochemical considerations for bottom-up synthetic biology. Emerg Top Life Sci 2019; 3:445-458. [PMID: 33523159 PMCID: PMC7289010 DOI: 10.1042/etls20190017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/18/2022]
Abstract
The bottom-up construction of synthetic cells from molecular components is arguably one of the most challenging areas of research in the life sciences. We review the impact of confining biological systems in synthetic vesicles. Complex cell-like systems require control of the internal pH, ionic strength, (macro)molecular crowding, redox state and metabolic energy conservation. These physicochemical parameters influence protein activity and need to be maintained within limits to ensure the system remains in steady-state. We present the physicochemical considerations for building synthetic cells with dimensions ranging from the smallest prokaryotes to eukaryotic cells.
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5
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Miller DM, Findlay HE, Ces O, Templer RH, Booth PJ. Light-activated control of protein channel assembly mediated by membrane mechanics. NANOTECHNOLOGY 2016; 27:494004. [PMID: 27831930 DOI: 10.1088/0957-4484/27/49/494004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photochemical processes provide versatile triggers of chemical reactions. Here, we use a photoactivated lipid switch to modulate the folding and assembly of a protein channel within a model biological membrane. In contrast to the information rich field of water-soluble protein folding, there is only a limited understanding of the assembly of proteins that are integral to biological membranes. It is however possible to exploit the foreboding hydrophobic lipid environment and control membrane protein folding via lipid bilayer mechanics. Mechanical properties such as lipid chain lateral pressure influence the insertion and folding of proteins in membranes, with different stages of folding having contrasting sensitivities to the bilayer properties. Studies to date have relied on altering bilayer properties through lipid compositional changes made at equilibrium, and thus can only be made before or after folding. We show that light-activation of photoisomerisable di-(5-[[4-(4-butylphenyl)azo]phenoxy]pentyl)phosphate (4-Azo-5P) lipids influences the folding and assembly of the pentameric bacterial mechanosensitive channel MscL. The use of a photochemical reaction enables the bilayer properties to be altered during folding, which is unprecedented. This mechanical manipulation during folding, allows for optimisation of different stages of the component insertion, folding and assembly steps within the same lipid system. The photochemical approach offers the potential to control channel assembly when generating synthetic devices that exploit the mechanosensitive protein as a nanovalve.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia. Department of Medical Biology, The University of Melbourne, 3052, Australia
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6
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Chi G, Rohde PR, Ridone P, Hankamer B, Martinac B, Landsberg MJ. Functional similarities between heterogeneously and homogenously expressed MscL constructs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:589-98. [PMID: 26233759 DOI: 10.1007/s00249-015-1062-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 06/29/2015] [Accepted: 07/14/2015] [Indexed: 11/30/2022]
Abstract
The mechanosensitive channel of large conductance MscL is a well-characterized mechanically gated non-selective ion channel, which often serves as a prototype mechanosensitive channel for mechanotransduction studies. However, there are some discrepancies between MscL constructs used in these studies, most notably unintended heterogeneous expression from some MscL expression constructs. In this study we investigate the possible cause of this expression pattern, and compare the original non-homogenously expressing constructs with our new homogeneously expressing one to confirm that there is little functional difference between them. In addition, a new MscL construct has been developed with an improved molar extinction coefficient at 280 nm, enabling more accurate protein quantification.
