251
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Doris SM, Smith DR, Beamesderfer JN, Raphael BJ, Nathanson JA, Gerbi SA. Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics. RNA (NEW YORK, N.Y.) 2015; 21:1719-1730. [PMID: 26283689 PMCID: PMC4574749 DOI: 10.1261/rna.051144.115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/07/2015] [Indexed: 06/01/2023]
Abstract
Comparative analysis of ribosomal RNA (rRNA) sequences has elucidated phylogenetic relationships. However, this powerful approach has not been fully exploited to address ribosome function. Here we identify stretches of evolutionarily conserved sequences, which correspond with regions of high functional importance. For this, we developed a structurally aligned database, FLORA (full-length organismal rRNA alignment) to identify highly conserved nucleotide elements (CNEs) in 23S-28S rRNA from each phylogenetic domain (Eukarya, Bacteria, and Archaea). Universal CNEs (uCNEs) are conserved in sequence and structural position in all three domains. Those in regions known to be essential for translation validate our approach. Importantly, some uCNEs reside in areas of unknown function, thus identifying novel sequences of likely great importance. In contrast to uCNEs, domain-specific CNEs (dsCNEs) are conserved in just one phylogenetic domain. This is the first report of conserved sequence elements in rRNA that are domain-specific; they are largely a eukaryotic phenomenon. The locations of the eukaryotic dsCNEs within the structure of the ribosome suggest they may function in nascent polypeptide transit through the ribosome tunnel and in tRNA exit from the ribosome. Our findings provide insights and a resource for ribosome function studies.
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Affiliation(s)
- Stephen M Doris
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Deborah R Smith
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Julia N Beamesderfer
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Benjamin J Raphael
- Department of Computer Science and Center for Computational Molecular Biology, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Judith A Nathanson
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
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252
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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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253
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Fung HYJ, Fu SC, Brautigam CA, Chook YM. Structural determinants of nuclear export signal orientation in binding to exportin CRM1. eLife 2015; 4:e10034. [PMID: 26349033 PMCID: PMC4596688 DOI: 10.7554/elife.10034] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/08/2015] [Indexed: 12/03/2022] Open
Abstract
The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). Comparison of minus and plus NESs identified structural and sequence determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.
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Affiliation(s)
- Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Szu-Chin Fu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
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254
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Translational arrest by a prokaryotic signal recognition particle is mediated by RNA interactions. Nat Struct Mol Biol 2015; 22:767-73. [PMID: 26344568 DOI: 10.1038/nsmb.3086] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 08/13/2015] [Indexed: 12/25/2022]
Abstract
The signal recognition particle (SRP) recognizes signal sequences of nascent polypeptides and targets ribosome-nascent chain complexes to membrane translocation sites. In eukaryotes, translating ribosomes are slowed down by the Alu domain of SRP to allow efficient targeting. In prokaryotes, however, little is known about the structure and function of Alu domain-containing SRPs. Here, we report a complete molecular model of SRP from the Gram-positive bacterium Bacillus subtilis, based on cryo-EM. The SRP comprises two subunits, 6S RNA and SRP54 or Ffh, and it facilitates elongation slowdown similarly to its eukaryotic counterpart. However, protein contacts with the small ribosomal subunit observed for the mammalian Alu domain are substituted in bacteria by RNA-RNA interactions of 6S RNA with the α-sarcin-ricin loop and helices H43 and H44 of 23S rRNA. Our findings provide a structural basis for cotranslational targeting and RNA-driven elongation arrest in prokaryotes.
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255
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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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256
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Dumesic PA, Rosenblad MA, Samuelsson T, Nguyen T, Moresco JJ, Yates JR, Madhani HD. Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. Nucleic Acids Res 2015; 43:9017-27. [PMID: 26275773 PMCID: PMC4605306 DOI: 10.1093/nar/gkv819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 08/01/2015] [Indexed: 12/21/2022] Open
Abstract
Despite conservation of the signal recognition particle (SRP) from bacteria to man, computational approaches have failed to identify SRP components from genomes of many lower eukaryotes, raising the possibility that they have been lost or altered in those lineages. We report purification and analysis of SRP in the human pathogen Cryptococcus neoformans, providing the first description of SRP in basidiomycetous yeast. The C. neoformans SRP RNA displays a predicted structure in which the universally conserved helix 8 contains an unprecedented stem-loop insertion. Guided by this sequence, we computationally identified 152 SRP RNAs throughout the phylum Basidiomycota. This analysis revealed additional helix 8 alterations including single and double stem-loop insertions as well as loop diminutions affecting RNA structural elements that are otherwise conserved from bacteria to man. Strikingly, these SRP RNA features in Basidiomycota are accompanied by phylum-specific alterations in the RNA-binding domain of Srp54, the SRP protein subunit that directly interacts with helix 8. Our findings reveal unexpected fungal SRP diversity and suggest coevolution of the two most conserved SRP features-SRP RNA helix 8 and Srp54-in basidiomycetes. Because members of this phylum include important human and plant pathogens, these noncanonical features provide new targets for antifungal compound development.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Magnus A Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tiffany Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
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257
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Abstract
Intracellular logistics are essential for delivery of newly synthesized material during polar growth of fungal hyphae. Proteins and lipids are actively transported throughout the cell by motor-dependent movement of small vesicles or larger units such as endosomes and the endoplasmic reticulum. A remarkably tight link is emerging between active membrane trafficking and mRNA transport, a process that determines the precise subcellular localization of translation products within the cell. Here, we report on recent insights into the mechanism and biological role of these intricate cotransport processes in fungal models such as Saccharomyces cerevisiae, Candida albicans, and Ustilago maydis. In the latter, we focus on the new finding of endosomal mRNA transport and its implications for protein targeting, complex assembly, and septin biology.
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Affiliation(s)
- Carl Haag
- Cluster of Excellence on Plant Sciences, Institute for Microbiology, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany; , ,
| | - Benedikt Steuten
- Cluster of Excellence on Plant Sciences, Institute for Microbiology, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany; , ,
| | - Michael Feldbrügge
- Cluster of Excellence on Plant Sciences, Institute for Microbiology, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany; , ,
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258
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Paths and determinants for Penicillium janthinellum to resist low and high copper. Sci Rep 2015; 5:10590. [PMID: 26265593 PMCID: PMC4642507 DOI: 10.1038/srep10590] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/20/2015] [Indexed: 01/21/2023] Open
Abstract
Copper (Cu) tolerance was well understood in fungi yeasts but not in filamentous fungi. Filamentous fungi are eukaryotes but unlike eukaryotic fungi yeasts, which are a collection of various fungi that are maybe classified into different taxa but all characterized by growth as filamentous hyphae cells and with a complex morphology. The current knowledge of Cu resistance of filamentous fungi is still fragmental and therefore needs to be bridged. In this study, we characterized Cu resistance of Penicillium janthinellum strain GXCR and its Cu-resistance-decreasing mutants (EC-6 and UC-8), and conducted sequencing of a total of 6 transcriptomes from wild-type GXCR and mutant EC-6 grown under control and external Cu. Taken all the results together, Cu effects on the basal metabolism were directed to solute transport by two superfamilies of solute carrier and major facilitator, the buffering free CoA and Acyl-CoA pool in the peroxisome, F-type H(+)-transporting ATPases-based ATP production, V-type H(+)-transporting ATPases-based transmembrane transport, protein degradation, and alternative splicing of pre-mRNAs. Roles of enzymatic and non-enzymatic antioxidants in resistance to low and high Cu were defined. The backbone paths, signaling systems, and determinants that involve resistance of filamentous fungi to high Cu were determined, discussed and outlined in a model.
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259
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Nelson WC, Stegen JC. The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. Front Microbiol 2015; 6:713. [PMID: 26257709 PMCID: PMC4508563 DOI: 10.3389/fmicb.2015.00713] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/29/2015] [Indexed: 11/21/2022] Open
Abstract
Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. “Housekeeping” genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.
