1
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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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2
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Pietz HL, Abbas A, Johnson ZL, Oldham ML, Suga H, Chen J. A macrocyclic peptide inhibitor traps MRP1 in a catalytically incompetent conformation. Proc Natl Acad Sci U S A 2023; 120:e2220012120. [PMID: 36893260 PMCID: PMC10089224 DOI: 10.1073/pnas.2220012120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
Adenosine triphosphate-binding cassette (ABC) transporters, such as multidrug resistance protein 1 (MRP1), protect against cellular toxicity by exporting xenobiotic compounds across the plasma membrane. However, constitutive MRP1 function hinders drug delivery across the blood-brain barrier, and MRP1 overexpression in certain cancers leads to acquired multidrug resistance and chemotherapy failure. Small-molecule inhibitors have the potential to block substrate transport, but few show specificity for MRP1. Here we identify a macrocyclic peptide, named CPI1, which inhibits MRP1 with nanomolar potency but shows minimal inhibition of a related multidrug transporter P-glycoprotein. A cryoelectron microscopy (cryo-EM) structure at 3.27 Å resolution shows that CPI1 binds MRP1 at the same location as the physiological substrate leukotriene C4 (LTC4). Residues that interact with both ligands contain large, flexible sidechains that can form a variety of interactions, revealing how MRP1 recognizes multiple structurally unrelated molecules. CPI1 binding prevents the conformational changes necessary for adenosine triphosphate (ATP) hydrolysis and substrate transport, suggesting it may have potential as a therapeutic candidate.
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Affiliation(s)
- Harlan L Pietz
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065
| | - Ata Abbas
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Zachary Lee Johnson
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065
| | - Michael L Oldham
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065
- HHMI, New York, NY 10065
| | - Hiroaki Suga
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Jue Chen
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY 10065
- HHMI, New York, NY 10065
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3
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Shivangi, Meena LS. A multifactorial assessment of the SRP pathway constituent FtsY as a vital mycobacterial constituent. Biotechnol Appl Biochem 2022; 69:2445-2453. [PMID: 34837716 DOI: 10.1002/bab.2294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
The signal recognition particle (SRP) system plays an imperative role in transporting the secretory protein to its intended location. The SRP pathway running in Mycobacterium tuberculosis constitutes FtsY (signal receptor), FfH (SRP), and 4.5S RNA in which signal receptor acts in the GTP-dependent manner. In this study, we are rendering the essential facts of FtsY with respect to mycobacterial growth. The growth study experiment showed that downexpressed FtsY slowed the growth of Mycobacterium smegmatis mc2 155 from the initial lag phase to stationary phase. Previously, we have showed that GTPase activity of FtsY is metal ion dependent and showed the maximum activity with 10 mM magnesium. The effect of Mg2+ and Mn2+ on mycobacterial growth showed that Mg2+ did not affect the growth, whereas higher concentration of Mn2+ decreases the bacterial growth. After searching the inhibitor database, 14 GTPase and ATPase inhibitors, Mac0182344, ML141, ITX3, NAV_2729, Br-GTP, Rhosin_HCl, Mac0182099, CCG_50014, CID_1067700, Mac0174809, Nsc_23766, Berberine, Nexinhib20, and EHT1864, were found to interact with FtsY. Further, ML141 and NAV2729 found to decrease the enzymatic activity of FtsY as well as the mycobacterial growth. Therefore, the conclusive statement of the present study can be stated as that the FtsY plays major role in mycobacterial cell survival and ML141 and NAV2729 can be used to constrain the SRP pathway.
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Affiliation(s)
- Shivangi
- Cardio Respiratory Disease Biology department, Mall Road, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Laxman S Meena
- Cardio Respiratory Disease Biology department, Mall Road, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
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4
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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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5
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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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6
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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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7
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Xu L, Xu S, Sun L, Zhang Y, Luo J, Bock R, Zhang J. Synergistic action of the gut microbiota in environmental RNA interference in a leaf beetle. MICROBIOME 2021; 9:98. [PMID: 33947455 PMCID: PMC8097945 DOI: 10.1186/s40168-021-01066-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/31/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND RNA interference (RNAi) has emerged as an efficient tool to control insect pests. When insects ingest double-stranded RNAs (dsRNAs) targeted against essential genes, strong gene silencing and mortality can be induced. To exert their function, dsRNA molecules must pass through the insect's gut and enter epithelial cells and/or the hemolymph. Gut bacteria are known to play multifarious roles in food digestion and nutrition, and confer protection against pathogens and parasites. Whether there is a cross talk between gut bacteria and ingested dsRNAs and whether the microbiome affects RNAi efficiency are unknown. RESULTS Here, using a leaf beetle gut microbiota system, we investigated whether gut bacteria interact with dsRNA molecules and how the gut microbiota affects RNAi responses in insects. We first showed that the leaf beetle Plagiodera versicolora (Coleoptera) is highly susceptible to RNAi. We then demonstrated that ingestion of dsRNAs by non-axenic P. versicolora larvae results in (i) significantly accelerated mortality compared with axenic larvae, and (ii) overgrowth and dysbiosis of the gut microbiota. The latter may be caused by bacterial utilization of dsRNA degradation products. Furthermore, we found that Pseudomonas putida, a gut bacterium of P. versicolora, acts as major accelerator of the death of P. versicolora larvae by transitioning from commensal to pathogenic lifestyle. CONCLUSIONS The present study illuminates the complex interplay between lethal dsRNA, the insect host, and its gut microbiota. The ingestion of dsRNA by the leaf beetle caused a dysbiosis of gut bacterial community, and the dsRNA degradation products by host insect preferentially promoted the growth of an entomopathogenic bacterium, which accelerated dsRNA lethality to the insect. Our findings reveal a synergistic role of the gut microbiota in dsRNA-induced mortality of pest insects, and provide new insights in the mechanisms of RNAi-based pest control. Video abstract.