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Affiliation(s)
- Gamma Chi
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
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7
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Geng Y, Kedrov A, Caumanns JJ, Crevenna AH, Lamb DC, Beckmann R, Driessen AJM. Role of the Cytosolic Loop C2 and the C Terminus of YidC in Ribosome Binding and Insertion Activity. J Biol Chem 2015; 290:17250-61. [PMID: 26023232 DOI: 10.1074/jbc.m115.650309] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/06/2022] Open
Abstract
Members of the YidC/Oxa1/Alb3 protein family mediate membrane protein insertion, and this process is initiated by the assembly of YidC·ribosome nascent chain complexes at the inner leaflet of the lipid bilayer. The positively charged C terminus of Escherichia coli YidC plays a significant role in ribosome binding but is not the sole determinant because deletion does not completely abrogate ribosome binding. The positively charged cytosolic loops C1 and C2 of YidC may provide additional docking sites. We performed systematic sequential deletions within these cytosolic domains and studied their effect on the YidC insertase activity and interaction with translation-stalled (programmed) ribosome. Deletions within loop C1 strongly affected the activity of YidC in vivo but did not influence ribosome binding or substrate insertion, whereas loop C2 appeared to be involved in ribosome binding. Combining the latter deletion with the removal of the C terminus of YidC abolished YidC-mediated insertion. We propose that these two regions play an crucial role in the formation and stabilization of an active YidC·ribosome nascent chain complex, allowing for co-translational membrane insertion, whereas loop C1 may be involved in the downstream chaperone activity of YidC or in other protein-protein interactions.
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Affiliation(s)
- Yanping Geng
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | - Joseph J Caumanns
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Alvaro H Crevenna
- the Physical Chemistry, Department for Chemistry, Center for Nanoscience, the NanoSystems Initiative Munich and the Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Don C Lamb
- the Physical Chemistry, Department for Chemistry, Center for Nanoscience, the NanoSystems Initiative Munich and the Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 81377 Munich, Germany
| | | | - Arnold J M Driessen
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, Nijenborgh 7, 9747 AG Groningen, The Netherlands,
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8
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Miller DM, Gulbis JM. Engineering protocells: prospects for self-assembly and nanoscale production-lines. Life (Basel) 2015; 5:1019-53. [PMID: 25815781 PMCID: PMC4500129 DOI: 10.3390/life5021019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic "organisms" with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. Until now, artificial cell technology has been largely restricted to the modification and metabolic engineering of living unicellular organisms. This review discusses emerging possibilities for developing synthetic protocell "machines" assembled entirely from individual biological components. We describe a host of recent technological advances that could potentially be harnessed in design and construction of synthetic protocells, some of which have already been utilized toward these ends. More elaborate designs include options for building self-assembling machines by incorporating cellular transport and assembly machinery. We also discuss production in miniature, using microfluidic production lines. While there are still many unknowns in the design, engineering and optimization of protocells, current technologies are now tantalizingly close to the capabilities required to build the first prototype protocells with potential real-world applications.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
| | - Jacqueline M Gulbis
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
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9
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Sachse R, Dondapati SK, Fenz SF, Schmidt T, Kubick S. Membrane protein synthesis in cell-free systems: From bio-mimetic systems to bio-membranes. FEBS Lett 2014; 588:2774-81. [DOI: 10.1016/j.febslet.2014.06.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 01/28/2023]
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10
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Friddin MS, Smithers NP, Beaugrand M, Marcotte I, Williamson PTF, Morgan H, de Planque MRR. Single-channel electrophysiology of cell-free expressed ion channels by direct incorporation in lipid bilayers. Analyst 2013; 138:7294-8. [DOI: 10.1039/c3an01540h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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11
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Halža E, Bro TH, Bilenberg B, Koçer A. Well-Defined Microapertures for Ion Channel Biosensors. Anal Chem 2012; 85:811-5. [DOI: 10.1021/ac303005g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erik Halža
- Groningen Biomolecular Sciences and Biotechnology Institute & BioMaDe Technology Foundation, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | | | - Brian Bilenberg
- NIL Technology ApS, Diplomvej 381, DK-2800, Kongens Lyngby, Denmark
| | - Armağan Koçer
- Groningen Biomolecular Sciences and Biotechnology Institute & BioMaDe Technology Foundation, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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12
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Balleza D. Mechanical properties of lipid bilayers and regulation of mechanosensitive function: from biological to biomimetic channels. Channels (Austin) 2012; 6:220-33. [PMID: 22790280 DOI: 10.4161/chan.21085] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Material properties of lipid bilayers, including thickness, intrinsic curvature and compressibility regulate the function of mechanosensitive (MS) channels. This regulation is dependent on phospholipid composition, lateral packing and organization within the membrane. Therefore, a more complete framework to understand the functioning of MS channels requires insights into bilayer structure, thermodynamics and phospholipid structure, as well as lipid-protein interactions. Phospholipids and MS channels interact with each other mainly through electrostatic forces and hydrophobic matching, which are also crucial for antimicrobial peptides. They are excellent models for studying the formation and stabilization of membrane pores. Importantly, they perform equivalent responses as MS channels: (1) tilting in response to tension and (2) dissipation of osmotic gradients. Lessons learned from pore forming peptides could enrich our knowledge of mechanisms of action and evolution of these channels. Here, the current state of the art is presented and general principles of membrane regulation of mechanosensitive function are discussed.