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Affiliation(s)
- William C Nelson
- Microbiology, Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - James C Stegen
- Microbiology, Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
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260
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Schuhmacher JS, Thormann KM, Bange G. How bacteria maintain location and number of flagella? FEMS Microbiol Rev 2015. [PMID: 26195616 DOI: 10.1093/femsre/fuv034] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bacteria differ in number and location of their flagella that appear in regular patterns at the cell surface (flagellation pattern). Despite the plethora of bacterial species, only a handful of these patterns exist. The correct flagellation pattern is a prerequisite for motility, but also relates to biofilm formation and the pathogenicity of disease-causing flagellated bacteria. However, the mechanisms that maintain location and number of flagella are far from being understood. Here, we review our knowledge on mechanisms that enable bacteria to maintain their appropriate flagellation pattern. While some peritrichous flagellation patterns might occur by rather simple stochastic processes, other bacterial species appear to rely on landmark systems to define the designated flagellar position. Such landmarks are the Tip system of Caulobacter crescentus or the signal recognition particle (SRP)-GTPase FlhF and the MinD/ParA-type ATPase FlhG (synonyms: FleN, YlxH and MinD2). The latter two proteins constitute a regulatory circuit essential for diverse flagellation patterns in many Gram-positive and negative species. The interactome of FlhF/G (e.g. C-ring proteins FliM, FliN, FliY or the transcriptional regulator FleQ/FlrA) seems evolutionary adapted to meet the specific needs for a respective pattern. This variability highlights the importance of the correct flagellation pattern for motile species.
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Affiliation(s)
- Jan S Schuhmacher
- LOEWE Center for Synthetic Microbiology & Dep. of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
| | - Kai M Thormann
- Justus-Liebig University, Department of Microbiology and Molecular Biology, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology & Dep. of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
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261
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Abstract
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
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Affiliation(s)
- Viachaslau Bernat
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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262
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Regulation by a chaperone improves substrate selectivity during cotranslational protein targeting. Proc Natl Acad Sci U S A 2015; 112:E3169-78. [PMID: 26056263 DOI: 10.1073/pnas.1422594112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ribosome exit site is a crowded environment where numerous factors contact nascent polypeptides to influence their folding, localization, and quality control. Timely and accurate selection of nascent polypeptides into the correct pathway is essential for proper protein biogenesis. To understand how this is accomplished, we probe the mechanism by which nascent polypeptides are accurately sorted between the major cotranslational chaperone trigger factor (TF) and the essential cotranslational targeting machinery, signal recognition particle (SRP). We show that TF regulates SRP function at three distinct stages, including binding of the translating ribosome, membrane targeting via recruitment of the SRP receptor, and rejection of ribosome-bound nascent polypeptides beyond a critical length. Together, these mechanisms enhance the specificity of substrate selection into both pathways. Our results reveal a multilayered mechanism of molecular interplay at the ribosome exit site, and provide a conceptual framework to understand how proteins are selected among distinct biogenesis machineries in this crowded environment.
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263
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Walter B, Hristou A, Nowaczyk MM, Schünemann D. In vitro reconstitution of co-translational D1 insertion reveals a role of the cpSec-Alb3 translocase and Vipp1 in photosystem II biogenesis. Biochem J 2015; 468:315-24. [PMID: 25803492 DOI: 10.1042/bj20141425] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Photosystem II (PS II) is a multi-subunit complex localized in the thylakoid membrane that performs the light-dependent photosynthetic charge separation. The PS II reaction centre comprises, among others, the D1 protein. De novo synthesis and repair of PS II require efficient mechanisms for transport and insertion of plastid encoded D1 into the thylakoid membrane. To elucidate the process of D1 insertion, we used an in vitro translation system derived from pea chloroplasts to reconstitute the D1 insertion. Thereby, truncated D1 encoding psbA mRNAs lacking a stop codon were translated in the presence of thylakoid membranes and the translation was stalled by addition of chloramphenicol. The generated ribosome nascent chain complexes (RNCs) were tightly associated with the thylakoids. Subsequently, these D1 insertion intermediates were enriched from solubilized thylakoids by sucrose cushion centrifugation. Immunological analyses demonstrated the presence of the cpSec translocase, Alb3, cpFtsY, cpSRP54 and Vipp1 (vesicle-inducing protein in plastids 1) in the enriched D1 insertion intermediates. A complex formation between cpSecY, Alb3, cpFtsY and Vipp1 in thylakoid membranes was shown by gel filtration chromatography, BN (Blue Native)/SDS-PAGE and co-immunoprecipitation experiments. Furthermore, a stimulating effect of recombinant Vipp1 on the formation of a D1 insertion intermediate was observed in vitro. These results suggest a co-operative function of these proteins in D1 insertion.
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Affiliation(s)
- Björn Walter
- *Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Athina Hristou
- *Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Marc M Nowaczyk
- †Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Danja Schünemann
- *Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780 Bochum, Germany
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264
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Plumb R, Zhang ZR, Appathurai S, Mariappan M. A functional link between the co-translational protein translocation pathway and the UPR. eLife 2015; 4. [PMID: 25993558 PMCID: PMC4456659 DOI: 10.7554/elife.07426] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/19/2015] [Indexed: 12/12/2022] Open
Abstract
Upon endoplasmic reticulum (ER) stress, the transmembrane endoribonuclease Ire1α performs mRNA cleavage reactions to increase the ER folding capacity. It is unclear how the low abundant Ire1α efficiently finds and cleaves the majority of mRNAs at the ER membrane. Here, we reveal that Ire1α forms a complex with the Sec61 translocon to cleave its mRNA substrates. We show that Ire1α's key substrate, XBP1u mRNA, is recruited to the Ire1α-Sec61 translocon complex through its nascent chain, which contains a pseudo-transmembrane domain to utilize the signal recognition particle (SRP)-mediated pathway. Depletion of SRP, the SRP receptor or the Sec61 translocon in cells leads to reduced Ire1α-mediated splicing of XBP1u mRNA. Furthermore, mutations in Ire1α that disrupt the Ire1α-Sec61 complex causes reduced Ire1α-mediated cleavage of ER-targeted mRNAs. Thus, our data suggest that the Unfolded Protein Response is coupled with the co-translational protein translocation pathway to maintain protein homeostasis in the ER during stress conditions. DOI:http://dx.doi.org/10.7554/eLife.07426.001 Proteins are made up of long chains of smaller building blocks called amino acids. To build this chain, a molecule called mRNA is ‘translated’ into the sequence of amino acids by a molecular machine called a ribosome. In order to work, the protein chain must then be folded into a complex shape. For many proteins, this happens inside a cell compartment called the endoplasmic reticulum. Newly made proteins are guided to the endoplasmic reticulum by ‘signal recognition particles’, and then enter the endoplasmic reticulum through a channel protein called Sec61. If too many protein chains arrive at once, or they are folded too slowly, the accumulation of unfolded proteins can stress the endoplasmic reticulum. To fix this, cells trigger a process called the unfolded protein response. In mammals, an enzyme called Ire1α detects when the endoplasmic reticulum is becoming stressed and responds by cleaving mRNA molecules. One particular target of Ire1α is the mRNA molecule that encodes a protein called XBP1, which can activate hundreds of genes to increase the size—and hence reduce the stress—of the endoplasmic reticulum. This protein is only made if a section of the mRNA molecule is removed from it; thus, by cleaving the mRNA, Ire1α enables the protein to be made. It remains unknown, however, how Ire1α finds and cleaves its mRNA targets. Plumb, Zhang et al. identified the proteins that bind to Ire1α in human cells, and found that the Sec61 channel is one such protein. This interaction localizes Ire1α to the Sec61 channel in the endoplasmic reticulum membrane. The XBP1 protein is then brought to this channel by a signal recognition particle while it is still being translated—that is, when it is still attached to the ribosome and its mRNA molecule. Ire1α can then cleave the XBP1 mRNA. In cells that lack the signal recognition particle or the Sec61 channel protein, Ire1α cannot efficiently cleave the XBP1 mRNA molecule. In addition, if Ire1α is unable to interact with the channel protein, it does not efficiently cleave mRNA molecules at the endoplasmic reticulum membrane. This work establishes a new link between the unfolded protein response and the pathway that brings new proteins to the endoplasmic reticulum membrane. It provides a basis for future studies examining the details of Ire1α signaling in mammals and, in particular, work investigating the mechanism of insulin mRNA cleavage by Ire1α, which has been implicated in type 2 diabetes. DOI:http://dx.doi.org/10.7554/eLife.07426.002
