1
|
Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
Collapse
Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| |
Collapse
|
2
|
Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
Collapse
Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
| |
Collapse
|
3
|
Sarmah P, Shang W, Origi A, Licheva M, Kraft C, Ulbrich M, Lichtenberg E, Wilde A, Koch HG. mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria. Cell Rep 2023; 42:112140. [PMID: 36842086 PMCID: PMC10066597 DOI: 10.1016/j.celrep.2023.112140] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 01/10/2023] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
Signal-sequence-dependent protein targeting is essential for the spatiotemporal organization of eukaryotic and prokaryotic cells and is facilitated by dedicated protein targeting factors such as the signal recognition particle (SRP). However, targeting signals are not exclusively contained within proteins but can also be present within mRNAs. By in vivo and in vitro assays, we show that mRNA targeting is controlled by the nucleotide content and by secondary structures within mRNAs. mRNA binding to bacterial membranes occurs independently of soluble targeting factors but is dependent on the SecYEG translocon and YidC. Importantly, membrane insertion of proteins translated from membrane-bound mRNAs occurs independently of the SRP pathway, while the latter is strictly required for proteins translated from cytosolic mRNAs. In summary, our data indicate that mRNA targeting acts in parallel to the canonical SRP-dependent protein targeting and serves as an alternative strategy for safeguarding membrane protein insertion when the SRP pathway is compromised.
Collapse
Affiliation(s)
- Pinku Sarmah
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University Freiburg, 79104 Freiburg, Germany
| | - Maximilian Ulbrich
- Internal Medicine IV, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | | | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
| |
Collapse
|
4
|
Mayer M, Winer L, Karniel A, Pinner E, Yardeni EH, Morgenstern D, Bibi E. Co-translational membrane targeting and holo-translocon docking of ribosomes translating the SRP receptor. J Mol Biol 2022; 434:167459. [DOI: 10.1016/j.jmb.2022.167459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 10/19/2022]
|
5
|
Lewis AJO, Hegde RS. A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC. BMC Biol 2021; 19:266. [PMID: 34911545 PMCID: PMC8675477 DOI: 10.1186/s12915-021-01171-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Protein transporters translocate hydrophilic segments of polypeptide across hydrophobic cell membranes. Two protein transporters are ubiquitous and date back to the last universal common ancestor: SecY and YidC. SecY consists of two pseudosymmetric halves, which together form a membrane-spanning protein-conducting channel. YidC is an asymmetric molecule with a protein-conducting hydrophilic groove that partially spans the membrane. Although both transporters mediate insertion of membrane proteins with short translocated domains, only SecY transports secretory proteins and membrane proteins with long translocated domains. The evolutionary origins of these ancient and essential transporters are not known. RESULTS The features conserved by the two halves of SecY indicate that their common ancestor was an antiparallel homodimeric channel. Structural searches with SecY's halves detect exceptional similarity with YidC homologs. The SecY halves and YidC share a fold comprising a three-helix bundle interrupted by a helical hairpin. In YidC, this hairpin is cytoplasmic and facilitates substrate delivery, whereas in SecY, it is transmembrane and forms the substrate-binding lateral gate helices. In both transporters, the three-helix bundle forms a protein-conducting hydrophilic groove delimited by a conserved hydrophobic residue. Based on these similarities, we propose that SecY originated as a YidC homolog which formed a channel by juxtaposing two hydrophilic grooves in an antiparallel homodimer. We find that archaeal YidC and its eukaryotic descendants use this same dimerisation interface to heterodimerise with a conserved partner. YidC's sufficiency for the function of simple cells is suggested by the results of reductive evolution in mitochondria and plastids, which tend to retain SecY only if they require translocation of large hydrophilic domains. CONCLUSIONS SecY and YidC share previously unrecognised similarities in sequence, structure, mechanism, and function. Our delineation of a detailed correspondence between these two essential and ancient transporters enables a deeper mechanistic understanding of how each functions. Furthermore, key differences between them help explain how SecY performs its distinctive function in the recognition and translocation of secretory proteins. The unified theory presented here explains the evolution of these features, and thus reconstructs a key step in the origin of cells.
Collapse
Affiliation(s)
- Aaron J O Lewis
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| |
Collapse
|
6
|
Potteth US, Upadhyay T, Saini S, Saraogi I. Novel Antibacterial Targets in Protein Biogenesis Pathways. Chembiochem 2021; 23:e202100459. [PMID: 34643994 DOI: 10.1002/cbic.202100459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/12/2021] [Indexed: 11/11/2022]
Abstract
Antibiotic resistance has emerged as a global threat due to the ability of bacteria to quickly evolve in response to the selection pressure induced by anti-infective drugs. Thus, there is an urgent need to develop new antibiotics against resistant bacteria. In this review, we discuss pathways involving bacterial protein biogenesis as attractive antibacterial targets since many of them are essential for bacterial survival and virulence. We discuss the structural understanding of various components associated with bacterial protein biogenesis, which in turn can be utilized for rational antibiotic design. We highlight efforts made towards developing inhibitors of these pathways with insights into future possibilities and challenges. We also briefly discuss other potential targets related to protein biogenesis.
Collapse
Affiliation(s)
- Upasana S Potteth
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Tulsi Upadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Snehlata Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India.,Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal - 462066, Madhya Pradesh, India
| |
Collapse
|
7
|
Oswald J, Njenga R, Natriashvili A, Sarmah P, Koch HG. The Dynamic SecYEG Translocon. Front Mol Biosci 2021; 8:664241. [PMID: 33937339 PMCID: PMC8082313 DOI: 10.3389/fmolb.2021.664241] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The spatial and temporal coordination of protein transport is an essential cornerstone of the bacterial adaptation to different environmental conditions. By adjusting the protein composition of extra-cytosolic compartments, like the inner and outer membranes or the periplasmic space, protein transport mechanisms help shaping protein homeostasis in response to various metabolic cues. The universally conserved SecYEG translocon acts at the center of bacterial protein transport and mediates the translocation of newly synthesized proteins into and across the cytoplasmic membrane. The ability of the SecYEG translocon to transport an enormous variety of different substrates is in part determined by its ability to interact with multiple targeting factors, chaperones and accessory proteins. These interactions are crucial for the assisted passage of newly synthesized proteins from the cytosol into the different bacterial compartments. In this review, we summarize the current knowledge about SecYEG-mediated protein transport, primarily in the model organism Escherichia coli, and describe the dynamic interaction of the SecYEG translocon with its multiple partner proteins. We furthermore highlight how protein transport is regulated and explore recent developments in using the SecYEG translocon as an antimicrobial target.
Collapse
Affiliation(s)
- Julia Oswald
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Robert Njenga
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Ana Natriashvili
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Pinku Sarmah
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| |
Collapse
|
8
|
Steinberg R, Koch HG. The largely unexplored biology of small proteins in pro- and eukaryotes. FEBS J 2021; 288:7002-7024. [PMID: 33780127 DOI: 10.1111/febs.15845] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022]
Abstract
The large abundance of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes and the plethora of smORF-encoded small proteins became only apparent with the constant advancements in bioinformatic, genomic, proteomic, and biochemical tools. Small proteins are typically defined as proteins of < 50 amino acids in prokaryotes and of less than 100 amino acids in eukaryotes, and their importance for cell physiology and cellular adaptation is only beginning to emerge. In contrast to antimicrobial peptides, which are secreted by prokaryotic and eukaryotic cells for combatting pathogens and competitors, small proteins act within the producing cell mainly by stabilizing protein assemblies and by modifying the activity of larger proteins. Production of small proteins is frequently linked to stress conditions or environmental changes, and therefore, cells seem to use small proteins as intracellular modifiers for adjusting cell metabolism to different intra- and extracellular cues. However, the size of small proteins imposes a major challenge for the cellular machinery required for protein folding and intracellular trafficking and recent data indicate that small proteins can engage distinct trafficking pathways. In the current review, we describe the diversity of small proteins in prokaryotes and eukaryotes, highlight distinct and common features, and illustrate how they are handled by the protein trafficking machineries in prokaryotic and eukaryotic cells. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.