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Affiliation(s)
- Daniel Balleza
- Unidad de Biofísica, CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain.
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13
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Neugebauer SA, Baulig A, Kuhn A, Facey SJ. Membrane Protein Insertion of Variant MscL Proteins Occurs at YidC and SecYEG of Escherichia coli. J Mol Biol 2012; 417:375-86. [DOI: 10.1016/j.jmb.2012.01.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/23/2011] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
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14
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Bonardi F, Nouwen N, Feringa BL, Driessen AJM. Protein conducting channels—mechanisms, structures and applications. MOLECULAR BIOSYSTEMS 2012; 8:709-19. [DOI: 10.1039/c2mb05433g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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15
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Luirink J, Yu Z, Wagner S, de Gier JW. Biogenesis of inner membrane proteins in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:965-76. [PMID: 22201544 DOI: 10.1016/j.bbabio.2011.12.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 12/05/2011] [Accepted: 12/12/2011] [Indexed: 11/26/2022]
Abstract
The inner membrane proteome of the model organism Escherichia coli is composed of inner membrane proteins, lipoproteins and peripherally attached soluble proteins. Our knowledge of the biogenesis of inner membrane proteins is rapidly increasing. This is in particular true for the early steps of biogenesis - protein targeting to and insertion into the membrane. However, our knowledge of inner membrane protein folding and quality control is still fragmentary. Furthering our knowledge in these areas will bring us closer to understand the biogenesis of individual inner membrane proteins in the context of the biogenesis of the inner membrane proteome of Escherichia coli as a whole. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
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Affiliation(s)
- Joen Luirink
- Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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16
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Characterization of the consequences of YidC depletion on the inner membrane proteome of E. coli using 2D blue native/SDS-PAGE. J Mol Biol 2011; 409:124-35. [PMID: 21497606 DOI: 10.1016/j.jmb.2011.03.068] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/28/2011] [Accepted: 03/28/2011] [Indexed: 11/20/2022]
Abstract
In the bacterium Escherichia coli, the essential inner membrane protein (IMP) YidC assists in the biogenesis of IMPs and IMP complexes. Our current ideas about the function of YidC are based on targeted approaches using only a handful of model IMPs. Proteome-wide approaches are required to further our understanding of the significance of YidC and to find new YidC substrates. Here, using two-dimensional blue native/SDS-PAGE methodology that is suitable for comparative analysis, we have characterized the consequences of YidC depletion for the steady-state levels and oligomeric state of the constituents of the inner membrane proteome. Our analysis showed that (i) YidC depletion reduces the levels of a variety of complexes without changing their composition, (ii) the levels of IMPs containing only soluble domains smaller than 100 amino acids are likely to be reduced upon YidC depletion, whereas the levels of IMPs with at least one soluble domain larger than 100 amino acids do not, and (iii) the levels of a number of proteins with established or putative chaperone activity (HflC, HflK, PpiD, OppA, GroEL and DnaK) are strongly increased in the inner membrane fraction upon YidC depletion. In the absence of YidC, these proteins may assist the folding of sizeable soluble domains of IMPs, thereby supporting their folding and oligomeric assembly. In conclusion, our analysis identifies many new IMPs/IMP complexes that depend on YidC for their biogenesis, responses that accompany depletion of YidC and an IMP characteristic that is associated with YidC dependence.
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