1
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Bischoff A, Ortelt J, Dünschede B, Zegarra V, Bedrunka P, Bange G, Schünemann D. The role of chloroplast SRP54 domains and its C-terminal tail region in post- and co-translational protein transport in vivo. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5734-5749. [PMID: 38989593 PMCID: PMC11427828 DOI: 10.1093/jxb/erae293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/10/2024] [Indexed: 07/12/2024]
Abstract
In the chloroplast, the 54 kDa subunit of the signal recognition particle (cpSRP54) is involved in the post-translational transport of the light-harvesting chlorophyll a/b-binding proteins (LHCPs) and the co-translational transport of plastid-encoded subunits of the photosynthetic complexes to the thylakoid membrane. It forms a high-affinity complex with plastid-specific cpSRP43 for post-translational transport, while a ribosome-associated pool coordinates its co-translational function. CpSRP54 constitutes a conserved multidomain protein, comprising a GTPase (NG) and a methionine-rich (M) domain linked by a flexible region. It is further characterized by a plastid-specific C-terminal tail region containing the cpSRP43-binding motif. To characterize the physiological role of the various regions of cpSRP54 in thylakoid membrane protein transport, we generated Arabidopsis cpSRP54 knockout (ffc1-2) lines producing truncated cpSRP54 variants or a GTPase point mutation variant. Phenotypic characterization of the complementation lines demonstrated that the C-terminal tail region of cpSRP54 plays an important role exclusively in post-translational LHCP transport. Furthermore, we show that the GTPase activity of cpSRP54 plays an essential role in the transport pathways for both nuclear as well as plastid-encoded proteins. In addition, our data revealed that plants expressing cpSRP54 without the C-terminal region exhibit a strongly increased accumulation of a photosystem I assembly intermediate.
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Affiliation(s)
- Annika Bischoff
- Molecular Biology of Plant Organelles, Ruhr University Bochum, Bochum, Germany
| | - Jennifer Ortelt
- Molecular Biology of Plant Organelles, Ruhr University Bochum, Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Ruhr University Bochum, Bochum, Germany
| | - Victor Zegarra
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Marburg, Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Marburg, Germany
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr University Bochum, Bochum, Germany
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2
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Chen S, Collart MA. Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression. J Mol Biol 2024; 436:168579. [PMID: 38648968 DOI: 10.1016/j.jmb.2024.168579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.
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Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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3
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Dornes A, Mais CN, Bange G. Structure of the GDP-bound state of the SRP GTPase FlhF. Acta Crystallogr F Struct Biol Commun 2024; 80:53-58. [PMID: 38376823 PMCID: PMC10910532 DOI: 10.1107/s2053230x24000979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/27/2024] [Indexed: 02/21/2024] Open
Abstract
The GTPase FlhF, a signal recognition particle (SRP)-type enzyme, is pivotal for spatial-numerical control and bacterial flagella assembly across diverse species, including pathogens. This study presents the X-ray structure of FlhF in its GDP-bound state at a resolution of 2.28 Å. The structure exhibits the classical N- and G-domain fold, consistent with related SRP GTPases such as Ffh and FtsY. Comparative analysis with GTP-loaded FlhF elucidates the conformational changes associated with GTP hydrolysis. These topological reconfigurations are similarly evident in Ffh and FtsY, and play a pivotal role in regulating the functions of these hydrolases.
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Affiliation(s)
- Anita Dornes
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
| | - Christopher-Nils Mais
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
- Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
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4
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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.
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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.
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5
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Pool MR. Targeting of Proteins for Translocation at the Endoplasmic Reticulum. Int J Mol Sci 2022; 23:ijms23073773. [PMID: 35409131 PMCID: PMC8998515 DOI: 10.3390/ijms23073773] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
The endoplasmic reticulum represents the gateway to the secretory pathway. Here, proteins destined for secretion, as well as soluble and membrane proteins that reside in the endomembrane system and plasma membrane, are triaged from proteins that will remain in the cytosol or be targeted to other cellular organelles. This process requires the faithful recognition of specific targeting signals and subsequent delivery mechanisms to then target them to the translocases present at the ER membrane, which can either translocate them into the ER lumen or insert them into the lipid bilayer. This review focuses on the current understanding of the first step in this process representing the targeting phase. Targeting is typically mediated by cleavable N-terminal hydrophobic signal sequences or internal membrane anchor sequences; these can either be captured co-translationally at the ribosome or recognised post-translationally and then delivered to the ER translocases. Location and features of the targeting sequence dictate which of several overlapping targeting pathway substrates will be used. Mutations in the targeting machinery or targeting signals can be linked to diseases.
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Affiliation(s)
- Martin R Pool
- School of Biological Science, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
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6
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How to save a bacterial ribosome in times of stress. Semin Cell Dev Biol 2022; 136:3-12. [PMID: 35331628 DOI: 10.1016/j.semcdb.2022.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/01/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022]
Abstract
Biogenesis of ribosomes is one of the most cost- and resource-intensive processes in all living cells. In bacteria, ribosome biogenesis is rate-limiting for growth and must be tightly coordinated to yield maximum fitness of the cells. Since bacteria are continuously facing environmental changes and stress conditions, they have developed sophisticated systems to sense and regulate their nutritional status. Amino acid starvation leads to the synthesis and accumulation of the nucleotide-based second messengers ppGpp and pppGpp [(p)ppGpp], which in turn function as central players of a pleiotropic metabolic adaptation mechanism named the stringent response. Here, we review our current knowledge on the multiple roles of (p)ppGpp in the stress-related modulation of the prokaryotic protein biosynthesis machinery with the ribosome as its core constituent. The alarmones ppGpp/pppGpp act as competitors of their GDP/GTP counterparts, to affect a multitude of ribosome-associated P-loop GTPases involved in the translation cycle, ribosome biogenesis and hibernation. A similar mode of inhibition has been found for the GTPases of the proteins involved in the SRP-dependent membrane-targeting machinery present in the periphery of the ribosome. In this sense, during stringent conditions, binding of (p)ppGpp restricts the membrane insertion and secretion of proteins. Altogether, we highlight the enormously resource-intensive stages of ribosome biogenesis as a critical regulatory hub of the stringent response that ultimately tunes the protein synthesis capacity and consequently the survival of the cell.
