51
|
Fluman N, Navon S, Bibi E, Pilpel Y. mRNA-programmed translation pauses in the targeting of E. coli membrane proteins. eLife 2014; 3. [PMID: 25135940 PMCID: PMC4359368 DOI: 10.7554/elife.03440] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/16/2014] [Indexed: 02/05/2023] Open
Abstract
In all living organisms, ribosomes translating membrane proteins are targeted to membrane translocons early in translation, by the ubiquitous signal recognition particle (SRP) system. In eukaryotes, the SRP Alu domain arrests translation elongation of membrane proteins until targeting is complete. Curiously, however, the Alu domain is lacking in most eubacteria. In this study, by analyzing genome-wide data on translation rates, we identified a potential compensatory mechanism in E. coli that serves to slow down the translation during membrane protein targeting. The underlying mechanism is likely programmed into the coding sequence, where Shine-Dalgarno-like elements trigger elongation pauses at strategic positions during the early stages of translation. We provide experimental evidence that slow translation during targeting and improves membrane protein production fidelity, as it correlates with better folding of overexpressed membrane proteins. Thus, slow elongation is important for membrane protein targeting in E. coli, which utilizes mechanisms different from the eukaryotic one to control the translation speed.
Collapse
Affiliation(s)
- Nir Fluman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sivan Navon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eitan Bibi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
52
|
Nilsson I, Lara P, Hessa T, Johnson AE, von Heijne G, Karamyshev AL. The code for directing proteins for translocation across ER membrane: SRP cotranslationally recognizes specific features of a signal sequence. J Mol Biol 2014; 427:1191-201. [PMID: 24979680 DOI: 10.1016/j.jmb.2014.06.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/17/2014] [Accepted: 06/20/2014] [Indexed: 10/25/2022]
Abstract
The signal recognition particle (SRP) cotranslationally recognizes signal sequences of secretory proteins and targets ribosome-nascent chain complexes to the SRP receptor in the endoplasmic reticulum membrane, initiating translocation of the nascent chain through the Sec61 translocon. Although signal sequences do not have homology, they have similar structural regions: a positively charged N-terminus, a hydrophobic core and a more polar C-terminal region that contains the cleavage site for the signal peptidase. Here, we have used site-specific photocrosslinking to study SRP-signal sequence interactions. A photoreactive probe was incorporated into the middle of wild-type or mutated signal sequences of the secretory protein preprolactin by in vitro translation of mRNAs containing an amber-stop codon in the signal peptide in the presence of the N(ε)-(5-azido-2 nitrobenzoyl)-Lys-tRNA(amb) amber suppressor. A homogeneous population of SRP-ribosome-nascent chain complexes was obtained by the use of truncated mRNAs in translations performed in the presence of purified canine SRP. Quantitative analysis of the photoadducts revealed that charged residues at the N-terminus of the signal sequence or in the early part of the mature protein have only a mild effect on the SRP-signal sequence association. However, deletions of amino acid residues in the hydrophobic portion of the signal sequence severely affect SRP binding. The photocrosslinking data correlate with targeting efficiency and translocation across the membrane. Thus, the hydrophobic core of the signal sequence is primarily responsible for its recognition and binding by SRP, while positive charges fine-tune the SRP-signal sequence affinity and targeting to the translocon.
Collapse
Affiliation(s)
- IngMarie Nilsson
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Patricia Lara
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Tara Hessa
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Arthur E Johnson
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA; Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden; Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden
| | - Andrey L Karamyshev
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75235, USA.
| |
Collapse
|
53
|
Denks K, Vogt A, Sachelaru I, Petriman NA, Kudva R, Koch HG. The Sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol 2014; 31:58-84. [DOI: 10.3109/09687688.2014.907455] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
54
|
Construction of a Laccase Chimerical Gene: Recombinant Protein Characterization and Gene Expression via Yeast Surface Display. Appl Biochem Biotechnol 2014; 172:2916-31. [DOI: 10.1007/s12010-014-0734-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
|
55
|
Castanié-Cornet MP, Bruel N, Genevaux P. Chaperone networking facilitates protein targeting to the bacterial cytoplasmic membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1442-56. [PMID: 24269840 DOI: 10.1016/j.bbamcr.2013.11.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/10/2013] [Accepted: 11/13/2013] [Indexed: 12/22/2022]
Abstract
Nascent polypeptides emerging from the ribosome are assisted by a pool of molecular chaperones and targeting factors, which enable them to efficiently partition as cytosolic, integral membrane or exported proteins. Extensive genetic and biochemical analyses have significantly expanded our knowledge of chaperone tasking throughout this process. In bacteria, it is known that the folding of newly-synthesized cytosolic proteins is mainly orchestrated by three highly conserved molecular chaperones, namely Trigger Factor (TF), DnaK (HSP70) and GroEL (HSP60). Yet, it has been reported that these major chaperones are strongly involved in protein translocation pathways as well. This review describes such essential molecular chaperone functions, with emphasis on both the biogenesis of inner membrane proteins and the post-translational targeting of presecretory proteins to the Sec and the twin-arginine translocation (Tat) pathways. Critical interplay between TF, DnaK, GroEL and other molecular chaperones and targeting factors, including SecB, SecA, the signal recognition particle (SRP) and the redox enzyme maturation proteins (REMPs) is also discussed. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
Collapse
Affiliation(s)
- Marie-Pierre Castanié-Cornet
- Laboratoire de Microbiologie et Génétique Moléculaire (LMGM), Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France
| | - Nicolas Bruel
- Laboratoire de Microbiologie et Génétique Moléculaire (LMGM), Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaire (LMGM), Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France.
| |
Collapse
|
56
|
Reithinger JH, Kim JEH, Kim H. Sec62 protein mediates membrane insertion and orientation of moderately hydrophobic signal anchor proteins in the endoplasmic reticulum (ER). J Biol Chem 2013; 288:18058-67. [PMID: 23632075 DOI: 10.1074/jbc.m113.473009] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Nascent chains are known to be targeted to the endoplasmic reticulum membrane either by a signal recognition particle (SRP)-dependent co-translational or by an SRP-independent post-translational translocation route depending on signal sequences. Using a set of model and cellular proteins carrying an N-terminal signal anchor sequence of controlled hydrophobicity and yeast mutant strains defective in SRP or Sec62 function, the hydrophobicity-dependent targeting efficiency and targeting pathway preference were systematically evaluated. Our results suggest that an SRP-dependent co-translational and an SRP-independent post-translational translocation are not mutually exclusive for signal anchor proteins and that moderately hydrophobic ones require both SRP and Sec62 for proper targeting and translocation to the endoplasmic reticulum. Further, defect in Sec62 selectively reduced signal sequences inserted in an N(in)-C(out) (type II) membrane topology, implying an undiscovered role of Sec62 in regulating the orientation of the signal sequence in an early stage of translocation.
Collapse
|
57
|
Ast T, Cohen G, Schuldiner M. A network of cytosolic factors targets SRP-independent proteins to the endoplasmic reticulum. Cell 2013; 152:1134-45. [PMID: 23452858 DOI: 10.1016/j.cell.2013.02.003] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 11/08/2012] [Accepted: 02/04/2013] [Indexed: 12/23/2022]
Abstract
Translocation into the endoplasmic reticulum (ER) is an initial and crucial biogenesis step for all secreted and endomembrane proteins in eukaryotes. ER insertion can take place through the well-characterized signal recognition particle (SRP)-dependent pathway or the less-studied route of SRP-independent translocation. To better understand the prevalence of the SRP-independent pathway, we systematically defined the translocational dependence of the yeast secretome. By combining hydropathy-based analysis and microscopy, we uncovered that a previously unappreciated fraction of the yeast secretome translocates without the aid of the SRP. Furthermore, we validated a family of SRP-independent substrates-the glycosylphosphatidylinositol (GPI)-anchored proteins. Studying this family, we identified a determinant for ER targeting and uncovered a network of cytosolic proteins that facilitate SRP-independent targeting and translocation. These findings highlight the underappreciated complexity of SRP-independent translocation, which enables this pathway to efficiently cope with its extensive substrate flux.