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Affiliation(s)
- Rachel Plumb
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, West Haven, United States
| | - Zai-Rong Zhang
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, West Haven, United States
| | - Suhila Appathurai
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, West Haven, United States
| | - Malaiyalam Mariappan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, West Haven, United States
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265
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Prokesch A, Smorlesi A, Perugini J, Manieri M, Ciarmela P, Mondini E, Trajanoski Z, Kristiansen K, Giordano A, Bogner-Strauss JG, Cinti S. Molecular aspects of adipoepithelial transdifferentiation in mouse mammary gland. Stem Cells 2015; 32:2756-66. [PMID: 24898182 DOI: 10.1002/stem.1756] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/28/2014] [Accepted: 04/20/2014] [Indexed: 01/09/2023]
Abstract
The circular, reversible conversion of the mammary gland during pregnancy and involution is a paradigm of physiological tissue plasticity. The two most prominent cell types in mammary gland, adipocytes and epithelial cells, interact in an orchestrated way to coordinate this process. Previously, we showed that this conversion is at least partly achieved by reciprocal transdifferentiation between mammary adipocytes and lobulo-alveolar epithelial cells. Here, we aim to shed more light on the regulators of mammary transdifferentiation. Using immunohistochemistry with cell type-specific lipid droplet-coating markers (Perilipin1 and 2), we show that cells with an intermediate adipoepithelial phenotype exist during and after pregnancy. Nuclei of cells with similar transitional structural characteristics are highly positive for Elf5, a master regulator of alveologenesis. In cultured adipocytes, we could show that transient and stable ectopic expression of Elf5 induces expression of the milk component whey acidic protein, although the general adipocyte phenotype is not affected suggesting that additional pioneering factors are necessary. Furthermore, the lack of transdifferentiation of adipocytes during pregnancy after clearing of the epithelial compartment indicates that transdifferentiation signals must emanate from the epithelial part. To explore candidate genes potentially involved in the transdifferentiation process, we devised a high-throughput gene expression study to compare cleared mammary fat pads with developing, contralateral controls at several time points during pregnancy. Incorporation of bioinformatic predictions of secretory proteins provides new insights into possible paracrine signaling pathways and downstream transdifferentiation factors. We discuss a potential role for osteopontin (secreted phosphoprotein 1 [Spp1]) signaling through integrins to induce adipoepithelial transdifferentiation.
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Affiliation(s)
- A Prokesch
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse, Graz, Austria; Institute of Biochemistry, Graz University of Technology, Petersgasse, Graz, Austria
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266
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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267
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van de Weijer ML, Luteijn RD, Wiertz EJHJ. Viral immune evasion: Lessons in MHC class I antigen presentation. Semin Immunol 2015; 27:125-37. [PMID: 25887630 DOI: 10.1016/j.smim.2015.03.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/13/2015] [Indexed: 12/19/2022]
Abstract
The MHC class I antigen presentation pathway enables cells infected with intracellular pathogens to signal the presence of the invader to the immune system. Cytotoxic T lymphocytes are able to eliminate the infected cells through recognition of pathogen-derived peptides presented by MHC class I molecules at the cell surface. In the course of evolution, many viruses have acquired inhibitors that target essential stages of the MHC class I antigen presentation pathway. Studies on these immune evasion proteins reveal fascinating strategies used by viruses to elude the immune system. Viral immunoevasins also constitute great research tools that facilitate functional studies on the MHC class I antigen presentation pathway, allowing the investigation of less well understood routes, such as TAP-independent antigen presentation and cross-presentation of exogenous proteins. Viral immunoevasins have also helped to unravel more general cellular processes. For instance, basic principles of ER-associated protein degradation via the ubiquitin-proteasome pathway have been resolved using virus-induced degradation of MHC class I as a model. This review highlights how viral immunoevasins have increased our understanding of MHC class I-restricted antigen presentation.
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Affiliation(s)
| | - Rutger D Luteijn
- Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Emmanuel J H J Wiertz
- Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands.
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268
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Walter B, Pieta T, Schünemann D. Arabidopsis thaliana mutants lacking cpFtsY or cpSRP54 exhibit different defects in photosystem II repair. FRONTIERS IN PLANT SCIENCE 2015; 6:250. [PMID: 25918516 PMCID: PMC4394663 DOI: 10.3389/fpls.2015.00250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/27/2015] [Indexed: 05/24/2023]
Abstract
Photosystem II (PS II) is a multi subunit protein complex embedded in the thylakoid membrane of cyanobacteria and chloroplasts. As the PS II reaction center protein D1 is prone to a light induced damage that inhibits PS II function especially at elevated light intensities, a highly ordered repair process including synthesis, targeting and insertion of D1 has evolved. To elucidate the function of the chloroplast signal recognition particle subunits, cpSRP43 and cpSRP54, and the cpSRP-receptor cpFtsY in D1 biogenesis we investigated the efficiency of the PS II repair cycle in the corresponding mutants of Arabidopsis thaliana. Immunological analyses, PAM measurements and in vivo labeling experiments demonstrate an impaired replacement of damaged D1 in the cpftsy mutant, while the chaos and the ffc mutant lacking cpSRP43 and cpSRP54, respectively, were not or hardly affected. The defect in cpftsy was neither caused by an impaired psbA transcript accumulation, D1 translation initiation nor by an enhanced D1 degradation. Further experiments revealed a decreased amount of salt stable, thylakoid membrane-associated translating ribosomes in the cpftsy mutant, while the amount of membrane-associated translating ribosomes is unaltered in the chaos and the ffc mutants. Therefore, our data indicate that the lack of cpFtsY leads to an inefficient PS II repair cycle caused by an impaired binding of translating ribosomes to the thylakoid membrane.
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Affiliation(s)
- Björn Walter
- Molecular Biology of Plant Organelles, Ruhr-University BochumBochum, Germany
| | - Thomas Pieta
- Plant Cell Physiology and Molecular Biology, Ruhr-University BochumBochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr-University BochumBochum, Germany
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269
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Dünschede B, Träger C, Schröder CV, Ziehe D, Walter B, Funke S, Hofmann E, Schünemann D. Chloroplast SRP54 Was Recruited for Posttranslational Protein Transport via Complex Formation with Chloroplast SRP43 during Land Plant Evolution. J Biol Chem 2015; 290:13104-14. [PMID: 25833951 DOI: 10.1074/jbc.m114.597922] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Indexed: 01/05/2023] Open
Abstract
In bacteria, membrane proteins are targeted cotranslationally via a signal recognition particle (SRP). During the evolution of higher plant chloroplasts from cyanobacteria, the SRP pathway underwent striking adaptations that enable the posttranslational transport of the abundant light-harvesting chlorophyll-a/b-binding proteins (LHCPs). The conserved 54-kDa SRP subunit in higher plant chloroplasts (cpSRP54) is not bound to an SRP RNA, an essential SRP component in bacteria, but forms a stable heterodimer with the chloroplast-specific cpSRP43. This heterodimeric cpSRP recognizes LHCP and delivers it to the thylakoid membrane whereby cpSRP43 plays a central role. This study shows that the cpSRP system in the green alga Chlamydomonas reinhardtii differs significantly from that of higher plants as cpSRP43 is not complexed to cpSRP54 in Chlamydomonas and cpSRP54 is not involved in LHCP recognition. This divergence is attributed to altered residues within the cpSRP54 tail and the second chromodomain of cpSRP43 that are crucial for the formation of the binding interface in Arabidopsis. These changes are highly conserved among chlorophytes, whereas all land plants contain cpSRP proteins with typical interaction motifs. These data demonstrate that the coevolution of LHCPs and cpSRP43 occurred independently of complex formation with cpSRP54 and that the interaction between cpSRP54 and cpSRP43 evolved later during the transition from chlorophytes to land plants. Furthermore, our data show that in higher plants a heterodimeric form of cpSRP is required for the formation of a low molecular weight transit complex with LHCP.