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7
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Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp. Nat Commun 2022; 13:1069. [PMID: 35217658 PMCID: PMC8881573 DOI: 10.1038/s41467-022-28675-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/07/2022] [Indexed: 11/08/2022] Open
Abstract
The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known as (p)ppGpp. Here, we report that (p)ppGpp inhibits the signal recognition particle (SRP)-dependent protein targeting pathway, which is essential for membrane protein biogenesis and protein secretion. More specifically, (p)ppGpp binds to the SRP GTPases Ffh and FtsY, and inhibits the formation of the SRP receptor-targeting complex, which is central for the coordinated binding of the translating ribosome to the SecYEG translocon. Cryo-EM analysis of SRP bound to translating ribosomes suggests that (p)ppGpp may induce a distinct conformational stabilization of the NG domain of Ffh and FtsY in Bacillus subtilis but not in E. coli. Bacterial responses to nutrient limitation and other stress conditions are often modulated by the nucleotide-based second messenger (p)ppGpp. Here, the authors show that (p)ppGpp inhibits the SRP membrane-protein insertion and secretion pathway by binding to GTPases Ffh and FtsY.
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8
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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]
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9
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Hsieh HH, Shan SO. Fidelity of Cotranslational Protein Targeting to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:ijms23010281. [PMID: 35008707 PMCID: PMC8745203 DOI: 10.3390/ijms23010281] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 02/04/2023] Open
Abstract
Fidelity of protein targeting is essential for the proper biogenesis and functioning of organelles. Unlike replication, transcription and translation processes, in which multiple mechanisms to recognize and reject noncognate substrates are established in energetic and molecular detail, the mechanisms by which cells achieve a high fidelity in protein localization remain incompletely understood. Signal recognition particle (SRP), a conserved pathway to mediate the localization of membrane and secretory proteins to the appropriate cellular membrane, provides a paradigm to understand the molecular basis of protein localization in the cell. In this chapter, we review recent progress in deciphering the molecular mechanisms and substrate selection of the mammalian SRP pathway, with an emphasis on the key role of the cotranslational chaperone NAC in preventing protein mistargeting to the ER and in ensuring the organelle specificity of protein localization.
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10
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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11
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Take Me Home, Protein Roads: Structural Insights into Signal Peptide Interactions during ER Translocation. Int J Mol Sci 2021; 22:ijms222111871. [PMID: 34769302 PMCID: PMC8584900 DOI: 10.3390/ijms222111871] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/14/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Cleavable endoplasmic reticulum (ER) signal peptides (SPs) and other non-cleavable signal sequences target roughly a quarter of the human proteome to the ER. These short peptides, mostly located at the N-termini of proteins, are highly diverse. For most proteins targeted to the ER, it is the interactions between the signal sequences and the various ER targeting and translocation machineries such as the signal recognition particle (SRP), the protein-conducting channel Sec61, and the signal peptidase complex (SPC) that determine the proteins’ target location and provide translocation fidelity. In this review, we follow the signal peptide into the ER and discuss the recent insights that structural biology has provided on the governing principles of those interactions.
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12
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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.
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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
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13
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Mysore VP, Zhou ZW, Ambrogio C, Li L, Kapp JN, Lu C, Wang Q, Tucker MR, Okoro JJ, Nagy-Davidescu G, Bai X, Plückthun A, Jänne PA, Westover KD, Shan Y, Shaw DE. A structural model of a Ras-Raf signalosome. Nat Struct Mol Biol 2021; 28:847-857. [PMID: 34625747 PMCID: PMC8643099 DOI: 10.1038/s41594-021-00667-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/25/2021] [Indexed: 01/29/2023]
Abstract
The protein K-Ras functions as a molecular switch in signaling pathways regulating cell growth. In the human mitogen-activated protein kinase (MAPK) pathway, which is implicated in many cancers, multiple K-Ras proteins are thought to assemble at the cell membrane with Ras effector proteins from the Raf family. Here we propose an atomistic structural model for such an assembly. Our starting point was an asymmetric guanosine triphosphate-mediated K-Ras dimer model, which we generated using unbiased molecular dynamics simulations and verified with mutagenesis experiments. Adding further K-Ras monomers in a head-to-tail fashion led to a compact helical assembly, a model we validated using electron microscopy and cell-based experiments. This assembly stabilizes K-Ras in its active state and presents composite interfaces to facilitate Raf binding. Guided by existing experimental data, we then positioned C-Raf, the downstream kinase MEK1 and accessory proteins (Galectin-3 and 14-3-3σ) on and around the helical assembly. The resulting Ras-Raf signalosome model offers an explanation for a large body of data on MAPK signaling.
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Affiliation(s)
| | - Zhi-Wei Zhou
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chiara Ambrogio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Turin, Italy
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonas N Kapp
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Chunya Lu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qi Wang
- D. E. Shaw Research, New York, NY, USA
| | | | - Jeffrey J Okoro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Xiaochen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - David E Shaw
- D. E. Shaw Research, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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14
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Lee JH, Jomaa A, Chung S, Hwang Fu YH, Qian R, Sun X, Hsieh HH, Chandrasekar S, Bi X, Mattei S, Boehringer D, Weiss S, Ban N, Shan SO. Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER. SCIENCE ADVANCES 2021; 7:eabg0942. [PMID: 34020957 PMCID: PMC8139590 DOI: 10.1126/sciadv.abg0942] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/01/2021] [Indexed: 05/07/2023]
Abstract
The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)-driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54G226E linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results provide a molecular model for the structural and functional transitions of SRP throughout the targeting cycle and show that these transitions provide important points for biological regulation that can be perturbed in genetic diseases.
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Affiliation(s)
- Jae Ho Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ahmad Jomaa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yu-Hsien Hwang Fu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ruilin Qian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xuemeng Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hao-Hsuan Hsieh
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sowmya Chandrasekar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Simone Mattei
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
- Cryo-EM Knowledge Hub, ETH Zurich, 8093 Zurich, Switzerland
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, 52900 Ramat-Gan, Israel
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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15
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Mayer B, Schwan M, Oviedo-Bocanegra LM, Bange G, Thormann KM, Graumann PL. Dynamics of Bacterial Signal Recognition Particle at a Single Molecule Level. Front Microbiol 2021; 12:663747. [PMID: 33995327 PMCID: PMC8120034 DOI: 10.3389/fmicb.2021.663747] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/18/2021] [Indexed: 11/21/2022] Open
Abstract
We have studied the localization and dynamics of bacterial Ffh, part of the SRP complex, its receptor FtsY, and of ribosomes in the Gamma-proteobacterium Shewanella putrefaciens. Using structured illumination microscopy, we show that ribosomes show a pronounced accumulation at the cell poles, whereas SRP and FtsY are distributed at distinct sites along the cell membrane, but they are not accumulated at the poles. Single molecule dynamics can be explained by assuming that all three proteins/complexes move as three distinguishable mobility fractions: a low mobility/static fraction may be engaged in translation, medium-fast diffusing fractions may be transition states, and high mobility populations likely represent freely diffusing molecules/complexes. Diffusion constants suggest that SRP and FtsY move together with slow-mobile ribosomes. Inhibition of transcription leads to loss of static molecules and reduction of medium-mobile fractions, in favor of freely diffusing subunits, while inhibition of translation appears to stall the medium mobile fractions. Depletion of FtsY leads to aggregation of Ffh, but not to loss of the medium mobile fraction, indicating that Ffh/SRP can bind to ribosomes independently from FtsY. Heat maps visualizing the three distinct diffusive populations show that while static molecules are mostly clustered at the cell membrane, diffusive molecules are localized throughout the cytosol. The medium fast populations show an intermediate pattern of preferential localization, suggesting that SRP/FtsY/ribosome transition states may form within the cytosol to finally find a translocon.