Collapse
Affiliation(s)
- Ruth Steinberg
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
| |
Collapse
|
9
|
Han R, Fang J, Jiang J, Gaidamakova EK, Tkavc R, Daly MJ, Contreras LM. Signal Recognition Particle RNA Contributes to Oxidative Stress Response in Deinococcus radiodurans by Modulating Catalase Localization. Front Microbiol 2020; 11:613571. [PMID: 33391243 PMCID: PMC7775534 DOI: 10.3389/fmicb.2020.613571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
The proper functioning of many proteins requires their transport to the correct cellular compartment or their secretion. Signal recognition particle (SRP) is a major protein transport pathway responsible for the co-translational movement of integral membrane proteins as well as periplasmic proteins. Deinococcus radiodurans is a ubiquitous bacterium that expresses a complex phenotype of extreme oxidative stress resistance, which depends on proteins involved in DNA repair, metabolism, gene regulation, and antioxidant defense. These proteins are located extracellularly or subcellularly, but the molecular mechanism of protein localization in D. radiodurans to manage oxidative stress response remains unexplored. In this study, we characterized the SRP complex in D. radiodurans R1 and showed that the knockdown (KD) of the SRP RNA (Qpr6) reduced bacterial survival under hydrogen peroxide and growth under chronic ionizing radiation. Through LC-mass spectrometry (MS/MS) analysis, we detected 162 proteins in the periplasm of wild-type D. radiodurans, of which the transport of 65 of these proteins to the periplasm was significantly reduced in the Qpr6 KD strain. Through Western blotting, we further demonstrated the localization of the catalases in D. radiodurans, DR_1998 (KatE1) and DR_A0259 (KatE2), in both the cytoplasm and periplasm, respectively, and showed that the accumulation of KatE1 and KatE2 in the periplasm was reduced in the SRP-defective strains. Collectively, this study establishes the importance of the SRP pathway in the survival and the transport of antioxidant proteins in D. radiodurans under oxidative stress.
Collapse
Affiliation(s)
- Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Jaden Fang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Jessie Jiang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Elena K Gaidamakova
- Uniformed Services University of the Health Sciences, Department of Pathology, Bethesda, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Rok Tkavc
- Uniformed Services University of the Health Sciences, Department of Pathology, Bethesda, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.,Uniformed Services University of the Health Sciences, Department of Microbiology and Immunology, Bethesda, MD, United States
| | - Michael J Daly
- Uniformed Services University of the Health Sciences, Department of Pathology, Bethesda, MD, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular & Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| |
Collapse
|
10
|
Miyazaki R, Akiyama Y, Mori H. Fine interaction profiling of VemP and mechanisms responsible for its translocation-coupled arrest-cancelation. eLife 2020; 9:62623. [PMID: 33320090 PMCID: PMC7793623 DOI: 10.7554/elife.62623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/11/2020] [Indexed: 12/24/2022] Open
Abstract
Bacterial cells utilize monitoring substrates, which undergo force-sensitive translation elongation arrest, to feedback-regulate a Sec-related gene. Vibrio alginolyticus VemP controls the expression of SecD/F that stimulates a late step of translocation by undergoing export-regulated elongation arrest. Here, we attempted at delineating the pathway of the VemP nascent-chain interaction with Sec-related factors, and identified the signal recognition particle (SRP) and PpiD (a membrane-anchored periplasmic chaperone) in addition to other translocon components and a ribosomal protein as interacting partners. Our results showed that SRP is required for the membrane-targeting of VemP, whereas PpiD acts cooperatively with SecD/F in the translocation and arrest-cancelation of VemP. We also identified the conserved Arg-85 residue of VemP as a crucial element that confers PpiD-dependence to VemP and plays an essential role in the regulated arrest-cancelation. We propose a scheme of the arrest-cancelation processes of VemP, which likely monitors late steps in the protein translocation pathway.
Collapse
Affiliation(s)
- Ryoji Miyazaki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| |
Collapse
|
11
|
Abstract
To identify the translocation components in cells, and to understand how they function in protein transport and membrane insertion, a variety of techniques have been used such as genetics, biochemistry, structural biology and single molecule methods. In particular, site-directed crosslinking between the client proteins and components of the translocation machineries have contributed significantly in the past and will do so in the future. One advantage of this technology is that it can be applied in vivo as well as in vitro and a comparison of the two approaches can be made. Also, the in vivo techniques allow time-dependent protocols which are essential for studying cellular pathways. Protein purification and reconstitution into proteoliposomes are the gold standard for studying membrane-based transport and translocation systems. With these biochemically defined approaches the function of each component in protein transport can be addressed individually with a plethora of biophysical techniques. Recently, the use of nanodiscs for reconstitution has added another extension of this reductionistic approach. Fluorescence based studies, cryo-microscopy and NMR spectroscopy have significantly added to our understanding how proteins move into and across membranes and will do this also in future.
Collapse
Affiliation(s)
- Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599, Stuttgart, Germany.
| |
Collapse
|
12
|
Jauss B, Petriman NA, Drepper F, Franz L, Sachelaru I, Welte T, Steinberg R, Warscheid B, Koch HG. Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands the global view on the SecYEG interactome in Escherichia coli. J Biol Chem 2019; 294:19167-19183. [PMID: 31699901 DOI: 10.1074/jbc.ra119.010686] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
The SecYEG translocon constitutes the major protein transport channel in bacteria and transfers an enormous variety of different secretory and inner-membrane proteins. The minimal core of the SecYEG translocon consists of three inner-membrane proteins, SecY, SecE, and SecG, which, together with appropriate targeting factors, are sufficient for protein transport in vitro However, in vivo the SecYEG translocon has been shown to associate with multiple partner proteins, likely allowing the SecYEG translocon to process its diverse substrates. To obtain a global view on SecYEG plasticity in Escherichia coli, here we performed a quantitative interaction proteomic analysis, which identified several known SecYEG-interacting proteins, verified the interaction of SecYEG with quality-control proteins, and revealed several previously unknown putative SecYEG-interacting proteins. Surprisingly, we found that the chaperone complex PpiD/YfgM is the most prominent interaction partner of SecYEG. Detailed analyses of the PpiD-SecY interaction by site-directed cross-linking revealed that PpiD and the established SecY partner protein YidC use almost completely-overlapping binding sites on SecY. Both PpiD and YidC contacted the lateral gate, the plug domain, and the periplasmic cavity of SecY. However, quantitative MS and cross-linking analyses revealed that despite having almost identical binding sites, their binding to SecY is noncompetitive. This observation suggests that the SecYEG translocon forms different substrate-independent subassemblies in which SecYEG either associates with YidC or with the PpiD/YfgM complex. In summary, the results of this study indicate that the PpiD/YfgM chaperone complex is a primary interaction partner of the SecYEG translocon.
Collapse
Affiliation(s)
- Benjamin Jauss
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Narcis-Adrian Petriman
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Lisa Franz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Ilie Sachelaru
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Thomas Welte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
13
|
Steinberg R, Knüpffer L, Origi A, Asti R, Koch HG. Co-translational protein targeting in bacteria. FEMS Microbiol Lett 2019; 365:4966980. [PMID: 29790984 DOI: 10.1093/femsle/fny095] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/09/2018] [Indexed: 01/16/2023] Open
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and have to be transported into or across the cytoplasmic membrane. Bacteria use multiple protein transport systems in parallel, but the majority of proteins engage two distinct targeting systems. One is the co-translational targeting by two universally conserved GTPases, the signal recognition particle (SRP) and its receptor FtsY, which deliver inner membrane proteins to either the SecYEG translocon or the YidC insertase for membrane insertion. The other targeting system depends on the ATPase SecA, which targets secretory proteins, i.e. periplasmic and outer membrane proteins, to SecYEG for their subsequent ATP-dependent translocation. While SRP selects its substrates already very early during their synthesis, the recognition of secretory proteins by SecA is believed to occur primarily after translation termination, i.e. post-translationally. In this review we highlight recent progress on how SRP recognizes its substrates at the ribosome and how the fidelity of the targeting reaction to SecYEG is maintained. We furthermore discuss similarities and differences in the SRP-dependent targeting to either SecYEG or YidC and summarize recent results that suggest that some membrane proteins are co-translationally targeted by SecA.