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Affiliation(s)
- Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Shijing Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Liuwei Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yiqiu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jing Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Ralph Bock
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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8
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Fry MY, Saladi SM, Clemons WM. The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. Protein Sci 2021; 30:882-898. [PMID: 33620121 PMCID: PMC7980504 DOI: 10.1002/pro.4049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/05/2023]
Abstract
STI1-domains are present in a variety of co-chaperone proteins and are required for the transfer of hydrophobic clients in various cellular processes. The domains were first identified in the yeast Sti1 protein where they were referred to as DP1 and DP2. Based on hidden Markov model searches, this domain had previously been found in other proteins including the mammalian co-chaperone SGTA, the DNA damage response protein Rad23, and the chloroplast import protein Tic40. Here, we refine the domain definition and carry out structure-based sequence alignment of STI1-domains showing conservation of five amphipathic helices. Upon examinations of these identified domains, we identify a preceding helix 0 and unifying sequence properties, determine new molecular models, and recognize that STI1-domains nearly always occur in pairs. The similarity at the sequence, structure, and molecular levels likely supports a unified functional role.
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Affiliation(s)
- Michelle Y. Fry
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Shyam M. Saladi
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - William M. Clemons
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
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9
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Hutanu A, Hauser PC, Moritz B, Kiessig S, Noël A, Stracke JO, Wild M, Schwarz MA. Methionine oxidation of proteins analyzed by affinity capillary electrophoresis in presence of silver(I) and gold(III) ions. Electrophoresis 2021; 42:1209-1216. [PMID: 33651405 PMCID: PMC9291207 DOI: 10.1002/elps.202000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/25/2021] [Accepted: 02/12/2021] [Indexed: 11/08/2022]
Abstract
Oxidative damage of biopharmaceuticals during manufacturing and storage is a key concern throughout pharmaceutical development. However, few simple and robust analytical methods are available for the determination of oxidation sites. Here, the potential of affinity capillary electrophoresis (ACE) in the separation of proteins with oxidized methionine (Met) residues is shown. Silver(I) and gold(I) ions have the attribute to selectively form complexes with thioethers over sulfoxides. The addition of these ions to the BGE leads to a selective complexation of Met residues and, thus, to a change of charge allowing separation of species according to the different oxidation states of Met. The mechanisms of these interactions are discussed and binding constants for peptides containing Met with silver(I) are calculated. Additionally, the proposed method can be used as an indicator of oxidative stress in large proteins. The presented technique is easily accessible, economical, and has rapid analysis times, adding new approaches to the analytical toolbox of Met sulfoxide detection.
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Affiliation(s)
- Andrei Hutanu
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland.,Department of Chemistry, University of Basel, Basel, Switzerland
| | - Peter C Hauser
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Bernd Moritz
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Steffen Kiessig
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Aurélie Noël
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Jan O Stracke
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Markus Wild
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Maria A Schwarz
- Department of Chemistry, University of Basel, Basel, Switzerland.,Business Unit Biopharmaceuticals, Solvias AG, Kaiseraugst, Switzerland
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10
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Harris AJ, Goldman AD. The very early evolution of protein translocation across membranes. PLoS Comput Biol 2021; 17:e1008623. [PMID: 33684113 PMCID: PMC7987157 DOI: 10.1371/journal.pcbi.1008623] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 03/23/2021] [Accepted: 12/10/2020] [Indexed: 11/18/2022] Open
Abstract
In this study, we used a computational approach to investigate the early evolutionary history of a system of proteins that, together, embed and translocate other proteins across cell membranes. Cell membranes comprise the basis for cellularity, which is an ancient, fundamental organizing principle shared by all organisms and a key innovation in the evolution of life on Earth. Two related requirements for cellularity are that organisms are able to both embed proteins into membranes and translocate proteins across membranes. One system that accomplishes these tasks is the signal recognition particle (SRP) system, in which the core protein components are the paralogs, FtsY and Ffh. Complementary to the SRP system is the Sec translocation channel, in which the primary channel-forming protein is SecY. We performed phylogenetic analyses that strongly supported prior inferences that FtsY, Ffh, and SecY were all present by the time of the last universal common ancestor of life, the LUCA, and that the ancestor of FtsY and Ffh existed before the LUCA. Further, we combined ancestral sequence reconstruction and protein structure and function prediction to show that the LUCA had an SRP system and Sec translocation channel that were similar to those of extant organisms. We also show that the ancestor of Ffh and FtsY that predated the LUCA was more similar to FtsY than Ffh but could still have comprised a rudimentary protein translocation system on its own. Duplication of the ancestor of FtsY and Ffh facilitated the specialization of FtsY as a membrane bound receptor and Ffh as a cytoplasmic protein that could bind nascent proteins with specific membrane-targeting signal sequences. Finally, we analyzed amino acid frequencies in our ancestral sequence reconstructions to infer that the ancestral Ffh/FtsY protein likely arose prior to or just after the completion of the canonical genetic code. Taken together, our results offer a window into the very early evolutionary history of cellularity.
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Affiliation(s)
- AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, Oberlin, Ohio, United States of America
| | - Aaron David Goldman
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, Oberlin, Ohio, United States of America
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
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11
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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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12
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Ouyang M, Li X, Zhang J, Feng P, Pu H, Kong L, Bai Z, Rong L, Xu X, Chi W, Wang Q, Chen F, Lu C, Shen J, Zhang L. Liquid-Liquid Phase Transition Drives Intra-chloroplast Cargo Sorting. Cell 2020; 180:1144-1159.e20. [PMID: 32169217 DOI: 10.1016/j.cell.2020.02.045] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 01/14/2020] [Accepted: 02/20/2020] [Indexed: 12/21/2022]
Abstract
In eukaryotic cells, organelle biogenesis is pivotal for cellular function and cell survival. Chloroplasts are unique organelles with a complex internal membrane network. The mechanisms of the migration of imported nuclear-encoded chloroplast proteins across the crowded stroma to thylakoid membranes are less understood. Here, we identified two Arabidopsis ankyrin-repeat proteins, STT1 and STT2, that specifically mediate sorting of chloroplast twin arginine translocation (cpTat) pathway proteins to thylakoid membranes. STT1 and STT2 form a unique hetero-dimer through interaction of their C-terminal ankyrin domains. Binding of cpTat substrate by N-terminal intrinsically disordered regions of STT complex induces liquid-liquid phase separation. The multivalent nature of STT oligomer is critical for phase separation. STT-Hcf106 interactions reverse phase separation and facilitate cargo targeting and translocation across thylakoid membranes. Thus, the formation of phase-separated droplets emerges as a novel mechanism of intra-chloroplast cargo sorting. Our findings highlight a conserved mechanism of phase separation in regulating organelle biogenesis.