Collapse
Affiliation(s)
- Tslil Ast
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | |
Collapse
|
58
|
von Loeffelholz O, Knoops K, Ariosa A, Zhang X, Karuppasamy M, Huard K, Schoehn G, Berger I, Shan SO, Schaffitzel C. Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex. Nat Struct Mol Biol 2013; 20:604-10. [PMID: 23563142 DOI: 10.1038/nsmb.2546] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/21/2013] [Indexed: 11/09/2022]
Abstract
Signal-recognition particle (SRP)-dependent targeting of translating ribosomes to membranes is a multistep quality-control process. Ribosomes that are translating weakly hydrophobic signal sequences can be rejected from the targeting reaction even after they are bound to the SRP. Here we show that the early complex, formed by Escherichia coli SRP and its receptor FtsY with ribosomes translating the incorrect cargo EspP, is unstable and rearranges inefficiently into subsequent conformational states, such that FtsY dissociation is favored over successful targeting. The N-terminal extension of EspP is responsible for these defects in the early targeting complex. The cryo-electron microscopy structure of this 'false' early complex with EspP revealed an ordered M domain of SRP protein Ffh making two ribosomal contacts, and the NG domains of Ffh and FtsY forming a distorted, flexible heterodimer. Our results provide a structural basis for SRP-mediated signal-sequence selection during recruitment of the SRP receptor.
Collapse
|
59
|
Islam ST, Lam JS. Topological mapping methods for α-helical bacterial membrane proteins--an update and a guide. Microbiologyopen 2013; 2:350-64. [PMID: 23408725 PMCID: PMC3633358 DOI: 10.1002/mbo3.72] [Citation(s) in RCA: 17] [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: 10/24/2012] [Revised: 01/04/2013] [Accepted: 01/10/2013] [Indexed: 12/19/2022] Open
Abstract
Integral membrane proteins with α-helical transmembrane segments (TMS) are known to play important and diverse roles in prokaryotic cell physiology. The net hydrophobicity of TMS directly corresponds to the observed difficulties in expressing and purifying these proteins, let alone producing sufficient yields for structural studies using two-/three-dimensional (2D/3D) crystallographic or nuclear magnetic resonance methods. To gain insight into the function of these integral membrane proteins, topological mapping has become an important tool to identify exposed and membrane-embedded protein domains. This approach has led to the discovery of protein tracts of functional importance and to the proposition of novel mechanistic hypotheses. In this review, we synthesize the various methods available for topological mapping of α-helical integral membrane proteins to provide investigators with a comprehensive reference for choosing techniques suited to their particular topological queries and available resources.
Collapse
Affiliation(s)
- Salim T Islam
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | | |
Collapse
|
60
|
Ast T, Schuldiner M. All roads lead to Rome (but some may be harder to travel): SRP-independent translocation into the endoplasmic reticulum. Crit Rev Biochem Mol Biol 2013; 48:273-88. [PMID: 23530742 DOI: 10.3109/10409238.2013.782999] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Translocation into the endoplasmic reticulum (ER) is the first biogenesis step for hundreds of eukaryotic secretome proteins. Over the past 30 years, groundbreaking biochemical, structural and genetic studies have delineated one conserved pathway that enables ER translocation- the signal recognition particle (SRP) pathway. However, it is clear that this is not the only pathway which can mediate ER targeting and insertion. In fact, over the past decade, several SRP-independent pathways have been uncovered, which recognize proteins that cannot engage the SRP and ensure their subsequent translocation into the ER. These SRP-independent pathways face the same challenges that the SRP pathway overcomes: chaperoning the preinserted protein while in the cytosol, targeting it rapidly to the ER surface and generating vectorial movement that inserts the protein into the ER. This review strives to summarize the various mechanisms and machineries which mediate these stages of SRP-independent translocation, as well as examine why SRP-independent translocation is utilized by the cell. This emerging understanding of the various pathways utilized by secretory proteins to insert into the ER draws light to the complexity of the translocational task, and underlines that insertion into the ER might be more varied and tailored than previously appreciated.
Collapse
Affiliation(s)
- Tslil Ast
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | | |
Collapse
|
61
|
Optimizing heterologous protein production in the periplasm of E. coli by regulating gene expression levels. Microb Cell Fact 2013; 12:24. [PMID: 23497240 PMCID: PMC3605120 DOI: 10.1186/1475-2859-12-24] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 03/05/2013] [Indexed: 11/10/2022] Open
Abstract
Background In Escherichia coli many heterologous proteins are produced in the periplasm. To direct these proteins to the periplasm, they are equipped with an N-terminal signal sequence so that they can traverse the cytoplasmic membrane via the protein-conducting Sec-translocon. For poorly understood reasons, the production of heterologous secretory proteins is often toxic to the cell thereby limiting yields. To gain insight into the mechanism(s) that underlie this toxicity we produced two secretory heterologous proteins, super folder green fluorescent protein and a single-chain variable antibody fragment, in the Lemo21(DE3) strain. In this strain, the expression intensity of the gene encoding the target protein can be precisely controlled. Results Both SFGFP and the single-chain variable antibody fragment were equipped with a DsbA-derived signal sequence. Producing these proteins following different gene expression levels in Lemo21(DE3) allowed us to identify the optimal expression level for each target gene. Too high gene expression levels resulted in saturation of the Sec-translocon capacity as shown by hampered translocation of endogenous secretory proteins and a protein misfolding/aggregation problem in the cytoplasm. At the optimal gene expression levels, the negative effects of the production of the heterologous secretory proteins were minimized and yields in the periplasm were optimized. Conclusions Saturating the Sec-translocon capacity can be a major bottleneck hampering heterologous protein production in the periplasm. This bottleneck can be alleviated by harmonizing expression levels of the genes encoding the heterologous secretory proteins with the Sec-translocon capacity. Mechanistic insight into the production of proteins in the periplasm is key to optimizing yields in this compartment.
Collapse
|
62
|
Dominant negative lptE mutation that supports a role for LptE as a plug in the LptD barrel. J Bacteriol 2013; 195:1327-34. [PMID: 23316047 DOI: 10.1128/jb.02142-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lipopolysaccharide (LPS) is the major outer leaflet constituent of the Gram-negative outer membrane (OM) bilayer. A bipartite protein complex of LptD and LptE assembles LPS into the OM. It has been established that LptE assists folding and assembly of its β-barrel partner LptD, yet reported biochemical evidence suggested additional LptE functions. Here, we isolated dominant negative lptE mutations, seeking to inform these functions. The lptE14 mutation increased OM permeability to erythromycin, even when the wild-type lptE gene was present. We show that the lptE14 mutation does not cause a defect in either LptD assembly or LPS export. A spontaneous IS1 insertion in secA suppressed lptE14 erythromycin sensitivity by removing the C-terminal SecB-binding domain of SecA. While this suppressor mutation broadly impeded SecB-dependent secretion of preproteins, we show that suppression was a direct and specific consequence of reduced LptD levels in the OM. We suggest that lptE14 causes poor plugging of the LptD β barrel and that a reduction of ineffectively plugged LptD-LptE14 complexes in the OM decreases permeability to erythromycin. Hence, lptE14 supports a proposed plug-and-barrel LptE-LptD arrangement.