Collapse
Affiliation(s)
- Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Lara Knüpffer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, Freiburg D-79104, Germany
| | - Rossella Asti
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| |
Collapse
|
14
|
Abstract
Bacterial protein transport via the conserved SecYEG translocon is generally classified as either cotranslational, i.e., when transport is coupled to translation, or posttranslational, when translation and transport are separated. We show here that the ATPase SecA, which is considered to bind its substrates posttranslationally, already scans the ribosomal tunnel for potential substrates. In the presence of a nascent chain, SecA retracts from the tunnel but maintains contact with the ribosomal surface. This is remarkably similar to the ribosome-binding mode of the signal recognition particle, which mediates cotranslational transport. Our data reveal a striking plasticity of protein transport pathways, which likely enable bacteria to efficiently recognize and transport a large number of highly different substrates within their short generation time. Bacteria execute a variety of protein transport systems for maintaining the proper composition of their different cellular compartments. The SecYEG translocon serves as primary transport channel and is engaged in transporting two different substrate types. Inner membrane proteins are cotranslationally inserted into the membrane after their targeting by the signal recognition particle (SRP). In contrast, secretory proteins are posttranslationally translocated by the ATPase SecA. Recent data indicate that SecA can also bind to ribosomes close to the tunnel exit. We have mapped the interaction of SecA with translating and nontranslating ribosomes and demonstrate that the N terminus and the helical linker domain of SecA bind to an acidic patch on the surface of the ribosomal protein uL23. Intriguingly, both also insert deeply into the ribosomal tunnel to contact the intratunnel loop of uL23, which serves as a nascent chain sensor. This binding pattern is remarkably similar to that of SRP and indicates an identical interaction mode of the two targeting factors with ribosomes. In the presence of a nascent chain, SecA retracts from the tunnel but maintains contact with the surface of uL23. Our data further demonstrate that ribosome and membrane binding of SecA are mutually exclusive, as both events depend on the N terminus of SecA. Our study highlights the enormous plasticity of bacterial protein transport systems and reveals that the discrimination between SRP and SecA substrates is already initiated at the ribosome.
Collapse
|
15
|
Miyazaki R, Akiyama Y, Mori H. A photo-cross-linking approach to monitor protein dynamics in living cells. Biochim Biophys Acta Gen Subj 2019; 1864:129317. [PMID: 30851405 DOI: 10.1016/j.bbagen.2019.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND Proteins, which comprise one of the major classes of biomolecules that constitute a cell, interact with other cellular factors during both their biogenesis and functional states. Studying not only static but also transient interactions of proteins is important to understand their physiological roles and regulation mechanisms. However, only a limited number of methods are available to analyze the dynamic behaviors of proteins at the molecular level in a living cell. The site-directed in vivo photo-cross-linking approach is an elegant technique to capture protein interactions with high spatial resolution in a living cell. SCOPE OF REVIEW Here, we review the in vivo photo-cross-linking approach including its recent applications and the potential problems to be considered. We also introduce a new in vivo photo-cross-linking-based technique (PiXie) to study protein dynamics with high spatiotemporal resolution. MAJOR CONCLUSIONS In vivo photo-cross-linking enables us to capture weak/transient protein interactions with high spatial resolution, and allows for identification of interacting factors. Moreover, the PiXie approach can be used to monitor rapid folding/assembly processes of proteins in living cells. GENERAL SIGNIFICANCE In vivo photo-cross-linking is a simple method that has been used to analyze the dynamic interactions of many cellular proteins. Originally developed in Escherichia coli, this system has been extended to studies in various organisms, making it a fundamental technique for investigating dynamic protein interactions in many cellular processes. This article is part of a Special issue entitled "Novel major techniques for visualizing 'live' protein molecules" edited by Dr. Daisuke Kohda.
Collapse
Affiliation(s)
- Ryoji Miyazaki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
| |
Collapse
|
16
|
Kempf G, Stjepanovic G, Sloan J, Hendricks A, Lapouge K, Sinning I. The Escherichia coli SRP Receptor Forms a Homodimer at the Membrane. Structure 2018; 26:1440-1450.e5. [PMID: 30146170 DOI: 10.1016/j.str.2018.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/14/2018] [Accepted: 07/22/2018] [Indexed: 01/19/2023]
Abstract
The Escherichia coli signal recognition particle (SRP) receptor, FtsY, plays a fundamental role in co-translational targeting of membrane proteins via the SRP pathway. Efficient targeting relies on membrane interaction of FtsY and heterodimerization with the SRP protein Ffh, which is driven by detachment of α helix (αN1) in FtsY. Here we show that apart from the heterodimer, FtsY forms a nucleotide-dependent homodimer on the membrane, and upon αN1 removal also in solution. Homodimerization triggers reciprocal stimulation of GTP hydrolysis and occurs in vivo. Biochemical characterization together with integrative modeling suggests that the homodimer employs the same interface as the heterodimer. Structure determination of FtsY NG+1 with GMPPNP shows that a dimerization-induced conformational switch of the γ-phosphate is conserved in Escherichia coli, filling an important gap in SRP GTPase activation. Our findings add to the current understanding of SRP GTPases and may challenge previous studies that did not consider homodimerization of FtsY.
Collapse
Affiliation(s)
- Georg Kempf
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Goran Stjepanovic
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Jeremy Sloan
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Astrid Hendricks
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany.
| |
Collapse
|
17
|
Draycheva A, Lee S, Wintermeyer W. Cotranslational protein targeting to the membrane: Nascent-chain transfer in a quaternary complex formed at the translocon. Sci Rep 2018; 8:9922. [PMID: 29967439 PMCID: PMC6028451 DOI: 10.1038/s41598-018-28262-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/20/2018] [Indexed: 11/29/2022] Open
Abstract
Membrane proteins in bacteria are cotranslationally inserted into the plasma membrane through the SecYEG translocon. Ribosomes exposing the signal-anchor sequence (SAS) of a membrane protein are targeted to the translocon by the signal recognition particle (SRP) pathway. SRP scans translating ribosomes and forms high-affinity targeting complexes with those exposing a SAS. Recognition of the SAS activates SRP for binding to its receptor, FtsY, which, in turn, is primed for SRP binding by complex formation with SecYEG, resulting in a quaternary targeting complex. Here we examine the effect of SecYEG docking to ribosome-nascent-chain complexes (RNCs) on SRP binding and SAS transfer, using SecYEG embedded in phospholipid-containing nanodiscs and monitoring FRET between fluorescence-labeled constituents of the targeting complex. SecYEG–FtsY binding to RNC–SRP complexes lowers the affinity of SRP to both ribosome and FtsY, indicating a general weakening of the complex due to partial binding competition near the ribosomal peptide exit. The rearrangement of the quaternary targeting complex to the pre-transfer complex requires an at least partially exposed SAS. The presence of SecYEG-bound FtsY and the length of the nascent chain strongly influence nascent-chain transfer from SRP to the translocon and repositioning of SRP in the post-transfer complex.
Collapse
Affiliation(s)
- Albena Draycheva
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Sejeong Lee
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Chemistry Research Laboratory, University of Oxford, OX1 3TA, Oxford, UK
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| |
Collapse
|
18
|
Knyazev DG, Kuttner R, Zimmermann M, Sobakinskaya E, Pohl P. Driving Forces of Translocation Through Bacterial Translocon SecYEG. J Membr Biol 2018; 251:329-343. [PMID: 29330604 PMCID: PMC6028853 DOI: 10.1007/s00232-017-0012-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 12/22/2017] [Indexed: 11/09/2022]
Abstract
This review focusses on the energetics of protein translocation via the Sec translocation machinery. First we complement structural data about SecYEG's conformational rearrangements by insight obtained from functional assays. These include measurements of SecYEG permeability that allow assessment of channel gating by ligand binding and membrane voltage. Second we will discuss the power stroke and Brownian ratcheting models of substrate translocation and the role that the two models assign to the putative driving forces: (i) ATP (SecA) and GTP (ribosome) hydrolysis, (ii) interaction with accessory proteins, (iii) membrane partitioning and folding, (iv) proton motive force (PMF), and (v) entropic contributions. Our analysis underlines how important energized membranes are for unravelling the translocation mechanism in future experiments.