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Affiliation(s)
- Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaoyi Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jing Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Peiqiang Feng
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hua Pu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lingxi Kong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zechen Bai
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Liwei Rong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiumei Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Fan Chen
- State Key Laboratory of Molecular Developmental Biology, Chinese Academy of Sciences, Beijing 100086, China
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jianren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China.
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13
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Abstract
Cells in all domains of life must translocate newly synthesized proteins both across membranes and into membranes. In eukaryotes, proteins are translocated into the lumen of the ER or the ER membrane. In prokaryotes, proteins are translocated into the cytoplasmic membrane or through the membrane into the periplasm for Gram-negative bacteria or the extracellular space for Gram-positive bacteria. Much of what we know about protein translocation was learned through genetic selections and screens utilizing lacZ gene fusions in Escherichia coli. This review covers the basic principles of protein translocation and how they were discovered and developed. In particular, we discuss how lacZ gene fusions and the phenotypes conferred were exploited to identify the genes involved in protein translocation and provide insights into their mechanisms of action. These approaches, which allowed the elucidation of processes that are conserved throughout the domains of life, illustrate the power of seemingly simple experiments.
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14
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Heiby JC, Goretzki B, Johnson CM, Hellmich UA, Neuweiler H. Methionine in a protein hydrophobic core drives tight interactions required for assembly of spider silk. Nat Commun 2019; 10:4378. [PMID: 31558722 PMCID: PMC6763431 DOI: 10.1038/s41467-019-12365-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/05/2019] [Indexed: 01/21/2023] Open
Abstract
Web spiders connect silk proteins, so-called spidroins, into fibers of extraordinary toughness. The spidroin N-terminal domain (NTD) plays a pivotal role in this process: it polymerizes spidroins through a complex mechanism of dimerization. Here we analyze sequences of spidroin NTDs and find an unusually high content of the amino acid methionine. We simultaneously mutate all methionines present in the hydrophobic core of a spidroin NTD from a nursery web spider’s dragline silk to leucine. The mutated NTD is strongly stabilized and folds at the theoretical speed limit. The structure of the mutant is preserved, yet its ability to dimerize is substantially impaired. We find that side chains of core methionines serve to mobilize the fold, which can thereby access various conformations and adapt the association interface for tight binding. Methionine in a hydrophobic core equips a protein with the capacity to dynamically change shape and thus to optimize its function. Spider silk is of interest in material science research. Here the authors show that the tight binding of a spider silk protein domain relies on the amino acid methionine, which is abundant in the domain core where it facilitates dynamic shape adaption of the binding interface.
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Affiliation(s)
- Julia C Heiby
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Benedikt Goretzki
- Institute for Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim Becherweg 30, 55128, Mainz, Germany.,Center for Biomolecular Magnetic Resonance, Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Christopher M Johnson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ute A Hellmich
- Institute for Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim Becherweg 30, 55128, Mainz, Germany. .,Center for Biomolecular Magnetic Resonance, Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
| | - Hannes Neuweiler
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074, Würzburg, Germany.
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15
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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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16
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Abstract
Bacterial protein transport via the conserved SecYEG translocon is generally classified as either cotranslational, i.e., when transport is coupled to translation, or posttranslational, when translation and transport are separated. We show here that the ATPase SecA, which is considered to bind its substrates posttranslationally, already scans the ribosomal tunnel for potential substrates. In the presence of a nascent chain, SecA retracts from the tunnel but maintains contact with the ribosomal surface. This is remarkably similar to the ribosome-binding mode of the signal recognition particle, which mediates cotranslational transport. Our data reveal a striking plasticity of protein transport pathways, which likely enable bacteria to efficiently recognize and transport a large number of highly different substrates within their short generation time. Bacteria execute a variety of protein transport systems for maintaining the proper composition of their different cellular compartments. The SecYEG translocon serves as primary transport channel and is engaged in transporting two different substrate types. Inner membrane proteins are cotranslationally inserted into the membrane after their targeting by the signal recognition particle (SRP). In contrast, secretory proteins are posttranslationally translocated by the ATPase SecA. Recent data indicate that SecA can also bind to ribosomes close to the tunnel exit. We have mapped the interaction of SecA with translating and nontranslating ribosomes and demonstrate that the N terminus and the helical linker domain of SecA bind to an acidic patch on the surface of the ribosomal protein uL23. Intriguingly, both also insert deeply into the ribosomal tunnel to contact the intratunnel loop of uL23, which serves as a nascent chain sensor. This binding pattern is remarkably similar to that of SRP and indicates an identical interaction mode of the two targeting factors with ribosomes. In the presence of a nascent chain, SecA retracts from the tunnel but maintains contact with the surface of uL23. Our data further demonstrate that ribosome and membrane binding of SecA are mutually exclusive, as both events depend on the N terminus of SecA. Our study highlights the enormous plasticity of bacterial protein transport systems and reveals that the discrimination between SRP and SecA substrates is already initiated at the ribosome.
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17
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Physiological Roles of Plant Methionine Sulfoxide Reductases in Redox Homeostasis and Signaling. Antioxidants (Basel) 2018; 7:antiox7090114. [PMID: 30158486 PMCID: PMC6162775 DOI: 10.3390/antiox7090114] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/24/2018] [Accepted: 08/26/2018] [Indexed: 01/09/2023] Open
Abstract
Oxidation of methionine (Met) leads to the formation of two S- and R-diastereoisomers of Met sulfoxide (MetO) that are reduced back to Met by methionine sulfoxide reductases (MSRs), A and B, respectively. Here, we review the current knowledge about the physiological functions of plant MSRs in relation with subcellular and tissue distribution, expression patterns, mutant phenotypes, and possible targets. The data gained from modified lines of plant models and crop species indicate that MSRs play protective roles upon abiotic and biotic environmental constraints. They also participate in the control of the ageing process, as shown in seeds subjected to adverse conditions. Significant advances were achieved towards understanding how MSRs could fulfil these functions via the identification of partners among Met-rich or MetO-containing proteins, notably by using redox proteomic approaches. In addition to a global protective role against oxidative damage in proteins, plant MSRs could specifically preserve the activity of stress responsive effectors such as glutathione-S-transferases and chaperones. Moreover, several lines of evidence indicate that MSRs fulfil key signaling roles via interplays with Ca2+- and phosphorylation-dependent cascades, thus transmitting ROS-related information in transduction pathways.