Collapse
|
63
|
Dammeyer T, Tinnefeld P. Engineered fluorescent proteins illuminate the bacterial periplasm. Comput Struct Biotechnol J 2012; 3:e201210013. [PMID: 24688673 PMCID: PMC3962181 DOI: 10.5936/csbj.201210013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/02/2012] [Accepted: 11/12/2012] [Indexed: 12/21/2022] Open
Abstract
The bacterial periplasm is of special interest whenever cell factories are designed and engineered. Recombinantely produced proteins are targeted to the periplasmic space of Gram negative bacteria to take advantage of the authentic N-termini, disulfide bridge formation and easy accessibility for purification with less contaminating cellular proteins. The oxidizing environment of the periplasm promotes disulfide bridge formation - a prerequisite for proper folding of many proteins into their active conformation. In contrast, the most popular reporter protein in all of cell biology, Green Fluorescent Protein (GFP), remains inactive if translocated to the periplasmic space prior to folding. Here, the self-catalyzed chromophore maturation is blocked by formation of covalent oligomers via interchain disulfide bonds in the oxidizing environment. However, different protein engineering approaches addressing folding and stability of GFP resulted in improved proteins with enhanced folding properties. Recent studies describe GFP variants that are not only active if translocated in their folded form via the twin-arginine translocation (Tat) pathway, but actively fold in the periplasm following general secretory pathway (Sec) and signal recognition particle (SRP) mediated secretion. This mini-review highlights the progress that enables new insights into bacterial export and periplasmic protein organization, as well as new biotechnological applications combining the advantages of the periplasmic production and the Aequorea-based fluorescent reporter proteins.
Collapse
Affiliation(s)
- Thorben Dammeyer
- Institut für Physikalische und Theoretische Chemie, NanoBioSciences, Technische Universität Braunschweig, Hans Sommer Str. 10, 38106 Braunschweig, Germany
| | - Philip Tinnefeld
- Institut für Physikalische und Theoretische Chemie, NanoBioSciences, Technische Universität Braunschweig, Hans Sommer Str. 10, 38106 Braunschweig, Germany
| |
Collapse
|
64
|
Liechti G, Goldberg JB. Outer membrane biogenesis in Escherichia coli, Neisseria meningitidis, and Helicobacter pylori: paradigm deviations in H. pylori. Front Cell Infect Microbiol 2012; 2:29. [PMID: 22919621 PMCID: PMC3417575 DOI: 10.3389/fcimb.2012.00029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 02/28/2012] [Indexed: 12/16/2022] Open
Abstract
The bacterial pathogen Helicobacter pylori is capable of colonizing the gastric mucosa of the human stomach using a variety of factors associated with or secreted from its outer membrane (OM). Lipopolysaccharide (LPS) and numerous OM proteins have been shown to be involved in adhesion and immune stimulation/evasion. Many of these factors are essential for colonization and/or pathogenesis in a variety of animal models. Despite this wide array of potential targets present on the bacterial surface, the ability of H. pylori to vary its OM profile limits the effectiveness of vaccines or therapeutics that target any single one of these components. However, it has become evident that the proteins comprising the complexes that transport the majority of these molecules to the OM are highly conserved and often essential. The field of membrane biogenesis has progressed remarkably in the last few years, and the possibility now exists for targeting the mechanisms by which β-barrel proteins, lipoproteins, and LPS are transported to the OM, resulting in loss of bacterial fitness and significant altering of membrane permeability. In this review, the OM transport machinery for LPS, lipoproteins, and outer membrane proteins (OMPs) are discussed. While the principal investigations of these transport mechanisms have been conducted in Escherichia coli and Neisseria meningitidis, here these systems will be presented in the genetic context of ε proteobacteria. Bioinformatic analysis reveals that minimalist genomes, such as that of Helicobacter pylori, offer insight into the smallest number of components required for these essential pathways to function. Interestingly, in the majority of ε proteobacteria, while the inner and OM associated apparatus of LPS, lipoprotein, and OMP transport pathways appear to all be intact, most of the components associated with the periplasmic compartment are either missing or are almost unrecognizable when compared to their E. coli counterparts. Eventual targeting of these pathways would have the net effect of severely limiting the delivery/transport of components to the OM and preventing the bacterium's ability to infect its human host.
Collapse
Affiliation(s)
- George Liechti
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville VA, USA
| | | |
Collapse
|
65
|
From self sufficiency to dependence: mechanisms and factors important for autotransporter biogenesis. Nat Rev Microbiol 2012; 10:213-25. [PMID: 22337167 DOI: 10.1038/nrmicro2733] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Autotransporters are a superfamily of proteins that use the type V secretion pathway for their delivery to the surface of Gram-negative bacteria. At first glance, autotransporters look to contain all the functional elements required to promote their own secretion: an amino-terminal signal peptide to mediate translocation across the inner membrane, a central passenger domain that is the secreted functional moiety, and a channel-forming carboxyl terminus that facilitates passenger domain translocation across the outer membrane. However, recent discoveries of common structural themes, translocation intermediates and accessory interactions have challenged the perceived simplicity of autotransporter secretion. Here, we discuss how these studies have led to an improved understanding of the mechanisms responsible for autotransporter biogenesis.
Collapse
|
66
|
Zhang D, Shan SO. Translation elongation regulates substrate selection by the signal recognition particle. J Biol Chem 2012; 287:7652-60. [PMID: 22228766 DOI: 10.1074/jbc.m111.325001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The signal recognition particle (SRP) is a universally conserved cellular machinery responsible for delivering membrane and secretory proteins to the proper cellular destination. The precise mechanism by which fidelity is achieved by the SRP pathway within the in vivo environment is yet to be understood. Previous studies have focused on the SRP pathway in isolation. Here we describe another important factor that modulates substrate selection by the SRP pathway: the ongoing synthesis of the nascent polypeptide chain by the ribosome. A slower translation elongation rate rescues the targeting defect of substrate proteins bearing mutant, suboptimal signal sequences both in vitro and in vivo. Consistent with a kinetic origin of this effect, similar rescue of protein targeting was also observed with mutant SRP receptors or SRP RNAs that specifically compromise the kinetics of SRP-receptor interaction during protein targeting. These data are consistent with a model in which ongoing protein translation is in constant kinetic competition with the targeting of the nascent proteins by the SRP and provides an important factor to regulate the fidelity of substrate selection by the SRP.
Collapse
Affiliation(s)
- Dawei Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | | |
Collapse
|
67
|
Zhang D, Sweredoski MJ, Graham RLJ, Hess S, Shan SO. Novel proteomic tools reveal essential roles of SRP and importance of proper membrane protein biogenesis. Mol Cell Proteomics 2011; 11:M111.011585. [PMID: 22030350 DOI: 10.1074/mcp.m111.011585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The signal recognition particle (SRP), which mediates cotranslational protein targeting to cellular membranes, is universally conserved and essential for bacterial and mammalian cells. However, the current understanding of the role of SRP in cell physiology and pathology is still poor, and the reasons behind its essential role in cell survival remain unclear. Here, we systematically analyzed the consequences of SRP loss in E. coli using time-resolved quantitative proteomic analyses. A series of snapshots of the steady-state and newly synthesized proteome unveiled three stages of cellular responses to SRP depletion, and demonstrated essential roles of SRP in metabolism, membrane potential, and protein and energy homeostasis in both the membrane and cytoplasm. We also identified a group of periplasmic proteins, including key molecular chaperones, whose localization was impaired by the loss of SRP; this and additional results showed that SRP is crucial for protein homeostasis in the bacterial envelope. These results reveal the extensive roles that SRP plays in bacterial physiology, emphasize the importance of proper membrane protein biogenesis, and demonstrate the ability of time-resolved quantitative proteomic analysis to provide new biological insights.
Collapse
Affiliation(s)
- Dawei Zhang
- Division of Chemistry and Chemical Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA.
| | | | | | | | | |
Collapse
|
68
|
Ricci DP, Silhavy TJ. The Bam machine: a molecular cooper. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1067-84. [PMID: 21893027 DOI: 10.1016/j.bbamem.2011.08.020] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/08/2011] [Accepted: 08/15/2011] [Indexed: 11/24/2022]
Abstract
The bacterial outer membrane (OM) is an exceptional biological structure with a unique composition that contributes significantly to the resiliency of Gram-negative bacteria. Since all OM components are synthesized in the cytosol, the cell must efficiently transport OM-specific lipids and proteins across the cell envelope and stably integrate them into a growing membrane. In this review, we discuss the challenges associated with these processes and detail the elegant solutions that cells have evolved to address the topological problem of OM biogenesis. Special attention will be paid to the Bam machine, a highly conserved multiprotein complex that facilitates OM β-barrel folding. This article is part of a Special Issue entitled: Protein Folding in Membranes.