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Affiliation(s)
- Benjamin Mayer
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Meike Schwan
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Luis M. Oviedo-Bocanegra
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Kai M. Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Peter L. Graumann
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
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16
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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.
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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
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17
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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18
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Two Signal Recognition Particle Sequences Are Present in the Amino-Terminal Domain of the C-Tailed Protein SciP. J Bacteriol 2020; 203:JB.00312-20. [PMID: 33020223 DOI: 10.1128/jb.00312-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/01/2020] [Indexed: 01/22/2023] Open
Abstract
During their synthesis, the C-tailed membrane proteins expose the membrane-spanning segment late from the ribosome and consequently can insert into the membrane only posttranslationally. However, the C-tailed type 6 secretion system (T6SS) component SciP uses the bacterial signal recognition particle (SRP) system for membrane targeting, which operates cotranslationally. Analysis of possible sequence regions in the amino-terminal part of the protein revealed two candidates that were then tested for whether they function as SRP signal peptides. Both sequences were tested positive as synthetic peptides for binding to SRP. In addition, purified ribosomes with stalled nascent chains exposing either sequence were capable of binding to SRP and SRP-FtsY complexes with high affinity. Together, the data suggest that both peptides can serve as an SRP signal sequence promoting an early membrane targeting of SciP during its synthesis. Like observed for multispanning membrane proteins, the two cytoplasmic SRP signal sequences of SciP may also facilitate a retargeting event, making the targeting more efficient.IMPORTANCE C-tail proteins are anchored in the inner membrane with a transmembrane segment at the C terminus in an N-in/C-out topology. Due to this topology, membrane insertion occurs only posttranslationally. Nevertheless, the C-tail-anchored protein SciP is targeted cotranslationally by SRP. We report here that two amino-terminal hydrophobic stretches in SciP are individually recognized by SRP and target the nascent protein to FtsY. The presence of two signal sequences may enable a retargeting mechanism, as already observed for multispanning membrane proteins, to make the posttranslational insertion of SciP by YidC more efficient.
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19
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Juaire KD, Lapouge K, Becker MMM, Kotova I, Michelhans M, Carapito R, Wild K, Bahram S, Sinning I. Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia. Structure 2020; 29:15-28.e7. [PMID: 33053321 DOI: 10.1016/j.str.2020.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/22/2020] [Accepted: 09/23/2020] [Indexed: 01/12/2023]
Abstract
The SRP54 GTPase is a key component of co-translational protein targeting by the signal recognition particle (SRP). Point mutations in SRP54 have been recently shown to lead to a form of severe congenital neutropenia displaying symptoms overlapping with those of Shwachman-Diamond syndrome. The phenotype includes severe neutropenia, exocrine pancreatic deficiency, and neurodevelopmental as well as skeletal disorders. Using a combination of X-ray crystallography, hydrogen-deuterium exchange coupled to mass spectrometry and complementary biochemical and biophysical methods, we reveal extensive structural defects in three disease-causing SRP54 variants resulting in critical protein destabilization. GTP binding is mostly abolished as a consequence of an altered GTPase core. The mutations located in conserved sequence fingerprints of SRP54 eliminate targeting complex formation with the SRP receptor as demonstrated in yeast and human cells. These specific defects critically influence the entire SRP pathway, thereby causing this life-threatening disease.
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Affiliation(s)
- Keven D Juaire
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Matthias M M Becker
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Irina Kotova
- BIOMICA SAS, 4 rue Boussingault, 67000 Strasbourg, France
| | - Michelle Michelhans
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 4 rue Kirschleger, 67085 Strasbourg, France
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 4 rue Kirschleger, 67085 Strasbourg, France
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.
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20
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Regulation of the Single Polar Flagellar Biogenesis. Biomolecules 2020; 10:biom10040533. [PMID: 32244780 PMCID: PMC7226244 DOI: 10.3390/biom10040533] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
Some bacterial species, such as the marine bacterium Vibrio alginolyticus, have a single polar flagellum that allows it to swim in liquid environments. Two regulators, FlhF and FlhG, function antagonistically to generate only one flagellum at the cell pole. FlhF, a signal recognition particle (SRP)-type guanosine triphosphate (GTP)ase, works as a positive regulator for flagellar biogenesis and determines the location of flagellar assembly at the pole, whereas FlhG, a MinD-type ATPase, works as a negative regulator that inhibits flagellar formation. FlhF intrinsically localizes at the cell pole, and guanosine triphosphate (GTP) binding to FlhF is critical for its polar localization and flagellation. FlhG also localizes at the cell pole via the polar landmark protein HubP to directly inhibit FlhF function at the cell pole, and this localization depends on ATP binding to FlhG. However, the detailed regulatory mechanisms involved, played by FlhF and FlhG as the major factors, remain largely unknown. This article reviews recent studies that highlight the post-translational regulation mechanism that allows the synthesis of only a single flagellum at the cell pole.
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21
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Wild K, Juaire KD, Soni K, Shanmuganathan V, Hendricks A, Segnitz B, Beckmann R, Sinning I. Reconstitution of the human SRP system and quantitative and systematic analysis of its ribosome interactions. Nucleic Acids Res 2019; 47:3184-3196. [PMID: 30649417 PMCID: PMC6451106 DOI: 10.1093/nar/gky1324] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/22/2022] Open
Abstract
Co-translational protein targeting to membranes depends on the regulated interaction of two ribonucleoprotein particles (RNPs): the ribosome and the signal recognition particle (SRP). Human SRP is composed of an SRP RNA and six proteins with the SRP GTPase SRP54 forming the targeting complex with the heterodimeric SRP receptor (SRαβ) at the endoplasmic reticulum membrane. While detailed structural and functional data are available especially for the bacterial homologs, the analysis of human SRP was impeded by the unavailability of recombinant SRP. Here, we describe the large-scale production of all human SRP components and the reconstitution of homogeneous SRP and SR complexes. Binding to human ribosomes is determined by microscale thermophoresis for individual components, assembly intermediates and entire SRP, and binding affinities are correlated with structural information available for all ribosomal contacts. We show that SRP RNA does not bind to the ribosome, while SRP binds with nanomolar affinity involving a two-step mechanism of the key-player SRP54. Ultrasensitive binding of SRP68/72 indicates avidity by multiple binding sites that are dominated by the C-terminus of SRP72. Our data extend the experimental basis to understand the mechanistic principles of co-translational targeting in mammals and may guide analyses of complex RNP–RNP interactions in general.