Collapse
Affiliation(s)
- Denis G Knyazev
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria.
| | - Roland Kuttner
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | - Mirjam Zimmermann
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | | | - Peter Pohl
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| |
Collapse
|
19
|
Co-translational Folding Intermediate Dictates Membrane Targeting of the Signal Recognition Particle Receptor. J Mol Biol 2018; 430:1607-1620. [PMID: 29704493 DOI: 10.1016/j.jmb.2018.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 11/22/2022]
Abstract
Much of our knowledge on the function of proteins is deduced from their mature, folded states. However, it is unknown whether partially synthesized nascent protein segments can execute biological functions during translation and whether their premature folding states matter. A recent observation that a nascent chain performs a distinct function, co-translational targeting in vivo, has been made with the Escherichia coli signal recognition particle receptor FtsY, a major player in the conserved pathway of membrane protein biogenesis. FtsY functions as a membrane-associated entity, but very little is known about the mode of its targeting to the membrane. Here we investigated the underlying structural mechanism of the co-translational FtsY targeting to the membrane. Our results show that helices N2-4, which mediate membrane targeting, form a stable folding intermediate co-translationally that greatly differs from its fold in the mature FtsY. These results thus resolve a long-standing mystery of how the receptor targets the membrane even when deleted of its alleged membrane targeting sequence. The structurally distinct targeting determinant of FtsY exists only co-translationally. Our studies will facilitate further efforts to seek cellular factors required for proper targeting and association of FtsY with the membrane. Moreover, the results offer a hallmark example for how co-translational nascent intermediates may dictate biological functions.
Collapse
|
20
|
Petriman NA, Jauß B, Hufnagel A, Franz L, Sachelaru I, Drepper F, Warscheid B, Koch HG. The interaction network of the YidC insertase with the SecYEG translocon, SRP and the SRP receptor FtsY. Sci Rep 2018; 8:578. [PMID: 29330529 PMCID: PMC5766551 DOI: 10.1038/s41598-017-19019-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/20/2017] [Indexed: 12/26/2022] Open
Abstract
YidC/Oxa1/Alb3 are essential proteins that operate independently or cooperatively with the Sec machinery during membrane protein insertion in bacteria, archaea and eukaryotic organelles. Although the interaction between the bacterial SecYEG translocon and YidC has been observed in multiple studies, it is still unknown which domains of YidC are in contact with the SecYEG translocon. By in vivo and in vitro site-directed and para-formaldehyde cross-linking we identified the auxiliary transmembrane domain 1 of E. coli YidC as a major contact site for SecY and SecG. Additional SecY contacts were observed for the tightly packed globular domain and the C1 loop of YidC, which reveals that the hydrophilic cavity of YidC faces the lateral gate of SecY. Surprisingly, YidC-SecYEG contacts were only observed when YidC and SecYEG were present at about stoichiometric concentrations, suggesting that the YidC-SecYEG contact in vivo is either very transient or only observed for a very small SecYEG sub-population. This is different for the YidC-SRP and YidC-FtsY interaction, which involves the C1 loop of YidC and is efficiently observed even at sub-stoichiometric concentrations of SRP/FtsY. In summary, our data provide a first detailed view on how YidC interacts with the SecYEG translocon and the SRP-targeting machinery.
Collapse
Affiliation(s)
- Narcis-Adrian Petriman
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Benjamin Jauß
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Antonia Hufnagel
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Lisa Franz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Ilie Sachelaru
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Friedel Drepper
- Institute of Biology II, Biochemistry - Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry - Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany.
| |
Collapse
|
21
|
Zhou H, Wang C. Purification and function analysis of the Δ-17 fatty acid desaturase with or without transmembrane domain. Exp Ther Med 2017; 14:2117-2125. [PMID: 28962132 PMCID: PMC5609165 DOI: 10.3892/etm.2017.4790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 04/11/2017] [Indexed: 11/05/2022] Open
Abstract
Fatty acid desaturation enzymes perform dehydrogenation reactions leading to the insertion of double bonds in fatty acids. ω-3 desaturase has an important role in converting ω-6 fatty acids into ω-3 fatty acids. Although genes for this desaturase have been identified, the enzymatic activity of Δ-17 with or without transmembrane domain, and the function of the Δ-17 desaturase is poorly understood. In the present study, a transgenic microorganism was used to clone the Δ-17 full length (Δ-17FL) and Δ-17 without transmembrane domain (Δ-17NT), the expression efficiency was improved and western blotting was used to detect the protein expression level. The purification of Δ-17 was precipitated using saturated ammonium sulfate solution, dissolved in phosphate buffered saline buffer, and then filtered using a 10 kDa ultrafiltration cube. Gas chromatography analysis was used to measure the effect of Δ-17NT or Δ-17FL expression on Pichia pastoris fatty acid composition. Furthermore, the function of Δ-17NT in HepG2 cells was measured and the mechanism was explored. It was demonstrated that Δ-17NT decreased cell growth and increased apoptosis in hepatocellular carcinoma cell lines in vitro. In conclusion, successful expression of high levels of recombinant Δ-17NT represents a critical step towards the elucidation of the function of membrane fatty acid desaturases.
Collapse
Affiliation(s)
- Haoyu Zhou
- Department of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430000, P.R. China
| | - Chengming Wang
- Department of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430000, P.R. China
| |
Collapse
|
22
|
Rouck J, Krapf J, Roy J, Huff H, Das A. Recent advances in nanodisc technology for membrane protein studies (2012-2017). FEBS Lett 2017; 591:2057-2088. [PMID: 28581067 PMCID: PMC5751705 DOI: 10.1002/1873-3468.12706] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 01/01/2023]
Abstract
Historically, the main barrier to membrane protein investigations has been the tendency of membrane proteins to aggregate (due to their hydrophobic nature), in aqueous solution as well as on surfaces. The introduction of biomembrane mimetics has since stimulated momentum in the field. One such mimetic, the nanodisc (ND) system, has proved to be an exceptional system for solubilizing membrane proteins. Herein, we critically evaluate the advantages and imperfections of employing nanodiscs in biophysical and biochemical studies. Specifically, we examine the techniques that have been modified to study membrane proteins in nanodiscs. Techniques discussed here include fluorescence microscopy, solution-state/solid-state nuclear magnetic resonance, electron microscopy, small-angle X-ray scattering, and several mass spectroscopy methods. Newer techniques such as SPR, charge-sensitive optical detection, and scintillation proximity assays are also reviewed. Lastly, we cover how nanodiscs are advancing nanotechnology through nanoplasmonic biosensing, lipoprotein-nanoplatelets, and sortase-mediated labeling of nanodiscs.
Collapse
Affiliation(s)
- John Rouck
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - John Krapf
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Jahnabi Roy
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Hannah Huff
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Aditi Das
- Department of Comparative Biosciences, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
- Beckman Institute for Advanced Science, Division of Nutritional Sciences, Neuroscience Program and Department of Bioengineering, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| |
Collapse
|
23
|
Sachelaru I, Winter L, Knyazev DG, Zimmermann M, Vogt A, Kuttner R, Ollinger N, Siligan C, Pohl P, Koch HG. YidC and SecYEG form a heterotetrameric protein translocation channel. Sci Rep 2017; 7:101. [PMID: 28273911 PMCID: PMC5427846 DOI: 10.1038/s41598-017-00109-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/08/2017] [Indexed: 11/26/2022] Open
Abstract
The heterotrimeric SecYEG complex cooperates with YidC to facilitate membrane protein insertion by an unknown mechanism. Here we show that YidC contacts the interior of the SecY channel resulting in a ligand-activated and voltage-dependent complex with distinct ion channel characteristics. The SecYEG pore diameter decreases from 8 Å to only 5 Å for the YidC-SecYEG pore, indicating a reduction in channel cross-section by YidC intercalation. In the presence of a substrate, YidC relocates to the rim of the pore as indicated by increased pore diameter and loss of YidC crosslinks to the channel interior. Changing the surface charge of the pore by incorporating YidC into the channel wall increases the anion selectivity, and the accompanying change in wall hydrophobicity is liable to alter the partition of helices from the pore into the membrane. This could explain how the exit of transmembrane domains from the SecY channel is facilitated by YidC.
Collapse
Affiliation(s)
- Ilie Sachelaru
- grid.5963.9Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, Freiburg, 79104 Germany ,grid.5963.9Fakultät für Biologie, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, 79104 Freiburg, Germany
| | - Lukas Winter
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Denis G. Knyazev
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Mirjam Zimmermann
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Andreas Vogt
- grid.5963.9Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, Freiburg, 79104 Germany ,grid.5963.9Fakultät für Biologie, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, 79104 Freiburg, Germany ,grid.5963.9Spemann-Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Roland Kuttner
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Nicole Ollinger
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Christine Siligan
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020, Linz, Austria.