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Affiliation(s)
| | | | | | | | - Björn Walter
- From the Molecular Biology of Plant Organelles and
| | - Silke Funke
- From the Molecular Biology of Plant Organelles and
| | - Eckhard Hofmann
- Protein Crystallography, Ruhr University Bochum, 44780 Bochum, Germany
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270
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Decoding mechanisms by which silent codon changes influence protein biogenesis and function. Int J Biochem Cell Biol 2015; 64:58-74. [PMID: 25817479 DOI: 10.1016/j.biocel.2015.03.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/02/2015] [Accepted: 03/14/2015] [Indexed: 02/07/2023]
Abstract
SCOPE Synonymous codon usage has been a focus of investigation since the discovery of the genetic code and its redundancy. The occurrences of synonymous codons vary between species and within genes of the same genome, known as codon usage bias. Today, bioinformatics and experimental data allow us to compose a global view of the mechanisms by which the redundancy of the genetic code contributes to the complexity of biological systems from affecting survival in prokaryotes, to fine tuning the structure and function of proteins in higher eukaryotes. Studies analyzing the consequences of synonymous codon changes in different organisms have revealed that they impact nucleic acid stability, protein levels, structure and function without altering amino acid sequence. As such, synonymous mutations inevitably contribute to the pathogenesis of complex human diseases. Yet, fundamental questions remain unresolved regarding the impact of silent mutations in human disorders. In the present review we describe developments in this area concentrating on mechanisms by which synonymous mutations may affect protein function and human health. PURPOSE This synopsis illustrates the significance of synonymous mutations in disease pathogenesis. We review the different steps of gene expression affected by silent mutations, and assess the benefits and possible harmful effects of codon optimization applied in the development of therapeutic biologics. PHYSIOLOGICAL AND MEDICAL RELEVANCE Understanding mechanisms by which synonymous mutations contribute to complex diseases such as cancer, neurodegeneration and genetic disorders, including the limitations of codon-optimized biologics, provides insight concerning interpretation of silent variants and future molecular therapies.
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271
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Rawat S, Zhu L, Lindner E, Dalbey RE, White SH. SecA drives transmembrane insertion of RodZ, an unusual single-span membrane protein. J Mol Biol 2015; 427:1023-37. [PMID: 24846669 PMCID: PMC4233018 DOI: 10.1016/j.jmb.2014.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/16/2014] [Accepted: 05/07/2014] [Indexed: 10/25/2022]
Abstract
The transmembrane (TM) helices of most type II single-span membrane proteins (S-SMPs) of Escherichia coli occur near the N-terminus, where the cell's targeting mechanisms can readily identify it as it emerges from the ribosome. However, the TM helices of a few S-SMPs, such as RodZ, occur a hundred or more residues downstream from the N-terminus, which raises fundamental questions about targeting and assembly. Because of RodZ's novelty and potential usefulness for understanding TM helix insertion in vivo, we examined its membrane targeting and assembly. We used RodZ constructs containing immunotags before the TM domain to assess membrane insertion using proteinase K digestion. We confirmed the N(in)-C(out) (type II) topology of RodZ and established the absence of a targeting signal other than the TM domain. RodZ was not inserted into the membrane under SecA depletion conditions or in the presence of sodium azide, which is known to inhibit SecA. Insertion failed when the TM proton gradient was abolished with Carbonyl cyanide m-chlorophenyl hydrazone. Insertion also failed when RodZ was expressed in SecE-depleted E. coli, indicating that the SecYEG translocon is required for RodZ assembly. Protease accessibility assays of RodZ in other E. coli depletion strains revealed that insertion is independent of SecB, YidC, and SecD/F. Insertion was found to be only weakly dependent on the signal recognition particle pathway: insertion was weakly dependent on the Ffh but independent of FtsY. We conclude that membrane insertion of RodZ requires only the SecYEG translocon, the SecA ATPase motor, and the TM proton motive force.
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Affiliation(s)
- Swati Rawat
- Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California at Irvine, Irvine, CA 92697-4560, USA
| | - Lu Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Lindner
- Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California at Irvine, Irvine, CA 92697-4560, USA
| | - Ross E Dalbey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Stephen H White
- Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California at Irvine, Irvine, CA 92697-4560, USA.
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272
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Mateja A, Paduch M, Chang HY, Szydlowska A, Kossiakoff AA, Hegde RS, Keenan RJ. Protein targeting. Structure of the Get3 targeting factor in complex with its membrane protein cargo. Science 2015; 347:1152-5. [PMID: 25745174 PMCID: PMC4413028 DOI: 10.1126/science.1261671] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Tail-anchored (TA) proteins are a physiologically important class of membrane proteins targeted to the endoplasmic reticulum by the conserved guided-entry of TA proteins (GET) pathway. During transit, their hydrophobic transmembrane domains (TMDs) are chaperoned by the cytosolic targeting factor Get3, but the molecular nature of the functional Get3-TA protein targeting complex remains unknown. We reconstituted the physiologic assembly pathway for a functional targeting complex and showed that it comprises a TA protein bound to a Get3 homodimer. Crystal structures of Get3 bound to different TA proteins showed an α-helical TMD occupying a hydrophobic groove that spans the Get3 homodimer. Our data elucidate the mechanism of TA protein recognition and shielding by Get3 and suggest general principles of hydrophobic domain chaperoning by cellular targeting factors.
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Affiliation(s)
- Agnieszka Mateja
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Hsin-Yang Chang
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anna Szydlowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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273
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Herschlag D, Allred BE, Gowrishankar S. From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function. Curr Opin Struct Biol 2015; 30:125-133. [PMID: 25744941 DOI: 10.1016/j.sbi.2015.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/11/2015] [Accepted: 02/11/2015] [Indexed: 12/18/2022]
Abstract
To understand RNA, it is necessary to move beyond a descriptive categorization towards quantitative predictions of its molecular conformations and functional behavior. An incisive approach to understanding the function and folding of biological RNA systems involves characterizing small, simple components that are largely responsible for the behavior of complex systems including helix-junction-helix elements and tertiary motifs. State-of-the-art methods have permitted unprecedented insight into the conformational ensembles of these elements revealing, for example, that conformations of helix-junction-helix elements are confined to a small region of the ensemble, that this region is highly dependent on the junction's topology, and that the correct alignment of tertiary motifs may be a rare conformation on the overall folding landscape. Further characterization of RNA components and continued development of experimental and computational methods with the goal of quantitatively predicting RNA folding and functional behavior will be critical to understanding biological RNA systems.
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Affiliation(s)
- Daniel Herschlag
- Department of Biochemistry, Beckman Center, B400, 279 W. Campus Dr. MC: 5307, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, 333 Campus Drive, Mudd Building, Room 121, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, 443 Via Ortega, Room 129, Stanford University, Stanford, CA 94305, USA.
| | - Benjamin E Allred
- Department of Biochemistry, Beckman Center, B400, 279 W. Campus Dr. MC: 5307, Stanford University, Stanford, CA 94305, USA
| | - Seshadri Gowrishankar
- Department of Chemical Engineering, 443 Via Ortega, Room 129, Stanford University, Stanford, CA 94305, USA
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274
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Morgunov AS, Babu MM. Optimizing membrane-protein biogenesis through nonoptimal-codon usage. Nat Struct Mol Biol 2015; 21:1023-5. [PMID: 25469841 DOI: 10.1038/nsmb.2926] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Alexey S Morgunov
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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275
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Kinori A, Bibi E. Co-translational membrane association of the Escherichia coli SRP receptor. J Cell Sci 2015; 128:1444-52. [DOI: 10.1242/jcs.166116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The signal recognition particle (SRP) receptor is a major player in the pathway of membrane protein biogenesis in all organisms. The receptor functions as a membrane bound entity but very little is known about its targeting to the membrane. Here we demonstrate in vivo that the Escherichia coli SRP receptor targets the membrane co-translationally. This requires emergence from the ribosome of the 4 helix-long N-domain of the receptor of which only helices 2–4 are required for co-translational membrane attachment. The results also suggest that the targeting might be regulated co-translationally. Together, our in vivo studies shed light on the biogenesis of the SRP receptor and its hypothetical role in targeting ribosomes to the Escherichia coli membrane.