Collapse
Affiliation(s)
- Dante P Ricci
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | |
Collapse
|
69
|
Yap MN, Bernstein HD. The translational regulatory function of SecM requires the precise timing of membrane targeting. Mol Microbiol 2011; 81:540-53. [PMID: 21635582 DOI: 10.1111/j.1365-2958.2011.07713.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In Escherichia coli, secA expression is regulated at the translational level by an upstream gene (secM) that encodes a presecretory protein. SecM contains a C-terminal sequence motif that induces a transient translation arrest. Inhibition of SecM membrane targeting prolongs the translation arrest and increases SecA synthesis by concomitantly altering the structure of the secM-secA mRNA. Here we show that the SecM signal peptide plays an essential role in this regulatory process by acting as a molecular timer that co-ordinates membrane targeting with the synthesis of the arrest motif. We found that signal peptide mutations that alter targeting kinetics and insertions or deletions that change the distance between the SecM signal peptide and the arrest motif perturb the balance between the onset and release of arrest that is required to regulate SecA synthesis. Furthermore, we found that the strength of the interaction between the ribosome and the SecM arrest motif is calibrated to ensure the release of arrest upon membrane targeting. Our results strongly suggest that several distinctive features of the SecM protein evolved as a consequence of constraints imposed by the ribosome and the Sec machinery.
Collapse
Affiliation(s)
- Mee-Ngan Yap
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | |
Collapse
|
70
|
Zalucki YM, Beacham IR, Jennings MP. Coupling between codon usage, translation and protein export in Escherichia coli. Biotechnol J 2011; 6:660-7. [PMID: 21567959 DOI: 10.1002/biot.201000334] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 11/07/2022]
Abstract
Proteins destined for export via the Sec-dependent pathway are synthesized with a short N-terminal signal peptide. A requirement for export is that the proteins are in a translocationally competent state. This is a loosely folded state that allows the protein to pass through the SecYEG apparatus and pass into the periplasm. In order to maintain pre-secretory proteins in an export-competent state, there are many factors that slow the folding of the pre-secretory protein in the cytoplasm. These include cytoplasmic chaperones, such as SecB, and the signal recognition particle, which bind the pre-secretory protein and direct it to the cytoplasmic membrane for export. Recently, evidence has been published that non-optimal codons in the signal sequence are important for a time-critical early event to allow the correct folding of pre-secretory proteins. This review details the recent developments in folding of the signal peptide and the pre-secretory protein.
Collapse
Affiliation(s)
- Yaramah M Zalucki
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | | | | |
Collapse
|
71
|
Aronson DE, Costantini LM, Snapp EL. Superfolder GFP is fluorescent in oxidizing environments when targeted via the Sec translocon. Traffic 2011; 12:543-8. [PMID: 21255213 DOI: 10.1111/j.1600-0854.2011.01168.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The ability to study proteins in live cells using genetically encoded fluorescent proteins (FPs) has revolutionized cell biology (1-3). Researchers have created numerous FP biosensors and optimized FPs for specific organisms and subcellular environments in a rainbow of colors (4,5). However, expressing FPs in oxidizing environments such as the eukaryotic endoplasmic reticulum (ER) or the bacterial periplasm can impair folding, thereby preventing fluorescence (6,7). A substantial fraction of enhanced green fluorescent protein (EGFP) oligomerizes to form non-fluorescent mixed disulfides in the ER (6) and EGFP does not fluoresce in the periplasm when targeted via the SecYEG translocon (7). To overcome these obstacles, we exploited the highly efficient folding capability of superfolder GFP (sfGFP) (8). Here, we report sfGFP does not form disulfide-linked oligomers in the ER and maltose-binding protein (MBP) signal sequence (peri)-sfGFP (9) is brightly fluorescent in the periplasm of Escherichia coli. Thus, sfGFP represents an important research tool for studying resident proteins of oxidizing environments.
Collapse
Affiliation(s)
- Deborah E Aronson
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | | | | |
Collapse
|
72
|
Hainzl T, Huang S, Meriläinen G, Brännström K, Sauer-Eriksson AE. Structural basis of signal-sequence recognition by the signal recognition particle. Nat Struct Mol Biol 2011; 18:389-91. [PMID: 21336278 DOI: 10.1038/nsmb.1994] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 12/01/2010] [Indexed: 12/29/2022]
Abstract
The signal recognition particle (SRP) recognizes and binds the signal sequence of nascent proteins as they emerge from the ribosome. We present here the 3.0-Å structure of a signal sequence bound to the Methanococcus jannaschii SRP core. Structural comparison with the free SRP core shows that signal-sequence binding induces formation of the GM-linker helix and a 180° flip of the NG domain-structural changes that ensure a hierarchical succession of events during protein targeting.
Collapse
Affiliation(s)
- Tobias Hainzl
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | | | | | | | | |
Collapse
|
73
|
Peterson JH, Woolhead CA, Bernstein HD. The conformation of a nascent polypeptide inside the ribosome tunnel affects protein targeting and protein folding. Mol Microbiol 2010; 78:203-17. [PMID: 20804452 DOI: 10.1111/j.1365-2958.2010.07325.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this report, we describe insights into the function of the ribosome tunnel that were obtained through an analysis of an unusual 25 residue N-terminal motif (EspP(1-25) ) associated with the signal peptide of the Escherichia coli EspP protein. It was previously shown that EspP(1-25) inhibits signal peptide recognition by the signal recognition particle, and we now show that fusion of EspP(1-25) to a cytoplasmic protein causes it to aggregate. We obtained two lines of evidence that both of these effects are attributable to the conformation of EspP(1-25) inside the ribosome tunnel. First, we found that mutations in EspP(1-25) that abolished its effects on protein targeting and protein folding altered the cross-linking of short nascent chains to ribosomal components. Second, we found that a mutation in L22 that distorts the tunnel mimicked the effects of the EspP(1-25) mutations on protein biogenesis. Our results provide evidence that the conformation of a polypeptide inside the ribosome tunnel can influence protein folding under physiological conditions and suggest that ribosomal mutations might increase the solubility of at least some aggregation-prone proteins produced in E. coli.
Collapse
Affiliation(s)
- Janine H Peterson
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0538, USA
| | | | | |
Collapse
|
74
|
Bibi E. Early targeting events during membrane protein biogenesis in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:841-50. [PMID: 20682283 DOI: 10.1016/j.bbamem.2010.07.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
Abstract
All living cells have co-translational pathways for targeting membrane proteins. Co-translation pathways for secretory proteins also exist but mostly in eukaryotes. Unlike secretory proteins, the biosynthetic pathway of most membrane proteins is conserved through evolution and these proteins are usually synthesized by membrane-bound ribosomes. Translation on the membrane requires that both the ribosomes and the mRNAs be properly localized. Theoretically, this can be achieved by several means. (i) The current view is that the targeting of cytosolic mRNA-ribosome-nascent chain complexes (RNCs) to the membrane is initiated by information in the emerging hydrophobic nascent polypeptides. (ii) The alternative model suggests that ribosomes may be targeted to the membrane also constitutively, whereas the appropriate mRNAs may be carried on small ribosomal subunits or targeted by other cellular factors to the membrane-bound ribosomes. Importantly, the available experimental data do not rule out the possibility that cells may also utilize both pathways in parallel. In any case, it is well documented that a major player in the targeting pathway is the signal recognition particle (SRP) system composed of the SRP and its receptor (SR). Although the functional core of the SRP system is evolutionarily conserved, its composition and biological practice come with different flavors in various organisms. This review is dedicated mainly to the Escherichia (E.) coli SRP, where the biochemical and structural properties of components of the SRP system have been relatively characterized, yielding essential information about various aspects of the pathway. In addition, several cellular interactions of the SRP and its receptor have been described in E. coli, providing insights into their spatial function. Collectively, these in vitro studies have led to the current view of the targeting pathway [see (i) above]. Interestingly, however, in vivo studies of the role of the SRP and its receptor, with emphasis on the temporal progress of the pathway, elicited an alternative hypothesis [see (ii) above]. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
Collapse
Affiliation(s)
- Eitan Bibi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
75
|
Facey SJ, Kuhn A. Biogenesis of bacterial inner-membrane proteins. Cell Mol Life Sci 2010; 67:2343-62. [PMID: 20204450 PMCID: PMC11115511 DOI: 10.1007/s00018-010-0303-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 02/01/2010] [Accepted: 02/03/2010] [Indexed: 11/26/2022]
Abstract
All cells must traffic proteins into and across their membranes. In bacteria, several pathways have evolved to enable protein transfer across the inner membrane, the periplasm, and the outer membrane. The major route of protein translocation in and across the cytoplasmic membrane is the general secretion pathway (Sec-pathway). The biogenesis of membrane proteins not only requires protein translocation but also coordinated targeting to the membrane beforehand and folding and assembly into their protein complexes afterwards to function properly in the cell. All these processes are responsible for the biogenesis of membrane proteins that mediate essential functions of the cell such as selective transport, energy conversion, cell division, extracellular signal sensing, and motility. This review will highlight the most recent developments on the structure and function of bacterial membrane proteins, focusing on the journey that integral membrane proteins take to find their final destination in the inner membrane.