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, Freiburg, 79104, Germany. .,Spemann-Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany.
| |
Collapse
|
24
|
Abstract
The insertion and assembly of proteins into the inner membrane of bacteria are crucial for many cellular processes, including cellular respiration, signal transduction, and ion and pH homeostasis. This process requires efficient membrane targeting and insertion of proteins into the lipid bilayer in their correct orientation and proper conformation. Playing center stage in these events are the targeting components, signal recognition particle (SRP) and the SRP receptor FtsY, as well as the insertion components, the Sec translocon and the YidC insertase. Here, we will discuss new insights provided from the recent high-resolution structures of these proteins. In addition, we will review the mechanism by which a variety of proteins with different topologies are inserted into the inner membrane of Gram-negative bacteria. Finally, we report on the energetics of this process and provide information on how membrane insertion occurs in Gram-positive bacteria and Archaea. It should be noted that most of what we know about membrane protein assembly in bacteria is based on studies conducted in Escherichia coli.
Collapse
Affiliation(s)
- Andreas Kuhn
- Institute for Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Ross E Dalbey
- Department of Chemistry, The Ohio State University, Columbus, OH 43210
| |
Collapse
|
25
|
Draycheva A, Bornemann T, Ryazanov S, Lakomek N, Wintermeyer W. The bacterial SRP receptor, FtsY, is activated on binding to the translocon. Mol Microbiol 2016; 102:152-67. [DOI: 10.1111/mmi.13452] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Albena Draycheva
- Department of Physical BiochemistryMax Planck Institute for Biophysical ChemistryGöttingen Germany
| | - Thomas Bornemann
- Department of Physical BiochemistryMax Planck Institute for Biophysical ChemistryGöttingen Germany
| | - Sergey Ryazanov
- Department of NMR‐based Structural BiologyMax Planck Institute for Biophysical ChemistryGöttingen Germany
| | - Nils‐Alexander Lakomek
- Department of NMR‐based Structural BiologyMax Planck Institute for Biophysical ChemistryGöttingen Germany
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, Solid‐state NMRETH ZürichZürich Switzerland
| | - Wolfgang Wintermeyer
- Department of Physical BiochemistryMax Planck Institute for Biophysical ChemistryGöttingen Germany
| |
Collapse
|
26
|
Lakomek NA, Draycheva A, Bornemann T, Wintermeyer W. Electrostatics and Intrinsic Disorder Drive Translocon Binding of the SRP Receptor FtsY. Angew Chem Int Ed Engl 2016; 55:9544-7. [PMID: 27346853 PMCID: PMC5094494 DOI: 10.1002/anie.201602905] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/19/2016] [Indexed: 01/18/2023]
Abstract
Integral membrane proteins in bacteria are co‐translationally targeted to the SecYEG translocon for membrane insertion via the signal recognition particle (SRP) pathway. The SRP receptor FtsY and its N‐terminal A domain, which is lacking in any structural model of FtsY, were studied using NMR and fluorescence spectroscopy. The A domain is mainly disordered and highly flexible; it binds to lipids via its N terminus and the C‐terminal membrane targeting sequence. The central A domain binds to the translocon non‐specifically and maintains disorder. Translocon targeting and binding of the A domain is driven by electrostatic interactions. The intrinsically disordered A domain tethers FtsY to the translocon, and because of its flexibility, allows the FtsY NG domain to scan a large area for binding to the NG domain of ribosome‐bound SRP, thereby promoting the formation of the quaternary transfer complex at the membrane.
Collapse
Affiliation(s)
- Nils-Alexander Lakomek
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany. .,ETH Zurich, Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Physical Chemistry (LPC), Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Albena Draycheva
- Max-Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Thomas Bornemann
- Max-Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Wolfgang Wintermeyer
- Max-Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| |
Collapse
|
27
|
Lakomek NA, Draycheva A, Bornemann T, Wintermeyer W. Electrostatics and Intrinsic Disorder Drive Translocon Binding of the SRP Receptor FtsY. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nils-Alexander Lakomek
- Department of NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
- ETH Zurich; Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Physical Chemistry (LPC); Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Albena Draycheva
- Max-Planck Institute for Biophysical Chemistry; Department of Physical Biochemistry; Am Fassberg 11 37077 Göttingen Germany
| | - Thomas Bornemann
- Max-Planck Institute for Biophysical Chemistry; Department of Physical Biochemistry; Am Fassberg 11 37077 Göttingen Germany
| | - Wolfgang Wintermeyer
- Max-Planck Institute for Biophysical Chemistry; Department of Physical Biochemistry; Am Fassberg 11 37077 Göttingen Germany
| |
Collapse
|
28
|
|
29
|
Kuhn P, Draycheva A, Vogt A, Petriman NA, Sturm L, Drepper F, Warscheid B, Wintermeyer W, Koch HG. Ribosome binding induces repositioning of the signal recognition particle receptor on the translocon. J Cell Biol 2016; 211:91-104. [PMID: 26459600 PMCID: PMC4602035 DOI: 10.1083/jcb.201502103] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The cotranslational transfer of nascent membrane proteins to the SecYEG translocon is facilitated by a reorientation of the SecY-bound signal recognition particle (SRP) receptor, FtsY, which accompanies the formation of a quaternary targeting complex consisting of SecYEG, FtsY, SRP, and the ribosome. Cotranslational protein targeting delivers proteins to the bacterial cytoplasmic membrane or to the eukaryotic endoplasmic reticulum membrane. The signal recognition particle (SRP) binds to signal sequences emerging from the ribosomal tunnel and targets the ribosome-nascent-chain complex (RNC) to the SRP receptor, termed FtsY in bacteria. FtsY interacts with the fifth cytosolic loop of SecY in the SecYEG translocon, but the functional role of the interaction is unclear. By using photo-cross-linking and fluorescence resonance energy transfer measurements, we show that FtsY–SecY complex formation is guanosine triphosphate independent but requires a phospholipid environment. Binding of an SRP–RNC complex exposing a hydrophobic transmembrane segment induces a rearrangement of the SecY–FtsY complex, which allows the subsequent contact between SecY and ribosomal protein uL23. These results suggest that direct RNC transfer to the translocon is guided by the interaction between SRP and translocon-bound FtsY in a quaternary targeting complex.
Collapse
Affiliation(s)
- Patrick Kuhn
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Albena Draycheva
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Andreas Vogt
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Narcis-Adrian Petriman
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Lukas Sturm
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
30
|
Hannemann L, Suppanz I, Ba Q, MacInnes K, Drepper F, Warscheid B, Koch HG. Redox Activation of the Universally Conserved ATPase YchF by Thioredoxin 1. Antioxid Redox Signal 2016; 24:141-56. [PMID: 26160547 PMCID: PMC4742990 DOI: 10.1089/ars.2015.6272] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
AIMS YchF/Ola1 are unconventional members of the universally conserved GTPase family because they preferentially hydrolyze ATP rather than GTP. These ATPases have been associated with various cellular processes and pathologies, including DNA repair, tumorigenesis, and apoptosis. In particular, a possible role in regulating the oxidative stress response has been suggested for both bacterial and human YchF/Ola1. In this study, we analyzed how YchF responds to oxidative stress and how it potentially regulates the antioxidant response. RESULTS Our data identify a redox-regulated monomer-dimer equilibrium of YchF as a key event in the functional cycle of YchF. Upon oxidative stress, the oxidation of a conserved and surface-exposed cysteine residue promotes YchF dimerization, which is accompanied by inhibition of the ATPase activity. No dimers were observed in a YchF mutant lacking this cysteine. In vitro, the YchF dimer is dissociated by thioredoxin 1 (TrxA) and this stimulates the ATPase activity. The physiological significance of the YchF-thioredoxin 1 interaction was demonstrated by in vivo cross-linking, which validated this interaction in living cells. This approach also revealed that both the ATPase domain and the helical domain of YchF are in contact with TrxA. INNOVATION YchF/Ola1 are the first redox-regulated members of the universally conserved GTPase family and are inactivated by oxidation of a conserved cysteine residue within the nucleotide-binding motif. CONCLUSION Our data provide novel insights into the regulation of the so far ill-defined YchF/Ola1 family of proteins and stipulate their role as negative regulators of the oxidative stress response.