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Affiliation(s)
- Klemens Wild
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Keven D Juaire
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Komal Soni
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Vivekanandan Shanmuganathan
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Astrid Hendricks
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Bernd Segnitz
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
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22
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Faoro C, Ataide SF. Structural insights into the G-loop dynamics of E. coli FtsY NG domain. J Struct Biol 2019; 208:107387. [PMID: 31520694 DOI: 10.1016/j.jsb.2019.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/27/2019] [Accepted: 09/10/2019] [Indexed: 10/26/2022]
Abstract
The bacterial signal recognition particle (SRP) receptor, FtsY, participates with the SRP in co-translation targeting of proteins. Multiple crystal structures of the NG domain of E. coli FtsYNG have been determined at high-resolution (1.22-1.88 Å), in the nucleotide-free (apo) form as well as bound to GDP and non-hydrolysable GTP analogues. The combination of high-resolution and multiple solved structures of FtsYNG in different states revealed a new sensor-relay system of this unique GTPase receptor. A nucleotide sensing function of the P-loop assists FtsYNG in nucleotide-binding and contributes to modulate nucleotide binding properties in SRP GTPases. A reorganization of the other G-loops and the insertion binding domain (IBD) is observed only upon transition from a diphosphate to a triphosphate nucleotide. The role of a magnesium ion during the GDP and GTP-bound states has also been observed. The binding of magnesium in the nucleotide site causes the reorientation of the β- and γ- phosphate groups toward the jaws of the P-loop and stabilizes the binding of the nucleotide, creating a network of hydrogen and water-bridge interactions.
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Affiliation(s)
- Camilla Faoro
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Sandro F Ataide
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia.
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23
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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.
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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
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24
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Wild K, Becker MM, Kempf G, Sinning I. Structure, dynamics and interactions of large SRP variants. Biol Chem 2019; 401:63-80. [DOI: 10.1515/hsz-2019-0282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022]
Abstract
Abstract
Co-translational protein targeting to membranes relies on the signal recognition particle (SRP) system consisting of a cytosolic ribonucleoprotein complex and its membrane-associated receptor. SRP recognizes N-terminal cleavable signals or signal anchor sequences, retards translation, and delivers ribosome-nascent chain complexes (RNCs) to vacant translocation channels in the target membrane. While our mechanistic understanding is well advanced for the small bacterial systems it lags behind for the large bacterial, archaeal and eukaryotic SRP variants including an Alu and an S domain. Here we describe recent advances on structural and functional insights in domain architecture, particle dynamics and interplay with RNCs and translocon and GTP-dependent regulation of co-translational protein targeting stimulated by SRP RNA.
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Affiliation(s)
- Klemens Wild
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| | - Matthias M.M. Becker
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| | - Georg Kempf
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
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25
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Kramer G, Shiber A, Bukau B. Mechanisms of Cotranslational Maturation of Newly Synthesized Proteins. Annu Rev Biochem 2019; 88:337-364. [DOI: 10.1146/annurev-biochem-013118-111717] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The timely production of functional proteins is of critical importance for the biological activity of cells. To reach the functional state, newly synthesized polypeptides have to become enzymatically processed, folded, and assembled into oligomeric complexes and, for noncytosolic proteins, translocated across membranes. Key activities of these processes occur cotranslationally, assisted by a network of machineries that transiently engage nascent polypeptides at distinct phases of translation. The sequence of events is tuned by intrinsic features of the nascent polypeptides and timely association of factors with the translating ribosome. Considering the dynamics of translation, the heterogeneity of cellular proteins, and the diversity of interaction partners, it is a major cellular achievement that these processes are temporally and spatially so precisely coordinated, minimizing the generation of damaged proteins. This review summarizes the current progress we have made toward a comprehensive understanding of the cotranslational interactions of nascent chains, which pave the way to their functional state.
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Affiliation(s)
- Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;,
| | - Ayala Shiber
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;,
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;,
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26
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Abstract
KdpD is a four-spanning membrane protein that has two large cytoplasmic domains at the amino- and at the carboxyterminus, respectively. During its biogenesis KdpD binds to the signal recognition particle (SRP) of Escherichia coli that consists of a 48-kDa protein Ffh and a 4.5S RNA. The protein is targeted to the inner membrane surface and is released after contacting the SRP receptor protein FtsY. The information within the KdpD protein that confers SRP interaction was found in the amino-terminal cytoplasmic domain of KdpD, particularly at residues 22–48. Within this sequence a Walker A motif is present at residues 30–38. To determine the actual sequence specificity to SRP, a collection of mutants was constructed. When the KdpD peptides (residues 22–48) were fused to sfGFP the targeting to the membrane was observed by fluorescence microscopy. Further, nascent chains of KdpD bound to ribosomes were purified and their binding to SRP was analysed by microscale thermophoresis. We found that the amino acid residues R22, K24 and K26 are important for SRP interaction, whereas the residues G30, G34 and G36, essential for a functional Walker A motif, can be replaced with alanines without affecting the affinity to SRP-FtsY and membrane targeting.
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27
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Abstract
Single-molecule studies provide unprecedented details about processes that are difficult to grasp by bulk biochemical assays that yield ensemble-averaged results. One of these processes is the translocation and insertion of proteins across and into the bacterial cytoplasmic membrane. This process is facilitated by the universally conserved secretion (Sec) system, a multi-subunit membrane protein complex that consists of dissociable cytoplasmic targeting components, a molecular motor, a protein-conducting membrane pore, and accessory membrane proteins. Here, we review recent insights into the mechanisms of protein translocation and membrane protein insertion from single-molecule studies.