Collapse
Affiliation(s)
- Sandra J. Facey
- Institute of Microbiology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Andreas Kuhn
- Institute of Microbiology, University of Hohenheim, 70599 Stuttgart, Germany
| |
Collapse
|
76
|
Zimmermann R, Eyrisch S, Ahmad M, Helms V. Protein translocation across the ER membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:912-24. [PMID: 20599535 DOI: 10.1016/j.bbamem.2010.06.015] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 06/11/2010] [Accepted: 06/14/2010] [Indexed: 01/02/2023]
Abstract
Protein translocation into the endoplasmic reticulum (ER) is the first and decisive step in the biogenesis of most extracellular and many soluble organelle proteins in eukaryotic cells. It is mechanistically related to protein export from eubacteria and archaea and to the integration of newly synthesized membrane proteins into the ER membrane and the plasma membranes of eubacteria and archaea (with the exception of tail anchored membrane proteins). Typically, protein translocation into the ER involves cleavable amino terminal signal peptides in precursor proteins and sophisticated transport machinery components in the cytosol, the ER membrane, and the ER lumen. Depending on the hydrophobicity and/or overall amino acid content of the precursor protein, transport can occur co- or posttranslationally. The respective mechanism determines the requirements for certain cytosolic transport components. The two mechanisms merge at the level of the ER membrane, specifically, at the heterotrimeric Sec61 complex present in the membrane. The Sec61 complex provides a signal peptide recognition site and forms a polypeptide conducting channel. Apparently, the Sec61 complex is gated by various ligands, such as signal peptides of the transport substrates, ribosomes (in cotranslational transport), and the ER lumenal molecular chaperone, BiP. Binding of BiP to the incoming polypeptide contributes to efficiency and unidirectionality of transport. Recent insights into the structure of the Sec61 complex and the comparison of the transport mechanisms and machineries in the yeast Saccharomyces cerevisiae, the human parasite Trypanosoma brucei, and mammals have various important mechanistic as well as potential medical implications. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
Collapse
Affiliation(s)
- Richard Zimmermann
- Medical Biochemistry & Molecular Biology, Saarland University, D-66041 Homburg, Germany.
| | | | | | | |
Collapse
|
77
|
Hoffmann A, Bukau B, Kramer G. Structure and function of the molecular chaperone Trigger Factor. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:650-61. [PMID: 20132842 DOI: 10.1016/j.bbamcr.2010.01.017] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 01/22/2010] [Indexed: 01/16/2023]
Abstract
Newly synthesized proteins often require the assistance of molecular chaperones to efficiently fold into functional three-dimensional structures. At first, ribosome-associated chaperones guide the initial folding steps and protect growing polypeptide chains from misfolding and aggregation. After that folding into the native structure may occur spontaneously or require support by additional chaperones which do not bind to the ribosome such as DnaK and GroEL. Here we review the current knowledge on the best-characterized ribosome-associated chaperone at present, the Escherichia coli Trigger Factor. We describe recent progress on structural and dynamic aspects of Trigger Factor's interactions with the ribosome and substrates and discuss how these interactions affect co-translational protein folding. In addition, we discuss the newly proposed ribosome-independent function of Trigger Factor as assembly factor of multi-subunit protein complexes. Finally, we cover the functional cooperation between Trigger Factor, DnaK and GroEL in folding of cytosolic proteins and the interplay between Trigger Factor and other ribosome-associated factors acting in enzymatic processing and translocation of nascent polypeptide chains.
Collapse
Affiliation(s)
- Anja Hoffmann
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | | | | |
Collapse
|
78
|
Luo J, Choulet J, Samuelson JC. Rational design of a fusion partner for membrane protein expression in E. coli. Protein Sci 2009; 18:1735-44. [PMID: 19530231 PMCID: PMC2771104 DOI: 10.1002/pro.189] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We have designed a novel protein fusion partner (P8CBD) to utilize the co-translational SRP pathway in order to target heterologous proteins to the E. coli inner membrane. SRP-dependence was demonstrated by analyzing the membrane translocation of P8CBD-PhoA fusion proteins in wt and SRP-ffh77 mutant cells. We also demonstrate that the P8CBD N-terminal fusion partner promotes over-expression of a Thermotoga maritima polytopic membrane protein by replacement of the native signal anchor sequence. Furthermore, the yeast mitochondrial inner membrane protein Oxa1p was expressed as a P8CBD fusion and shown to function within the E. coli inner membrane. In this example, the mitochondrial targeting peptide was replaced by P8CBD. Several practical features were incorporated into the P8CBD expression system to aid in protein detection, purification, and optional in vitro processing by enterokinase. The basis of membrane protein over-expression toxicity is discussed and solutions to this problem are presented. We anticipate that this optimized expression system will aid in the isolation and study of various recombinant forms of membrane-associated protein.
Collapse
Affiliation(s)
- Jianying Luo
- New England Biolabs, Inc. Gene Expression Division, Ipswich, Massachusetts 01938, USA
| | | | | |
Collapse
|
79
|
Abstract
Large amounts of antibiotics used for human therapy, as well as for farm animals and even for fish in aquaculture, resulted in the selection of pathogenic bacteria resistant to multiple drugs. Multidrug resistance in bacteria may be generated by one of two mechanisms. First, these bacteria may accumulate multiple genes, each coding for resistance to a single drug, within a single cell. This accumulation occurs typically on resistance (R) plasmids. Second, multidrug resistance may also occur by the increased expression of genes that code for multidrug efflux pumps, extruding a wide range of drugs. This review discusses our current knowledge on the molecular mechanisms involved in both types of resistance.
Collapse
Affiliation(s)
- Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.
| |
Collapse
|
80
|
Abstract
The Signal Recognition Particle (SRP) plays a critical role in the sorting of nascent secretory and membrane proteins. Remarkably, this function has been conserved from bacteria, where SRP delivers proteins to the inner membrane, through to eukaryotes, where SRP is required for targeting of proteins to the endoplasmic reticulum. This review focuses on present understanding of SRP structure and function and the relationship between the two. Furthermore, the similarities and differences in the structure, function and cellular role of SRP in bacteria, chloroplasts, fungi and mammals will be stressed.