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276
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Lewis NE, Brady LJ. Breaking the bacterial protein targeting and translocation model: oral organisms as a case in point. Mol Oral Microbiol 2014; 30:186-97. [PMID: 25400073 DOI: 10.1111/omi.12088] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2014] [Indexed: 12/19/2022]
Abstract
Insights into the membrane biogenesis of oral and throat bacteria have highlighted key differences in protein localization by the general secretion pathway compared with the well-studied Escherichia coli model system. These intriguing novelties have advanced our understanding of both how these microorganisms have adapted to survive and cause disease in the oral cavity, and the field of protein translocation as a whole. This review focuses on findings that highlight where oral bacteria differ from the E. coli paradigm, why these differences are biologically important, and what questions remain about the differences in pathway function. The majority of insight into protein translocation in microbes of the oral cavity has come from streptococcal species, which will be the main topic of this review. However, other bacteria will be discussed when relevant. An overview of the E. coli model of protein targeting and translocation is provided for comparison.
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Affiliation(s)
- N E Lewis
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
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277
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Kunze M, Malkani N, Maurer-Stroh S, Wiesinger C, Schmid JA, Berger J. Mechanistic insights into PTS2-mediated peroxisomal protein import: the co-receptor PEX5L drastically increases the interaction strength between the cargo protein and the receptor PEX7. J Biol Chem 2014; 290:4928-4940. [PMID: 25538232 DOI: 10.1074/jbc.m114.601575] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The destination of peroxisomal matrix proteins is encoded by short peptide sequences, which have been characterized as peroxisomal targeting signals (PTS) residing either at the C terminus (PTS1) or close to the N terminus (PTS2). PTS2-carrying proteins interact with their cognate receptor protein PEX7 that mediates their transport to peroxisomes by a concerted action with a co-receptor protein, which in mammals is the PTS1 receptor PEX5L. Using a modified version of the mammalian two-hybrid assay, we demonstrate that the interaction strength between cargo and PEX7 is drastically increased in the presence of the co-receptor PEX5L. In addition, cargo binding is a prerequisite for the interaction between PEX7 and PEX5L and ectopic overexpression of PTS2-carrying cargo protein drastically increases the formation of PEX7-PEX5L complexes in this assay. Consistently, we find that the peroxisomal transfer of PEX7 depends on cargo binding and that ectopic overexpression of cargo protein stimulates this process. Thus, the sequential formation of a highly stable trimeric complex involving cargo protein, PEX7 and PEX5L stabilizes cargo binding and is a prerequisite for PTS2-mediated peroxisomal import.
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Affiliation(s)
- Markus Kunze
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria,.
| | - Naila Malkani
- Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671; School of Biological Sciences (SBS), Nanyang Technological University (NTU), 8 Medical Drive, Singapore 117597
| | - Christoph Wiesinger
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Johannes A Schmid
- Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Berger
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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278
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Gilet L, DiChiara JM, Figaro S, Bechhofer DH, Condon C. Small stable RNA maturation and turnover in Bacillus subtilis. Mol Microbiol 2014; 95:270-82. [PMID: 25402410 DOI: 10.1111/mmi.12863] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2014] [Indexed: 02/05/2023]
Abstract
Stable RNA maturation is a key process in the generation of functional RNAs, and failure to correctly process these RNAs can lead to their elimination through quality control mechanisms. Studies of the maturation pathways of ribosomal RNA and transfer RNA in Bacillus subtilis showed they were radically different from Escherichia coli and led to the identification of new B. subtilis-specific enzymes. We noticed that, despite their important roles in translation, a number of B. subtilis small stable RNAs still did not have characterised maturation pathways, notably the tmRNA, involved in ribosome rescue, and the RNase P RNA, involved in tRNA maturation. Here, we show that tmRNA is matured by RNase P and RNase Z at its 5' and 3' extremities, respectively, whereas the RNase P RNA is matured on its 3' side by RNase Y. Recent evidence that several RNases are not essential in B. subtilis prompted us to revisit maturation of the scRNA, a component of the signal recognition particle involved in co-translational insertion of specific proteins into the membrane. We show that RNase Y is also involved in 3' processing of scRNA. Lastly, we identified some of the enzymes involved in the turnover of these three stable RNAs.
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Affiliation(s)
- Laetitia Gilet
- CNRS FRE 3630 (affiliated with University Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
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279
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Williams CC, Jan CH, Weissman JS. Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. Science 2014; 346:748-51. [PMID: 25378625 DOI: 10.1126/science.1257522] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nearly all mitochondrial proteins are nuclear-encoded and are targeted to their mitochondrial destination from the cytosol. Here, we used proximity-specific ribosome profiling to comprehensively measure translation at the mitochondrial surface in yeast. Most inner-membrane proteins were cotranslationally targeted to mitochondria, reminiscent of proteins entering the endoplasmic reticulum (ER). Comparison between mitochondrial and ER localization demonstrated that the vast majority of proteins were targeted to a specific organelle. A prominent exception was the fumarate reductase Osm1, known to reside in mitochondria. We identified a conserved ER isoform of Osm1, which contributes to the oxidative protein-folding capacity of the organelle. This dual localization was enabled by alternative translation initiation sites encoding distinct targeting signals. These findings highlight the exquisite in vivo specificity of organellar targeting mechanisms.
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Affiliation(s)
| | | | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA. These authors contributed equally to this work.
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280
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Pechmann S, Chartron JW, Frydman J. Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo. Nat Struct Mol Biol 2014; 21:1100-5. [PMID: 25420103 DOI: 10.1038/nsmb.2919] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/20/2014] [Indexed: 02/07/2023]
Abstract
The genetic code allows most amino acids a choice of optimal and nonoptimal codons. We report that synonymous codon choice is tuned to promote interaction of nascent polypeptides with the signal recognition particle (SRP), which assists in protein translocation across membranes. Cotranslational recognition by the SRP in vivo is enhanced when mRNAs contain nonoptimal codon clusters 35-40 codons downstream of the SRP-binding site, the distance that spans the ribosomal polypeptide exit tunnel. A local translation slowdown upon ribosomal exit of SRP-binding elements in mRNAs containing these nonoptimal codon clusters is supported experimentally by ribosome profiling analyses in yeast. Modulation of local elongation rates through codon choice appears to kinetically enhance recognition by ribosome-associated factors. We propose that cotranslational regulation of nascent-chain fate may be a general constraint shaping codon usage in the genome.
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Affiliation(s)
| | - Justin W Chartron
- Department of Biology, Stanford University, Stanford, California, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California, USA
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281
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Wang H, Stefanovic B. Role of LARP6 and nonmuscle myosin in partitioning of collagen mRNAs to the ER membrane. PLoS One 2014; 9:e108870. [PMID: 25271881 PMCID: PMC4182744 DOI: 10.1371/journal.pone.0108870] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/01/2014] [Indexed: 02/07/2023] Open
Abstract
Type I collagen is extracellular matrix protein composed of two α1(I) and one α2(I) polypeptides that fold into triple helix. Collagen polypeptides are translated in coordination to synchronize the rate of triple helix folding to the rate of posttranslational modifications of individual polypeptides. This is especially important in conditions of high collagen production, like fibrosis. It has been assumed that collagen mRNAs are targeted to the membrane of the endoplasmic reticulum (ER) after translation of the signal peptide and by signal peptide recognition particle (SRP). Here we show that collagen mRNAs associate with the ER membrane even when translation is inhibited. Knock down of LARP6, an RNA binding protein which binds 5' stem-loop of collagen mRNAs, releases a small amount of collagen mRNAs from the membrane. Depolimerization of nonmuscle myosin filaments has a similar, but stronger effect. In the absence of LARP6 or nonmuscle myosin filaments collagen polypeptides become hypermodified, are poorly secreted and accumulate in the cytosol. This indicates lack of coordination of their synthesis and retro-translocation due to hypermodifications and misfolding. Depolimerization of nonmuscle myosin does not alter the secretory pathway through ER and Golgi, suggesting that the role of nonmuscle myosin is primarily to partition collagen mRNAs to the ER membrane. We postulate that collagen mRNAs directly partition to the ER membrane prior to synthesis of the signal peptide and that LARP6 and nonmuscle myosin filaments mediate this process. This allows coordinated initiation of translation on the membrane bound collagen α1(I) and α2(I) mRNAs, a necessary step for proper synthesis of type I collagen.