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Affiliation(s)
- Anne-Bart Seinen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute; and the Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Current affiliation: Biophysics Group, AMOLF, 1098 XG Amsterdam, Netherlands
| | - Arnold J.M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute; and the Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
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28
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Lang S, Nguyen D, Pfeffer S, Förster F, Helms V, Zimmermann R. Functions and Mechanisms of the Human Ribosome-Translocon Complex. Subcell Biochem 2019; 93:83-141. [PMID: 31939150 DOI: 10.1007/978-3-030-28151-9_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane of the endoplasmic reticulum (ER) in human cells harbors the protein translocon, which facilitates membrane insertion and translocation of almost every newly synthesized polypeptide targeted to organelles of the secretory pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins, which are associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, Sec61 channel opening and closing, and modification of precursor polypeptides in transit through the Sec61 complex. Recently, cryoelectron tomography of translocons in native ER membranes has given unprecedented insights into the architecture and dynamics of the native, ribosome-associated translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion or translocation of newly synthesized polypeptides as well as the possible roles of the Sec61 channel as a passive ER calcium leak channel and regulator of ATP/ADP exchange between cytosol and ER.
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Affiliation(s)
- Sven Lang
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany.
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- ZMBH, 69120, Heidelberg, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Richard Zimmermann
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany
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29
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Pohlschroder M, Pfeiffer F, Schulze S, Abdul Halim MF. Archaeal cell surface biogenesis. FEMS Microbiol Rev 2018; 42:694-717. [PMID: 29912330 PMCID: PMC6098224 DOI: 10.1093/femsre/fuy027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis. These include those facilitating co- and post-translational protein targeting to the cell surface, transport into and across the archaeal lipid membrane, and protein anchoring strategies. We also discuss, in some detail, the assembly of specific cell surface structures, such as the archaeal S-layer and the type IV pili. We will highlight the importance of post-translational protein modifications, such as lipid attachment and glycosylation, in the biosynthesis as well as the regulation of the functions of these cell surface structures and present the differences and similarities in the biogenesis of type IV pili across prokaryotic domains.
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Affiliation(s)
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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30
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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.
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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.
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31
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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.
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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.
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32
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Chu F, Thornton DT, Nguyen HT. Chemical cross-linking in the structural analysis of protein assemblies. Methods 2018; 144:53-63. [PMID: 29857191 DOI: 10.1016/j.ymeth.2018.05.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
For decades, chemical cross-linking of proteins has been an established method to study protein interaction partners. The chemical cross-linking approach has recently been revived by mass spectrometric analysis of the cross-linking reaction products. Chemical cross-linking and mass spectrometric analysis (CXMS) enables the identification of residues that are close in three-dimensional (3D) space but not necessarily close in primary sequence. Therefore, this approach provides medium resolution information to guide de novo structure prediction, protein interface mapping and protein complex model building. The robustness and compatibility of the CXMS approach with multiple biochemical methods have made it especially appealing for challenging systems with multiple biochemical compositions and conformation states. This review provides an overview of the CXMS approach, describing general procedures in sample processing, data acquisition and analysis. Selection of proper chemical cross-linking reagents, strategies for cross-linked peptide identification, and successful application of CXMS in structural characterization of proteins and protein complexes are discussed.
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Affiliation(s)
- Feixia Chu
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, United States.
| | - Daniel T Thornton
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Hieu T Nguyen
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
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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.
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Venkatesan A, Palaniyandi K, Sharma D, Bisht D, Narayanan S. Characterization of FtsY, its interaction with Ffh, and proteomic identification of their potential substrates in Mycobacterium tuberculosis. Can J Microbiol 2018; 64:243-251. [PMID: 29361248 DOI: 10.1139/cjm-2017-0385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The universally conserved signal recognition particle (SRP) pathway that mediates co-translational targeting of membrane and secretory proteins is essential for eukaryotic and prokaryotic cells. The Mycobacterium tuberculosis SRP pathway consists of 2 proteins, Ffh and FtsY, and a 4.5S RNA molecule. Although the Escherichia coli SRP pathway is well studied, understanding of the M. tuberculosis SRP pathway components is very limited. In this study, we have overexpressed and characterized the M. tuberculosis SRP receptor (SR) FtsY as a GTP binding protein. Further, we established the direct protein-protein interaction between Ffh and FtsY. The Ffh-FtsY complex formation resulted in mutual stimulation of their GTP hydrolysis activity. We also attempted to biochemically characterize the SRP components by constructing the antisense gene knockdown strains of ffh and ftsY in M. tuberculosis. Loss of ffh and ftsY resulted in a decreased in vitro growth rate of the antisense ffh strain as compared with the antisense ftsY strain. Finally, 2-D gel electrophoresis of antisense depleted ffh and ftsY strains identified differential expression of 14 proteins.
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Affiliation(s)
- Arunkumar Venkatesan
- a Department of Immunology, National Institute for Research in Tuberculosis, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600031, India
| | - Kannan Palaniyandi
- a Department of Immunology, National Institute for Research in Tuberculosis, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600031, India
| | - Divakar Sharma
- b Department of Biochemistry, National JALMA Institute for Leprosy & other Mycobacterial Diseases, Dr. Matsuki Miyazaki Road, Tajganj, Agra 282004, India
| | - Deepa Bisht
- b Department of Biochemistry, National JALMA Institute for Leprosy & other Mycobacterial Diseases, Dr. Matsuki Miyazaki Road, Tajganj, Agra 282004, India
| | - Sujatha Narayanan
- a Department of Immunology, National Institute for Research in Tuberculosis, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600031, India
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35
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Carapito R, Konantz M, Paillard C, Miao Z, Pichot A, Leduc MS, Yang Y, Bergstrom KL, Mahoney DH, Shardy DL, Alsaleh G, Naegely L, Kolmer A, Paul N, Hanauer A, Rolli V, Müller JS, Alghisi E, Sauteur L, Macquin C, Morlon A, Sancho CS, Amati-Bonneau P, Procaccio V, Mosca-Boidron AL, Marle N, Osmani N, Lefebvre O, Goetz JG, Unal S, Akarsu NA, Radosavljevic M, Chenard MP, Rialland F, Grain A, Béné MC, Eveillard M, Vincent M, Guy J, Faivre L, Thauvin-Robinet C, Thevenon J, Myers K, Fleming MD, Shimamura A, Bottollier-Lemallaz E, Westhof E, Lengerke C, Isidor B, Bahram S. Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features. J Clin Invest 2017; 127:4090-4103. [PMID: 28972538 DOI: 10.1172/jci92876] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
Shwachman-Diamond syndrome (SDS) (OMIM #260400) is a rare inherited bone marrow failure syndrome (IBMFS) that is primarily characterized by neutropenia and exocrine pancreatic insufficiency. Seventy-five to ninety percent of patients have compound heterozygous loss-of-function mutations in the Shwachman-Bodian-Diamond syndrome (sbds) gene. Using trio whole-exome sequencing (WES) in an sbds-negative SDS family and candidate gene sequencing in additional SBDS-negative SDS cases or molecularly undiagnosed IBMFS cases, we identified 3 independent patients, each of whom carried a de novo missense variant in srp54 (encoding signal recognition particle 54 kDa). These 3 patients shared congenital neutropenia linked with various other SDS phenotypes. 3D protein modeling revealed that the 3 variants affect highly conserved amino acids within the GTPase domain of the protein that are critical for GTP and receptor binding. Indeed, we observed that the GTPase activity of the mutated proteins was impaired. The level of SRP54 mRNA in the bone marrow was 3.6-fold lower in patients with SRP54-mutations than in healthy controls. Profound reductions in neutrophil counts and chemotaxis as well as a diminished exocrine pancreas size in a SRP54-knockdown zebrafish model faithfully recapitulated the human phenotype. In conclusion, autosomal dominant mutations in SRP54, a key member of the cotranslation protein-targeting pathway, lead to syndromic neutropenia with a Shwachman-Diamond-like phenotype.