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18
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Möller-Hergt BV, Carlström A, Stephan K, Imhof A, Ott M. The ribosome receptors Mrx15 and Mba1 jointly organize cotranslational insertion and protein biogenesis in mitochondria. Mol Biol Cell 2018; 29:2386-2396. [PMID: 30091672 PMCID: PMC6233058 DOI: 10.1091/mbc.e18-04-0227] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial gene expression in Saccharomyces cerevisiae is responsible for the production of highly hydrophobic subunits of the oxidative phosphorylation system. Membrane insertion occurs cotranslationally on membrane-bound mitochondrial ribosomes. Here, by employing a systematic mass spectrometry–based approach, we discovered the previously uncharacterized membrane protein Mrx15 that interacts via a soluble C-terminal domain with the large ribosomal subunit. Mrx15 contacts mitochondrial translation products during their synthesis and plays, together with the ribosome receptor Mba1, an overlapping role in cotranslational protein insertion. Taken together, our data reveal how these ribosome receptors organize membrane protein biogenesis in mitochondria.
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Affiliation(s)
| | - Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Katharina Stephan
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University of Munich, DE-82152 Planegg-Martinsried, Germany
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
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19
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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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20
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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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21
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McLean R, Inglis GD, Mosimann SC, Uwiera RRE, Abbott DW. Determining the Localization of Carbohydrate Active Enzymes Within Gram-Negative Bacteria. Methods Mol Biol 2017; 1588:199-208. [PMID: 28417370 DOI: 10.1007/978-1-4939-6899-2_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Investigating the subcellular location of secreted proteins is valuable for illuminating their biological function. Although several bioinformatics programs currently exist to predict the destination of a trafficked protein using its signal peptide sequence, these programs have limited accuracy and often require experimental validation. Here, we present a systematic method to fractionate gram-negative cells and characterize the subcellular localization of secreted carbohydrate active enzymes (CAZymes). This method involves four parallel approaches that reveal the relative abundance of protein within the cytoplasm, periplasm, outer membrane, and extracellular environment. Cytoplasmic and periplasmic proteins are fractionated by lysis and osmotic shock, respectively. Outer membrane bound proteins are determined by comparing cells before and after exoproteolytic digestion. Extracellularly secreted proteins are collected from the media and concentrated. These four different fractionations can then be probed for the presence and quantity of target proteins using immunochemical methods such as Western blots and ELISAs, or enzyme activity assays.
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Affiliation(s)
- Richard McLean
- Functional Genomics of Complex Carbohydrate Utilization, Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave. South, Lethbridge, T1J 4B1 AB, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, T1K 3M4 AB, Canada
| | - G Douglas Inglis
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, T1K 3M4 AB, Canada
| | - Steven C Mosimann
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, T1K 3M4 AB, Canada
| | - Richard R E Uwiera
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5
| | - D Wade Abbott
- Functional Genomics of Complex Carbohydrate Utilization, Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave. South, Lethbridge, T1J 4B1 AB, Canada. .,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, T1K 3M4 AB, Canada.
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22
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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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23
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Abstract
In this issue of Structure, Borowska et al. (2015) report the crystal structure and provide experimental evidence on an archaeal membrane insertase, the DUF106 protein from Methanocaldococcus jannaschii, demonstrating that YidC/Oxa1/Alb3-like insertases exist in the archaeal plasma membrane.
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Affiliation(s)
- Ross E Dalbey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany.
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24
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Itakura E, Zavodszky E, Shao S, Wohlever ML, Keenan RJ, Hegde RS. Ubiquilins Chaperone and Triage Mitochondrial Membrane Proteins for Degradation. Mol Cell 2016; 63:21-33. [PMID: 27345149 PMCID: PMC4942676 DOI: 10.1016/j.molcel.2016.05.020] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/04/2016] [Accepted: 05/16/2016] [Indexed: 12/14/2022]
Abstract
We investigated how mitochondrial membrane proteins remain soluble in the cytosol until their delivery to mitochondria or degradation at the proteasome. We show that Ubiquilin family proteins bind transmembrane domains in the cytosol to prevent aggregation and temporarily allow opportunities for membrane targeting. Over time, Ubiquilins recruit an E3 ligase to ubiquitinate bound clients. The attached ubiquitin engages Ubiquilin's UBA domain, normally bound to an intramolecular UBL domain, and stabilizes the Ubiquilin-client complex. This conformational change precludes additional chances at membrane targeting for the client, while simultaneously freeing Ubiquilin's UBL domain for targeting to the proteasome. Loss of Ubiquilins by genetic ablation or sequestration in polyglutamine aggregates leads to accumulation of non-inserted mitochondrial membrane protein precursors. These findings define Ubiquilins as a family of chaperones for cytosolically exposed transmembrane domains and explain how they use ubiquitin to triage clients for degradation via coordinated intra- and intermolecular interactions.
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Affiliation(s)
- Eisuke Itakura
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Biology, Faculty of Science, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Eszter Zavodszky
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sichen Shao
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthew L Wohlever
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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25
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Abstract
Serine resolvases are an interesting group of site-specific recombinases that, in their native contexts, resolve large fused replicons into smaller separated ones. Some resolvases are encoded by replicative transposons and resolve the transposition product, in which the donor and recipient molecules are fused, into separate replicons. Other resolvases are encoded by plasmids and function to resolve plasmid dimers into monomers. Both types are therefore involved in the spread and maintenance of antibiotic-resistance genes. Resolvases and the closely related invertases were the first serine recombinases to be studied in detail, and much of our understanding of the unusual strand exchange mechanism of serine recombinases is owed to those early studies. Resolvases and invertases have also served as paradigms for understanding how DNA topology can be harnessed to regulate enzyme activity. Finally, their relatively modular structure, combined with a wealth of structural and biochemical data, has made them good choices for engineering chimeric recombinases with designer specificity. This chapter focuses on the current understanding of serine resolvases, with a focus on the contributions of structural studies.