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Affiliation(s)
- Hao Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
| | - Branko Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
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282
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Jagannathan S, Reid DW, Cox AH, Nicchitta CV. De novo translation initiation on membrane-bound ribosomes as a mechanism for localization of cytosolic protein mRNAs to the endoplasmic reticulum. RNA (NEW YORK, N.Y.) 2014; 20:1489-98. [PMID: 25142066 PMCID: PMC4174431 DOI: 10.1261/rna.045526.114] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/25/2014] [Indexed: 05/21/2023]
Abstract
The specialized protein synthesis functions of the cytosol and endoplasmic reticulum compartments are conferred by the signal recognition particle (SRP) pathway, which directs the cotranslational trafficking of signal sequence-encoding mRNAs from the cytosol to the endoplasmic reticulum (ER). Although subcellular mRNA distributions largely mirror the binary pattern predicted by the SRP pathway model, studies in mammalian cells, yeast, and Drosophila have also demonstrated that cytosolic protein-encoding mRNAs are broadly represented on ER-bound ribosomes. A mechanism for such noncanonical mRNA localization remains, however, to be identified. Here, we examine the hypothesis that de novo translation initiation on ER-bound ribosomes serves as a mechanism for localizing cytosolic protein-encoding mRNAs to the ER. As a test of this hypothesis, we performed single molecule RNA fluorescence in situ hybridization studies of subcellular mRNA distributions and report that a substantial fraction of mRNAs encoding the cytosolic protein GAPDH resides in close proximity to the ER. Consistent with these data, analyses of subcellular mRNA and ribosome distributions in multiple cell lines demonstrated that cytosolic protein mRNA-ribosome distributions were strongly correlated, whereas signal sequence-encoding mRNA-ribosome distributions were divergent. Ribosome footprinting studies of ER-bound polysomes revealed a substantial initiation codon read density enrichment for cytosolic protein-encoding mRNAs. We also demonstrate that eukaryotic initiation factor 2α is bound to the ER via a salt-sensitive, ribosome-independent mechanism. Combined, these data support ER-localized translation initiation as a mechanism for mRNA recruitment to the ER.
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Affiliation(s)
- Sujatha Jagannathan
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Amanda H Cox
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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283
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Abstract
The Alu domain of the signal recognition particle (SRP) arrests protein biosynthesis by competition with elongation factor binding on the ribosome. The mammalian Alu domain is a protein-RNA complex, while prokaryotic Alu domains are protein-free with significant extensions of the RNA. Here we report the crystal structure of the complete Alu domain of Bacillus subtilis SRP RNA at 2.5 Å resolution. The bacterial Alu RNA reveals a compact fold, which is stabilized by prokaryote-specific extensions and interactions. In this 'closed' conformation, the 5' and 3' regions are clamped together by the additional helix 1, the connecting 3-way junction and a novel minor groove interaction, which we term the 'minor-saddle motif' (MSM). The 5' region includes an extended loop-loop pseudoknot made of five consecutive Watson-Crick base pairs. Homology modeling with the human Alu domain in context of the ribosome shows that an additional lobe in the pseudoknot approaches the large subunit, while the absence of protein results in the detachment from the small subunit. Our findings provide the structural basis for purely RNA-driven elongation arrest in prokaryotes, and give insights into the structural adaption of SRP RNA during evolution.
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Affiliation(s)
- Georg Kempf
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
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284
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Cymer F, von Heijne G, White SH. Mechanisms of integral membrane protein insertion and folding. J Mol Biol 2014; 427:999-1022. [PMID: 25277655 DOI: 10.1016/j.jmb.2014.09.014] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/13/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022]
Abstract
The biogenesis, folding, and structure of α-helical membrane proteins (MPs) are important to understand because they underlie virtually all physiological processes in cells including key metabolic pathways, such as the respiratory chain and the photosystems, as well as the transport of solutes and signals across membranes. Nearly all MPs require translocons--often referred to as protein-conducting channels--for proper insertion into their target membrane. Remarkable progress toward understanding the structure and functioning of translocons has been made during the past decade. Here, we review and assess this progress critically. All available evidence indicates that MPs are equilibrium structures that achieve their final structural states by folding along thermodynamically controlled pathways. The main challenge for cells is the targeting and membrane insertion of highly hydrophobic amino acid sequences. Targeting and insertion are managed in cells principally by interactions between ribosomes and membrane-embedded translocons. Our review examines the biophysical and biological boundaries of MP insertion and the folding of polytopic MPs in vivo. A theme of the review is the under-appreciated role of basic thermodynamic principles in MP folding and assembly. Thermodynamics not only dictates the final folded structure but also is the driving force for the evolution of the ribosome-translocon system of assembly. We conclude the review with a perspective suggesting a new view of translocon-guided MP insertion.
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Affiliation(s)
- Florian Cymer
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm.,Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden
| | - Stephen H White
- Department of Physiology and Biophysics and the Center for Biomembrane Systems University of California, Irvine Irvine, CA 92697
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285
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Wang CY, Miller TF. Allosteric response and substrate sensitivity in peptide binding of the signal recognition particle. J Biol Chem 2014; 289:30868-30879. [PMID: 25237192 DOI: 10.1074/jbc.m114.584912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We characterize the conformational dynamics and substrate selectivity of the signal recognition particle (SRP) using a thermodynamic free energy cycle approach and microsecond timescale molecular dynamics simulations. The SRP is a central component of the co-translational protein targeting machinery that binds to the N-terminal signal peptide (SP) of nascent proteins. We determined the shift in relative conformational stability of the SRP upon substrate binding to quantify allosteric coupling between SRP domains. In particular, for dipeptidyl aminopeptidase, an SP that is recognized by the SRP for co-translational targeting, it is found that substrate binding induces substantial changes in the SRP toward configurations associated with targeting of the nascent protein, and it is found that the changes are modestly enhanced by a mutation that increases the hydrophobicity of the SP. However, for alkaline phosphatase, an SP that is recognized for post-translational targeting, substrate binding induces the reverse change in the SRP conformational distribution away from targeting configurations. Microsecond timescale trajectories reveal the intrinsic flexibility of the SRP conformational landscape and provide insight into recent single molecule studies by illustrating that 10-nm lengthscale changes between FRET pairs occur via the rigid-body movement of SRP domains connected by the flexible linker region. In combination, these results provide direct evidence for the hypothesis that substrate-controlled conformational switching in the SRP provides a mechanism for discriminating between different SPs and for connecting substrate binding to downstream steps in the protein targeting pathway.
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Affiliation(s)
- Connie Y Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106.