Collapse
Affiliation(s)
- Liya Hannemann
- 1 Institut für Biochemie und Molekularbiologie, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany
| | - Ida Suppanz
- 2 Faculty of Biology, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany .,3 BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany
| | - Qiaorui Ba
- 1 Institut für Biochemie und Molekularbiologie, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany .,2 Faculty of Biology, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany
| | - Katherine MacInnes
- 1 Institut für Biochemie und Molekularbiologie, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany
| | - Friedel Drepper
- 2 Faculty of Biology, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany .,3 BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany
| | - Bettina Warscheid
- 2 Faculty of Biology, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany .,3 BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany
| | - Hans-Georg Koch
- 1 Institut für Biochemie und Molekularbiologie, Albert-Ludwigs-Universität Freiburg , Freiburg, Germany
| |
Collapse
|
31
|
Elvekrog MM, Walter P. Dynamics of co-translational protein targeting. Curr Opin Chem Biol 2015; 29:79-86. [PMID: 26517565 DOI: 10.1016/j.cbpa.2015.09.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/15/2015] [Indexed: 12/20/2022]
Abstract
Most membrane and secretory proteins are delivered co-translationally to protein translocation channels in their destination membrane by the signal recognition particle (SRP) and its receptor. This co-translational molecular machinery is conserved across all kingdoms of life, though it varies in composition and function. Here we report recent progress towards understanding the mechanism of SRP function, focusing on findings about Escherichia coli SRP's conformational dynamics throughout the targeting process. These insights shed light on a key checkpoint in the targeting cycle: how SRP regulates engagement of an actively translating ribosome with the translocation machinery at the membrane.
Collapse
Affiliation(s)
- Margaret M Elvekrog
- The Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, United States
| | - Peter Walter
- The Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, United States.
| |
Collapse
|
32
|
Walter B, Hristou A, Nowaczyk MM, Schünemann D. In vitro reconstitution of co-translational D1 insertion reveals a role of the cpSec-Alb3 translocase and Vipp1 in photosystem II biogenesis. Biochem J 2015; 468:315-24. [PMID: 25803492 DOI: 10.1042/bj20141425] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Photosystem II (PS II) is a multi-subunit complex localized in the thylakoid membrane that performs the light-dependent photosynthetic charge separation. The PS II reaction centre comprises, among others, the D1 protein. De novo synthesis and repair of PS II require efficient mechanisms for transport and insertion of plastid encoded D1 into the thylakoid membrane. To elucidate the process of D1 insertion, we used an in vitro translation system derived from pea chloroplasts to reconstitute the D1 insertion. Thereby, truncated D1 encoding psbA mRNAs lacking a stop codon were translated in the presence of thylakoid membranes and the translation was stalled by addition of chloramphenicol. The generated ribosome nascent chain complexes (RNCs) were tightly associated with the thylakoids. Subsequently, these D1 insertion intermediates were enriched from solubilized thylakoids by sucrose cushion centrifugation. Immunological analyses demonstrated the presence of the cpSec translocase, Alb3, cpFtsY, cpSRP54 and Vipp1 (vesicle-inducing protein in plastids 1) in the enriched D1 insertion intermediates. A complex formation between cpSecY, Alb3, cpFtsY and Vipp1 in thylakoid membranes was shown by gel filtration chromatography, BN (Blue Native)/SDS-PAGE and co-immunoprecipitation experiments. Furthermore, a stimulating effect of recombinant Vipp1 on the formation of a D1 insertion intermediate was observed in vitro. These results suggest a co-operative function of these proteins in D1 insertion.
Collapse
Affiliation(s)
- Björn Walter
- *Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Athina Hristou
- *Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Marc M Nowaczyk
- †Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Danja Schünemann
- *Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780 Bochum, Germany
| |
Collapse
|
33
|
Kinori A, Bibi E. Co-translational membrane association of the Escherichia coli SRP receptor. J Cell Sci 2015; 128:1444-52. [DOI: 10.1242/jcs.166116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The signal recognition particle (SRP) receptor is a major player in the pathway of membrane protein biogenesis in all organisms. The receptor functions as a membrane bound entity but very little is known about its targeting to the membrane. Here we demonstrate in vivo that the Escherichia coli SRP receptor targets the membrane co-translationally. This requires emergence from the ribosome of the 4 helix-long N-domain of the receptor of which only helices 2–4 are required for co-translational membrane attachment. The results also suggest that the targeting might be regulated co-translationally. Together, our in vivo studies shed light on the biogenesis of the SRP receptor and its hypothetical role in targeting ribosomes to the Escherichia coli membrane.
Collapse
|
34
|
Sachelaru I, Petriman NA, Kudva R, Koch HG. Dynamic interaction of the sec translocon with the chaperone PpiD. J Biol Chem 2014; 289:21706-15. [PMID: 24951590 DOI: 10.1074/jbc.m114.577916] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Sec translocon constitutes a ubiquitous protein transport channel that consists in bacteria of the three core components: SecY, SecE, and SecG. Additional proteins interact with SecYEG during different stages of protein transport. During targeting, SecYEG interacts with SecA, the SRP receptor, or the ribosome. Protein transport into or across the membrane is then facilitated by the interaction of SecYEG with YidC and the SecDFYajC complex. During protein transport, SecYEG is likely to interact also with the protein quality control machinery, but details about this interaction are missing. By in vivo and in vitro site-directed cross-linking, we show here that the periplasmic chaperone PpiD is located in front of the lateral gate of SecY, through which transmembrane domains exit the SecY channel. The strongest contacts were found to helix 2b of SecY. Blue native PAGE analyses verify the presence of a SecYEG-PpiD complex in native Escherichia coli membranes. The PpiD-SecY interaction was not influenced by the addition of SecA and only weakly influenced by binding of nontranslating ribosomes to SecYEG. In contrast, PpiD lost contact to the lateral gate of SecY during membrane protein insertion. These data identify PpiD as an additional and transient subunit of the bacterial SecYEG translocon. The data furthermore demonstrate the highly modular and versatile composition of the Sec translocon, which is probably essential for its ability to transport a wide range of substrates across membranes in bacteria and eukaryotes.
Collapse
Affiliation(s)
- Ilie Sachelaru
- From the Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, the Faculty of Biology, and
| | - Narcis-Adrian Petriman
- From the Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, the Faculty of Biology, and
| | - Renuka Kudva
- From the Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, the Faculty of Biology, and the Spemann-Graduate School of Biology and Medicine, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- From the Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, the Spemann-Graduate School of Biology and Medicine, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
35
|
Visualization of a polytopic membrane protein during SecY-mediated membrane insertion. Nat Commun 2014; 5:4103. [PMID: 24912953 DOI: 10.1038/ncomms5103] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 05/13/2014] [Indexed: 01/16/2023] Open
Abstract
The biogenesis of polytopic membrane proteins occurs co-translationally on ribosomes that are tightly bound to a membrane-embedded protein-conducting channel: the Sec-complex. The path that is followed by nascent proteins inside the ribosome and the Sec-complex is relatively well established; however, it is not clear what the fate of the N-terminal transmembrane domains (TMDs) of polytopic membrane proteins is when the C-terminal TMDs domains are not yet synthesized. Here, we present the sub-nanometer cryo-electron microscopy structure of an in vivo generated ribosome-SecY complex that carries a membrane insertion intermediate of proteorhodopsin (PR). The structure reveals a pre-opened Sec-complex and the first two TMDs of PR already outside the SecY complex directly in front of its proposed lateral gate. Thus, our structure is in agreement with positioning of N-terminal TMDs at the periphery of SecY, and in addition, it provides clues for the molecular mechanism underlying membrane protein topogenesis.
Collapse
|
36
|
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]
|
37
|
Zhou Y, Ueda T, Müller M. Signal recognition particle and SecA cooperate during export of secretory proteins with highly hydrophobic signal sequences. PLoS One 2014; 9:e92994. [PMID: 24717922 PMCID: PMC3981701 DOI: 10.1371/journal.pone.0092994] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/28/2014] [Indexed: 12/03/2022] Open
Abstract
The Sec translocon of bacterial plasma membranes mediates the linear translocation of secretory proteins as well as the lateral integration of membrane proteins. Integration of many membrane proteins occurs co-translationally via the signal recognition particle (SRP)-dependent targeting of ribosome-associated nascent chains to the Sec translocon. In contrast, translocation of classical secretory proteins across the Sec translocon is a post-translational event requiring no SRP but the motor protein SecA. Secretory proteins were, however, reported to utilize SRP in addition to SecA, if the hydrophobicity of their signal sequences exceeds a certain threshold value. Here we have analyzed transport of this subgroup of secretory proteins across the Sec translocon employing an entirely defined in vitro system. We thus found SecA to be both necessary and sufficient for translocation of secretory proteins with hydrophobic signal sequences, whereas SRP and its receptor improved translocation efficiency. This SRP-mediated boost of translocation is likely due to the early capture of the hydrophobic signal sequence by SRP as revealed by site-specific photo cross-linking of ribosome nascent chain complexes.