Collapse
Affiliation(s)
- Martin R Pool
- Faculty of Life Sciences, University of Manchester, Manchester, UK.
| |
Collapse
|
81
|
The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat Struct Mol Biol 2009; 16:589-97. [PMID: 19491936 DOI: 10.1038/nsmb.1614] [Citation(s) in RCA: 347] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The early events in the life of newly synthesized proteins in the cellular environment are remarkably complex. Concurrently with their synthesis by the ribosome, nascent polypeptides are subjected to enzymatic processing, chaperone-assisted folding or targeting to translocation pores at membranes. The ribosome itself has a key role in these different tasks and governs the interplay between the various factors involved. Indeed, the ribosome serves as a platform for the spatially and temporally regulated association of enzymes, targeting factors and chaperones that act upon the nascent polypeptides emerging from the exit tunnel. Furthermore, the ribosome provides opportunities to coordinate the protein-synthesis activity of its peptidyl transferase center with the protein targeting and folding processes. Here we review the early co-translational events involving the ribosome that guide cytosolic proteins to their native state.
Collapse
|
82
|
Shukla A, Huang W, Depaz IM, Gillam EMJ. Membrane integration of recombinant human P450 forms. Xenobiotica 2009; 39:495-507. [DOI: 10.1080/00498250902934884] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
83
|
Kol S, Majczak W, Heerlien R, van der Berg JP, Nouwen N, Driessen AJM. Subunit a of the F(1)F(0) ATP synthase requires YidC and SecYEG for membrane insertion. J Mol Biol 2009; 390:893-901. [PMID: 19497329 DOI: 10.1016/j.jmb.2009.05.074] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 05/22/2009] [Accepted: 05/27/2009] [Indexed: 11/16/2022]
Abstract
The insertion of inner membrane proteins in Escherichia coli occurs almost exclusively via the SecYEG pathway, while some membrane proteins require the membrane protein insertase YidC. In vitro analysis demonstrates that subunit a of the F(1)F(0) ATP synthase (F(0)a) is strictly dependent on Ffh, SecYEG and YidC for its membrane insertion but independent of the proton motive force. The insertion of the first transmembrane segment of F(0)a also depends on Ffh and SecYEG but not on YidC, whereas the insertion is strongly dependent on the proton motive force, unlike the full-length F(0)a protein. These data demonstrate an extensive role of YidC in the assembly of the F(0) sector of the F(1)F(0) ATP synthase.
Collapse
Affiliation(s)
- Stefan Kol
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | | | | | | | | | | |
Collapse
|
84
|
Tian P, Bernstein HD. Identification of a post-targeting step required for efficient cotranslational translocation of proteins across the Escherichia coli inner membrane. J Biol Chem 2009; 284:11396-404. [PMID: 19211555 PMCID: PMC2670145 DOI: 10.1074/jbc.m900375200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Indexed: 11/06/2022] Open
Abstract
Recent studies have shown that cytoplasmic proteins are exported efficiently in Escherichia coli only if they are attached to signal peptides that are recognized by the signal recognition particle and are thereby targeted to the SecYEG complex cotranslationally. The evidence suggests that the entry of these proteins into the secretory pathway at an early stage of translation is necessary to prevent them from folding into a translocation-incompetent conformation. We found, however, that several glycolytic enzymes attached to signal peptides that are recognized by the signal recognition particle were exported inefficiently. Based on previous studies of post-translational export, we hypothesized that the export block was due to the presence of basic residues at the extreme N terminus of each enzyme. Consistent with our hypothesis, we found that the introduction of negatively charged residues into this segment increased the efficiency of export. Export efficiency was sensitive to the number, position, and sequence context of charged residues. The importance of charge for efficient export was underscored by an in silico analysis that revealed a conserved negative charge bias at the N terminus of the mature region of bacterial presecretory proteins. Our results demonstrate that cotranslational targeting of a protein to the E. coli SecYEG complex does not ensure its export but that export also depends on a subsequent event (most likely the initiation of translocation) that involves sequences both within and just beyond the signal peptide.
Collapse
Affiliation(s)
- Pu Tian
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0538, USA
| | | |
Collapse
|
85
|
Abstract
Correct protein function depends on delivery to the appropriate cellular or subcellular compartment. Following the initiation of protein synthesis in the cytosol, many bacterial and eukaryotic proteins must be integrated into or transported across a membrane to reach their site of function. Whereas in the post-translational delivery pathway ATP-dependent factors bind to completed polypeptides and chaperone them until membrane translocation is initiated, a GTP-dependent co-translational pathway operates to couple ongoing protein synthesis to membrane transport. These distinct pathways provide different solutions for the maintenance of proteins in a state that is competent for membrane translocation and their delivery for export from the cytosol.
Collapse
|
86
|
Zimmermann R, Blatch GL. A novel twist to protein secretion in eukaryotes. Trends Parasitol 2009; 25:147-50. [PMID: 19269249 DOI: 10.1016/j.pt.2009.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 11/29/2022]
Abstract
A recent functional analysis of the protein translocase, which is present in the trypanosomal endoplasmic reticulum membrane, by Michaeli and co-workers has indicated an unexpected diversity in the mechanisms and components of protein secretion in eukaryotes and might eventually pave the way for the development of anti-trypanosomal drugs. Furthermore, the work on these human parasites also supports conclusions that were drawn previously for components of protein secretion in human cells on the basis of in vitro studies.
Collapse
Affiliation(s)
- Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany.
| | | |
Collapse
|
87
|
Clérico EM, Szymańska A, Gierasch LM. Exploring the interactions between signal sequences and E. coli SRP by two distinct and complementary crosslinking methods. Biopolymers 2009; 92:201-11. [PMID: 19280642 PMCID: PMC2896254 DOI: 10.1002/bip.21181] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Photoaffinity crosslinking comprises a group of invaluable techniques used to investigate in detail a binding interaction between two polypeptides. As the diverse photo crosslinking techniques available display inherent differences, the method of choice will provide specific information about a particular system under study. We used two complementary crosslinking approaches: photo-induced crosslinking of unmodified proteins (PICUP) and benzophenone-mediated (BPM) crosslinking to extensively examine the interaction between the signal recognition particle (SRP) and signal sequences. Signal peptide binding by SRP presents a central puzzle in the protein targeting process because signal sequences must be recognized with fidelity but lack strict primary structural homology. The concurrent use of PICUP and BPM crosslinking to link signal peptides to E. coli SRP allowed us to explore the crosslinking pattern resulting from using different crosslinking chemistries, varying the position of the photoprobe in the hydrophobic core of the signal sequence, and shifting the crosslinking reactive group away from the signal peptide backbone. By PICUP, signal peptides crosslinked exclusively to the NG domain of the SRP protein Ffh, regardless of the position of the reactive residue. Benzophenone-modified amino acids preferentially crosslinked the signal peptide to the C-terminal (M) domain of Ffh. We conclude that signal peptide binding is largely mediated by the M domain. Importantly, our data also indicate intimate, at least transient, contacts between the hydrophobic core of the signal peptide and the NG domain. These results reopen the possibility of a direct involvement of the NG domain in signal sequence recognition.
Collapse
Affiliation(s)
- Eugenia M. Clérico
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst MA 01003, U.S.A
- Department of Chemistry, University of Massachusetts, Amherst MA 01003, U.S.A
| | - Aneta Szymańska
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst MA 01003, U.S.A
- Department of Chemistry, University of Massachusetts, Amherst MA 01003, U.S.A
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst MA 01003, U.S.A
- Department of Chemistry, University of Massachusetts, Amherst MA 01003, U.S.A
| |
Collapse
|
88
|
Goldshmidt H, Sheiner L, Bütikofer P, Roditi I, Uliel S, Günzel M, Engstler M, Michaeli S. Role of protein translocation pathways across the endoplasmic reticulum in Trypanosoma brucei. J Biol Chem 2008; 283:32085-98. [PMID: 18768469 DOI: 10.1074/jbc.m801499200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The translocation of secretory and membrane proteins across the endoplasmic reticulum (ER) membrane is mediated by co-translational (via the signal recognition particle (SRP)) and post-translational mechanisms. In this study, we investigated the relative contributions of these two pathways in trypanosomes. A homologue of SEC71, which functions in the post-translocation chaperone pathway in yeast, was identified and silenced by RNA interference. This factor is essential for parasite viability. In SEC71-silenced cells, signal peptide (SP)-containing proteins traversed the ER, but several were mislocalized, whereas polytopic membrane protein biogenesis was unaffected. Surprisingly trypanosomes can interchangeably utilize two of the pathways to translocate SP-containing proteins except for glycosylphosphatidylinositol-anchored proteins, whose level was reduced in SEC71-silenced cells but not in cells depleted for SRP68, an SRP-binding protein. Entry of SP-containing proteins to the ER was significantly blocked only in cells co-silenced for the two translocation pathways (SEC71 and SRP68). SEC63, a factor essential for both translocation pathways in yeast, was identified and silenced by RNA interference. SEC63 silencing affected entry to the ER of both SP-containing proteins and polytopic membrane proteins, suggesting that, as in yeast, this factor is essential for both translocation pathways in vivo. This study suggests that, unlike bacteria or other eukaryotes, trypanosomes are generally promiscuous in their choice of mechanism for translocating SP-containing proteins to the ER, although the SRP-independent pathway is favored for glycosylphosphatidylinositol-anchored proteins, which are the most abundant surface proteins in these parasites.