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Affiliation(s)
- Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Martina Konantz
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Catherine Paillard
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Onco-hématologie Pédiatrique, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Zhichao Miao
- Architecture et Réactivité de l'ARN, CNRS UPR 9002, LabEx NetRNA, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Angélique Pichot
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Magalie S Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Holcombe, Houston, Texas, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Katie L Bergstrom
- Department of Pediatrics, Hematology-Oncology Section, Texas Children's Hematology and Cancer Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Donald H Mahoney
- Department of Pediatrics, Hematology-Oncology Section, Texas Children's Hematology and Cancer Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Deborah L Shardy
- Department of Pediatrics, Hematology-Oncology Section, Texas Children's Hematology and Cancer Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Ghada Alsaleh
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Lydie Naegely
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Aline Kolmer
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Nicodème Paul
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Antoine Hanauer
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Véronique Rolli
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Joëlle S Müller
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Elisa Alghisi
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Loïc Sauteur
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Cécile Macquin
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | | | - Consuelo Sebastia Sancho
- Service de Radiologie Pédiatrique, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Patrizia Amati-Bonneau
- CNRS UMR 6015, INSERM UMR - S1083, MitoVasc Institute, Angers University, Angers, France.,Department of Biochemistry and Genetics, Angers Hospital, Angers, France
| | - Vincent Procaccio
- CNRS UMR 6015, INSERM UMR - S1083, MitoVasc Institute, Angers University, Angers, France.,Department of Biochemistry and Genetics, Angers Hospital, Angers, France
| | - Anne-Laure Mosca-Boidron
- Laboratoire de Cytogénétique, Pôle de Biologie, Centre Hospitalier Universitaire (CHU) de Dijon, Dijon, France
| | - Nathalie Marle
- Laboratoire de Cytogénétique, Pôle de Biologie, Centre Hospitalier Universitaire (CHU) de Dijon, Dijon, France
| | - Naël Osmani
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Olivier Lefebvre
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Jacky G Goetz
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Sule Unal
- Division of Pediatric Hematology, Hacettepe University Medical Faculty, Sihhiye, Ankara, Turkey
| | - Nurten A Akarsu
- Gene Mapping Laboratory, Department of Medical Genetics, Hacettepe University Medical Faculty, Sihhiye, Ankara, Turkey
| | - Mirjana Radosavljevic
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Marie-Pierre Chenard
- Département de Pathologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Fanny Rialland
- Service d'Oncologie et Hématologie Pédiatrique, Hôpital Femmes-enfants-adolescents, CHU de Nantes, Nantes, France
| | - Audrey Grain
- Service d'Oncologie et Hématologie Pédiatrique, Hôpital Femmes-enfants-adolescents, CHU de Nantes, Nantes, France
| | | | | | - Marie Vincent
- Service de Génétique Médicale, Hôpital Femmes-enfants-adolescents, CHU de Nantes, Nantes, France
| | - Julien Guy
- Service d'Hématologie Biologique, Pôle Biologie, CHU de Dijon, Dijon, France
| | - Laurence Faivre
- Service de Génétique, Hôpital d'enfants, CHU de Dijon, Dijon, France
| | | | - Julien Thevenon
- Service de Génétique, Hôpital d'enfants, CHU de Dijon, Dijon, France
| | - Kasiani Myers
- Division of Blood and Marrow Transplantation and Immune Deficiency, The Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, and
| | - Akiko Shimamura
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Eric Westhof
- Architecture et Réactivité de l'ARN, CNRS UPR 9002, LabEx NetRNA, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Claudia Lengerke
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.,Division of Hematology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Bertrand Isidor
- Service de Génétique Médicale, Hôpital Femmes-enfants-adolescents, CHU de Nantes, Nantes, France.,Laboratoire de Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, INSERM UMR - S957, Faculté de Médecine, Nantes, France
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
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36
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Haßdenteufel S, Sicking M, Schorr S, Aviram N, Fecher-Trost C, Schuldiner M, Jung M, Zimmermann R, Lang S. hSnd2 protein represents an alternative targeting factor to the endoplasmic reticulum in human cells. FEBS Lett 2017; 591:3211-3224. [PMID: 28862756 DOI: 10.1002/1873-3468.12831] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022]
Abstract
Recently, understanding of protein targeting to the endoplasmic reticulum (ER) was expanded by the discovery of multiple pathways that function in parallel to the signal recognition particle (SRP). Guided entry of tail-anchored proteins and SRP independent (SND) are two such targeting pathways described in yeast. So far, no human SND component is functionally characterized. Here, we report hSnd2 as the first constituent of the human SND pathway able to support substrate-specific protein targeting to the ER. Similar to its yeast counterpart, hSnd2 is assumed to function as a membrane-bound receptor preferentially targeting precursors carrying C-terminal transmembrane domains. Our genetic and physical interaction studies show that hSnd2 is part of a complex network of targeting and translocation that is dynamically regulated.