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26
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Kuhn P, Draycheva A, Vogt A, Petriman NA, Sturm L, Drepper F, Warscheid B, Wintermeyer W, Koch HG. Ribosome binding induces repositioning of the signal recognition particle receptor on the translocon. J Cell Biol 2016; 211:91-104. [PMID: 26459600 PMCID: PMC4602035 DOI: 10.1083/jcb.201502103] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The cotranslational transfer of nascent membrane proteins to the SecYEG translocon is facilitated by a reorientation of the SecY-bound signal recognition particle (SRP) receptor, FtsY, which accompanies the formation of a quaternary targeting complex consisting of SecYEG, FtsY, SRP, and the ribosome. Cotranslational protein targeting delivers proteins to the bacterial cytoplasmic membrane or to the eukaryotic endoplasmic reticulum membrane. The signal recognition particle (SRP) binds to signal sequences emerging from the ribosomal tunnel and targets the ribosome-nascent-chain complex (RNC) to the SRP receptor, termed FtsY in bacteria. FtsY interacts with the fifth cytosolic loop of SecY in the SecYEG translocon, but the functional role of the interaction is unclear. By using photo-cross-linking and fluorescence resonance energy transfer measurements, we show that FtsY–SecY complex formation is guanosine triphosphate independent but requires a phospholipid environment. Binding of an SRP–RNC complex exposing a hydrophobic transmembrane segment induces a rearrangement of the SecY–FtsY complex, which allows the subsequent contact between SecY and ribosomal protein uL23. These results suggest that direct RNC transfer to the translocon is guided by the interaction between SRP and translocon-bound FtsY in a quaternary targeting complex.
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Affiliation(s)
- Patrick Kuhn
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Albena Draycheva
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Andreas Vogt
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Narcis-Adrian Petriman
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Lukas Sturm
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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27
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Abstract
Secretion is the cellular process present in every organism that delivers soluble proteins and cargoes to the extracellular space. In eukaryotes, conventional protein secretion (CPS) is the trafficking route that secretory proteins undertake when are transported from the endoplasmic reticulum (ER) to the Golgi apparatus (GA), and subsequently to the plasma membrane (PM) via secretory vesicles or secretory granules. This book chapter recalls the fundamental steps in cell biology research contributing to the elucidation of CPS; it describes the most prominent examples of conventionally secreted proteins in eukaryotic cells and the molecular mechanisms necessary to regulate each step of this process.
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28
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Plagens A, Daume M, Wiegel J, Randau L. Circularization restores signal recognition particle RNA functionality in Thermoproteus. eLife 2015; 4. [PMID: 26499493 PMCID: PMC4731332 DOI: 10.7554/elife.11623] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/23/2015] [Indexed: 11/15/2022] Open
Abstract
Signal recognition particles (SRPs) are universal ribonucleoprotein complexes found in all three domains of life that direct the cellular traffic and secretion of proteins. These complexes consist of SRP proteins and a single, highly structured SRP RNA. Canonical SRP RNA genes have not been identified for some Thermoproteus species even though they contain SRP19 and SRP54 proteins. Here, we show that genome rearrangement events in Thermoproteus tenax created a permuted SRP RNA gene. The 5'- and 3'-termini of this SRP RNA are located close to a functionally important loop present in all known SRP RNAs. RNA-Seq analyses revealed that these termini are ligated together to generate circular SRP RNA molecules that can bind to SRP19 and SRP54. The circularization site is processed by the tRNA splicing endonuclease. This moonlighting activity of the tRNA splicing machinery permits the permutation of the SRP RNA and creates highly stable and functional circular RNA molecules. DOI:http://dx.doi.org/10.7554/eLife.11623.001 Cells make many proteins that are eventually released outside the cell or inserted into the cell’s membrane. As these proteins are still being made, they are captured by a “signal recognition particle” (or SRP); this molecular machine then guides the newly forming protein to the cell’s membrane. SRPs are found in all living organisms on Earth and contain several different proteins and a short RNA molecule. However, a few species belonging to the archaeal domain of life did not seem to contain an identifiable gene for the RNA component of the SRP. Now Plagens et al. have sought to solve the mystery of the “missing” component of this essential protein-targeting machine. This involved searching through the RNAs that are produced by an archaeon called Thermoproteus tenax, a single-celled microbe which grows in the absence of oxygen and at temperatures of up to 95°C. Plagens et al. discovered that the “missing” SRP RNA gene had not yet been identified because rearrangements in this archaeon’s genome had swapped the left and right portions of the SRP RNA gene. Further experiments revealed that the correct sequence order is restored in mature SRP RNA molecules by the two ends of the molecule being linked to form a circle. These RNA circles are made by the cellular machinery that normally removes the unneeded sections from other RNA molecules (called transfer RNAs). Circular RNA is much more stable at high temperatures and does not degrade easily, and Plagens et al. suggest that this particular arrangement is therefore especially advantageous for this species. Future work will now aim to work out which selective pressures favor the evolution of such fragmented RNAs. DOI:http://dx.doi.org/10.7554/eLife.11623.002
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Affiliation(s)
- André Plagens
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Daume
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Wiegel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Synmikro, Marburg, Germany
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Kunze M, Berger J. The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance. Front Physiol 2015; 6:259. [PMID: 26441678 PMCID: PMC4585086 DOI: 10.3389/fphys.2015.00259] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/04/2015] [Indexed: 12/04/2022] Open
Abstract
The proper distribution of proteins between the cytosol and various membrane-bound compartments is crucial for the functionality of eukaryotic cells. This requires the cooperation between protein transport machineries that translocate diverse proteins from the cytosol into these compartments and targeting signal(s) encoded within the primary sequence of these proteins that define their cellular destination. The mechanisms exerting protein translocation differ remarkably between the compartments, but the predominant targeting signals for mitochondria, chloroplasts and the ER share the N-terminal position, an α-helical structural element and the removal from the core protein by intraorganellar cleavage. Interestingly, similar properties have been described for the peroxisomal targeting signal type 2 mediating the import of a fraction of soluble peroxisomal proteins, whereas other peroxisomal matrix proteins encode the type 1 targeting signal residing at the extreme C-terminus. The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments. Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals. Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
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Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. A YidC-like Protein in the Archaeal Plasma Membrane. Structure 2015; 23:1715-1724. [PMID: 26256539 PMCID: PMC4558205 DOI: 10.1016/j.str.2015.06.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/29/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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31
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Abstract
Accurate folding, assembly, localization, and maturation of newly synthesized proteins are essential to all cells and require high fidelity in the protein biogenesis machineries that mediate these processes. Here, we review our current understanding of how high fidelity is achieved in one of these processes, the cotranslational targeting of nascent membrane and secretory proteins by the signal recognition particle (SRP). Recent biochemical, biophysical, and structural studies have elucidated how the correct substrates drive a series of elaborate conformational rearrangements in the SRP and SRP receptor GTPases; these rearrangements provide effective fidelity checkpoints to reject incorrect substrates and enhance the fidelity of this essential cellular pathway. The mechanisms used by SRP to ensure fidelity share important conceptual analogies with those used by cellular machineries involved in DNA replication, transcription, and translation, and these mechanisms likely represent general principles for other complex cellular pathways.