Collapse
Affiliation(s)
- Yufan Zhou
- Institute of Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Zellforschung, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Takuya Ueda
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Matthias Müller
- Institute of Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Zellforschung, University of Freiburg, Freiburg, Germany
- * E-mail:
| |
Collapse
|
38
|
Parker MS, Sah R, Balasubramaniam A, Sallee FR, Park EA, Parker SL. On the expansion of ribosomal proteins and RNAs in eukaryotes. Amino Acids 2014; 46:1589-604. [PMID: 24633358 DOI: 10.1007/s00726-014-1704-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 02/18/2014] [Indexed: 01/11/2023]
Abstract
While the ribosome constitution is similar in all biota, there is a considerable increase in size of both ribosomal proteins (RPs) and RNAs in eukaryotes as compared to archaea and bacteria. This is pronounced in the large (60S) ribosomal subunit (LSU). In addition to enlargement (apparently maximized already in lower eukarya), the RP changes include increases in fraction, segregation and clustering of basic residues, and decrease in hydrophobicity. The acidic fraction is lower in eukaryote as compared to prokaryote RPs. In all eukaryote groups tested, the LSU RPs have significantly higher content of basic residues and homobasic segments than the SSU RPs. The vertebrate LSU RPs have much higher sequestration of basic residues than those of bacteria, archaea and even of the lower eukarya. The basic clusters are highly aligned in the vertebrate, but less in the lower eukarya, and only within families in archaea and bacteria. Increase in the basicity of RPs, besides helping transport to the nucleus, should promote stability of the assembled ribosome as well as the association with translocons and other intracellular matrix proteins. The size and GC nucleotide bias of the expansion segments of large LSU rRNAs also culminate in the vertebrate, and should support ribosome association with the endoplasmic reticulum and other intracellular networks. However, the expansion and nucleotide bias of eukaryote LSU rRNAs do not clearly correlate with changes in ionic parameters of LSU ribosomal proteins.
Collapse
Affiliation(s)
- Michael S Parker
- Department of Microbiology and Molecular Cell Sciences, University of Memphis, Memphis, TN, 38152, USA
| | | | | | | | | | | |
Collapse
|
39
|
Lim B, Miyazaki R, Neher S, Siegele DA, Ito K, Walter P, Akiyama Y, Yura T, Gross CA. Heat shock transcription factor σ32 co-opts the signal recognition particle to regulate protein homeostasis in E. coli. PLoS Biol 2013; 11:e1001735. [PMID: 24358019 PMCID: PMC3866087 DOI: 10.1371/journal.pbio.1001735] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022] Open
Abstract
The bacterial heat shock transcription factor, σ32, maintains proper protein homeostasis only after it is targeted to the inner membrane by the signal recognition particle (SRP), thereby enabling integration of protein folding information from both the cytoplasm and cell membrane. All cells must adapt to rapidly changing conditions. The heat shock response (HSR) is an intracellular signaling pathway that maintains proteostasis (protein folding homeostasis), a process critical for survival in all organisms exposed to heat stress or other conditions that alter the folding of the proteome. Yet despite decades of study, the circuitry described for responding to altered protein status in the best-studied bacterium, E. coli, does not faithfully recapitulate the range of cellular responses in response to this stress. Here, we report the discovery of the missing link. Surprisingly, we found that σ32, the central transcription factor driving the HSR, must be localized to the membrane rather than dispersed in the cytoplasm as previously assumed. Genetic analyses indicate that σ32 localization results from a protein targeting reaction facilitated by the signal recognition particle (SRP) and its receptor (SR), which together comprise a conserved protein targeting machine and mediate the cotranslational targeting of inner membrane proteins to the membrane. SRP interacts with σ32 directly and transports it to the inner membrane. Our results show that σ32 must be membrane-associated to be properly regulated in response to the protein folding status in the cell, explaining how the HSR integrates information from both the cytoplasm and bacterial cell membrane. All cells have to adjust to frequent changes in their environmental conditions. The heat shock response is a signaling pathway critical for survival of all organisms exposed to elevated temperatures. Under such conditions, the heat shock response maintains enzymes and other proteins in a properly folded state. The mechanisms for sensing temperature and the subsequent induction of the appropriate transcriptional response have been extensively studied. Prior to this work, however, the circuitry described in the best studied bacterium E. coli could not fully explain the range of cellular responses that are observed following heat shock. We report the discovery of this missing link. Surprisingly, we find that σ32, a transcription factor that induces gene expression during heat shock, needs to be localized to the membrane, rather than being active as a soluble cytoplasmic protein as previously thought. We show that, equally surprisingly, σ32 is targeted to the membrane by the signal recognition particle (SRP) and its receptor (SR). SRP and SR constitute a conserved protein targeting machine that normally only operates on membrane and periplasmic proteins that contain identifiable signal sequences. Intriguingly, σ32 does not have any canonical signal sequence for export or membrane-integration. Our results indicate that membrane-associated σ32, not soluble cytoplasmic σ32, is the preferred target of regulatory control in response to heat shock. Our new model thus explains how protein folding status from both the cytoplasm and bacterial cell membrane can be integrated to control the heat shock response.
Collapse
Affiliation(s)
- Bentley Lim
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California, United States of America
| | - Ryoji Miyazaki
- Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Saskia Neher
- Department of Biochemistry and Biophysics and Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California United States of America
| | - Deborah A. Siegele
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Koreaki Ito
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Peter Walter
- Department of Biochemistry and Biophysics and Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California United States of America
| | - Yoshinori Akiyama
- Institute for Virus Research, Kyoto University, Kyoto, Japan
- * E-mail: (Y.A.); (T.Y.); (C.A.G.)
| | - Takashi Yura
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- * E-mail: (Y.A.); (T.Y.); (C.A.G.)
| | - Carol A. Gross
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California, United States of America
- Department of Cell and Tissue Biology, University of California at San Francisco, San Francisco, California, United States
- * E-mail: (Y.A.); (T.Y.); (C.A.G.)
| |
Collapse
|
40
|
Saraogi I, Shan SO. Co-translational protein targeting to the bacterial membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1433-41. [PMID: 24513458 DOI: 10.1016/j.bbamcr.2013.10.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 12/18/2022]
Abstract
Co-translational protein targeting by the Signal Recognition Particle (SRP) is an essential cellular pathway that couples the synthesis of nascent proteins to their proper cellular localization. The bacterial SRP, which contains the minimal ribonucleoprotein core of this universally conserved targeting machine, has served as a paradigm for understanding the molecular basis of protein localization in all cells. In this review, we highlight recent biochemical and structural insights into the molecular mechanisms by which fundamental challenges faced by protein targeting machineries are met in the SRP pathway. Collectively, these studies elucidate how an essential SRP RNA and two regulatory GTPases in the SRP and SRP receptor (SR) enable this targeting machinery to recognize, sense and respond to its biological effectors, i.e. the cargo protein, the target membrane and the translocation machinery, thus driving efficient and faithful co-translational protein targeting. 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)
- Ishu Saraogi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|
41
|
Kedrov A, Kusters I, Driessen AJM. Single-Molecule Studies of Bacterial Protein Translocation. Biochemistry 2013; 52:6740-54. [DOI: 10.1021/bi400913x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Alexej Kedrov
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Ilja Kusters
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| |
Collapse
|
42
|
Kudva R, Denks K, Kuhn P, Vogt A, Müller M, Koch HG. Protein translocation across the inner membrane of Gram-negative bacteria: the Sec and Tat dependent protein transport pathways. Res Microbiol 2013; 164:505-34. [DOI: 10.1016/j.resmic.2013.03.016] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
|
43
|
Sachelaru I, Petriman NA, Kudva R, Kuhn P, Welte T, Knapp B, Drepper F, Warscheid B, Koch HG. YidC occupies the lateral gate of the SecYEG translocon and is sequentially displaced by a nascent membrane protein. J Biol Chem 2013; 288:16295-16307. [PMID: 23609445 DOI: 10.1074/jbc.m112.446583] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most membrane proteins are co-translationally inserted into the lipid bilayer via the universally conserved SecY complex and they access the lipid phase presumably via a lateral gate in SecY. In bacteria, the lipid transfer of membrane proteins from the SecY channel is assisted by the SecY-associated protein YidC, but details on the SecY-YidC interaction are unknown. By employing an in vivo and in vitro site-directed cross-linking approach, we have mapped the SecY-YidC interface and found YidC in contact with all four transmembrane domains of the lateral gate. This interaction did not require the SecDFYajC complex and was not influenced by SecA binding to SecY. In contrast, ribosomes dissociated the YidC contacts to lateral gate helices 2b and 8. The major contact between YidC and the lateral gate was lost in the presence of ribosome nascent chains and new SecY-YidC contacts appeared. These data demonstrate that the SecY-YidC interaction is influenced by nascent-membrane-induced lateral gate movements.