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Affiliation(s)
- Sarah Haßdenteufel
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Stefan Schorr
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Naama Aviram
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Claudia Fecher-Trost
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Saarland University, Homburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Martin Jung
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Richard Zimmermann
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
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37
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Hwang Fu YH, Huang WYC, Shen K, Groves JT, Miller T, Shan SO. Two-step membrane binding by the bacterial SRP receptor enable efficient and accurate Co-translational protein targeting. eLife 2017; 6. [PMID: 28753124 PMCID: PMC5533587 DOI: 10.7554/elife.25885] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 06/28/2017] [Indexed: 01/25/2023] Open
Abstract
The signal recognition particle (SRP) delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum, or the bacterial plasma membrane. The precise mechanism by which the bacterial SRP receptor, FtsY, interacts with and is regulated at the target membrane remain unclear. Here, quantitative analysis of FtsY-lipid interactions at single-molecule resolution revealed a two-step mechanism in which FtsY initially contacts membrane via a Dynamic mode, followed by an SRP-induced conformational transition to a Stable mode that activates FtsY for downstream steps. Importantly, mutational analyses revealed extensive auto-inhibitory mechanisms that prevent free FtsY from engaging membrane in the Stable mode; an engineered FtsY pre-organized into the Stable mode led to indiscriminate targeting in vitro and disrupted FtsY function in vivo. Our results show that the two-step lipid-binding mechanism uncouples the membrane association of FtsY from its conformational activation, thus optimizing the balance between the efficiency and fidelity of co-translational protein targeting. DOI:http://dx.doi.org/10.7554/eLife.25885.001
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Affiliation(s)
- Yu-Hsien Hwang Fu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - William Y C Huang
- Department of Chemistry, University of California at Berkeley, Berkeley, United States
| | - Kuang Shen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Jay T Groves
- Department of Chemistry, University of California at Berkeley, Berkeley, United States
| | - Thomas Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
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38
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Ziehe D, Dünschede B, Schünemann D. From bacteria to chloroplasts: evolution of the chloroplast SRP system. Biol Chem 2017; 398:653-661. [PMID: 28076289 DOI: 10.1515/hsz-2016-0292] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/04/2017] [Indexed: 02/02/2023]
Abstract
Chloroplasts derive from a prokaryotic symbiont that lost most of its genes during evolution. As a result, the great majority of chloroplast proteins are encoded in the nucleus and are posttranslationally imported into the organelle. The chloroplast genome encodes only a few proteins. These include several multispan thylakoid membrane proteins which are synthesized on thylakoid-bound ribosomes and cotranslationally inserted into the membrane. During evolution, ancient prokaryotic targeting machineries were adapted and combined with novel targeting mechanisms to facilitate post- and cotranslational protein transport in chloroplasts. This review focusses on the chloroplast signal recognition particle (cpSRP) protein transport system, which has been intensively studied in higher plants. The cpSRP system derived from the prokaryotic SRP pathway, which mediates the cotranslational protein transport to the bacterial plasma membrane. Chloroplasts contain homologs of several components of the bacterial SRP system. The function of these conserved components in post- and/or cotranslational protein transport and chloroplast-specific modifications of these transport mechanisms are described. Furthermore, recent studies of cpSRP systems in algae and lower plants are summarized and their impact on understanding the evolution of the cpSRP system are discussed.
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Affiliation(s)
- Dominik Ziehe
- Molecular Biology of Plant Organelles, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum
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39
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Abstract
Many proteins are translocated across the endoplasmic reticulum (ER) membrane in eukaryotes or the plasma membrane in prokaryotes. These proteins use hydrophobic signal sequences or transmembrane (TM) segments to trigger their translocation through the protein-conducting Sec61/SecY channel. Substrates are first directed to the channel by cytosolic targeting factors, which use hydrophobic pockets to bind diverse signal and TM sequences. Subsequently, these hydrophobic sequences insert into the channel, docking into a groove on the outside of the lateral gate of the channel, where they also interact with lipids. Structural data and biochemical experiments have elucidated how channel partners, the ribosome in cotranslational translocation, and the eukaryotic ER chaperone BiP or the prokaryotic cytosolic SecA ATPase in posttranslational translocation move polypeptides unidirectionally across the membrane. Structures of auxiliary components of the bacterial translocon, YidC and SecD/F, provide additional insight. Taken together, these recent advances result in mechanistic models of protein translocation.
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Affiliation(s)
- Tom A Rapoport
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Long Li
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Eunyong Park
- The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065;
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40
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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.
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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
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41
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Denks K, Sliwinski N, Erichsen V, Borodkina B, Origi A, Koch HG. The signal recognition particle contacts uL23 and scans substrate translation inside the ribosomal tunnel. Nat Microbiol 2017; 2:16265. [PMID: 28134917 DOI: 10.1038/nmicrobiol.2016.265] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 12/09/2016] [Indexed: 01/12/2023]
Abstract
The signal recognition particle (SRP) delivers ∼25% of all bacterial proteins to the membrane for cotranslational insertion. However, a comprehensive model on how the low-abundant SRP scans the vast number of translating ribosomes to identify the correct substrates is lacking. Here, we show that the C-terminal helix of the signal-sequence-binding domain of SRP penetrates into the ribosomal tunnel and contacts the intra-tunnel loop of ribosomal protein uL23. This allows SRP to obtain information about the translational status of the ribosome and possibly the character of the approaching nascent chain. Correct substrates reposition the C-terminal helix of SRP, which facilitates stable binding of the signal sequence by the M-domain of SRP. Thus, SRP already surveys translating ribosomes before the signal sequence is surface exposed. This early interaction probably enables the small number of SRP molecules to scan many ribosomes and to initiate efficient targeting of proper substrates.
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Affiliation(s)
- Kärt Denks
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany
| | - Nadine Sliwinski
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany
| | - Veronika Erichsen
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany
| | - Bogdana Borodkina
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany
| | - Andrea Origi
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany
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42
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Gupta S, Roy M, Ghosh A. The Archaeal Signal Recognition Particle: Present Understanding and Future Perspective. Curr Microbiol 2016; 74:284-297. [DOI: 10.1007/s00284-016-1167-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 11/21/2016] [Indexed: 10/20/2022]
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43
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Becker MMM, Lapouge K, Segnitz B, Wild K, Sinning I. Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction. Nucleic Acids Res 2016; 45:470-481. [PMID: 27899666 PMCID: PMC5224484 DOI: 10.1093/nar/gkw1124] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/21/2016] [Accepted: 10/28/2016] [Indexed: 12/30/2022] Open
Abstract
Co-translational protein targeting and membrane protein insertion is a fundamental process and depends on the signal recognition particle (SRP). In mammals, SRP is composed of the SRP RNA crucial for SRP assembly and function and six proteins. The two largest proteins SRP68 and SRP72 form a heterodimer and bind to a regulatory site of the SRP RNA. Despite their essential roles in the SRP pathway, structural information has been available only for the SRP68 RNA-binding domain (RBD). Here we present the crystal structures of the SRP68 protein-binding domain (PBD) in complex with SRP72-PBD and of the SRP72-RBD bound to the SRP S domain (SRP RNA, SRP19 and SRP68) detailing all interactions of SRP72 within SRP. The SRP72-PBD is a tetratricopeptide repeat, which binds an extended linear motif of SRP68 with high affinity. The SRP72-RBD is a flexible peptide crawling along the 5e- and 5f-loops of SRP RNA. A conserved tryptophan inserts into the 5e-loop forming a novel type of RNA kink-turn stabilized by a potassium ion, which we define as K+-turn. In addition, SRP72-RBD remodels the 5f-loop involved in ribosome binding and visualizes SRP RNA plasticity. Docking of the S domain structure into cryo-electron microscopy density maps reveals multiple contact sites between SRP68/72 and the ribosome, and explains the role of SRP72 in the SRP pathway.