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Affiliation(s)
- Xin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125;
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32
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Proteomic Analysis of theStreptomyces griseusRibosomal Fraction. Biosci Biotechnol Biochem 2014; 76:2267-74. [DOI: 10.1271/bbb.120556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Co-translational targeting and translocation of proteins to the endoplasmic reticulum. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2392-402. [DOI: 10.1016/j.bbamcr.2013.02.021] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 12/16/2022]
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34
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Generation of a Highly Active Folding Enzyme by Combining a Parvulin-Type Prolyl Isomerase from SurA with an Unrelated Chaperone Domain. J Mol Biol 2013; 425:4089-98. [DOI: 10.1016/j.jmb.2013.06.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 11/19/2022]
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Saraogi I, Shan SO. Co-translational protein targeting to the bacterial membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1433-41. [PMID: 24513458 DOI: 10.1016/j.bbamcr.2013.10.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 12/18/2022]
Abstract
Co-translational protein targeting by the Signal Recognition Particle (SRP) is an essential cellular pathway that couples the synthesis of nascent proteins to their proper cellular localization. The bacterial SRP, which contains the minimal ribonucleoprotein core of this universally conserved targeting machine, has served as a paradigm for understanding the molecular basis of protein localization in all cells. In this review, we highlight recent biochemical and structural insights into the molecular mechanisms by which fundamental challenges faced by protein targeting machineries are met in the SRP pathway. Collectively, these studies elucidate how an essential SRP RNA and two regulatory GTPases in the SRP and SRP receptor (SR) enable this targeting machinery to recognize, sense and respond to its biological effectors, i.e. the cargo protein, the target membrane and the translocation machinery, thus driving efficient and faithful co-translational protein targeting. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Ishu Saraogi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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36
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Reinstein J. Proximity effects on the protein domain level: engineering prolyl isomerases through combinatorial biochemistry. J Mol Biol 2013; 425:4065-6. [PMID: 23911550 DOI: 10.1016/j.jmb.2013.07.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Jochen Reinstein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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37
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Kudva R, Denks K, Kuhn P, Vogt A, Müller M, Koch HG. Protein translocation across the inner membrane of Gram-negative bacteria: the Sec and Tat dependent protein transport pathways. Res Microbiol 2013; 164:505-34. [DOI: 10.1016/j.resmic.2013.03.016] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
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38
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Molecular flexibility and structural instabilities in crystalline l-methionine. Biophys Chem 2013; 180-181:76-85. [PMID: 23886538 DOI: 10.1016/j.bpc.2013.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/14/2013] [Accepted: 06/14/2013] [Indexed: 11/22/2022]
Abstract
We have investigated the dynamics in polycrystalline samples of l-methionine related to the structural transition at about 307K by incoherent inelastic and quasielastic neutron scattering, X-ray powder diffraction as well as ab-initio calculations. l-Methionine is a sulfur amino acid which can be considered a derivative of alanine with the alanine R-group CH3 exchanged by CH3S(CH2)2. Using X-ray powder diffraction we have observed at ~190K an anomalous drop of the c-lattice parameter and an abrupt change of the β-monoclinic angle that could be correlated to the anomalies observed in previous specific heat measurements. Distinct changes in the quasielastic region of the neutron spectra are interpreted as being due to the onset and slowing-down of reorientational motions of the CH3-S group, are clearly distinguished above 130K in crystalline l-methionine. Large-amplitude motions observed at low frequencies are also activated above 275K, while other well-defined vibrations are damped. The ensemble of our results suggests that the crystalline structure of l-methionine is dynamically highly disordered above 275K, and such disorder can be linked to the flexibility of the molecular thiol-ether group.
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Abstract
The signal recognition particle (SRP) and its receptor compose a universally conserved and essential cellular machinery that couples the synthesis of nascent proteins to their proper membrane localization. The past decade has witnessed an explosion in in-depth mechanistic investigations of this targeting machine at increasingly higher resolutions. In this review, we summarize recent work that elucidates how the SRP and SRP receptor interact with the cargo protein and the target membrane, respectively, and how these interactions are coupled to a novel GTPase cycle in the SRP·SRP receptor complex to provide the driving force and enhance the fidelity of this fundamental cellular pathway. We also discuss emerging frontiers in which important questions remain to be addressed.
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Affiliation(s)
- David Akopian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Kuang Shen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Xin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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40
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Mandon EC, Trueman SF, Gilmore R. Protein translocation across the rough endoplasmic reticulum. Cold Spring Harb Perspect Biol 2013; 5:cshperspect.a013342. [PMID: 23251026 DOI: 10.1101/cshperspect.a013342] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The rough endoplasmic reticulum is a major site of protein biosynthesis in all eukaryotic cells, serving as the entry point for the secretory pathway and as the initial integration site for the majority of cellular integral membrane proteins. The core components of the protein translocation machinery have been identified, and high-resolution structures of the targeting components and the transport channel have been obtained. Research in this area is now focused on obtaining a better understanding of the molecular mechanism of protein translocation and membrane protein integration.