Collapse
Affiliation(s)
- Hanoch Goldshmidt
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | | | | | | | | | | | |
Collapse
|
89
|
Maier KS, Hubich S, Liebhart H, Krauss S, Kuhn A, Facey SJ. An amphiphilic region in the cytoplasmic domain of KdpD is recognized by the signal recognition particle and targeted to the Escherichia coli membrane. Mol Microbiol 2008; 68:1471-84. [PMID: 18433452 PMCID: PMC2440551 DOI: 10.1111/j.1365-2958.2008.06246.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sensor protein KdpD of Escherichia coli is composed of a large N-terminal hydrophilic region (aa 1–400), four transmembrane regions (aa 401–498) and a large hydrophilic region (aa 499–894) at the C-terminus. KdpD requires the signal recognition particle (SRP) for its targeting to the membrane. Deletions within KdpD show that the first 50 residues are required for SRP-driven membrane insertion. A fusion protein of the green fluorescent protein (GFP) with KdpD is found localized at the membrane only when SRP is present. The membrane targeting of GFP was not observed when the first 50 KdpD residues were deleted. A truncated mutant of KdpD containing only the first 25 amino acids fused to GFP lost its ability to specifically interact with SRP, whereas a specific interaction between SRP and the first 48 amino acids of KdpD fused to GFP was confirmed by pull-down experiments. Conclusively, a small amphiphilic region of 27 residues within the amino-terminal domain of KdpD (aa 22–48) is recognized by SRP and targets the protein to the membrane. This shows that membrane proteins with a large N-terminal region in the cytoplasm can be membrane-targeted early on to allow co-translational membrane insertion of their distant transmembrane regions.
Collapse
Affiliation(s)
- Katja S Maier
- Institute of Microbiology, University of Hohenheim, 70599 Stuttgart, Germany
| | | | | | | | | | | |
Collapse
|
90
|
The signal recognition particle pathway is required for virulence in Streptococcus pyogenes. Infect Immun 2008; 76:2612-9. [PMID: 18411293 DOI: 10.1128/iai.00239-07] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The signal recognition particle (SRP) pathway is a universally conserved pathway for targeting polypeptides for secretion via the cotranslational pathway. In particular, the SRP pathway is thought to be the main mechanism for targeting polypeptides in gram-positive bacteria, including a number of important human pathogens. Though widely considered to be an essential cellular component, recent advances have indicated this pathway may be dispensable in gram-positive bacteria of the genus Streptococcus under in vitro conditions. However, its importance for the pathogenesis of streptococcal disease is unknown. In this study, we investigated the importance of the SRP pathway for virulence factor secretion in the human pathogen Streptococcus pyogenes. While the SRP pathway was not found to be essential for viability in vitro, SRP mutants demonstrated a medium-specific growth defect that could be rescued by the addition of glucose. We also observed that a distinct subset of virulence factors were dependent upon the SRP pathway for secretion, whereas others were completely independent of this pathway. Significantly, deletion of the SRP pathway resulted in mutants that were highly attenuated in both a zebrafish model of necrotic myositis and a murine subcutaneous ulcer model, highlighting the importance of this pathway in vivo. These studies emphasize the importance of the SRP pathway for the in vivo survival and pathogenesis of S. pyogenes.
Collapse
|
91
|
The conserved extension of the Hbp autotransporter signal peptide does not determine targeting pathway specificity. Biochem Biophys Res Commun 2008; 368:522-7. [DOI: 10.1016/j.bbrc.2008.01.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 01/22/2008] [Indexed: 11/15/2022]
|
92
|
Dautin N, Bernstein HD. Protein secretion in gram-negative bacteria via the autotransporter pathway. Annu Rev Microbiol 2007; 61:89-112. [PMID: 17506669 DOI: 10.1146/annurev.micro.61.080706.093233] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Autotransporters are a large and diverse superfamily of proteins produced by pathogenic gram-negative bacteria that are composed of an N-terminal passenger domain, which typically harbors a virulence function, and a C-terminal beta domain. It has long been known that the beta domain anchors the protein to the outer membrane and facilitates transport of the passenger domain into the extracellular space. Despite the apparent simplicity of the autotransporter pathway, several aspects of autotransporter biogenesis remain poorly understood, most notably the mechanism by which the passenger domain is translocated across the outer membrane. Here we review recent evidence that the enormous sequence diversity of both passenger and beta domains belies a remarkable conservation of structure. We also discuss insights into each stage of autotransporter biogenesis that have emerged from recent structural, biochemical, and imaging studies.
Collapse
Affiliation(s)
- Nathalie Dautin
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0538, USA.
| | | |
Collapse
|
93
|
Lotz M, Haase W, Kühlbrandt W, Collinson I. Projection structure of yidC: a conserved mediator of membrane protein assembly. J Mol Biol 2007; 375:901-7. [PMID: 18054957 DOI: 10.1016/j.jmb.2007.10.089] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 10/13/2007] [Accepted: 10/17/2007] [Indexed: 11/28/2022]
Abstract
Bacteria, mitochondria and chloroplasts harbour factors that facilitate the insertion, folding and assembly of membrane proteins. In Escherichia coli, yidC is required for membrane insertion, acting in both a Sec-dependent and a Sec-independent manner. There is an expanding volume of biochemical work on its role in this process, but none so far on its structure. We present the first of this class of membrane proteins determined by electron cryomicroscopy in the near-nativelike state of the membrane. yidC forms dimers in the membrane and each monomer has an area of low density that may be part of the path transmembrane segments follow during their insertion. Upon consideration of the structures of yidC and SecYEG, we speculate on the nature of the interfaces that facilitate the alternative pathways (Sec-dependent and -independent) of membrane protein insertion.
Collapse
Affiliation(s)
- Mirko Lotz
- Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany
| | | | | | | |
Collapse
|
94
|
Tuteja R, Pradhan A, Sharma S. Plasmodium falciparum signal peptidase is regulated by phosphorylation and required for intra-erythrocytic growth. Mol Biochem Parasitol 2007; 157:137-47. [PMID: 18054093 DOI: 10.1016/j.molbiopara.2007.10.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Revised: 10/16/2007] [Accepted: 10/18/2007] [Indexed: 11/15/2022]
Abstract
The human malaria parasite Plasmodium falciparum exports a variety of its proteins through its endoplasmic reticulum (ER) based secretory pathway in order to survive in the host erythrocyte. Signal peptidases are membrane-bound endopeptidases and have an important role in the transport and maturation of these parasite proteins. Prokaryotic signal peptidases are indispensable enzymes required for the removal of N-terminal signal peptide from the secretory proteins. Eukaryotic signal peptidases exist as multimeric protein complex in the ER and the catalytic subunit of this complex catalyzes removal of the N-terminal signal peptide from preproteins. All the signal peptidases contain five regions of high-sequence similarity referred to as boxes A-E. Here we report characterization of the catalytic subunit of signal peptidase complex (SPC) from P. falciparum. This protein designated as PfSP21 shows homology with the similar subunit from other sources and contains all the conserved boxes A-E. PfSP21 is able to cleave the peptide substrate containing the signal peptidase cleavage site. PfSP21 is phosphorylated by protein kinase C and its enzyme activity was upregulated after this phosphorylation. Immunofluorescence assay studies revealed that PfSP21 is localized in the ER of P. falciparum. PfSP21 dsRNA specifically inhibits the growth of P. falciparum in culture and this inhibition is most likely due to the decrease in the amount of endogenous PfSP21 protein. These studies demonstrate the characterization of a functional subunit of SPC from P. falciparum and should make an important contribution in our better understanding of the complex process of protein translocation in the parasite.