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286
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mRNA transport meets membrane traffic. Trends Genet 2014; 30:408-17. [DOI: 10.1016/j.tig.2014.07.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/09/2014] [Accepted: 07/09/2014] [Indexed: 02/07/2023]
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287
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Paila YD, Richardson LGL, Schnell DJ. New insights into the mechanism of chloroplast protein import and its integration with protein quality control, organelle biogenesis and development. J Mol Biol 2014; 427:1038-1060. [PMID: 25174336 DOI: 10.1016/j.jmb.2014.08.016] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/20/2014] [Accepted: 08/23/2014] [Indexed: 01/04/2023]
Abstract
The translocons at the outer (TOC) and the inner (TIC) envelope membranes of chloroplasts mediate the targeting and import of several thousand nucleus-encoded preproteins that are required for organelle biogenesis and homeostasis. The cytosolic events in preprotein targeting remain largely unknown, although cytoplasmic chaperones have been proposed to facilitate delivery to the TOC complex. Preprotein recognition is mediated by the TOC GTPase receptors Toc159 and Toc34. The receptors constitute a GTP-regulated switch, which initiates membrane translocation via Toc75, a member of the Omp85 (outer membrane protein 85)/TpsB (two-partner secretion system B) family of bacterial, plastid and mitochondrial β-barrel outer membrane proteins. The TOC receptor systems have diversified to recognize distinct sets of preproteins, thereby maximizing the efficiency of targeting in response to changes in gene expression during developmental and physiological events that impact organelle function. The TOC complex interacts with the TIC translocon to allow simultaneous translocation of preproteins across the envelope. Both the two inner membrane complexes, the Tic110 and 1 MDa complexes, have been implicated as constituents of the TIC translocon, and it remains to be determined how they interact to form the TIC channel and assemble the import-associated chaperone network in the stroma that drives import across the envelope membranes. This review will focus on recent developments in our understanding of the mechanisms and diversity of the TOC-TIC systems. Our goal is to incorporate these recent studies with previous work and present updated or revised models for the function of TOC-TIC in protein import.
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Affiliation(s)
- Yamuna D Paila
- Department of Biochemistry and Molecular Biology, Life Sciences Laboratories Room N431, 240 Thatcher Rd, University of Massachusetts, Amherst MA 01003-9364, USA
| | - Lynn G L Richardson
- Department of Biochemistry and Molecular Biology, Life Sciences Laboratories Room N431, 240 Thatcher Rd, University of Massachusetts, Amherst MA 01003-9364, USA
| | - Danny J Schnell
- Department of Biochemistry and Molecular Biology, Life Sciences Laboratories Room N431, 240 Thatcher Rd, University of Massachusetts, Amherst MA 01003-9364, USA
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288
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APC rearrangements in familial adenomatous polyposis: heterogeneity of deletion lengths and breakpoint sequences underlies similar phenotypes. Fam Cancer 2014; 14:41-9. [DOI: 10.1007/s10689-014-9750-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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289
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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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290
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Fluman N, Navon S, Bibi E, Pilpel Y. mRNA-programmed translation pauses in the targeting of E. coli membrane proteins. eLife 2014; 3. [PMID: 25135940 PMCID: PMC4359368 DOI: 10.7554/elife.03440] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/16/2014] [Indexed: 02/05/2023] Open
Abstract
In all living organisms, ribosomes translating membrane proteins are targeted to membrane translocons early in translation, by the ubiquitous signal recognition particle (SRP) system. In eukaryotes, the SRP Alu domain arrests translation elongation of membrane proteins until targeting is complete. Curiously, however, the Alu domain is lacking in most eubacteria. In this study, by analyzing genome-wide data on translation rates, we identified a potential compensatory mechanism in E. coli that serves to slow down the translation during membrane protein targeting. The underlying mechanism is likely programmed into the coding sequence, where Shine-Dalgarno-like elements trigger elongation pauses at strategic positions during the early stages of translation. We provide experimental evidence that slow translation during targeting and improves membrane protein production fidelity, as it correlates with better folding of overexpressed membrane proteins. Thus, slow elongation is important for membrane protein targeting in E. coli, which utilizes mechanisms different from the eukaryotic one to control the translation speed.
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Affiliation(s)
- Nir Fluman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sivan Navon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eitan Bibi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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291
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Sommer MS, Schleiff E. Protein targeting and transport as a necessary consequence of increased cellular complexity. Cold Spring Harb Perspect Biol 2014; 6:6/8/a016055. [PMID: 25085907 DOI: 10.1101/cshperspect.a016055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
With increasing intracellular complexity, a new cell-biological problem that is the allocation of cytoplasmically synthesized proteins to their final destinations within the cell emerged. A special challenge is thereby the translocation of proteins into or across cellular membranes. The underlying mechanisms are only in parts well understood, but it can be assumed that the course of cellular evolution had a deep impact on the design of the required molecular machines. In this article, we aim to summarize the current knowledge and concepts of the evolutionary development of protein trafficking as a necessary premise and consequence of increased cellular complexity.
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Affiliation(s)
- Maik S Sommer
- Institute for Molecular Biosciences, Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany Centre of Membrane Proteomics, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
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292
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Wang F, Chan C, Weir NR, Denic V. The Get1/2 transmembrane complex is an endoplasmic-reticulum membrane protein insertase. Nature 2014; 512:441-4. [PMID: 25043001 DOI: 10.1038/nature13471] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 05/13/2014] [Indexed: 11/09/2022]
Abstract
Hundreds of tail-anchored proteins, including soluble N-ethylmaleimide-sensitive factor attachment receptors (SNAREs) involved in vesicle fusion, are inserted post-translationally into the endoplasmic reticulum membrane by a dedicated protein-targeting pathway. Before insertion, the carboxy-terminal transmembrane domains of tail-anchored proteins are shielded in the cytosol by the conserved targeting factor Get3 (in yeast; TRC40 in mammals). The Get3 endoplasmic-reticulum receptor comprises the cytosolic domains of the Get1/2 (WRB/CAML) transmembrane complex, which interact individually with the targeting factor to drive a conformational change that enables substrate release and, as a consequence, insertion. Because tail-anchored protein insertion is not associated with significant translocation of hydrophilic protein sequences across the membrane, it remains possible that Get1/2 cytosolic domains are sufficient to place Get3 in proximity with the endoplasmic-reticulum lipid bilayer and permit spontaneous insertion to occur. Here we use cell reporters and biochemical reconstitution to define mutations in the Get1/2 transmembrane domain that disrupt tail-anchored protein insertion without interfering with Get1/2 cytosolic domain function. These mutations reveal a novel Get1/2 insertase function, in the absence of which substrates stay bound to Get3 despite their proximity to the lipid bilayer; as a consequence, the notion of spontaneous transmembrane domain insertion is a non sequitur. Instead, the Get1/2 transmembrane domain helps to release substrates from Get3 by capturing their transmembrane domains, and these transmembrane interactions define a bona fide pre-integrated intermediate along a facilitated route for tail-anchor entry into the lipid bilayer. Our work sheds light on the fundamental point of convergence between co-translational and post-translational endoplasmic-reticulum membrane protein targeting and insertion: a mechanism for reducing the ability of a targeting factor to shield its substrates enables substrate handover to a transmembrane-domain-docking site embedded in the endoplasmic-reticulum membrane.
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Affiliation(s)
- Fei Wang
- Department of Molecular and Cellular Biology, Harvard University, Northwest Labs, Cambridge, Massachusetts 02138, USA
| | - Charlene Chan
- Department of Molecular and Cellular Biology, Harvard University, Northwest Labs, Cambridge, Massachusetts 02138, USA
| | - Nicholas R Weir
- Department of Molecular and Cellular Biology, Harvard University, Northwest Labs, Cambridge, Massachusetts 02138, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Harvard University, Northwest Labs, Cambridge, Massachusetts 02138, USA
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293
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Altegoer F, Schuhmacher J, Pausch P, Bange G. From molecular evolution to biobricks and synthetic modules: a lesson by the bacterial flagellum. Biotechnol Genet Eng Rev 2014; 30:49-64. [DOI: 10.1080/02648725.2014.921500] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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294
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Sachelaru I, Petriman NA, Kudva R, Koch HG. Dynamic interaction of the sec translocon with the chaperone PpiD. J Biol Chem 2014; 289:21706-15. [PMID: 24951590 DOI: 10.1074/jbc.m114.577916] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Sec translocon constitutes a ubiquitous protein transport channel that consists in bacteria of the three core components: SecY, SecE, and SecG. Additional proteins interact with SecYEG during different stages of protein transport. During targeting, SecYEG interacts with SecA, the SRP receptor, or the ribosome. Protein transport into or across the membrane is then facilitated by the interaction of SecYEG with YidC and the SecDFYajC complex. During protein transport, SecYEG is likely to interact also with the protein quality control machinery, but details about this interaction are missing. By in vivo and in vitro site-directed cross-linking, we show here that the periplasmic chaperone PpiD is located in front of the lateral gate of SecY, through which transmembrane domains exit the SecY channel. The strongest contacts were found to helix 2b of SecY. Blue native PAGE analyses verify the presence of a SecYEG-PpiD complex in native Escherichia coli membranes. The PpiD-SecY interaction was not influenced by the addition of SecA and only weakly influenced by binding of nontranslating ribosomes to SecYEG. In contrast, PpiD lost contact to the lateral gate of SecY during membrane protein insertion. These data identify PpiD as an additional and transient subunit of the bacterial SecYEG translocon. The data furthermore demonstrate the highly modular and versatile composition of the Sec translocon, which is probably essential for its ability to transport a wide range of substrates across membranes in bacteria and eukaryotes.