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Affiliation(s)
- Elisabet C Mandon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-2324, USA
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41
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Characterization of Ffh of Mycobacterium tuberculosis and its interaction with 4.5S RNA. Microbiol Res 2012; 167:520-5. [DOI: 10.1016/j.micres.2012.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 02/27/2012] [Accepted: 03/11/2012] [Indexed: 11/20/2022]
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42
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Govindarajan S, Nevo-Dinur K, Amster-Choder O. Compartmentalization and spatiotemporal organization of macromolecules in bacteria. FEMS Microbiol Rev 2012; 36:1005-22. [DOI: 10.1111/j.1574-6976.2012.00348.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 12/18/2022] Open
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43
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Jiang X, Ruiz T, Mintz KP. Characterization of the secretion pathway of the collagen adhesin EmaA of Aggregatibacter actinomycetemcomitans. Mol Oral Microbiol 2012; 27:382-96. [PMID: 22958387 DOI: 10.1111/j.2041-1014.2012.00652.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The extracellular matrix protein adhesin A (EmaA) surface antennae-like structures of the periodontal pathogen Aggregatibacter actinomycetemcomitans are composed of three identical protein monomers. Recently, we have demonstrated that the protein is synthesized with an extended signal peptide of 56 amino acids necessary for membrane targeting and protein translocation. In this study, EmaA secretion was demonstrated to be reliant on a chaperone-dependent secretion pathway. Deletion of secB partially reduced but did not abolish the amount of EmaA in the membrane. This observation was attributed to an increase in the synthesis of DnaK in the ΔsecB strain. Overexpression of a DnaK substitution mutant (A174T), with diminished activity, in the ΔsecB strain further reduced the amount of EmaA in the membrane. Expression of dnaK A174T in the wild-type strain did not affect the amount of EmaA in the membrane when grown under optimal growth conditions at 37°C. However, EmaA was found to be reduced when this strain was grown at heat-shock temperature. A chromosomal deletion of amino acids 16-39 of the EmaA extended signal peptide, transformed with either the wild-type or dnaK A174T-expressing plasmid, did not affect the amount of EmaA in the membrane. In addition, the level of EmaA in a ΔsecB/emaA(-) double mutant strain expressing EmaAΔ16-39 was unchanged when grown at both temperatures. The data suggest that chaperones are required for the targeting of EmaA to the membrane and a specific region of the signal peptide is necessary for secretion under stress conditions.
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Affiliation(s)
- X Jiang
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
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44
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Angerer H, Nasiri HR, Niedergesäß V, Kerscher S, Schwalbe H, Brandt U. Tracing the tail of ubiquinone in mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1776-84. [PMID: 22484275 DOI: 10.1016/j.bbabio.2012.03.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 12/01/2022]
Abstract
Mitochondrial complex I (proton pumping NADH:ubiquinone oxidoreductase) is the largest and most complicated component of the respiratory electron transfer chain. Despite its central role in biological energy conversion the structure and function of this membrane integral multiprotein complex is still poorly understood. Recent insights into the structure of complex I by X-ray crystallography have shown that iron-sulfur cluster N2, the immediate electron donor for ubiquinone, resides about 30Å above the membrane domain and mutagenesis studies suggested that the active site for the hydrophobic substrate is located next to this redox-center. To trace the path for the hydrophobic tail of ubiquinone when it enters the peripheral arm of complex I, we performed an extensive structure/function analysis of complex I from Yarrowia lipolytica monitoring the interaction of site-directed mutants with five ubiquinone derivatives carrying different tails. The catalytic activity of a subset of mutants was strictly dependent on the presence of intact isoprenoid moieties in the tail. Overall a consistent picture emerged suggesting that the tail of ubiquinone enters through a narrow path at the interface between the 49-kDa and PSST subunits. Most notably we identified a set of methionines that seems to form a hydrophobic gate to the active site reminiscent to the M-domains involved in the interaction with hydrophobic targeting sequences with the signal recognition particle of the endoplasmic reticulum. Interestingly, two of the amino acids critical for the interaction with the ubiquinone tail are different in bovine complex I and we could show that one of these exchanges is responsible for the lower sensitivity of Y. lipolytica complex I towards the inhibitor rotenone. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Heike Angerer
- Goethe-University, Theodor-Stern-Kai 7, Frankfurt am Main, Germany
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45
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Tail-anchor targeting by a Get3 tetramer: the structure of an archaeal homologue. EMBO J 2011; 31:707-19. [PMID: 22124326 PMCID: PMC3273380 DOI: 10.1038/emboj.2011.433] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 11/09/2011] [Indexed: 11/09/2022] Open
Abstract
Efficient delivery of membrane proteins is a critical cellular process. The recently elucidated GET (Guided Entry of TA proteins) pathway is responsible for the targeted delivery of tail-anchored (TA) membrane proteins to the endoplasmic reticulum. The central player is the ATPase Get3, which in its free form exists as a dimer. Biochemical evidence suggests a role for a tetramer of Get3. Here, we present the first crystal structure of an archaeal Get3 homologue that exists as a tetramer and is capable of TA protein binding. The tetramer generates a hydrophobic chamber that we propose binds the TA protein. We use small-angle X-ray scattering to provide the first structural information of a fungal Get3/TA protein complex showing that the overall molecular envelope is consistent with the archaeal tetramer structure. Moreover, we show that this fungal tetramer complex is capable of TA insertion. This allows us to suggest a model where a tetramer of Get3 sequesters a TA protein during targeting to the membrane.
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46
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Knörzer P, Silakov A, Foster CE, Armstrong FA, Lubitz W, Happe T. Importance of the protein framework for catalytic activity of [FeFe]-hydrogenases. J Biol Chem 2011; 287:1489-99. [PMID: 22110126 DOI: 10.1074/jbc.m111.305797] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The active center (H-cluster) of [FeFe]-hydrogenases is embedded into a hydrophobic pocket within the protein. We analyzed several amino acids, located in the vicinity of this niche, by site-directed mutagenesis of the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1). These amino acids are highly conserved and predicted to be involved in H-cluster coordination. Characterization of two hydrogenase variants confirmed this hypothesis. The exchange of residues CrHydA1Met(415) and CrHydA1Lys(228) resulted in inactive proteins, which, according to EPR and FTIR analyses, contain no intact H-cluster. However, [FeFe]-hydrogenases in which CpIMet(353) (CrHydA1Met(223)) and CpICys(299) (CrHydA1Cys(169)) were exchanged to leucine and serine, respectively, showed a structurally intact H-cluster with catalytic activity either absent (CpIC299S) or strongly diminished (CpIM353L). In the case of CrHydA1C169S, the H-cluster was trapped in an inactive state exhibiting g values and vibrational frequencies that resembled the H(trans) state of DdH from Desulfovibrio desulfuricans. This cysteine residue, interacting with the bridge head nitrogen of the di(methyl)amine ligand, seems therefore to represent an essential contribution of the immediate protein environment to the reaction mechanism. Exchanging methionine CpIM(353) (CrHydA1M(223)) to leucine led to a strong decrease in turnover without affecting the K(m) value of the electron donor. We suggest that this methionine constitutes a "fine-tuning" element of hydrogenase activity.