Collapse
Affiliation(s)
- Renu Tuteja
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.
| | | | | |
Collapse
|
95
|
Lustig Y, Vagima Y, Goldshmidt H, Erlanger A, Ozeri V, Vince J, McConville MJ, Dwyer DM, Landfear SM, Michaeli S. Down-regulation of the trypanosomatid signal recognition particle affects the biogenesis of polytopic membrane proteins but not of signal peptide-containing proteins. EUKARYOTIC CELL 2007; 6:1865-75. [PMID: 17715370 PMCID: PMC2043396 DOI: 10.1128/ec.00134-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Protein translocation across the endoplasmic reticulum is mediated by the signal recognition particle (SRP). In this study, the SRP pathway in trypanosomatids was down-regulated by two approaches: RNA interference (RNAi) silencing of genes encoding SRP proteins in Trypanosoma brucei and overexpression of dominant-negative mutants of 7SL RNA in Leptomonas collosoma. The biogenesis of both signal peptide-containing proteins and polytopic membrane proteins was examined using endogenous and green fluorescent protein-fused proteins. RNAi silencing of SRP54 or SRP68 in T. brucei resulted in reduced levels of polytopic membrane proteins, but no effect on the level of signal peptide-containing proteins was observed. When SRP deficiency was achieved in L. collosoma by overexpression of dominant-negative mutated 7SL RNA, a major effect was observed on polytopic membrane proteins but not on signal peptide-containing proteins. This study included two trypanosomatid species, tested various protein substrates, and induced depletion of the SRP pathway by affecting either the levels of SRP binding proteins or that of SRP RNA. Our results demonstrate that, as in bacteria but in contrast to mammalian cells, the trypanosome SRP is mostly essential for the biogenesis of membrane proteins.
Collapse
Affiliation(s)
- Yaniv Lustig
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | | | | | | | | | | | | | | | | | | |
Collapse
|
96
|
Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane--distinct translocases and mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1778:1735-56. [PMID: 17935691 DOI: 10.1016/j.bbamem.2007.07.015] [Citation(s) in RCA: 343] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 07/23/2007] [Accepted: 07/24/2007] [Indexed: 11/20/2022]
Abstract
In bacteria, two major pathways exist to secrete proteins across the cytoplasmic membrane. The general Secretion route, termed Sec-pathway, catalyzes the transmembrane translocation of proteins in their unfolded conformation, whereupon they fold into their native structure at the trans-side of the membrane. The Twin-arginine translocation pathway, termed Tat-pathway, catalyses the translocation of secretory proteins in their folded state. Although the targeting signals that direct secretory proteins to these pathways show a high degree of similarity, the translocation mechanisms and translocases involved are vastly different.
Collapse
|
97
|
Abstract
Understanding the transport of hydrophilic proteins across biological membranes continues to be an important undertaking. The general secretory (Sec) pathway in Escherichia coli transports the majority of E. coli proteins from their point of synthesis in the cytoplasm to their sites of final localization, associating sequentially with a number of protein components of the transport machinery. The targeting signals for these substrates must be discriminated from those of proteins transported via other pathways. While targeting signals for each route have common overall characteristics, individual signal peptides vary greatly in their amino acid sequences. How do these diverse signals interact specifically with the proteins that comprise the appropriate transport machinery and, at the same time, avoid targeting to an alternate route? The recent publication of the crystal structures of components of the Sec transport machinery now allows a more thorough consideration of the interactions of signal sequences with these components.
Collapse
Affiliation(s)
| | - Debra A. Kendall
- To whom correspondence should be addressed. Mailing address: Department of Molecular and Cell Biology, 91 North Eagleville Road, The University of Connecticut, Storrs, CT 06269-3125. Phone: (860) 486-1891. Fax: (860) 486-4331. E-mail:
| |
Collapse
|
98
|
Retallack DM, Schneider JC, Mitchell J, Chew L, Liu H. Transport of heterologous proteins to the periplasmic space of Pseudomonas fluorescens using a variety of native signal sequences. Biotechnol Lett 2007; 29:1483-91. [PMID: 17541504 DOI: 10.1007/s10529-007-9415-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 05/02/2007] [Indexed: 10/23/2022]
Abstract
Bacterial expression of recombinant proteins containing disulfide bonds is facilitated by transport of the proteins to the periplasmic space. Several Pseudomonas fluorescens signal sequences have been identified that efficiently direct proteins to the periplasm and provide solubility and yield advantages over the production of proteins fused to the PelB signal sequence in E. coli. For a single chain antibody fragment, the final yield varied from about 1 g/l to 10 g/l when expression in P. fluorescens involved fusion to various P. fluorescens signal sequences.
Collapse
Affiliation(s)
- Diane M Retallack
- The Dow Chemical Company, Core Biotechnology Research and Development, 5501 Oberlin Dr, San Diego, CA 92121, USA.
| | | | | | | | | |
Collapse
|
99
|
Bradshaw N, Walter P. The signal recognition particle (SRP) RNA links conformational changes in the SRP to protein targeting. Mol Biol Cell 2007; 18:2728-34. [PMID: 17507650 PMCID: PMC1924838 DOI: 10.1091/mbc.e07-02-0117] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The RNA component of the signal recognition particle (SRP) is universally required for cotranslational protein targeting. Biochemical studies have shown that SRP RNA participates in the central step of protein targeting by catalyzing the interaction of the SRP with the SRP receptor (SR). SRP RNA also accelerates GTP hydrolysis in the SRP.SR complex once formed. Using a reverse-genetic and biochemical analysis, we identified mutations in the E. coli SRP protein, Ffh, that abrogate the activity of the SRP RNA and cause corresponding targeting defects in vivo. The mutations in Ffh that disrupt SRP RNA activity map to regions that undergo dramatic conformational changes during the targeting reaction, suggesting that the activity of the SRP RNA is linked to the major conformational changes in the signal sequence-binding subunit of the SRP. In this way, the SRP RNA may coordinate the interaction of the SRP and the SR with ribosome recruitment and transfer to the translocon, explaining why the SRP RNA is an indispensable component of the protein targeting machinery.
Collapse
Affiliation(s)
- Niels Bradshaw
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158
| | - Peter Walter
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158
| |
Collapse
|
100
|
Flower AM. The SecY translocation complex: convergence of genetics and structure. Trends Microbiol 2007; 15:203-10. [PMID: 17368028 DOI: 10.1016/j.tim.2007.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 01/26/2007] [Accepted: 03/01/2007] [Indexed: 11/19/2022]
Abstract
All organisms share a requirement for translocation of proteins across membranes. The major mechanism for this process is the universally conserved SecY/Sec61 pathway. Many years of extensive genetic and biochemical analyses identified the components of the SecY/Sec61 pathway, demonstrated that most exported proteins use this route for translocation, and led to understanding of many functions of the components. Recently, structural predictions based on genetic analyses in Escherichia coli were confirmed, in a striking and satisfying manner, by the solution of an X-ray crystal structure from an archaeal SecY complex. This review discusses the genetic background that led to those hypotheses and the convergence of genetic studies with structural data.
Collapse
Affiliation(s)
- Ann M Flower
- Department of Microbiology and Immunology, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202-9037, USA.
| |
Collapse
|