Collapse
Affiliation(s)
- Ilie Sachelaru
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Fakultät für Biologie, 79104 Freiburg, Germany
| | - Narcis Adrian Petriman
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Fakultät für Biologie, 79104 Freiburg, Germany
| | - Renuka Kudva
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Fakultät für Biologie, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), 79104 Freiburg, Germany
| | - Patrick Kuhn
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Fakultät für Biologie, 79104 Freiburg, Germany
| | - Thomas Welte
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany
| | | | - Friedel Drepper
- Fakultät für Biologie, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Zentrum für Biologische Signalstudien, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Fakultät für Biologie, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Zentrum für Biologische Signalstudien, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), 79104 Freiburg, Germany.
| |
Collapse
|
44
|
Abstract
The signal recognition particle (SRP) and its receptor compose a universally conserved and essential cellular machinery that couples the synthesis of nascent proteins to their proper membrane localization. The past decade has witnessed an explosion in in-depth mechanistic investigations of this targeting machine at increasingly higher resolutions. In this review, we summarize recent work that elucidates how the SRP and SRP receptor interact with the cargo protein and the target membrane, respectively, and how these interactions are coupled to a novel GTPase cycle in the SRP·SRP receptor complex to provide the driving force and enhance the fidelity of this fundamental cellular pathway. We also discuss emerging frontiers in which important questions remain to be addressed.
Collapse
Affiliation(s)
- David Akopian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Kuang Shen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Xin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| |
Collapse
|
45
|
Akopian D, Dalal K, Shen K, Duong F, Shan SO. SecYEG activates GTPases to drive the completion of cotranslational protein targeting. ACTA ACUST UNITED AC 2013; 200:397-405. [PMID: 23401005 PMCID: PMC3575545 DOI: 10.1083/jcb.201208045] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
SecYEG drives conformational changes in the cotranslational targeting complex to activate it for GTP hydrolysis and the handover of the translating ribosome. Signal recognition particle (SRP) and its receptor (SR) comprise a highly conserved cellular machine that cotranslationally targets proteins to a protein-conducting channel, the bacterial SecYEG or eukaryotic Sec61p complex, at the target membrane. Whether SecYEG is a passive recipient of the translating ribosome or actively regulates this targeting machinery remains unclear. Here we show that SecYEG drives conformational changes in the cargo-loaded SRP–SR targeting complex that activate it for GTP hydrolysis and for handover of the translating ribosome. These results provide the first evidence that SecYEG actively drives the efficient delivery and unloading of translating ribosomes at the target membrane.
Collapse
Affiliation(s)
- David Akopian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | | | | |
Collapse
|
46
|
Lohmeyer E, Schröder S, Pawlik G, Trasnea PI, Peters A, Daldal F, Koch HG. The ScoI homologue SenC is a copper binding protein that interacts directly with the cbb₃-type cytochrome oxidase in Rhodobacter capsulatus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:2005-15. [PMID: 22771512 DOI: 10.1016/j.bbabio.2012.06.621] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 11/28/2022]
Abstract
Sco proteins are widespread assembly factors for the Cu(A) centre of aa₃-type cytochrome oxidases in eukaryotic and prokaryotic organisms. However, Sco homologues are also found in bacteria like Rhodobacter capsulatus which lack aa₃-type cytochrome oxidases and instead use a cbb₃-type cytochrome oxidase (cbb₃ Cox) without a Cu(A) centre as a terminal oxidase. In the current study, we have analyzed the role of Sco (SenC) during cbb₃ Cox assembly in R. capsulatus. In agreement with earlier works, we found a strong cbb₃ Cox defect in the absence of SenC that impairs the steady-state stability of the CcoN, CcoO and CcoP core subunits, without the accumulation of detectable assembly intermediates. In vivo cross-linking results demonstrate that SenC is in close proximity to the CcoP and CcoH subunits of cbb₃ Cox, suggesting that SenC interacts directly with cbb₃ Cox during its assembly. SenC binds copper and the cbb₃ Cox assembly defect in the absence of SenC can be rescued by the addition of least 0.5μM Cu. Neither copper nor SenC influenced the transcription of the ccoNOQP operon encoding for cbb₃ Cox. Transcription of senC itself was also not influenced by Cu unless the putative Cu-export ATPase CcoI was absent. As CcoI is specifically required for the cbb₃ Cox assembly, these data provide a direct link between Cu delivery to cbb₃ Cox and SenC function.
Collapse
Affiliation(s)
- Eva Lohmeyer
- Institut für Biochemie und Molekularbiologie, ZBMZ, Stefan-Meier-Strasse 17, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.
| | | | | | | | | | | | | |
Collapse
|
47
|
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]
|
48
|
Wu ZC, de Keyzer J, Kedrov A, Driessen AJM. Competitive binding of the SecA ATPase and ribosomes to the SecYEG translocon. J Biol Chem 2012; 287:7885-95. [PMID: 22267723 DOI: 10.1074/jbc.m111.297911] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During co-translational membrane insertion of membrane proteins with large periplasmic domains, the bacterial SecYEG complex needs to interact both with the ribosome and the SecA ATPase. Although the binding sites for SecA and the ribosome overlap, it has been suggested that these ligands can interact simultaneously with SecYEG. We used surface plasmon resonance and fluorescence correlation spectroscopy to examine the interaction of SecA and ribosomes with the SecYEG complex present in membrane vesicles and the purified SecYEG complex present in a detergent-solubilized state or reconstituted into nanodiscs. Ribosome binding to the SecYEG complex is strongly stimulated when the ribosomes are charged with nascent chains of the monotopic membrane protein FtsQ. This binding is competed by an excess of SecA, indicating that binding of SecA and ribosomes to SecYEG is mutually exclusive.
Collapse
Affiliation(s)
- Zht Cheng Wu
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | | | | |
Collapse
|
49
|
Zhang XX, Chan CS, Bao H, Fang Y, Foster LJ, Duong F. Nanodiscs and SILAC-based mass spectrometry to identify a membrane protein interactome. J Proteome Res 2011; 11:1454-9. [PMID: 22129326 DOI: 10.1021/pr200846y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Integral membrane proteins are challenging to work with biochemically given their insoluble nature; the nanodisc circumvents the difficulty by stabilizing them in small patches of lipid bilayer. Here, we show that nanodiscs combined with SILAC-based quantitative proteomics can be used to identify the soluble interacting partners of virtually any membrane protein. As a proof of principle, we applied the method to the bacterial SecYEG protein-conducting channel, the maltose transporter MalFGK(2) and the membrane integrase YidC. In contrast to the detergent micelles, which tend to destabilize interactions, the nanodisc was able to capture out of a complex whole cell extract the proteins SecA, Syd, and MalE with a high degree of confidence and specificity. The method was sensitive enough to isolate these interactors as a function of the lipid composition in the disc and the culture conditions. In agreement with a previous photo-cross linking analysis, YidC did not show any high-affinity interactions with cytosolic or periplasmic proteins. These three examples illustrate the utility of nanoscale lipid bilayers to identify the soluble peripheral partners of proteins intergrated in the lipid bilayer.
Collapse
Affiliation(s)
- Xiao X Zhang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | | | | |
Collapse
|
50
|
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.
Collapse
Affiliation(s)
- Joen Luirink
- Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | | | | | | |
Collapse
|