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Affiliation(s)
- Philipp Knörzer
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Ruhr-Universität Bochum, 44780 Bochum, Germany
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47
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Abstract
The signal recognition particle (SRP) is a key component of the cellular machinery that couples the ongoing synthesis of proteins to their proper localization, and has often served as a paradigm for understanding the molecular basis of protein localization within the cell. The SRP pathway exemplifies several key molecular events required for protein targeting to cellular membranes: the specific recognition of signal sequences on cargo proteins, the efficient delivery of cargo to the target membrane, the productive unloading of cargo to the translocation machinery and the precise spatial and temporal coordination of these molecular events. Here we highlight recent advances in our understanding of the molecular mechanisms underlying this pathway, and discuss new questions raised by these findings.
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Affiliation(s)
- Ishu Saraogi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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48
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Abstract
The mitochondrial rhomboid protease Parl governs apoptosis, morphology, metabolism and might be implicated in Parkinson's disease, but the structural basis of its activity and complex regulation remain unknown. We report the discovery of γ-cleavage, a proteolytic event on the loop connecting the first transmembrane helix (TMH) of Parl to the 6-TMH catalytic rhomboid domain of the protease. This cleavage disrupts the '1+6' structure that defines every mitochondrial rhomboid and generates a new form of Parl, PROD (Parl-rhomboid-domain). Structure-function analysis of Parl suggests that γ-cleavage could be implicated in eliminating Parl proteolytic activity, and structural modeling of PROD reveals structural conservation with the bacterial rhomboid GlpG. However, unlike bacterial rhomboids, which employ a diad-based mechanism of catalysis, Parl appears to use a conserved mitochondrial rhomboid-specific Asp residue on TMH-5 in a triad-based mechanism of catalysis. This work provides unexpected insights into the structural determinants regulating Parl stability and activity in vivo, and reveals a complex cascade of proteolytic events controlling the function of the protease in the mitochondrion.
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49
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Bibi E. Early targeting events during membrane protein biogenesis in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:841-50. [PMID: 20682283 DOI: 10.1016/j.bbamem.2010.07.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
Abstract
All living cells have co-translational pathways for targeting membrane proteins. Co-translation pathways for secretory proteins also exist but mostly in eukaryotes. Unlike secretory proteins, the biosynthetic pathway of most membrane proteins is conserved through evolution and these proteins are usually synthesized by membrane-bound ribosomes. Translation on the membrane requires that both the ribosomes and the mRNAs be properly localized. Theoretically, this can be achieved by several means. (i) The current view is that the targeting of cytosolic mRNA-ribosome-nascent chain complexes (RNCs) to the membrane is initiated by information in the emerging hydrophobic nascent polypeptides. (ii) The alternative model suggests that ribosomes may be targeted to the membrane also constitutively, whereas the appropriate mRNAs may be carried on small ribosomal subunits or targeted by other cellular factors to the membrane-bound ribosomes. Importantly, the available experimental data do not rule out the possibility that cells may also utilize both pathways in parallel. In any case, it is well documented that a major player in the targeting pathway is the signal recognition particle (SRP) system composed of the SRP and its receptor (SR). Although the functional core of the SRP system is evolutionarily conserved, its composition and biological practice come with different flavors in various organisms. This review is dedicated mainly to the Escherichia (E.) coli SRP, where the biochemical and structural properties of components of the SRP system have been relatively characterized, yielding essential information about various aspects of the pathway. In addition, several cellular interactions of the SRP and its receptor have been described in E. coli, providing insights into their spatial function. Collectively, these in vitro studies have led to the current view of the targeting pathway [see (i) above]. Interestingly, however, in vivo studies of the role of the SRP and its receptor, with emphasis on the temporal progress of the pathway, elicited an alternative hypothesis [see (ii) above]. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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Affiliation(s)
- Eitan Bibi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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Escherichia coli SRP, its protein subunit Ffh, and the Ffh M domain are able to selectively limit membrane protein expression when overexpressed. mBio 2010; 1. [PMID: 20714446 PMCID: PMC2921155 DOI: 10.1128/mbio.00020-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 05/06/2010] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli signal recognition particle (SRP) system plays an important role in membrane protein biogenesis. Previous studies have suggested indirectly that in addition to its role during the targeting of ribosomes translating membrane proteins to translocons, the SRP might also have a quality control role in preventing premature synthesis of membrane proteins in the cytoplasm. This proposal was studied here using cells simultaneously overexpressing various membrane proteins and either SRP, the SRP protein Ffh, its 4.5S RNA, or the Ffh M domain. The results show that SRP, Ffh, and the M domain are all able to selectively inhibit the expression of membrane proteins. We observed no apparent changes in the steady-state mRNA levels or membrane protein stability, suggesting that inhibition may occur at the level of translation, possibly through the interaction between Ffh and ribosome-hydrophobic nascent chain complexes. Since E. coli SRP does not have a eukaryote-like translation arrest domain, we discuss other possible mechanisms by which this SRP might regulate membrane protein translation when overexpressed. The eukaryotic SRP slows down translation of SRP substrates by cytoplasmic ribosomes. This activity is important for preventing premature synthesis of secretory and membrane proteins in the cytoplasm. It is likely that an analogous quality control step would be required in all living cells. However, on the basis of its composition and domain structure and limited in vitro studies, it is believed that the E. coli SRP is unable to regulate ribosomes translating membrane proteins. Nevertheless, several in vivo studies have suggested otherwise. To address this issue further in vivo, we utilized unbalanced conditions under which E. coli simultaneously overexpresses SRP and each of several membrane or cytosolic proteins. Surprisingly, our results clearly show that the E. coli SRP is capable of regulating membrane protein synthesis and demonstrate that the M domain of Ffh mediates this activity. These results thus open the way for mechanistic characterization of this quality control process in bacteria.
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