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Affiliation(s)
- Ilie Sachelaru
- From the Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, the Faculty of Biology, and
| | - Narcis-Adrian Petriman
- From the Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, the Faculty of Biology, and
| | - Renuka Kudva
- From the Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, the Faculty of Biology, and the Spemann-Graduate School of Biology and Medicine, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- From the Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, the Spemann-Graduate School of Biology and Medicine, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
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295
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Sørensen DM, Holen HW, Holemans T, Vangheluwe P, Palmgren MG. Towards defining the substrate of orphan P5A-ATPases. Biochim Biophys Acta Gen Subj 2014; 1850:524-35. [PMID: 24836520 DOI: 10.1016/j.bbagen.2014.05.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 11/16/2022]
Abstract
BACKGROUND P-type ATPases are ubiquitous ion and lipid pumps found in cellular membranes. P5A-ATPases constitute a poorly characterized subfamily of P-type ATPases present in all eukaryotic organisms but for which a transported substrate remains to be identified. SCOPE OF REVIEW This review aims to discuss the available evidence which could lead to identification of possible substrates of P5A-ATPases. MAJOR CONCLUSIONS The complex phenotypes resulting from the loss of P5A-ATPases in model organisms can be explained by a role of the P5A-ATPase in the endoplasmic reticulum (ER), where loss of function leads to broad and unspecific phenotypes related to the impairment of basic ER functions such as protein folding and processing. Genetic interactions in Saccharomyces cerevisiae point to a role of the endogenous P5A-ATPase Spf1p in separation of charges in the ER, in sterol metabolism, and in insertion of tail-anchored proteins in the ER membrane. A role for P5A-ATPases in vesicle formation would explain why sterol transport and distribution are affected in knock out cells, which in turn has a negative impact on the spontaneous insertion of tail-anchored proteins. It would also explain why secretory proteins destined for the Golgi and the cell wall have difficulties in reaching their final destination. Cations and phospholipids could both be transported substrates of P5A-ATPases and as each carry charges, transport of either might explain why a charge difference arises across the ER membrane. GENERAL SIGNIFICANCE Identification of the substrate of P5A-ATPases would throw light on an important general process in the ER that is still not fully understood. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Danny Mollerup Sørensen
- Centre for Membrane Pumps in Cells and Disease-PUMPkin, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Henrik Waldal Holen
- Centre for Membrane Pumps in Cells and Disease-PUMPkin, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Tine Holemans
- Department of Cellular and Molecular Medicine, ON1 Campus Gasthuisberg, Katholieke Universiteit Leuven, Herestraat 49, Box 802, B3000 Leuven, Belgium
| | - Peter Vangheluwe
- Department of Cellular and Molecular Medicine, ON1 Campus Gasthuisberg, Katholieke Universiteit Leuven, Herestraat 49, Box 802, B3000 Leuven, Belgium
| | - Michael G Palmgren
- Centre for Membrane Pumps in Cells and Disease-PUMPkin, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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296
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Denks K, Vogt A, Sachelaru I, Petriman NA, Kudva R, Koch HG. The Sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol 2014; 31:58-84. [DOI: 10.3109/09687688.2014.907455] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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297
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Grotwinkel JT, Wild K, Segnitz B, Sinning I. SRP RNA remodeling by SRP68 explains its role in protein translocation. Science 2014; 344:101-4. [PMID: 24700861 DOI: 10.1126/science.1249094] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The signal recognition particle (SRP) is central to membrane protein targeting; SRP RNA is essential for SRP assembly, elongation arrest, and activation of SRP guanosine triphosphatases. In eukaryotes, SRP function relies on the SRP68-SRP72 heterodimer. We present the crystal structures of the RNA-binding domain of SRP68 (SRP68-RBD) alone and in complex with SRP RNA and SRP19. SRP68-RBD is a tetratricopeptide-like module that binds to a RNA three-way junction, bends the RNA, and inserts an α-helical arginine-rich motif (ARM) into the major groove. The ARM opens the conserved 5f RNA loop, which in ribosome-bound SRP establishes a contact to ribosomal RNA. Our data provide the structural basis for eukaryote-specific, SRP68-driven RNA remodeling required for protein translocation.
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Affiliation(s)
- Jan Timo Grotwinkel
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
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298
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Bar-Peled L, Sabatini DM. Regulation of mTORC1 by amino acids. Trends Cell Biol 2014; 24:400-6. [PMID: 24698685 DOI: 10.1016/j.tcb.2014.03.003] [Citation(s) in RCA: 591] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/04/2014] [Accepted: 03/05/2014] [Indexed: 12/31/2022]
Abstract
The mechanistic target of rapamycin complex I (mTORC1) is a central regulator of cellular and organismal growth, and hyperactivation of this pathway is implicated in the pathogenesis of many human diseases including cancer and diabetes. mTORC1 promotes growth in response to the availability of nutrients, such as amino acids, which drive mTORC1 to the lysosomal surface, its site of activation. How amino acid levels are communicated to mTORC1 is only recently coming to light by the discovery of a lysosome-based signaling system composed of Rags (Ras-related GTPases) and Ragulator v-ATPase, GATOR (GAP activity towards Rags), and folliculin (FLCN) complexes. Increased understanding of this pathway will not only provide insight into growth control but also into the human pathologies triggered by its deregulation.
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Affiliation(s)
- Liron Bar-Peled
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Nine Cambridge Center, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Cambridge MA 02142, USA.
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299
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An mRNA-derived noncoding RNA targets and regulates the ribosome. Mol Cell 2014; 54:147-155. [PMID: 24685157 PMCID: PMC3988847 DOI: 10.1016/j.molcel.2014.02.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/26/2014] [Accepted: 02/12/2014] [Indexed: 12/02/2022]
Abstract
The structural and functional repertoire of small non-protein-coding RNAs (ncRNAs) is central for establishing gene regulation networks in cells and organisms. Here, we show that an mRNA-derived 18-nucleotide-long ncRNA is capable of downregulating translation in Saccharomyces cerevisiae by targeting the ribosome. This 18-mer ncRNA binds to polysomes upon salt stress and is crucial for efficient growth under hyperosmotic conditions. Although the 18-mer RNA originates from the TRM10 locus, which encodes a tRNA methyltransferase, genetic analyses revealed the 18-mer RNA nucleotide sequence, rather than the mRNA-encoded enzyme, as the translation regulator. Our data reveal the ribosome as a target for a small regulatory ncRNA and demonstrate the existence of a yet unkown mechanism of translation regulation. Ribosome-targeted small ncRNAs are found in all domains of life and represent a prevalent but so far largely unexplored class of regulatory molecules. This study reveals the yeast ribosome as direct target for small regulatory ncRNAs An 18-nt-long exon-derived RNA fragment from the TRM10 locus binds to ribosomes This 18-mer ncRNA inhibits global protein biosynthesis in vivo and in vitro This translation attenuation is crucial for adaption under hyperosmotic stress
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300
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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