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Affiliation(s)
- Matthias M M Becker
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Bernd Segnitz
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
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44
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Chandrasekar S, Shan SO. Anionic Phospholipids and the Albino3 Translocase Activate Signal Recognition Particle-Receptor Interaction during Light-harvesting Chlorophyll a/b-binding Protein Targeting. J Biol Chem 2016; 292:397-406. [PMID: 27895124 DOI: 10.1074/jbc.m116.752956] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/14/2016] [Indexed: 01/12/2023] Open
Abstract
The universally conserved signal recognition particle (SRP) co-translationally delivers newly synthesized membrane and secretory proteins to the target cellular membrane. The only exception is found in the chloroplast of green plants, where the chloroplast SRP (cpSRP) post-translationally targets light-harvesting chlorophyll a/b-binding proteins (LHCP) to the thylakoid membrane. The mechanism and regulation of this post-translational mode of targeting by cpSRP remain unclear. Using biochemical and biophysical methods, here we show that anionic phospholipids activate the cpSRP receptor cpFtsY to promote rapid and stable cpSRP54·cpFtsY complex assembly. Furthermore, the stromal domain of the Alb3 translocase binds with high affinity to and regulates GTP hydrolysis in the cpSRP54·cpFtsY complex, suggesting that cpFtsY is primarily responsible for initial recruitment of the targeting complex to Alb3. These results suggest a new model for the sequential recruitment, remodeling, and unloading of the targeting complex at membrane translocase sites in the post-translational cpSRP pathway.
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Affiliation(s)
- Sowmya Chandrasekar
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Shu-Ou Shan
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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45
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Chandrasekar S, Sweredoski MJ, Sohn CH, Hess S, Shan SO. Co-evolution of Two GTPases Enables Efficient Protein Targeting in an RNA-less Chloroplast Signal Recognition Particle Pathway. J Biol Chem 2016; 292:386-396. [PMID: 27895118 DOI: 10.1074/jbc.m116.752931] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/17/2016] [Indexed: 11/06/2022] Open
Abstract
The signal recognition particle (SRP) is an essential ribonucleoprotein particle that mediates the co-translational targeting of newly synthesized proteins to cellular membranes. The SRP RNA is a universally conserved component of SRP that mediates key interactions between two GTPases in SRP and its receptor, thus enabling rapid delivery of cargo to the target membrane. Notably, this essential RNA is bypassed in the chloroplast (cp) SRP of green plants. Previously, we showed that the cpSRP and cpSRP receptor GTPases (cpSRP54 and cpFtsY, respectively) interact efficiently by themselves without the SRP RNA. Here, we explore the molecular mechanism by which this is accomplished. Fluorescence analyses showed that, in the absence of SRP RNA, the M-domain of cpSRP54 both accelerates and stabilizes complex assembly between cpSRP54 and cpFtsY. Cross-linking coupled with mass spectrometry and mutational analyses identified a new interaction between complementarily charged residues on the cpFtsY G-domain and the vicinity of the cpSRP54 M-domain. These residues are specifically conserved in plastids, and their evolution coincides with the loss of SRP RNA in green plants. These results provide an example of how proteins replace the functions of RNA during evolution.
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Affiliation(s)
| | - Michael J Sweredoski
- the Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Chang Ho Sohn
- From the Division of Chemistry and Chemical Engineering and
| | - Sonja Hess
- the Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Shu-Ou Shan
- From the Division of Chemistry and Chemical Engineering and
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46
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ATPase and GTPase Tangos Drive Intracellular Protein Transport. Trends Biochem Sci 2016; 41:1050-1060. [PMID: 27658684 DOI: 10.1016/j.tibs.2016.08.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 11/24/2022]
Abstract
The GTPase superfamily of proteins provides molecular switches to regulate numerous cellular processes. The 'GTPase switch' paradigm, in which external regulatory factors control the switch of a GTPase between 'on' and 'off' states, has been used to interpret the regulatory mechanism of many GTPases. However, recent work unveiled a class of nucleotide hydrolases that do not adhere to this classical paradigm. Instead, they use nucleotide-dependent dimerization cycles to regulate key cellular processes. In this review article, recent studies of dimeric GTPases and ATPases involved in intracellular protein targeting are summarized. It is suggested that these proteins can use the conformational plasticity at their dimer interface to generate multiple points of regulation, thereby providing the driving force and spatiotemporal coordination of complex cellular pathways.
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47
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Daumke O, Praefcke GJK. Invited review: Mechanisms of GTP hydrolysis and conformational transitions in the dynamin superfamily. Biopolymers 2016; 105:580-93. [PMID: 27062152 PMCID: PMC5084822 DOI: 10.1002/bip.22855] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/29/2022]
Abstract
Dynamin superfamily proteins are multidomain mechano-chemical GTPases which are implicated in nucleotide-dependent membrane remodeling events. A prominent feature of these proteins is their assembly- stimulated mechanism of GTP hydrolysis. The molecular basis for this reaction has been initially clarified for the dynamin-related guanylate binding protein 1 (GBP1) and involves the transient dimerization of the GTPase domains in a parallel head-to-head fashion. A catalytic arginine finger from the phosphate binding (P-) loop is repositioned toward the nucleotide of the same molecule to stabilize the transition state of GTP hydrolysis. Dynamin uses a related dimerization-dependent mechanism, but instead of the catalytic arginine, a monovalent cation is involved in catalysis. Still another variation of the GTP hydrolysis mechanism has been revealed for the dynamin-like Irga6 which bears a glycine at the corresponding position in the P-loop. Here, we highlight conserved and divergent features of GTP hydrolysis in dynamin superfamily proteins and show how nucleotide binding and hydrolysis are converted into mechano-chemical movements. We also describe models how the energy of GTP hydrolysis can be harnessed for diverse membrane remodeling events, such as membrane fission or fusion. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 580-593, 2016.
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Affiliation(s)
- Oliver Daumke
- Kristallographie, Max-Delbrück Centrum Für Molekulare Medizin, Robert-Rössle-Straße 10, Berlin, 13125, Germany
- Institut Für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, Berlin, 14195, Germany
| | - Gerrit J K Praefcke
- Abteilung Hämatologie/Transfusionsmedizin, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, Langen, 63225, Germany
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48
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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
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49
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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.
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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.
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50
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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
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